@inbook {12141,
	title = {A Short History of Membrane Physics},
	booktitle = {Handbook of Lipid Membranes: Molecular, Functional, and Materials Aspects.    Editors:  C. Safinya and J. Raedler },
	year = {In Press},
	month = {2017},
	publisher = {Taylor and Francis },
	organization = {Taylor and Francis },
	author = {Erich Sackman and Ben-Shaul, Avinoam}
}
@article { ISI:000379457200050,
	title = {A Prufer-Sequence Based Algorithm for Calculating the Size of Ideal Randomly Branched Polymers},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {120},
	year = {2016},
	month = {JUL 7},
	pages = {6231-6237},
	abstract = {Branched polymers can be represented as tree graphs. A one-to-one correspondence exists between a tree graph comprised of N labeled vertices and a sequence of N 2 integers, known as the Prufer sequence. Permutations of this sequence yield sequences corresponding to tree graphs with the same vertex-degree distribution but (generally) different branching patterns. Repeatedly shuffling the Prufer sequence we have generated large ensembles of random tree graphs, all with the same degree distributions. We also present and apply an efficient algorithm to determine graph distances directly from their Prufer sequences. From the (Prufer sequence derived) graph distances, 3D size metrics, e.g., the polymer{\textquoteright}s radius of gyration, R-g, and average end-to-end distance, were then calculated using several different theoretical approaches. Applying our method to ideal randomly branched polymers of different vertex-degree distributions, all their 3D size measures are found to obey the usual N-1/4 scaling law. Among the branched polymers analyzed are RNA molecules comprised of equal proportions of the four-randomly distributed-nucleotides. Prior to Prufer shuffling, the vertices of their representative tree graphs, these {\textquoteleft}{\textquoteleft}random-sequence{\textquoteright}{\textquoteright} RNAs exhibit an R-g similar to N-1/3 scaling.},
	issn = {1520-6106},
	doi = {10.1021/acs.jpcb.6b02258},
	author = {Singaram, Surendra W. and Gopal, Ajaykumar and Ben-Shaul, Avinoam}
}
@article { ISI:000388545600002,
	title = {Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {111},
	year = {2016},
	month = {NOV 15},
	pages = {2077-2085},
	abstract = {Long RNA molecules are at the core of gene regulation across all kingdoms of life, while also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with non repeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. To test whether a branched polymer model can estimate the overall sizes of large RNAs, we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long noncoding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of maximum ladder distance. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low ionic-strength sizes. These results suggest that sizes of long RNA molecules are determined by the branching pattern of their secondary structures. We also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs.
http://www.sciencedirect.com/science/article/pii/S0006349516309419

},
	issn = {0006-3495},
	doi = {10.1016/j.bpj.2016.10.014},
	author = {Borodavka, Alexander and Singaram, Surendra W. and Stockley, Peter G. and Gelbart, William M and Ben-Shaul, Avinoam and Tuma, Roman}
}
@article { ISI:000364435500006,
	title = {Role of RNA Branchedness in the Competition for Viral Capsid Proteins},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {119},
	year = {2015},
	month = {NOV 5},
	pages = {13991-14002},
	abstract = {To optimize binding-and packaging-by their capsid proteins (CP), single-stranded (ss) RNA viral genomes often have local secondary/tertiary structures with high CP affinity, with these {\textquoteleft}{\textquoteleft}packaging signals{\textquoteright}{\textquoteright} serving as heterogeneous nucleation sites for the formation of capsids. Under typical in vitro self-assembly conditions, however, and in particular for the case of many ssRNA viruses whose CP have cationic N-termini, the adsorption of CP by RNA is nonspecific because the CP concentration exceeds the largest dissociation constant for CP RNA binding. Consequently, the RNA is saturated by bound protein before lateral interactions between CP drive the homogeneous nucleation of capsids. But, before capsids are formed, the binding of protein remains reversible and introduction of another RNA species with a different length and/or sequence is found experimentally to result in significant redistribution of protein. Here we argue that, for a given RNA mass, the sequence with the highest affinity for protein is the one with the most compact secondary structure arising from self-complementarity; similarly, a long RNA steals protein from an equal mass of shorter ones. In both cases, it is the lateral attractions between bound proteins that determines the relative CP affinities of the RNA templates, even though the individual binding sites are identical. We demonstrate this with Monte Carlo simulations, generalizing the Rosenbluth method for excludedvolume polymers to include branching of the polymers and their reversible binding by protein.},
	issn = {1520-6106},
	doi = {10.1021/acs.jpcb.5b06445},
	author = {Singararn, Surendra W. and Garmann, Rees F. and Knobler, Charles M. and Gelbart, William M and Ben-Shaul, Avinoam}
}
@article { ISI:000347468900004,
	title = {Viral ssRNAs Are Indeed Compact},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {108},
	year = {2015},
	month = {JAN 6},
	pages = {14-16},
	issn = {0006-3495},
	doi = {10.1016/j.bpj.2014.11.010},
	author = {Ben-Shaul, A and Gelbart, W.M.}
}
@article { ISI:000338981200005,
	title = {Characterization of Viral Capsid Protein Self-Assembly around Short Single-Stranded RNA},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {118},
	year = {2014},
	month = {JUL 10},
	pages = {7510-7519},
	abstract = {For many viruses, the packaging of a single-stranded RNA (ss-RNA) genome is spontaneous, driven by capsid protein-capsid protein (CP) and CP-RNA interactions. Furthermore, for some multipartite ss-RNA viruses, copackaging of two or more RNA molecules is a common strategy. Here we focus on RNA copackaging in vitro by using cowpea chlorotic mottle virus (CCMV) CP and an RNA molecule that is short (500 nucleotides (nts)) compared to the lengths (approximate to 3000 nts) packaged in wild-type virions. We show that the degree of cooperativity of virus assembly depends not only on the relative strength of the CP-CP and CP-RNA interactions but also on the RNA being short: a 500-nt RNA molecule cannot form a capsid by itself, so its packaging requires the aggregation of multiple CP-RNA complexes. By using fluorescence correlation spectroscopy (FCS), we show that at neutral pH and sufficiently low concentrations RNA and CP form complexes that are smaller than the wild-type capsid and that four 500-nt RNAs are packaged into virus-like particles (VLPs) only upon lowering the pH. Further, a variety of bulk-solution techniques confirm that fully ordered VLPs are formed only upon acidification. On the basis of these results, we argue that the observed high degree of cooperativity involves equilibrium between multiple CP/RNA complexes.},
	issn = {1520-6106},
	doi = {10.1021/jp503050z},
	author = {Comas-Garcia, Mauricio and Garmann, Rees F. and Singaram, Surendra W. and Ben-Shaul, Avinoam and Knobler, Charles M. and Gebart, William M.}
}
@article { ISI:000330132500019,
	title = {Reply to the Comment by S. Harvey on {\textquoteleft}{\textquoteleft}Entropy, Energy, and Bending of DNA in Viral Capsids{\textquoteright}{\textquoteright}},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {106},
	year = {2014},
	month = {JAN 21},
	pages = {493-496},
	abstract = {The comment by Stephen Harvey in this issue of the Biophysical Journal concludes with two statements regarding my recent letter about DNA packaging into viral capsids. Harvey agrees with my interpretation of the origin of the large confinement entropy predicted by the molecular-dynamics simulations of his group, and its sensitive dependence on the molecular parameters of their wormlike chain model of double-stranded DNA. On the other hand, he doubts my assertion that the confinement entropy is already included in the interstrand repulsion free energy derived from osmotic stress measurements, which constitutes the major contribution to the packaging free energy used in recent continuum theories of this process. Harvey suggests instead that the confinement entropy should be added to this free energy as a separate term (using, for instance, the method described in my letter). I will argue that this addition is redundant, and, in a brief discussion of continuum theories, will also discuss his comments as relates to the work of other researchers.},
	issn = {0006-3495},
	doi = {10.1016/j.bpj.2013.11.4497},
	author = {Ben-Shaul, Avinoam}
}
@article { ISI:000341271500016,
	title = {Viral RNAs Are Unusually Compact},
	journal = {PLOS ONE},
	volume = {9},
	year = {2014},
	month = {SEP 4},
	abstract = {A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly.},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0105875},
	author = {Gopal, Ajaykumar and Egecioglu, Defne E. and Yoffe, Aron M. and Ben-Shaul, Avinoam and Rao, Ayala L. N. and Knobler, Charles M. and Gelbart, William M}
}
@article { ISI:000324303603734,
	title = {Theory and simulations of receptor binding in inter-cell adhesion and junction formation},
	journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
	volume = {245},
	year = {2013},
	note = {245th National Spring Meeting of the American-Chemical-Society (ACS), New Orleans, LA, APR 07-11, 2013},
	month = {APR 7},
	publisher = {Amer Chem Soc},
	issn = {0065-7727},
	author = {Wu, Yinghao and Shapiro, Lawrence and Honig, Barry and Ben-Shaul, Avinoam}
}
@article { ISI:000324755200001,
	title = {Counterion release in membrane-biopolymer interactions},
	journal = {SOFT MATTER},
	volume = {9},
	year = {2013},
	pages = {9268-9284},
	abstract = {When two oppositely charged macroions are brought into contact, a large fraction of the mobile counterions that previously surrounded each isolated macromolecule is released into the bulk solution, thereby increasing the counterions{\textquoteright} translational entropy. The entropy gain associated with this counterion release mechanism is the driving force for various macroion binding processes, such as protein-membrane, protein-DNA, and DNA-membrane complexation. In this review we focus on the role of counterion release in the interaction between charged macromolecules and oppositely charged lipid membranes. The electrostatic interaction is generally coupled to other degrees of freedom of the membrane, or of the adsorbed macroion. Thus, for example, when a basic protein adsorbs onto a binary fluid membrane comprising anionic and neutral lipids then, in addition to the release of the mobile counterions to the bulk solution, the protein polarizes the membrane composition by attracting the charged lipids to its immediate vicinity. This process, which enhances the electrostatic attraction, is partly hampered by the concomitant loss of two-dimensional (2D) lipid mixing entropy, so that the resulting lipid distribution reflects the balance between these opposing tendencies. In membranes containing both monovalent and multivalent lipids, as is often the case with biological membranes, the peripheral protein preferentially interacts with (and thus immobilizes) the multivalent lipids, because a smaller number of these lipids are needed to neutralize its charge. The monovalent {\textquoteleft}{\textquoteleft}counterlipids{\textquoteright}{\textquoteright} are thus free to translate in the remaining area of the membrane. This entropy-driven counterlipid release mechanism in 2D is analogous to the extensively studied phenomenon of DNA condensation by polyvalent cations in 3D. Being self-assembled fluid aggregates, lipid bilayers can respond to interactions with peripheral or integral (whether charged or neutral) macromolecules in various ways. Of particular interest in this review is the interplay between electrostatic interactions, the lipid composition degrees of freedom mentioned above, and the membrane curvature elasticity, as will be discussed in some detail in the context of the thermodynamic stability and phase behavior of lipid-DNA complexes (also known as {\textquoteleft}{\textquoteleft}lipoplexes{\textquoteright}{\textquoteright}). This article is primarily theoretical, but the systems and phenomena considered are directly related to and motivated by specific experiments. The theoretical modeling is generally based on mean-field level approaches, specifically the Poisson-Boltzmann theory for electrostatic interactions, sometimes in conjunction with coarse grained computer simulations.},
	issn = {1744-683X},
	doi = {10.1039/c3sm51419f},
	author = {Harries, Daniel and May, Sylvio and Ben-Shaul, Avinoam}
}
@article { ISI:000319318400001,
	title = {Entropy, Energy, and Bending of DNA in Viral Capsids},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {104},
	year = {2013},
	month = {MAY 21},
	pages = {L15-L17},
	abstract = {Inspired by novel single-molecule and bulk solution measurements, the physics underlying the forces and pressures involved in DNA packaging into bacteriophage capsids became the focus of numerous recent theoretical models. These fall into two general categories: Continuum-elastic theories (CT), and simulation studies-mostly of the molecular dynamics (MD) genre. Both types of models account for the dependence of the force, and hence the packaging free energy (Delta F), on the loaded DNA length, but differ markedly in interpreting their origin. While DNA confinement entropy is a dominant contribution to DF in the MD simulations, in the CT theories this role is fulfilled by interstrand repulsion, and there is no explicit entropy term. The goal of this letter is to resolve this apparent contradiction, elucidate the origin of the entropic term in the MD simulations, and point out its tacit presence in the CT treatments.},
	issn = {0006-3495},
	doi = {10.1016/j.bpj.2013.04.006},
	author = {Ben-Shaul, Avinoam}
}
@article { ISI:000316525600006,
	title = {Theory and Simulations of Adhesion Receptor Dimerization on Membrane Surfaces},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {104},
	year = {2013},
	month = {MAR 19},
	pages = {1221-1229},
	abstract = {The equilibrium constants of trans and cis dimerization of membrane bound (2D) and freely moving (3D) adhesion receptors are expressed and compared using elementary statistical-thermodynamics. Both processes are mediated by the binding of extracellular subdomains whose range of motion in the 2D environment is reduced upon dimerization, defining a thin reaction shell where dimer formation and dissociation take place. We show that the ratio between the 2D and 3D equilibrium constants can be expressed as a product of individual factors describing, respectively, the spatial ranges of motions of the adhesive domains, and their rotational freedom within the reaction shell. The results predicted by the theory are compared to those obtained from a novel, to our knowledge, dynamical simulations methodology, whereby pairs of receptors perform realistic translational, internal, and rotational motions in 2D and 3D. We use cadherins as our model system. The theory and simulations explain how the strength of cis and trans interactions of adhesive receptors are affected both by their presence in the constrained intermembrane space and by the 2D environment of membrane surfaces. Our work provides fundamental insights as to the mechanism of lateral clustering of adhesion receptors after cell-cell contact and, more generally, to the formation of lateral microclusters of proteins on cell surfaces.},
	issn = {0006-3495},
	doi = {10.1016/j.bpj.2013.02.009},
	author = {Wu, Yinghao and Honig, Barry and Ben-Shaul, Avinoam}
}
@article { ISI:000286008500029,
	title = {The ends of a large RNA molecule are necessarily close},
	journal = {NUCLEIC ACIDS RESEARCH},
	volume = {39},
	year = {2011},
	month = {JAN},
	pages = {292-299},
	abstract = {We show on general theoretical grounds that the two ends of single-stranded (ss) RNA molecules (consisting of roughly equal proportions of A, C, G and U) are necessarily close together, largely independent of their length and sequence. This is demonstrated to be a direct consequence of two generic properties of the equilibrium secondary structures, namely that the average proportion of bases in pairs is similar to 60\% and that the average duplex length is similar to 4. Based on mfold and Vienna computations on large numbers of ssRNAs of various lengths (1000-10 000 nt) and sequences (both random and biological), we find that the 5{\textquoteright}-3{\textquoteright} distance-defined as the sum of H-bond and covalent (ss) links separating the ends of the RNA chain-is small, averaging 15-20 for each set of viral sequences tested. For random sequences this distance is similar to 12, consistent with the theory. We discuss the relevance of these results to evolved sequence complementarity and specific protein binding effects that are known to be important for keeping the two ends of viral and messenger RNAs in close proximity. Finally we speculate on how our conclusions imply indistinguishability in size and shape of equilibrated forms of linear and covalently circularized ssRNA molecules.},
	issn = {0305-1048},
	doi = {10.1093/nar/gkq642},
	author = {Yoffe, Aron M. and Prinsen, Peter and Gelbart, William M and Ben-Shaul, Avinoam}
}
@article { ISI:000288644700057,
	title = {A Sequential Folding Model Predicts Length-Independent Secondary Structure Properties of Long ssRNA},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {115},
	year = {2011},
	month = {MAR 31},
	pages = {3193-3199},
	abstract = {We introduce a simple model for folding random-sequence RNA molecules, arguing that it provides a direct route to predicting and rationalizing several average properties of RNA secondary structures. The first folding step involves identifying the longest possible duplex, thereby dividing the molecule into a pair of daughter loops. Successive steps involve identifying similarly the longest duplex in each new pair of daughter loops, with this process proceeding sequentially until the loops are too small for a viable duplex to form. Approximate analytical solutions are found for the average fraction of paired bases, the average duplex length, and the average loop size, all of which are shown to be independent of sequence length for long enough molecules. Numerical solutions to the model provide estimates for these average secondary structure properties that agree well with those obtained from more sophisticated folding algorithms. We also use the model to derive the asymptotic power law for the dependence of the maximum ladder distance on chain length.},
	issn = {1520-6106},
	doi = {10.1021/jp110680e},
	author = {Fang, Li Tai and Yoffe, Aron M. and Gelbart, William M and Ben-Shaul, Avinoam}
}
@article { ISI:000296516800052,
	title = {The size of RNA as an ideal branched polymer},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {135},
	year = {2011},
	month = {OCT 21},
	abstract = {Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e. g., denatured states) of the same sequence of monomers. To elucidate the dependence of compactness on the nature and extent of branching, we represent ssRNA secondary structures as tree graphs which we treat as ideal branched polymers, and use a theorem of Kramers for evaluating their root-mean-square radius of gyration, (R) over cap (g) = root \&lt; R(g)(2)\&gt;. We consider two sets of sequences-random and viral-with nucleotide sequence lengths (N) ranging from 100 to 10 000. The RNAs of icosahedral viruses are shown to be more compact (i.e., to have smaller (R) over cap (g) ) than the random RNAs. For the random sequences we find that (R) over cap (g) varies as N(1/3). These results are contrasted with the scaling of (R) over cap (g) for ideal randomly branched polymers (N(1/4)), and with that from recent modeling of (relatively short, N \&lt;= 161) RNA tertiary structures (N(2/5)). (C) 2011 American Institute of Physics. [doi: 10.1063/1.3652763]},
	issn = {0021-9606},
	doi = {10.1063/1.3652763},
	author = {Fang, Li Tai and Gelbart, William M and Ben-Shaul, Avinoam}
}
@article { ISI:000293167900043,
	title = {Transforming binding affinities from three dimensions to two with application to cadherin clustering},
	journal = {NATURE},
	volume = {475},
	year = {2011},
	month = {JUL 28},
	pages = {510-U107},
	abstract = {Membrane-bound receptors often form large assemblies resulting from binding to soluble ligands, cell-surface molecules on other cells and extracellular matrix proteins(1). For example, the association of membrane proteins with proteins on different cells (trans-interactions) can drive the oligomerization of proteins on the same cell(2) (cis-interactions). A central problem in understanding the molecular basis of such phenomena is that equilibrium constants are generally measured in three-dimensional solution and are thus difficult to relate to the two-dimensional environment of a membrane surface. Here we present a theoretical treatment that converts three-dimensional affinities to two dimensions, accounting directly for the structure and dynamics of the membrane-bound molecules. Using a multiscale simulation approach, we apply the theory to explain the formation of ordered, junction-like clusters by classical cadherin adhesion proteins. The approach features atomic-scale molecular dynamics simulations to determine interdomain flexibility, Monte Carlo simulations of multidomain motion and lattice simulations of junction formation(3). A finding of general relevance is that changes in interdomain motion on trans-binding have a crucial role in driving the lateral, cis-, clustering of adhesion receptors.},
	issn = {0028-0836},
	doi = {10.1038/nature10183},
	author = {Wu, Yinghao and Vendome, Jeremie and Shapiro, Lawrence and Ben-Shaul, Avinoam and Honig, Barry}
}
@article { ISI:000282809700029,
	title = {Cooperativity between trans and cis interactions in cadherin-mediated junction formation},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
	volume = {107},
	year = {2010},
	month = {OCT 12},
	pages = {17592-17597},
	abstract = {Intercellullar junctions formed by cadherins, including desmosomes and adherens junctions, comprise two dimensional arrays of {\textquoteleft}{\textquoteleft}trans{\textquoteright}{\textquoteright} dimers formed between monomers emanating from opposing cell surfaces. Lateral {\textquoteleft}{\textquoteleft}cis{\textquoteright}{\textquoteright} interfaces between cadherins from the same cell surface have been proposed to play a role in cadherin clustering. Although the molecular details of cis interactions remain uncertain, they must define an anisotropic arrangement where binding is favorable only in certain orientations. Here we report Monte Carlo simulations performed on a 2D lattice constructed to account for the anisotropy in cadherin cis interactions. A crucial finding is that the {\textquoteleft}{\textquoteleft}phase transition{\textquoteright}{\textquoteright} between freely diffusing cadherin monomers and dimers and a condensed ordered 2D junction formed by dimers alone is a cooperative process involving both trans and cis interactions. Moreover, cis interactions, despite being too weak to be measured in solution, are critical to the formation of an ordered junction structure. We discuss these results in light of available experimental information on cadherin binding free energies that are transformed from their bulk solution values to interaction energies on a 2D lattice.},
	issn = {0027-8424},
	doi = {10.1073/pnas.1011247107},
	author = {Wu, Yinghao and Jin, Xiangshu and Harrison, Oliver and Shapiro, Lawrence and Honig, Barry H. and Ben-Shaul, Avinoam}
}
@inbook {14539,
	title = {Matrix Formalism for Sequence-Specific Polymer Binding to Multicomponent Lipid Membranes},
	booktitle = {Membrane-Active Peptides: Methods and Results on Structure and Function},
	year = {2009},
	pages = {29-52},
	publisher = {International University Line},
	organization = {International University Line},
	address = {La Jolla, California},
	author = {Teif,  V.B. and Harries, D and Lando, D.Y. and Ben-Shaul, A},
	editor = {Castanho, M.}
}
@article { ISI:000272115200010,
	title = {From Branched Networks of Actin Filaments to Bundles},
	journal = {CHEMPHYSCHEM},
	volume = {10},
	year = {2009},
	month = {NOV 9},
	pages = {2818-2827},
	abstract = {Cross-linking proteins can mediate the emergence of rigid bundles from a dense branched network of actin filaments. To enable their binding, the filaments must first bend towards each other. We derive an explicit criterion for the onset of bundling, in terms of the initial length of filaments L, their spacing b, and cross-linker concentration f, reflecting the balance between bending and binding energies. Our model system contains actin, the branching complex Arp2/3 and the bundling protein fascin. In the first distinct stage, during which only actin and Arp2/3 are active, an entangled aster-like mesh of actin filaments is formed. Tens of seconds later, when filaments at the aster periphery are long and barely branched, a sharp transition takes place into a star-like structure, marking the onset of bundling. Now fascin and actin govern bundle growth; Arp2/3 plays no role. Using kinetic Monte Carlo simulations we calculate the temporal evolution of b and L, and predict the onset of bundling as a function of f. Our predictions are in good qualitative agreement with several new experiments that are reported herein and demonstrate how f controls the aster-star transition and bundle length. We also present two models for aster growth corresponding to different experimental realizations. The first treats filament and bundle association as an irreversible sequence of elongation-association steps. The second, applicable for low f, treats bundling as a reversible self-assembly process, where the optimal bundle size is dictated by the balance between surface and bending energies. Finally, we discuss the relevance of our conclusions for the lamellipodium to filopodia transition in living cells, noting that bundles are more likely nucleated by {\textquoteleft}{\textquoteleft}tip complex{\textquoteright}{\textquoteright} cross-linkers (e.g. mDia2 or Ena/VASP), whereas fascin is mainly involved in bundle maintenance.},
	issn = {1439-4235},
	doi = {10.1002/cphc.200900615},
	author = {Brill-Karniely, Yifat and Ideses, Yaron and Bernheim-Groswasser, Anne and Ben-Shaul, Avinoam}
}
@article { ISI:000267972700032,
	title = {Linking molecular affinity and cellular specificity in cadherin-mediated adhesion},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
	volume = {106},
	year = {2009},
	month = {JUL 14},
	pages = {11594-11599},
	abstract = {Many cell-cell adhesive events are mediated by the dimerization of cadherin proteins presented on apposing cell surfaces. Cadherin-mediated processes play a central role in the sorting of cells into separate tissues in vivo, but in vitro assays aimed at mimicking this behavior have yielded inconclusive results. In some cases, cells that express different cadherins exhibit homotypic cell sorting, forming separate cell aggregates, whereas in other cases, intermixed aggregates are formed. A third pattern is observed for mixtures of cells expressing either N- or E-cadherin, which form distinct homotypic aggregates that adhere to one another through a heterotypic interface. The molecular basis of cadherin-mediated cell patterning phenomena is poorly understood, in part because the relationship between cellular adhesive specificity and intermolecular binding free energies has not been established. To clarify this issue, we have measured the dimerization affinities of N-cadherin and E-cadherin. These proteins are similar in sequence and structure, yet are able to mediate homotypic cell patterning behavior in a variety of tissues. N-cadherin is found to form homodimers with higher affinity than does E-cadherin and, unexpectedly, the N/E-cadherin heterophilic binding affinity is intermediate in strength between the 2 homophilic affinities. We can account for observed cell aggregation behaviors by using a theoretical framework that establishes a connection between molecular affinities and cell-cell adhesive specificity. Our results illustrate how graded differences between different homophilic and heterophilic cadherin dimerizaton affinities can result in homotypic cell patterning and, more generally, show how proteins that are closely related can, nevertheless, be responsible for highly specific cellular adhesive behavior.},
	issn = {0027-8424},
	doi = {10.1073/pnas.0905349106},
	author = {Katsamba, P. and Carroll, K. and Ahlsena, G. and Bahna, F. and Vendome, J. and Posy, S. and Rajebhosale, M. and Price, S. and Jessell, T. M. and Ben-Shaul, A and L. Shapiro and Honig, Barry H.}
}
@article { ISI:000264432500007,
	title = {Arp2/3 Branched Actin Network Mediates Filopodia-Like Bundles Formation In Vitro},
	journal = {PLOS ONE},
	volume = {3},
	year = {2008},
	month = {SEP 29},
	abstract = {During cellular migration, regulated actin assembly takes place at the cell leading edge, with continuous disassembly deeper in the cell interior. Actin polymerization at the plasma membrane results in the extension of cellular protrusions in the form of lamellipodia and filopodia. To understand how cells regulate the transformation of lamellipodia into filopodia, and to determine the major factors that control their transition, we studied actin self-assembly in the presence of Arp2/3 complex, WASp-VCA and fascin, the major proteins participating in the assembly of lamellipodia and filopodia. We show that in the early stages of actin polymerization fascin is passive while Arp2/3 mediates the formation of dense and highly branched aster-like networks of actin. Once filaments in the periphery of an aster get long enough, fascin becomes active, linking the filaments into bundles which emanate radially from the aster{\textquoteright}s surface, resulting in the formation of star-like structures. We show that the number of bundles nucleated per star, as well as their thickness and length, is controlled by the initial concentration of Arp2/3 complex ([Arp2/3]). Specifically, we tested several values of [Arp2/3] and found that for given initial concentrations of actin and fascin, the number of bundles per star, as well as their length and thickness are larger when [Arp2/3] is lower. Our experimental findings can be interpreted and explained using a theoretical scheme which combines Kinetic Monte Carlo simulations for aster growth, with a simple mechanistic model for bundles{\textquoteright} formation and growth. According to this model, bundles emerge from the aster{\textquoteright}s (sparsely branched) surface layer. Bundles begin to form when the bending energy associated with bringing two filaments into contact is compensated by the energetic gain resulting from their fascin linking energy. As time evolves the initially thin and short bundles elongate, thus reducing their bending energy and allowing them to further associate and create thicker bundles, until all actin monomers are consumed. This process is essentially irreversible on the time scale of actin polymerization. Two structural parameters, L, which is proportional to the length of filament tips at the aster periphery and b, the spacing between their origins, dictate the onset of bundling; both depending on [Arp2/3]. Cells may use a similar mechanism to regulate filopodia formation along the cell leading edge. Such a mechanism may allow cells to have control over the localization of filopodia by recruiting specific proteins that regulate filaments length (e. g., Dia2) to specific sites along lamellipodia.},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0003297},
	author = {Ideses, Yaron and Brill-Karniely, Yifat and Haviv, Lior and Ben-Shaul, Avinoam and Bernheim-Groswasser, Anne}
}
@article { ISI:000257889400017,
	title = {The {\textquoteleft}{\textquoteleft}Electrostatic-Switch{\textquoteright}{\textquoteright} mechanism: Monte Carlo study of MARCKS-membrane interaction},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {95},
	year = {2008},
	month = {AUG 15},
	pages = {1745-1757},
	abstract = {The binding of the myristoylated alanine-rich C kinase substrate (MARCKS) to mixed, fluid, phospholipid membranes is modeled with a recently developed Monte Carlo simulation scheme. The central domain of MARCKS is both basic (zeta = +13) and hydrophobic (five Phe residues), and is flanked with two long chains, one ending with the myristoylated N-terminus. This natively unfolded protein is modeled as a flexible chain of {\textquoteleft}{\textquoteleft}beads{\textquoteright}{\textquoteright} representing the amino acid residues. The membranes contain neutral (zeta = 0), monovalent (zeta = -1), and tetravalent (zeta = -4) lipids, all of which are laterally mobile. MARCKS-membrane interaction is modeled by Debye-Huckel electrostatic potentials and semiempirical hydrophobic energies. In agreement with experiment, we find that membrane binding is mediated by electrostatic attraction of the basic domain to acidic lipids and membrane penetration of its hydrophobic moieties. The binding is opposed by configurational entropy losses and electrostatic membrane repulsion of the two long chains, and by lipid demixing upon adsorption. The simulations provide a physical model for how membrane-adsorbed MARCKS attracts several PIP2 lipids (zeta = -4) to its vicinity, and how phosphorylation of the central domain (zeta = +13 to zeta = +7) triggers an {\textquoteleft}{\textquoteleft}electrostatic switch{\textquoteright}{\textquoteright}, which weakens both the membrane interaction and PIP(2) sequestration. This scheme captures the essence of {\textquoteleft}{\textquoteleft}discreteness of charge{\textquoteright}{\textquoteright} at membrane surfaces and can examine the formation of membrane-mediated multicomponent macromolecular complexes that function in many cellular processes.},
	issn = {0006-3495},
	doi = {10.1529/biophysj.108.132522},
	author = {Tzlil, Shelly and Murray, Diana and Ben-Shaul, Avinoam}
}
@article { ISI:000254901300002,
	title = {Matrix formalism for site-specific binding of unstructured proteins to multicomponent lipid membranes},
	journal = {JOURNAL OF PEPTIDE SCIENCE},
	volume = {14},
	year = {2008},
	note = {2nd Workshop on Biophysics of Membrane-Active Peptides, Lisbon, PORTUGAL, 2007},
	month = {APR},
	pages = {368-373},
	abstract = {We describe a new approach to calculate the binding of flexible peptides and unfolded proteins to multicomponent lipid membranes. The method is based on the transfer matrix formalism of statistical mechanics recently described as a systematic tool to study DNA-protein-drug binding in gene regulation. Using the energies of interaction of the individual polymer segments with different membrane lipid species and the scaling corrections due to polymer looping, we calculate polymer adsorption characteristics and the degree of sequestration of specific membrane lipids. The method is applied to the effector domain of the MARCKS (myristoylated alanine rich C kinase substrate) protein known to be involved in signal transduction through membrane binding. The calculated binding constants of the MARCKS(151-175) peptide and a series of related peptides to mixed PC/PS/PIP2 membranes are in satisfactory agreement with in vitro experiments. Copyright (c) 2008 European Peptide Society and John Wiley \&amp; Sons, Ltd.},
	issn = {1075-2617},
	doi = {10.1002/pse.994},
	author = {Teif, Vladimir B and Harries, Daniel and Lando, Dmitri Y and Ben-Shaul, Avinoam}
}
@article { ISI:000256492300012,
	title = {Modulation of the spontaneous curvature and bending rigidity of lipid membranes by interfacially adsorbed amphipathic peptides},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {112},
	year = {2008},
	month = {JUN 12},
	pages = {6988-6996},
	abstract = {Amphipathic alpha-helical peptides are often ascribed an ability to induce curvature stress in lipid membranes. This may lead directly to a bending deformation of the host membrane, or it may promote the formation of defects that involve highly curved lipid layers present in membrane pores, fusion intermediates, and solubilized peptide-micelle complexes. The driving force is the same in all cases: peptides induce a spontaneous curvature in the host lipid layer, the sign of which depends sensitively on the peptide{\textquoteright}s structural properties. We provide a quantitative account for this observation on the basis of a molecular-level method. To this end, we consider a lipid membrane with peptides interfacially adsorbed onto one leaflet at high peptide-to-lipid ratio. The peptides are modeled generically as rigid cylinders that interact with the host membrane through a perturbation of the conformational properties of the lipid chains. Through the use of a molecular-level chain packing theory, we calculate the elastic properties, that is, the spontaneous curvature and bending stiffness, of the peptide-decorated lipid membrane as a function of the peptide{\textquoteright}s insertion depth. We find a positive spontaneous curvature (preferred bending of the membrane away from the peptide) for small penetration depths of the peptide. At a penetration depth roughly equal to half-insertion into the hydrocarbon core, the spontaneous curvature changes sign, implying negative spontaneous curvature (preferred bending of the membrane toward the peptide) for large penetration depths. Despite thinning of the membrane upon peptide insertion, we find an increase in the bending stiffness. We discuss these findings in terms of how the peptide induces elastic stress.},
	issn = {1520-6106},
	doi = {10.1021/jp711107y},
	author = {Zemel, Assaf and Ben-Shaul, Avinoam and May, Sylvio}
}
@article { ISI:000260597400018,
	title = {Predicting the sizes of large RNA molecules},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
	volume = {105},
	year = {2008},
	month = {OCT 21},
	pages = {16153-16158},
	abstract = {We present a theory of the dependence on sequence of the three-dimensional size of large single-stranded (ss) RNA molecules. The work is motivated by the fact that the genomes of many viruses are large ssRNA molecules-often several thousand nucleotides long-and that these RNAs are spontaneously packaged into small rigid protein shells. We argue that there has been evolutionary pressure for the genome to have overall spatial properties-including an appropriate radius of gyration, R-g-that facilitate this assembly process. For an arbitrary RNA sequence, we introduce the (thermal) average maximum ladder distance (\&lt; MLD \&gt;) and use it as a measure of the {\textquoteleft}{\textquoteleft}extendedness{\textquoteright}{\textquoteright} of the RNA secondary structure. The \&lt; MLD \&gt; values of viral ssRNAs that package into capsids of fixed size are shown to be consistently smaller than those for randomly permuted sequences of the same length and base composition, and also smaller than those of natural ssRNAs that are not under evolutionary pressure to have a compact native form. By mapping these secondary structures onto a linear polymer model and by using \&lt; MLD \&gt; as a measure of effective contour length, we predict the R-g values of viral ssRNAs are smaller than those of nonviral sequences. More generally, we predict the average \&lt; MLD \&gt; values of large nonviral ssRNAs scale as N-0.67 +/- 0.01, where N is the number of nucleotides, and that their R-g values vary as \&lt; MLD \&gt;(0.5) in an ideal solvent, and hence as N-0.34. An alternative analysis, which explicitly includes all branches, is introduced and shown to yield consistent results.},
	issn = {0027-8424},
	doi = {10.1073/pnas.0808089105},
	author = {Yoffe, Aron M. and Prinsen, Peter and Gopal, Ajaykumar and Knobler, Charles M. and Gelbart, William M and Ben-Shaul, Avinoam}
}
@article { ISI:000236472500023,
	title = {Reconstitution of the transition from lamellipodium to filopodium in a membrane-free system},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
	volume = {103},
	year = {2006},
	month = {MAR 28},
	pages = {4906-4911},
	abstract = {The cellular cytoskeleton is a complex dynamical network that constantly remodels as cells divide and move. This reorganization process occurs not only at the cell membrane, but also in the cell interior (bulk). During locomotion, regulated actin assembly near the plasma membrane produces lamellipodia and filopodia. Therefore, most in vitro experiments explore phenomena taking place in the vicinity of a surface. To understand how the molecular machinery of a cell self-organizes in a more general way, we studied bulk polymerization of actin in the presence of actin-related protein 2/3 complex and a nucleation promoting factor as a model for actin assembly in the cell interior separate from membranes. Bulk polymerization of actin in the presence of the verprolin homology, cofilin homology, and acidic region, domain of Wiskott-Aldrich syndrome protein, and actin-related protein 2/3 complex results in spontaneous formation of diffuse aster-like structures. In the presence of fascin these asters transition into stars with bundles of actin filaments growing from the surface, similar to star-like structures recently observed in vivo. The transition from asters to stars depends on the ratio [fascin]/[G actin]. The polarity of the actin filaments during the transition is preserved, as in the transition from lamellipodia to filopodia. Capping protein inhibits star formation. Based on these experiments and kinetic Monte Carlo simulations, we propose a model for the spontaneous self-assembly of asters and their transition into stars. This mechanism may apply to the transition from lamellipodia to filopodia in vivo.},
	issn = {0027-8424},
	doi = {10.1073/pnas.0508269103},
	author = {Haviv, L and Brill-Karniely, Y and Mahaffy, R and Backouche, F and Ben-Shaul, A and Pollard, TD and Bernheim-Groswasser, A}
}
@article { ISI:000227494600022,
	title = {Domain formation induced by the adsorption of charged proteins on mixed lipid membranes},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {88},
	year = {2005},
	month = {MAR},
	pages = {1702-1714},
	abstract = {Peripheral proteins can trigger the formation of domains in mixed. uid- like lipid membranes. We analyze the mechanism underlying this process for proteins that bind electrostatically onto a. at two- component membrane, composed of charged and neutral lipid species. Of particular interest are membranes in whichthe hydrocarbon lipid tails tend to segregate owing to nonideal chain mixing,but the ( protein- free) lipid membrane is nevertheless stable due to the electrostatic repulsion between the charged lipid headgroups. The adsorption of charged, say basic, proteins onto a membrane containing anionic lipids induces local lipid demixing, whereby charged lipids migrate toward ( or away from) the adsorption site, so as to minimize the electrostatic binding free energy. Apart from reducing lipid headgroup repulsion, this process creates a gradient in lipid composition around the adsorption zone, and hence a line energy whose magnitude depends on the protein{\textquoteright}s size and charge and the extent of lipid chain nonideality. Above a certain critical lipid nonideality, the line energy islarge enough to induce domain formation, i. e., protein aggregation and, concomitantly, macroscopic lipid phase separation. We quantitatively analyze the thermodynamic stability of the dressed membrane based on nonlinear Poisson- Boltzmann theory, accounting for both the microscopic characteristics of the proteins and lipid composition modulations at and around the adsorption zone. Spinodal surfaces and critical points of the dressed membranes are calculated for several different model proteins of spherical and disklike shapes. Among the models studied we. nd the most substantial protein- induced membrane destabilization for disk- like proteins whose charges are concentrated in the membrane- facing surface. If additional charges reside on the side faces of the proteins, direct protein- protein repulsion diminishes considerably the propensity fordomain formation. Generally, a highly charged. at face of a macroion appears most ef. cient in inducing large compositional gradients, hence a large and unfavorable line energy and consequently lateral macroion aggregation and, concomitantly, macroscopic lipid phase separation.},
	issn = {0006-3495},
	doi = {10.1529/biophysj.104.048132},
	author = {Mbamala, EC and Ben-Shaul, A and May, S}
}
@article { ISI:000232933300013,
	title = {Flexible charged macromolecules on mixed fluid lipid membranes: Theory and Monte Carlo simulations},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {89},
	year = {2005},
	month = {NOV},
	pages = {2972-2987},
	abstract = {Fluid membranes containing charged lipids enhance binding of oppositely charged proteins by mobilizing these lipids into the interaction zone, overcoming the concomitant entropic losses due to lipid segregation and lower conformational freedom upon macromolecule adsorption. We study this energetic-entropic interplay using Monte Carlo simulations and theory. Our model system consists of a flexible cationic polyelectrolyte, interacting, via Debye-Huckel and short-ranged repulsive potentials, with membranes containing neutral lipids, 1\% tetravalent, and 10\% ( or 1\%) monovalent anionic lipids. Adsorption onto a fluid membrane is invariably stronger than to an equally charged frozen or uniform membrane. Although monovalent lipids may suffice for binding rigid macromolecules, polyvalent counter-lipids ( e. g., phosphatidylinositol 4,5 bisphosphate), whose entropy loss upon localization is negligible, are crucial for binding flexible macromolecules, which lose conformational entropy upon adsorption. Extending Rosenbluth{\textquoteright}s Monte Carlo scheme we directly simulate polymer adsorption on fluid membranes. Yet, we argue that similar information could be derived from a biased superposition of quenched membrane simulations. Using a simple cell model we account for surface concentration effects, and show that the average adsorption probabilities on annealed and quenched membranes coincide at vanishing surface concentrations. We discuss the relevance of our model to the electrostatic-switch mechanism of, e. g., the myristoylated alanine-rich C kinase substrate protein.},
	issn = {0006-3495},
	doi = {10.1529/biophysj.105.068387},
	author = {Tzlil, S and Ben-Shaul, A}
}
@article { ISI:000228859400005,
	title = {Perturbation of a lipid membrane by amphipathic peptides and its role in pore formation},
	journal = {EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS},
	volume = {34},
	year = {2005},
	month = {MAY},
	pages = {230-242},
	abstract = {We study the structural and energetic consequences of (α-helical) amphipathic peptide adsorption onto a lipid membrane and the subsequent formation of a transmembrane peptide pore. Initially, each peptide binds to the membrane surface, with the hydrophobic face of its cylinder-like body inserted into the hydrocarbon core. Pore formation results from subsequent peptide crowding, oligomerization, and eventually reorientation along the membrane normal. We have theoretically analyzed three peptide-membrane association states: interfacially-adsorbed monomeric and dimeric peptides, and the multi-peptide transmembrane pore state. Our molecular-level model for the lipid bilayer is based on a combination of detailed chain packing theory and a phenomenological description of the headgroup region. We show that the membrane perturbation free energy depends critically on peptide orientation: in the transmembrane pore state the lipid perturbation energy, per peptide, is smaller than in the adsorbed state. This suggests that the gain in conformational freedom of the lipid chains is a central driving force for pore formation. We also find a weak, lipid-mediated, gain in membrane perturbation free energy upon dimerization of interfacially-adsorbed peptides. Although the results pertain mainly to weakly-charged peptides, they reveal general properties of the interaction of amphipathic peptides with lipid membranes.},
	issn = {0175-7571},
	doi = {10.1007/s00249-004-0445-9},
	author = {Zemel, A and Ben-Shaul, A and May, S}
}
@article { ISI:000229807200026,
	title = {Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through beta-strand swapping},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
	volume = {102},
	year = {2005},
	month = {JUN 14},
	pages = {8531-8536},
	abstract = {Cadherins constitute a family of cell-surface proteins that mediate intercellular adhesion through the association of protomers presented from juxtaposed cells. Differential cadherin expression leads to highly specific intercellular interactions in vivo. This cell-cell specificity is difficult to understand at the molecular level because individual cadherins within a given subfamily are highly similar to each other both in sequence and structure, and they dimerize with remarkably low binding affinities. Here, we provide a molecular model that accounts for these apparently contradictory observations. The model is based in part on the fact that cadherins bind to one another by {\textquoteleft}{\textquoteleft}swapping{\textquoteright}{\textquoteright} the N-terminal beta-strands of their adhesive domains. An inherent feature of strand swapping (or, more generally, the domain swapping phenomenon) is that {\textquoteleft}{\textquoteleft}closed{\textquoteright}{\textquoteright} monomeric conformations act as competitive inhibitors of dinner formation, thus lowering affinities even when the dimer interface has the characteristics of high-affinity complexes. The model describes quantitatively how small affinity differences between low-affinity cadherin dimers are amplified by multiple cadherin interactions to establish large specificity effects at the cellular level. It is shown that cellular specificity would not be observed if cadherins bound with high affinities, thus emphasizing the crucial role of strand swapping in cell-cell adhesion. Numerical estimates demonstrate that the strength of cellular adhesion is extremely sensitive to the concentration of cadherins expressed at the cell surface. We suggest that the domain swapping mechanism is used by a variety of cell-adhesion proteins and that related mechanisms to control affinity and specificity are exploited in other systems.},
	issn = {0027-8424},
	doi = {10.1073/pnas.0503319102},
	author = {Chen, CP and Posy, S. and Ben-Shaul, A and L. Shapiro and Honig, BH}
}
@article { ISI:000188535700043,
	title = {Enveloping of charged proteins by lipid bilayers},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {108},
	year = {2004},
	month = {JAN 29},
	pages = {1491-1496},
	abstract = {The ability of a mixed lipid bilayer composed of neutral and charged lipids to encapsulate an oppositely charged protein is studied with use of a simple theoretical model. The free energy of the bilayer-enveloped protein complex is expressed as a sum of electrostatic and curvature elasticity contributions, and compared to that of a protein adsorbed on a mixed planar bilayer. The electrostatic adsorption energy on the planar bilayer is calculated by using an extended Poisson-Boltzmann approach, which allows for local lipid charge modulation in the adsorption zone. We find that the electrostatic interactions favor the wrapped state, while the bending energy prefers the planar bilayer. To enable the transition from the adsorbed to enveloped protein geometry, there is a minimal necessary protein charge. This {\textquoteleft}{\textquoteleft}crossover{\textquoteright}{\textquoteright} charge depends on the bending rigidity of the lipid membrane and the (composition dependent) spontaneous curvature of its constituent monolayers. The values for the crossover charge predicted by the theory are in line with the charge necessary for peptide shuttles to penetrate cell membranes.},
	issn = {1520-6106},
	doi = {10.1021/jp036501z},
	author = {Harries, D and Ben-Shaul, A and Szleifeo, I}
}
@article { ISI:000222035200021,
	title = {Membrane perturbation induced by interfacially adsorbed peptides},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {86},
	year = {2004},
	month = {JUN},
	pages = {3607-3619},
	abstract = {The structural and energetic characteristics of the interaction between interfacially adsorbed (partially inserted) a-helical, amphipathic peptides and the lipid bilayer substrate are studied using a molecular level theory of lipid chain packing in membranes. The peptides are modeled as {\textquoteleft}{\textquoteleft}amphipathic cylinders{\textquoteright}{\textquoteright} characterized by a well-defined polar angle. Assuming two-dimensional nematic order of the adsorbed peptides, the membrane perturbation free energy is evaluated using a cell-like model; the peptide axes are parallel to the membrane plane. The elastic and interfacial contributions to the perturbation free energy of the {\textquoteleft}{\textquoteleft}peptide-dressed{\textquoteright}{\textquoteright} membrane are evaluated as a function of: the peptide penetration depth into the bilayer{\textquoteright}s hydrophobic core, the membrane thickness, the polar angle, and the lipid/peptide ratio. The structural properties calculated include the shape and extent of the distorted (stretched and bent) lipid chains surrounding the adsorbed peptide, and their orientational (C-H) bond order parameter profiles. The changes in bond order parameters attendant upon peptide adsorption are in good agreement with magnetic resonance measurements. Also consistent with experiment, our model predicts that peptide adsorption results in membrane thinning. Our calculations reveal pronounced, membrane-mediated, attractive interactions between the adsorbed peptides, suggesting a possible mechanism for lateral aggregation of membrane-bound peptides. As a special case of interest, we have also investigated completely hydrophobic peptides, for which we find a strong energetic preference for the transmembrane (inserted) orientation over the horizontal (adsorbed) orientation.},
	issn = {0006-3495},
	doi = {10.1529/biophysj.103.033605},
	author = {Zemel, A and Ben-Shaul, A and May, S}
}
@article { ISI:000187996400003,
	title = {Modeling of cationic lipid-DNA complexes},
	journal = {CURRENT MEDICINAL CHEMISTRY},
	volume = {11},
	year = {2004},
	month = {JAN},
	pages = {151-167},
	abstract = {Cationic lipid-DNA complexes, often referred to as lipoplexes, are formed spontaneously in aqueous solutions upon mixing DNA and liposomes composed of cationic and nonionic lipids. Understanding the mechanisms underlying lipoplex formation, structure and phase behavior is crucial for their further development and design as non-viral transfection vectors in gene therapy. From a physical point of view, lipoplexes are ordered, self-assembled, composite aggregates. Their preferred spatial geometry and phase behavior are governed by a delicate coupling between the electrostatic interactions which drive lipoplex formation and the elastic properties of the constituent lipid layers, both depending on the molecular nature and composition of the lipid mixture. In this review we outline some recent efforts to model the microscopic structure, energetic and phase behavior of cationic lipid-DNA mixtures, focusing on the two principal aggregation geometries: the lamellar (L-alpha(C)), or {\textquoteleft}{\textquoteleft}sandwich{\textquoteright}{\textquoteright} complexes, and the hexagonal (H-II(C)), or {\textquoteleft}{\textquoteleft}honeycomb{\textquoteright}{\textquoteright} complexes. We relate the structural and thermodynamic properties of these two {\textquoteleft}{\textquoteleft}canonical{\textquoteright}{\textquoteright} lipoplex morphologies to their appearance in phase diagrams of DNA-lipid mixtures, emphasizing the crucial role fulfilled by the molecular packing characteristics of the cationic and neutral lipids, as reflected in the curvature elastic properties of the mixed lipid layer.},
	issn = {0929-8673},
	doi = {10.2174/0929867043456142},
	author = {May, S and Ben-Shaul, A}
}
@article { ISI:000220567600012,
	title = {A statistical-thermodynamic model of viral budding},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {86},
	year = {2004},
	month = {APR},
	pages = {2037-2048},
	abstract = {We present a simple statistical thermodynamic model for budding of viral nucleocapsids at the cell membrane. The membrane is modeled as a flexible lipid bilayer embedding linker (spike) proteins, which serve to anchor and thus wrap the membrane around the viral capsids. The free energy of a single bud is expressed as a sum of the bending energy of its membrane coat, the spike-mediated capsid-membrane adhesion energy, and the line energy associated with the bud{\textquoteright}s rim, all depending on the extent of wrapping (i.e., bud size), and density of spikes in the curved membrane. This self-energy is incorporated into a simple free energy functional for the many-bud system, allowing for different spike densities, and hence entropy, in the curved (budding) and planar membrane regions, as well as for the configurational entropy of the polydisperse bud population. The equilibrium spike densities in the coexisting, curved and planar, membrane regions are calculated as a function of the membrane bending energy and the spike-mediated adhesion energy, for different spike and nucleocapsid concentrations in the membrane plane, as well as for several values of the bud{\textquoteright}s rim energy. We show that complete budding (full wrapping of nucleocapsids) can only take place if the adhesion energy exceeds a certain, critical, bending free energy. Whenever budding takes place, the spike density in the mature virions is saturated, i.e., all spike adhesion sites are occupied. The rim energy plays an important role in determining the size distribution of buds. The fraction of fully wrapped buds increases as this energy increases, resulting eventually in an all-or-nothing mechanism, whereby nucleocapsids at the plasma membrane are either fully enveloped or completely naked (just touching the membrane). We also find that at low concentrations all capsids arriving at the membrane get tightly and fully enveloped. Beyond a certain concentration, corresponding approximately to a stoichiometric spike/capsid ratio, newly arriving capsids cannot be fully wrapped; i.e., the budding yield decreases.},
	issn = {0006-3495},
	author = {Tzlil, S and Deserno, M and Gelbert, WM and Ben-Shaul, A}
}
@article { ISI:000223532500010,
	title = {Tilt modulus of a lipid monolayer},
	journal = {EUROPEAN PHYSICAL JOURNAL E},
	volume = {14},
	year = {2004},
	month = {JUL},
	pages = {299-308},
	abstract = {In addition to the familiar bending and stretching deformations, lipid monolayers and bilayers in their disordered state are often subjected to tilt deformations, occurring for instance in structural rearrangements accompanying membrane fusion, or upon insertion of {\textquoteleft}{\textquoteleft}oblique{\textquoteright}{\textquoteright} hydrophobic proteins into lipid bilayers. We study the elastic response of a flat lipid monolayer to a tilt deformation, using the spatial and conformational average of the chain end-to-end vector from the membrane normal to define a macroscopic membrane tilt. The physical origin and magnitude of the corresponding tilt modulus k(t) is analyzed using two complementary theoretical approaches. The first is a phenomenological model showing that the tilt and bending deformations are decoupled and the effects of inter-chain correlations on the tilt modulus is small. The second is based on a molecular-level mean-field theory of chain packing, enabling numerical evaluation of the tilt modulus for realistic, multi-conformation, chain models. Both approaches reveal that the tilt modulus involves two major contributions. The first is elastic in origin, arising from the stretching of the hydrocarbon chains upon a tilt deformation and reflecting the loss of chain conformational freedom associated with chain stretching. The second, purely entropic, contribution results from the constraints imposed by a tilt deformation on the fluctuations of chain director orientations. Using the chain-packing theory we compute the two contributions numerically as a function of the cross-sectional area per chain. The elastic and entropic terms are shown to dominate the value of k(t) for small and large areas per chain, respectively. For typical cross-sectional areas of lipid chains in biological membranes they areof comparable magnitude, yielding k(t) approximate to 0.2k(B)T/Angstrom(2).},
	issn = {1292-8941},
	doi = {10.1140/epje/i2004-10019-y},
	author = {May, S and Kozlovsky, Y and Ben-Shaul, A and Kozlov, MM}
}
@inbook {12343,
	title = {Membrane-Macromolecule Interactions and their Structural Consequences},
	booktitle = {Planar Lipid Bilayers (BLM{\textquoteright}s) and their Applications},
	volume = {7},
	year = {2003},
	pages = {315-346},
	publisher = {Elsevier Science},
	organization = {Elsevier Science},
	edition = {1st},
	address = {Amsterdam},
	author = {May, S and Ben-Shaul, A},
	editor = {H.T. Tien and A.L. Ottowa-Leitmanova}
}
@article { ISI:000182167500039,
	title = {Curvature and charge modulations in lamellar DNA-lipid complexes},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {107},
	year = {2003},
	month = {APR 17},
	pages = {3624-3630},
	abstract = {To model the possible formation of coupled spatial corrugations and charge density modulations in lamellar DNA-lipid complexes, we use a free energy functional which includes the electrostatic, lipid mixing, and elastic degrees of freedom in a self-consistent manner. We find that the balance of forces favors membrane corrugations that are expected to be stable with respect to thermal membrane undulations for a certain range of lipid (charged and uncharged) composition. This may lead to locking between DNA strands in adjacent galleries of the complex. Furthermore, the possibility of membrane corrugations renders the lamellar complex more stable with respect to another, hexagonal, DNA-lipid phase.},
	issn = {1520-6106},
	doi = {10.1021/jp026637h},
	author = {Harries, D and May, S and Ben-Shaul, A}
}
@article { ISI:000183123100011,
	title = {Energetics and self-assembly of amphipathic peptide pores in lipid membranes},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {84},
	year = {2003},
	month = {APR},
	pages = {2242-2255},
	abstract = {We present a theoretical study of the energetics, equilibrium size, and size distribution of membrane pores composed of electrically charged amphipathic peptides. The peptides are modeled as cylinders (mimicking alpha-helices) carrying different amounts of charge, with the charge being uniformly distributed over a hydrophilic face, defined by the angle subtended by polar amino acid residues. The free energy of a pore of a given radius, R, and a given number of peptides, s, is expressed as a sum of the peptides{\textquoteright} electrostatic charging energy (calculated using Poisson-Boltzmann theory), and the lipid-perturbation energy associated with the formation of a membrane rim (which we model as being semitoroidal) in the gap between neighboring peptides. A simple phenomenological model is used to calculate the membrane perturbation energy. The balance between the opposing forces (namely, the radial free energy derivatives) associated with the electrostatic free energy that favors large R, and the membrane perturbation term that favors small R, dictates the equilibrium properties of the pore. Systematic calculations are reported for circular pores composed of various numbers of peptides, carrying different amounts of charge (1-6 elementary, positive charges) and characterized by different polar angles. We find that the optimal R{\textquoteright}s, for all (except, possibly, very weakly) charged peptides conform to the {\textquoteleft}{\textquoteleft}toroidal{\textquoteright}{\textquoteright} pore model, whereby a membrane rim larger than similar to1 nm intervenes between neighboring peptides. Only weakly charged peptides are likely to form {\textquoteleft}{\textquoteleft}barrel-stave{\textquoteright}{\textquoteright} pores where the peptides essentially touch one another. Treating pore formation as a two-dimensional self-assembly phenomenon, a simple statistical thermodynamic model is formulated and used to calculate pore size distributions. We find that the average pore size and size polydispersity increase with peptide charge and with the amphipathic polar angle. We also argue that the transition of peptides from the adsorbed to the inserted (membrane pore) state is cooperative and thus occurs rather abruptly upon a change in ambient conditions.},
	issn = {0006-3495},
	doi = {10.1016/S0006-3495(03)75030-9},
	author = {Zemel, A and Fattal, DR and Ben-Shaul, A}
}
@article { ISI:000183123000016,
	title = {Forces and pressures in DNA packaging and release from viral capsids},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {84},
	year = {2003},
	month = {MAR},
	pages = {1616-1627},
	abstract = {In a previous communication (Kindt et al., 2001) we reported preliminary results of Brownian dynamics simulation and analytical theory which address the packaging and ejection forces involving DNA in bacteriophage capsids. In the present work we provide a systematic formulation of the underlying theory, featuring the energetic and structural aspects of the strongly confined DNA. The free energy of the DNA chain is expressed as a sum of contributions from its encapsidated and released portions, each expressed as a sum of bending and interstrand energies but subjected to different boundary conditions. The equilibrium structure and energy of the capsid-confined and free chain portions are determined, for each ejected length, by variational minimization of the free energy with respect to their shape profiles and interaxial spacings. Numerical results are derived for a model system mimicking the lambda-phage. We find that the fully encapsidated genome is highly compressed and strongly bent, forming a spool-like condensate, storing enormous elastic energy. The elastic stress is rapidly released during the first stage of DNA injection, indicating the large force (tens of pico Newtons) needed to complete the (inverse) loading process. The second injection stage sets in when similar to1/3 of the genome has been released, and the interaxial distance has nearly reached its equilibrium value (corresponding to that of a relaxed torus in solution); concomitantly the encapsidated genome begins a gradual morphological transformation from a spool to a torus. We also calculate the loading force, the average pressure on the capsid{\textquoteright}s walls, and the anisotropic pressure profile within the capsid. The results are interpreted in terms of the (competing) bending and interaction components of the packing energy, and are shown to be in good agreement with available experimental data.},
	issn = {0006-3495},
	author = {Tzlil, S and Kindt, JT and Gelbart, W.M. and Ben-Shaul, A}
}
@article { ISI:000183820600008,
	title = {Osmotic shock and the strength of viral capsids},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {85},
	year = {2003},
	month = {JUL},
	pages = {70-74},
	abstract = {Osmotic shock is a familiar means for rupturing viral capsids and exposing their genomes intact. The necessary conditions for providing this shock involve incubation in high-concentration salt solutions, and lower permeability of the capsids to salt ions than to water molecules. We discuss here how values of the capsid strength can be inferred from calculations of the osmotic pressure differences associated with measured values of the critical concentration of incubation solution.},
	issn = {0006-3495},
	author = {Cordova, A and Deserno, M and Gelbart, W.M. and Ben-Shaul, A}
}
@article { ISI:000177581200004,
	title = {Adsorption of charged macromolecules on mixed fluid membranes},
	journal = {COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS},
	volume = {208},
	year = {2002},
	note = {Current Trends in Interface Chemistry Polish-Israeli Symposium, LUBLIN, POLAND, JUL 03-07, 2000},
	month = {AUG 14},
	pages = {41-50},
	abstract = {The adsorption of charge rigid macromolecules, such as proteins from solution, on mixed (charged and neutral) lipid membranes is affected by several important factors. First, the mobile lipids in the membrane may rearrange, and demix locally to match the charge density of the apposed macromolecule, thus lowering the adsorption free energy. On the other hand, the (electrostatic) interaction between adsorbed macromolecules tends to lower the saturation coverage of the membrane. Additional factors, such as non-ideal lipid demixing or an elastic membrane response, enhanced by the presence of the charged macromolecules, may be at the base of the experimentally observed formation of high density protein domains and lateral macro-phase separation in lipid membranes. (C) 2002 Elsevier Science B.V. All rights reserved.},
	issn = {0927-7757},
	doi = {10.1016/S0927-7757(02)00100-0},
	author = {Harries, D and May, S and Ben-Shaul, A}
}
@article { ISI:000179878200054,
	title = {Macroion-induced compositional instability of binary fluid membranes},
	journal = {PHYSICAL REVIEW LETTERS},
	volume = {89},
	year = {2002},
	month = {DEC 23},
	abstract = {Macroion adsorption on a mixed, fluid, lipid membrane containing oppositely charged lipids induces local changes in lipid composition at the interaction zones, and gradients at their boundaries. Including these effects in the free energy of the macroion-dressed membrane we derive its spinodal equation, and show that nonideal lipid mixing can lead to (lipid-mediated) attraction between macroions and lateral phase separation in the composite membrane. The critical nonideality for this transition is substantially smaller than that of the bare lipid membrane, decreasing with macroion size and charge. That is, the lipid membrane is destabilized by macroion adsorption.},
	issn = {0031-9007},
	doi = {10.1103/PhysRevLett.89.268102},
	author = {May, S and Harries, D and Ben-Shaul, A}
}
@article { ISI:000172328100038,
	title = {DNA packaging and ejection forces in bacteriophage},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
	volume = {98},
	year = {2001},
	month = {NOV 20},
	pages = {13671-13674},
	abstract = {We calculate the forces required to package (or, equivalently, acting to eject) DNA into (from) a bacteriophage capsid, as a function of the loaded (ejected) length, under conditions for which the DNA is either self-repelling or self-attracting. Through computer simulation and analytical theory, we find the loading force to increase more than 10-fold (to tens of piconewtons) during the final third of the loading process; correspondingly, the internal pressure drops 10-fold to a few atmospheres (matching the osmotic pressure in the cell) upon ejection of just a small fraction of the phage genome. We also determine an evolution of the arrangement of packaged DNA from toroidal to spool-like structures.},
	issn = {0027-8424},
	doi = {10.1073/pnas.241486298},
	author = {Kindt, J and Tzlil, S and Ben-Shaul, A and Gelbart, W.M.}
}
@article { ISI:000167001200005,
	title = {Molecular theory of the sphere-to-rod transition and the second CMC in aqueous micellar solutions},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {105},
	year = {2001},
	month = {JAN 25},
	pages = {630-640},
	abstract = {We present a molecular-level theory for amphiphile packing in linear micelles, focusing on the early stages of micellar elongation, i.e., on small and {\textquoteleft}{\textquoteleft}intermediate-size{\textquoteright}{\textquoteright} micelles, whose endcaps are not yet molded into a final shape. The internal free energy of a micelle of given size and shape is expressed as an integral over local molecular packing free energies in different regions of the micelle. The free energy per molecule is expressed as a sum of interfacial ({\textquoteright}{\textquoteright}opposing forces{\textquoteright}{\textquoteright}) and chain conformational contributions, both depending on the local geometry. The equilibrium shape and energy of the micelle is determined by functional minimization of the total free energy. For amphiphiles exhibiting strong preference for packing in the cylindrical geometry, we show that the early stages of growth involve an energetic barrier, resulting in a {\textquoteleft}{\textquoteleft}gap{\textquoteright}{\textquoteright} in the micellar size distribution. That is, at low total amphiphile concentrations only small (globular) micelles appear in solution. Their concentration reaches a well-defined saturation value, beyond which, all added amphiphiles are incorporated in long micelles, whose {\textquoteleft}{\textquoteleft}non-interacting{\textquoteright}{\textquoteright} endcaps are well separated by the cylindrical middle part. This, {\textquoteleft}{\textquoteleft}second CMC{\textquoteright}{\textquoteright} behavior is demonstrated by numerical calculations of micellar size distributions and average aggregation numbers as a function of the total concentration. The conditions necessary for the appearance of a second CMC are analyzed theoretically, with explicit reference to the underlying molecular packing characteristics. In particular, it is shown that a necessary condition for the appearance of a sharply defined second CMC is that the endcap energies (of at least some) of the small or intermediate-size micelles must be considerably lower than the asymptotic (long micelle) value of this quantity. The diameter of the minimal, spherical micelles, as well as that of the final endcaps, is found to be larger than the diameter of the cylindrical body of the very long micelles. Our results are in good qualitative agreement with recent cryo-TEM imaging studies of micellar shape and growth, as well as with previous (less direct) experiments revealing second CMC behavior.},
	issn = {1089-5647},
	doi = {10.1021/jp003021o},
	author = {May, S and Ben-Shaul, A}
}
@article { ISI:000089060900002,
	title = {Association entropy in adsorption processes},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {79},
	year = {2000},
	month = {SEP},
	pages = {1180-1187},
	abstract = {The association of two species to form a bound complex, e.g., the binding of a ligand to a protein or the adsorption of a peptide on a lipid membrane, involves an entropy loss, reflecting the conversion of free translational and rotational degrees of freedom into bound motions. Previous theoretical estimates of the standard entropy change in bimolecular binding processes, Delta S degrees, have been derived from the root-mean-square fluctuations in protein crystals, suggesting Delta S degrees approximate to -50 e.u., i.e., T Delta S degrees approximate to -25 kT = -15 kcal/mol. In this work we focus on adsorption, rather than binding processes. We first present a simple statistical-thermodynamic scheme for calculating the adsorption entropy, including its resolution into translational and rotational contributions, using the known distance-orientation dependent binding (adsorption) potential. We then utilize this scheme to calculate the free energy of interaction and entropy of pentalysine adsorption onto a lipid membrane. obtaining T Delta S degrees approximate to -1.7 kT approximate to -1.3 kcal/mol. Most of this entropy change is due to the conversion of one free translation into a bound motion, the rest arising from the confinement of two rotational degrees of freedom. The smaller entropy loss in adsorption compared to binding processes arises partly because a smaller number of degrees of freedom become restricted, but mainly due to the fact that the binding potential is much {\textquoteleft}{\textquoteleft}softer.{\textquoteright}{\textquoteright}},
	issn = {0006-3495},
	author = {Ben-Tal, N and Honig, B and Bagdassarian, CK and Ben-Shaul, A}
}
@article { ISI:000084890100006,
	title = {Direct evidence for counterion release upon cationic lipid-DNA condensation},
	journal = {LANGMUIR},
	volume = {16},
	year = {2000},
	month = {JAN 25},
	pages = {303-306},
	abstract = {The cooperative condensation of DNA and cationic liposomes to form ordered aggregates in aqueous solution is associated with the release of partially bound counterions. We directly determine the extent of counterion release by separating the supernatant from the precipitated condensates, measuring the conductivity of the solution before and after the phase transition. The extent of counterion release is calculated for a range of lipid/DNA concentration ratios based on the nonlinear Poisson-Boltzmann theory. Both experiment and theory show maximal, essentially complete, release of counterions at the isoelectric point, where the positive (lipid)/negative (DNA) charge ratio is 1:1. Furthermore, at this point the entropic contribution to the condensation free energy is maximal and dominant.},
	issn = {0743-7463},
	doi = {10.1021/la991268a},
	author = {Wagner, K and Harries, D and May, S and Kahl, V and Radler, JO and Ben-Shaul, A}
}
@article { ISI:000089688000008,
	title = {Lipid demixing and protein-protein interactions in the adsorption of charged proteins on mixed membranes},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {79},
	year = {2000},
	month = {OCT},
	pages = {1747-1760},
	abstract = {The adsorption free energy of charged proteins on mixed membranes, containing varying amounts of (oppositely) charged lipids, is calculated based on a mean-field free energy expression that accounts explicitly for the ability of the lipids to demix locally, and for lateral interactions between the adsorbed proteins. Minimization of this free energy functional yields the familiar nonlinear Poisson-Boltzmann equation and the boundary condition at the membrane surface that allows for lipid charge rearrangement. These two self-consistent equations are solved simultaneously. The proteins are modeled as uniformly charged spheres and the (bare) membrane as an ideal two-dimensional binary mixture of charged and neutral lipids. Substantial variations in the lipid charge density profiles are found when highly charged proteins adsorb on weakly charged membranes; the lipids, at a certain demixing entropy penalty, adjust their concentration in the vicinity of the adsorbed protein to achieve optimal charge matching. Lateral repulsive interactions between the adsorbed proteins affect the lipid modulation profile and, at high densities, result in substantial lowering of the binding energy. Adsorption isotherms demonstrating the importance of lipid mobility and protein-protein interactions are calculated using an adsorption equation with a coverage-dependent binding constant. Typically, at bulk-surface equilibrium (i.e., when the membrane surface is {\textquoteleft}{\textquoteleft}saturated{\textquoteright}{\textquoteright} by adsorbed proteins), the membrane charges are {\textquoteleft}{\textquoteleft}overcompensated{\textquoteright}{\textquoteright} by the protein charges, because only about half of the protein charges (those on the hemispheres facing the membrane) are involved in charge neutralization. Finally, it is argued that the formation of lipid-protein domains may be enhanced by electrostatic adsorption of proteins, but its origin (e.g., elastic deformations associated with lipid demixing) is not purely electrostatic.},
	issn = {0006-3495},
	author = {May, S and Harries, D and Ben-Shaul, A}
}
@article { ISI:000089772500002,
	title = {A molecular model for lipid-mediated interaction between proteins in membranes},
	journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
	volume = {2},
	year = {2000},
	pages = {4494-4502},
	abstract = {The loss of conformational freedom experienced by lipid chains in the vicinity of one, or two, impenetrable walls, representing the surfaces of hydrophobic transmembrane proteins, is calculated using a mean-field molecular-level chain packing theory. The hydrophobic thickness of the protein is set equal to that of the unperturbed lipid membrane (i.e., no {\textquoteleft}{\textquoteleft}hydrophobic mismatch{\textquoteright}{\textquoteright}). The probability distributions of chain conformations, at all distances from the walls, are calculated by generating all conformations according to the rotational-isomeric-state model, and subjecting the system free energy to the requirement that the hydrophobic core of the membrane is liquid-like, and hence uniformly packed by chain segments. As long as the two protein surfaces are far apart, their interaction zones do not overlap, each extending over several molecular diameters. When the interaction zones begin to overlap, inter-protein repulsion sets in. At some intermediate distance the interaction turns strongly attractive, resulting from the depletion of (highly constrained) lipid tails from the volume separating the two surfaces. The chains confined between the hydrophobic surfaces are tilted away from the walls. Their tilt angle decreases monotonically with the distance from the walls, and with the distance between the walls. A nonmonotonic variation of the lipid-mediated interaction free energy between hydrophobic surfaces in membranes is also obtained using a simple, analytical, model in which chain conformations are grouped according to their director (end-to-end vector) orientations.},
	issn = {1463-9076},
	doi = {10.1039/b003570j},
	author = {May, S and Ben-Shaul, A}
}
@article { ISI:000086349500004,
	title = {The phase behavior of cationic lipid-DNA complexes},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {78},
	year = {2000},
	month = {APR},
	pages = {1681-1697},
	abstract = {We present a theoretical analysis of the phase behavior of solutions containing DNA, cationic lipids, and nonionic (helper) lipids. Our model allows for five possible structures, treated as incompressible macroscopic phases: two lipid-DNA composite (lipoplex) phases, namely, the lamellar (L-alpha(C)) and hexagonal (H-II(C)) complexes; two binary (cationic/neutral) lipid phases, that is, the bilayer (L-alpha) and inverse-hexagonal (H-II) structures, and uncomplexed DNA. The free energy of the four lipid-containing phases is expressed as a sum of composition-dependent electrostatic, elastic, and mixing terms. The electrostatic free energies of all phases are calculated based on Poisson-Boltzmann theory. The phase diagram of the system is evaluated by minimizing the total free energy of the three-component mixture with respect to all the compositional degrees of freedom. We show that the phase behavior, in particular the preferred lipid-DNA complex geometry, is governed by a subtle interplay between the electrostatic, elastic, and mixing terms, which depend, in turn, on the lipid composition and lipid/DNA ratio. Detailed calculations are presented for three prototypical systems, exhibiting markedly different phase behaviors. The simplest mixture corresponds to a rigid planar membrane as the lipid source, in which case, only lamellar complexes appear in solution. When the membranes are {\textquoteleft}{\textquoteleft}soft{\textquoteright}{\textquoteright} (i.e., low bending modulus) the system exhibits the formation of both lamellar and hexagonal complexes, sometimes coexisting with each other, and with pure lipid or DNA phases. The last system corresponds to a lipid mixture involving helper lipids with strong propensity toward the inverse-hexagonal phase. Here, again, the phase diagram is rather complex, revealing a multitude of phase transitions and coexistences. Lamellar and hexagonal complexes appear, sometimes together, in different regions of the phase diagram.},
	issn = {0006-3495},
	author = {May, S and Harries, D and Ben-Shaul, A}
}
@article { ISI:000078368800015,
	title = {Molecular theory of lipid-protein interaction and the L-alpha-H-II transition},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {76},
	year = {1999},
	month = {FEB},
	pages = {751-767},
	abstract = {We present a molecular-level theory for lipid-protein interaction and apply it to the study of lipid-mediated interactions between proteins and the protein-induced transition from the planar bilayer (L-alpha to the inverse-hexagonal (H-II phase. The proteins are treated as rigid, membrane-spanning, hydrophobic inclusions of different size and shape, e.g., {\textquoteleft}{\textquoteleft}cylinder-like,{\textquoteright}{\textquoteright} {\textquoteleft}{\textquoteleft}barrel-like,{\textquoteright}{\textquoteright} or {\textquoteleft}{\textquoteleft}vase-like.{\textquoteright}{\textquoteright} We assume strong hydrophobic coupling between the protein and its neighbor lipids. This means that, if necessary, the flexible lipid chains surrounding the protein will stretch, compress, and/or tilt to bridge the hydrophobic thickness mismatch between the protein and the unperturbed bilayer. The system free energy is expressed as an integral over local molecular contributions. the latter accounting for interheadgroup repulsion, hydrocarbon-water surface energy, and chain stretching-tilting effects. We show that the molecular interaction constants are intimately related to familiar elastic (continuum) characteristics of the membrane, such as the bending rigidity and spontaneous curvature, as well as to the less familiar tilt modulus. The equilibrium configuration of the membrane is determined by minimizing the free energy functional, subject to boundary conditions dictated by the size, shape. and spatial distribution of inclusions. A similar procedure is used to calculate the free energy and structure of peptide-free and peptide-rich hexagonal phases. Two degrees of freedom are involved in the variational minimization procedure: the local length and local tilt angle of the lipid chains. The inclusion of chain tilt is particularly important for studying noncylindrical (for instance, barrel-like) inclusions and analyzing the structure of the H-II lipid phase; e.g., we find that chain tilt relaxation implies strong faceting of the lipid monolayers in the hexagonal phase. Consistent with experiment, we find that only short peptides (large negative mismatch) can induce the L-alpha {\textendash}\&gt; H-II transition. At the transition, a peptide-poor L-alpha phase coexists with a peptide-rich H-II phase.},
	issn = {0006-3495},
	doi = {10.1016/S0006-3495(99)77241-3},
	author = {May, S and Ben-Shaul, A}
}
@article { ISI:000078514000039,
	title = {A statistical thermodynamic model for cross-bridge mediated condensation of vesicles},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY A},
	volume = {102},
	year = {1998},
	month = {NOV 19},
	pages = {9586-9592},
	abstract = {The phase behavior of a solution containing a mixture of large and small, cross-bridging ({\textquoteright}{\textquoteright}two-sided sticker{\textquoteright}{\textquoteright}) particles is studied using a lattice model analyzed with the aid of mean-field calculations and Monte Carlo simulations. Neither the large nor the small particles interact with each other (except for excluded volume effects). However, the small particles can adsorb onto the surface of one or two large particles, in the latter case providing a cross-bridge, i.e., an adhesive bond, between the large particles. The formulation of the model is motivated by experimental studies involving aqueous solutions of vesicles (the large particles) and biotin-avidin-biotin cross-bridges. This system exhibits a first-order phase transition from a dilute to a condensed phase of vesicles once the average number of stickers per vesicle exceeds a certain threshold value. The statistical thermodynamic description of the system becomes particularly simple upon (Legendre) transformation from the two-component canonical ensemble to a {\textquoteleft}{\textquoteleft}mixed{\textquoteright}{\textquoteright} ensemble involving a constant chemical potential of the cross-bridge particles. The phase separation behavior of the system is calculated for two sets of molecular parametrs, revealing good qualitative agreement with relevant experiments.},
	issn = {1089-5639},
	doi = {10.1021/jp9823300},
	author = {Farbman-Yogev, I and Bohbot-Raviv, Y and Ben-Shaul, A}
}
@article { ISI:000075246200014,
	title = {Structure, stability, and thermodynamics of lamellar DNA-lipid complexes},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {75},
	year = {1998},
	month = {JUL},
	pages = {159-173},
	abstract = {We develop a statistical thermodynamic model for the phase evolution of DNA-cationic lipid complexes in aqueous solution, as a function of the ratios of charged to neutral lipid and charged lipid to DNA. The complexes consist of parallel strands of DNA intercalated in the water layers of lamellar stacks of mixed lipid bilayers, as determined by recent synchrotron x-ray measurements Elastic deformations of the DNA and the lipid bilayers are neglected, but DNA-induced spatial inhomogeneities in the bilayer charge densities are included. The relevant nonlinear Poisson-Boltzmann equation is solved numerically, including self-consistent treatment of the boundary conditions at the polarized membrane surfaces. For a wide range of lipid compositions, the phase evolution is characterized by three regions of lipid to DNA charge ratio, rho: 1) for low rho, the complexes coexist with excess DNA, and the DNA-DNA spacing in the complex, d, is constant; 2) for intermediate rho, including the isoelectric point rho = 1, all of the lipid and DNA in solution is incorporated into the complex, whose inter-DNA distance d increases linearly with rho; and 3) for high rho, the complexes coexist with excess liposomes (whose lipid composition is different from that in the complex), and their spacing d is nearly, but not completely, independent of rho. These results can be understood in terms of a simple charging model that reflects the competition between counterion entropy and inter-DNA (rho \&lt; 1) and interbilayer (rho \&gt; 1) repulsions. Finally, our approach and conclusions are compared with theoretical work by others, and with relevant experiments.},
	issn = {0006-3495},
	author = {Harries, D and May, S and Gelbart, W.M. and Ben-Shaul, A}
}
@article { ISI:A1997WE31200035,
	title = {Conformational chain statistics in a model lipid bilayer: Comparison between mean field and Monte Carlo calculations},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {106},
	year = {1997},
	month = {JAN 22},
	pages = {1609-1619},
	abstract = {A comparison between a mean held theory of chain packing in membranes and micelles and Monte Carlo simulations is presented for model lipid bilayers. In both approaches the {\textquoteleft}{\textquoteright}lipids{\textquoteright}{\textquoteright} are modeled as freely jointed (but self-avoiding) chains of spherical segments. The first segment of the chain represents the head group, anchored to the bilayer interface by a harmonic binding potential. The simulations are performed for symmetric bilayers composed of 200 chains, with periodic boundary conditions. Both pure and mixed bilayers (composed of long and short chains) are analyzed. In the simulation nonbonded segments interact via Lennard-Jones potentials, ensuring nearly uniform segment density in the bilayer core, as assumed in the mean held theory. The lateral pressure profiles governing the probability distribution of chain conformations in the mean field theory are related and compared to the tangential pressure profiles calculated from the simulations using Kirkwood-Buff{\textquoteright}s molecular theory. The two pressure profiles show very good agreement. We also calculate two conformational chain properties: end-segment distributions and orientational bond order parameters. The end-segment distributions calculated by the two approaches show excellent agreement. The order parameters compare somewhat less satisfactorily, yet we found that the order parameters derived from the simulations depend rather sensitively on the details of the interaction potential. In general, the results of the simulations support the use of the mean held theory as a (simple) tool for studying conformational chain statistics in confined environments and related thermodynamic properties, such as membrane curvature elasticity. (C) 1997 American Institute Physics.},
	issn = {0021-9606},
	doi = {10.1063/1.473283},
	author = {Harries, D and Benshaul, A.}
}
@article { ISI:A1997YD84800016,
	title = {DNA-lipid complexes: Stability of honeycomb-like and spaghetti-like structures},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {73},
	year = {1997},
	month = {NOV},
	pages = {2427-2440},
	abstract = {A molecular level theory is presented for the thermodynamic stability of two (similar) types of structural complexes formed by (either single strand or supercoiled) DNA and cationic liposomes, both involving a monolayer-coated DNA as the central structural unit. In the {\textquoteleft}{\textquoteright}spaghetti{\textquoteright}{\textquoteright} complex the central unit is surrounded by another, oppositely curved, monolayer, thus forming a bilayer mantle. The {\textquoteleft}{\textquoteright}honeycomb{\textquoteright}{\textquoteright} complex is a bundle of hexagonally packed DNA-monolayer units. The formation free energy of these complexes, starting from a planar cationic/neutral lipid bilayer and bare DNA, is expressed as a sum of electrostatic, bending, mixing, and (for the honeycomb) chain frustration contributions. The electrostatic free energy is calculated using the Poisson-Boltzmann equation. The bending energy of the mixed lipid layers is treated in the quadratic curvature approximation with composition-dependent bending rigidity and spontaneous curvature. Ideal lipid mixing is assumed within each lipid monolayer. We found that the most stable monolayer-coated DNA units are formed when the charged/neutral lipid composition corresponds (nearly) to charge neutralization; the optimal monolayer radius corresponds to close DNA-monolayer contact. These conclusions are also valid for the honeycomb complex, as the chain frustration energy is found to be negligible. Typically, the stabilization energies for these structures are on the order of 1 k(B)T/Angstrom of DNA length, reflecting mainly the balance between the electrostatic and bending energies. The spaghetti complexes are less stable due to the additional bending energy of the external monolayer. A thermodynamic analysis is presented for calculating the equilibrium lipid compositions when the complexes coexist with excess bilayer.},
	issn = {0006-3495},
	author = {May, S and Benshaul, A.}
}
@article { ISI:A1997YD60400005,
	title = {Molecular theory of bending elasticity and branching of cylindrical micelles},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
	volume = {101},
	year = {1997},
	month = {OCT 23},
	pages = {8648-8657},
	abstract = {Two structural-thermodynamic characteristics of cylindrical, wormlike micelles in dilute solution are studied using a molecular-level model: (a) the bending elasticity of the micelles and (b) their tendency to form intermicellar junctions (branches). The internal (free) energy of the micelles, before and after a bending deformation and junction formation, are calculated using mean field theories for the free energies of the molecules constituting these structures. The molecular free energies, which depend on the local packing geometries, include the contributions of head group repulsion forces, the hydrocarbon-water interfacial energy, and the chain conformational free energy. We find that when only the head group and surface contributions to the packing energy art:taken into account, the one-dimensional bending constant of the micelles is negligibly small, When the chain contribution is included, and when reasonable molecular packing parameters are used, we find that the persistence length, which is proportional to the bending rigidity, is typically a few tens of nanometers. The free energy change associated with the formation of a trijoint intermicellar junction upon the {\textquoteleft}{\textquoteright}fusion{\textquoteright}{\textquoteright} of one micellar end cap with the cylindrical body of another micelle is found to be small but positive; about 10 k(B)T at room temperature. This conclusion does not refute ?he possibility that intermicellar junctions are metastable transients or that their formation may be favored entropically, due either to conformational degeneracy or excluded volume interactions between micelles. Our conclusions apply to aqueous solutions containing one, single-tail, surfactant species.},
	issn = {1089-5647},
	doi = {10.1021/jp971328q},
	author = {May, S and Bohbot, Y and Ben-Shaul, A}
}
@article { ISI:A1996VT40700014,
	title = {Effect of lateral repulsion on desorption acid diffusion kinetics SHG experiments and MC simulations},
	journal = {APPLIED SURFACE SCIENCE},
	volume = {106},
	year = {1996},
	note = {2nd International Conference on Photo-Excited Processes and Applications, JERUSALEM, ISRAEL, SEP 17-21, 1995},
	month = {OCT},
	pages = {80-89},
	abstract = {Activation energies for desorption and for diffusion were experimentally determined as a function of surface coverage for the system of ammonia on Re(001) utilizing optical second harmonic generation techniques, For the first time coverage grating with up to 5th order SH-diffraction is reported for K atoms on Re(001). Preliminary diffusion measurements were performed on this system as well. These systems may be considered as ideal model to study the effect of very strong lateral repulsion on the kinetics of desorption and diffusion. A MC study on the ammonia-Re(001) system is presented, which examines the significance of long range repulsive dipole-dipole interactions on the outcome desorption and diffusion kinetics, We found that a single set of parameters, within the dipole-dipole like (1/r(3)) dependence on adsorbates separation distance, explains qualitatively and in certain cases quantitatively the experimental observations. Interaction range up to 4th order neighbors must be computed in order to properly account for the results.},
	issn = {0169-4332},
	doi = {10.1016/S0169-4332(96)00371-6},
	author = {Wei, Z and Verhoef, R and M. Asscher and Farbman, I. and Benshaul, A.}
}
@article { ISI:A1996UD67000035,
	title = {Effects of adsorbate lateral repulsion on desorption and diffusion kinetics studied by Monte Carlo simulations},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {104},
	year = {1996},
	month = {APR 8},
	pages = {5674-5682},
	abstract = {The effects of adsorbate lateral interactions on the kinetics of surface diffusion and desorption are studied by means of kinetic and thermodynamic Monte Carlo simulations. This study is motivated by recent diffusion and desorption experiments on the NH3/Re(001) system, which show that the activation energies of these processes decrease (in different fashions) with increasing surface coverage, the interactions between the adsorbates are thus assumed to be repulsive. A long range dipole-dipole-like potential is used to simulate both the diffusion and desorption processes. Most calculations are carried out with the interaction range extending up to fourth-order neighbors. Longer ranges are found to barely affect the kinetic behavior. On the other hand, shorter ranges of interaction result in qualitatively and quantitatively different structural (thermodynamic phase) behaviors and, consequently, in very different kinetics of diffusion and desorption. The model used to calculate diffusion kinetics assumes that the activation barrier to particle diffusion depends, simultaneously, on the local environments of both the initial and the final sites involved in the elementary event of particle jumps. The chemical diffusion coefficient is evaluated based on thermodynamic and kinetic Monte Carlo simulations. It is found to increase with surface coverage, reflecting the repulsive nature of the interactions. Yet, unlike the experimental results, the increase is nonmonotonic but rather, somewhat oscillatory-reflecting the structural phase transitions of the adsorbed layer. The activation energy of desorption is found to decrease by about 15 kcal/mole as the coverage increases from 0 to 1, showing steeper slopes around the coverages corresponding to a perfectly ordered adlayer phase. These results are in satisfactory qualitative and quantitative agreement with experiment. Finally, it is shown that the coverage dependence of the activation barrier to diffusion can be reasonably well evaluated from equilibrium thermodynamic desorption data. (C) 1996 American Institute of Physics.},
	issn = {0021-9606},
	doi = {10.1063/1.471805},
	author = {Farbman, I. and M. Asscher and Benshaul, A.}
}
@article { ISI:A1996UB81800026,
	title = {Free-energy determinants of alpha-helix insertion into lipid bilayers},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {70},
	year = {1996},
	month = {APR},
	pages = {1803-1812},
	abstract = {A detailed treatment is provided of the various free-energy terms that contribute to the transfer of a polyalanine ct-helix from the aqueous phase into lipid bilayers. In agreement with previous work, the hydrophobic effect is found to provide the major driving force for helix insertion, However, an opposing effect of comparable magnitude is also identified and is attributed to the large free-energy penalty associated with the desolvation of peptide hydrogen bonds on transfer to the low dielectric environment of the bilayer. Lipid perturbation effects as well as the entropy loss associated with helix immobilization in the bilayer are also evaluated. Two configurations of a membrane-bound 25mer polyalanine helix were found to be lower in free energy than the isolated helix in the aqueous phase, The first corresponds to the case of vertical insertion, in which a helix terminus protrudes from each side of the bilayer. The second minimum is for the case of horizontal insertion, for which the helix is adsorbed upon the surface of the bilayer. The calculated free-energy minima are found to be in good agreement with recent measurements of related systems, Large free-energy barriers resulting from desolvation of unsatisfied hydrogen-bonding groups al the helix termini are obtained for both insertion processes. The barriers for insertion are significantly reduced if the helix termini are assumed to be {\textquoteleft}{\textquoteright}capped{\textquoteright}{\textquoteright} through the formation of hydrogen bonds with polar sidechains, For uncapped helices, our results support recently proposed models in which helices are inserted by first adsorbing on the membrane surface and then having one terminus {\textquoteleft}{\textquoteright}swing around{\textquoteright}{\textquoteright} so as to penetrate the bilayer,},
	issn = {0006-3495},
	author = {BenTal, N and Benshaul, A. and Nicholls, A and Honig, B}
}
@article { ISI:A1996VA59500034,
	title = {The {\textquoteleft}{\textquoteright}new{\textquoteright}{\textquoteright} science of {\textquoteleft}{\textquoteright}complex fluids{\textquoteright}{\textquoteright}},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {100},
	year = {1996},
	month = {AUG 1},
	pages = {13169-13189},
	abstract = {We present an overview of the modern study of complex fluids which, because of the overwhelming breadth and richness of this field, unavoidably neglects many interesting systems and research developments. In proposing a definition of the field. we discuss first the special role played by phenomenological theory and the limitations of molecular-level description. The remainder of the article is organized into sections which treat model colloids, micellized surfactant solutions, interfacial films and microemulsions, bilayers and membranes, and new materials. In each instance we try to provide a physical basis for the special nature of interactions and long-range ordering transitions in these novel colloidal and thin layer systems. At the heart of understanding these highly varied phenomena lie the curvature dependence of surface energies and the coupling between self-assembly on small length scales and phase changes at large ones..},
	issn = {0022-3654},
	doi = {10.1021/jp9606570},
	author = {Gelbart, W.M. and Benshaul, A.}
}
@article { ISI:A1996UV90800016,
	title = {Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {71},
	year = {1996},
	month = {JUL},
	pages = {130-137},
	abstract = {A statistical thermodynamic approach is used to analyze the various contributions to the free energy change associated with the insertion of proteins and protein fragments into lipid bilayers. The partition coefficient that determines the equilibrium distribution of proteins between the membrane and the solution is expressed as the ratio between the partition functions of the protein in the two phases. It is shown that when all of the relevant degrees of freedom (i.e., those that change their character upon insertion into the membrane) can be treated classically, the partition coefficient is fully determined by the ratio of the configurational integrals and thus does not involve any mass-dependent factors, a conclusion that is also valid for related processes such as protein adsorption on a membrane surface or substrate binding to proteins. The partition coefficient, and hence the transfer free energy, depend only on the potential energy of the protein in the membrane. Expressing this potential as a sum of a {\textquoteleft}{\textquoteright}static{\textquoteright}{\textquoteright} term, corresponding to the equilibrium (minimal free energy) configuration of the protein in the membrane, and a {\textquoteleft}{\textquoteright}dynamical{\textquoteright}{\textquoteright} term representing fluctuations around the equilibrium configuration, we show that the static term contains the {\textquoteleft}{\textquoteright}solvation{\textquoteright}{\textquoteright} and {\textquoteleft}{\textquoteright}lipid perturbation{\textquoteright}{\textquoteright} contributions to the transfer free energy. The dynamical term is responsible for the {\textquoteleft}{\textquoteright}immobilization{\textquoteright}{\textquoteright} Free energy, reflecting the loss of translational and rotational entropy of the protein upon incorporation into the membrane. Based on a recent molecular theory of lipid-protein interactions, the lipid perturbation and immobilization contributions are then expressed in terms of the elastic deformation free energy resulting from the perturbation of the lipid environment by the foreign (protein) inclusion; The model is formulated for cylindrically shaped proteins, and numerical estimates are given for the insertion of an a-helical peptide into a lipid bilayer. The immobilization free energy is shown to be considerably smaller than in previous estimates of this quantity, and the origin of the difference is discussed in detail.},
	issn = {0006-3495},
	author = {Benshaul, A. and BenTal, N and Honig, B}
}
@inbook {14538,
	title = {Molecular Theory of Acyl Chain Packing in Lipid and Lipid-Protein Membranes},
	booktitle = {Nonmedical Applications of Liposomes:Vol. 1 Liposomes: Theory and Basic Science},
	volume = {1},
	year = {1995},
	pages = {129-151},
	publisher = {CRC Press},
	organization = {CRC Press},
	address = {New York},
	author = {Fattal, DR and Ben-Shaul, A},
	editor = {Y. Barenholz and Lasic, D.P.}
}
@article { ISI:A1995QK48700056,
	title = {CELL MODEL AND COMPUTER-SIMULATION STUDIES OF LAYERED AND HEXAGONAL STATES OF ALIGNED, HARD DISKS VERSUS RODS},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {99},
	year = {1995},
	month = {MAR 2},
	pages = {2907-2914},
	abstract = {We consider the possibility of smectic and columnar phases in fluids and colloidal suspensions of aligned rods and disks interacting through excluded-volume forces. After briefly reviewing previous work, and applying known cell model techniques to compare the phase behaviors of disks and rods, we present and discuss the results from new Monte Carlo simulations of perfectly oriented rods (spherocylinders) and disks (torocylinders). We conclude tentatively that columnar phases are stable only in the case of disks.},
	issn = {0022-3654},
	doi = {10.1021/j100009a055},
	author = {SHARLOW, MF and SELINGER, RLB and Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1995QY25200058,
	title = {EFFECT OF TENSION ON PORE FORMATION IN DRUG-CONTAINING VESICLES},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {99},
	year = {1995},
	month = {MAY 11},
	pages = {7694-7697},
	abstract = {Pore formation in unilamellar lipid vesicles is believed to occur when the concentration of membrane-bound drug molecules exceeds a certain value. We treat this phenomenon in analogy with that of the micellization of surfactant in bulk aqueous solutions, thereby relating the threshold concentration of drug molecules to the free energy associated with transferring a molecule to a pore from its uniformly-dispersed state in the membrane. Incorporating the effect of lateral tension induced by osmotic pressure, we calculate the lowering of the pore-formation threshold with increasing tension. These predictions are tested by direct measurements on liposomal dispersions involving the antifungal drug amphotericin B.},
	issn = {0022-3654},
	doi = {10.1021/j100019a057},
	author = {WEAKLIEM, CL and FUJII, G and CHANG, JE and Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1995QP31600019,
	title = {HE SCATTERING FROM COMPACT CLUSTERS AND FROM DIFFUSION-LIMITED AGGREGATES ON SURFACES - OBSERVABLE SIGNATURES OF STRUCTURE},
	journal = {SURFACE SCIENCE},
	volume = {327},
	year = {1995},
	month = {APR 1},
	pages = {165-191},
	abstract = {The angular intensity distribution of He beams scattered from compact clusters and from diffusion limited aggregates, epitaxially grown on metal surfaces, is investigated theoretically. The purpose is two-fold: to distinguish compact cluster structures from diffusion limited aggregates, and to find observable signatures that can characterize the compact clusters at the atomic level of detail. To simplify the collision dynamics, the study is carried out in the framework of the sudden approximation, which assumes that momentum changes perpendicular to the surface are targe compared with momentum transfer due to surface corrugation. The diffusion limited aggregates on which the scattering calculations were done, were generated by kinetic Monte Carlo simulations, It is demonstrated, by focusing on the example of compact Pt heptamers, that signatures of structure of compact clusters may indeed be extracted from the scattering distribution. These signatures enable both an experimental distinction between diffusion limited aggregates and compact clusters, and a determination of the cluster structure, The characteristics comprising the signatures are, to varying degrees, the rainbow, Fraunhofer, specular and constructive interference peaks, all seen in the intensity distribution, It is also shown, how the distribution of adsorbate heights above the metal surface can be obtained by an analysis of the specuIar peak attenuation. The results contribute to establishing He scattering as a powerful tool in the investigation of surface disorder and epitaxial growth on surfaces, alongside with STM.},
	issn = {0039-6028},
	doi = {10.1016/0039-6028(94)00828-0},
	author = {Hamburger, D. A. and Yinnon, A. T. and Farbman, I. and Benshaul, A. and Gerber, R. B.}
}
@article { ISI:A1995TA65700015,
	title = {LIPID CHAIN PACKING AND LIPID-PROTEIN INTERACTION IN MEMBRANES},
	journal = {PHYSICA A},
	volume = {220},
	year = {1995},
	note = {XXIV Winter Meeting on Statistical Physics, CUERNAVACA, MEXICO, JAN 03-06, 1995},
	month = {OCT 15},
	pages = {192-216},
	publisher = {Conacyt; Acad Investigac Cient A C; Univ Nacl Autonoma Mexico, Inst Fis; Univ Nacl Autonoma Mexico, Fac Quim; Univ Autonoma Metropolitana},
	abstract = {This article describes briefly several applications of a molecular theory of lipid organization in membranes to systems of biophysical interest. After introducing the basic concepts of this mean field theory we outline three of its recent applications. i) Calculations of lipid chain conformational statistics in membrane bilayers, and comparison of the results (e.g. bond orientational order parameters) to experiment and molecular dynamics simulations. Good agreement is found. ii) A molecular model for lipid-protein interactions, which explicitly considers the effects of a rigid hydrophobic protein on the elastic (conformational) properties of the lipid bilayer. We also analyze the role of the {\textquoteleft}hydrophobic mismatch{\textquoteright} between the protein and lipid bilayer thickness. iii) A molecular level calculation of the vesicle to micelle transition, attendant upon the addition of ({\textquoteright}curvature loving{\textquoteright}) surfactant to a lipid bilayer vesicle. Future applications, e.g. to the calculation of the free energy barriers involved in membrane fusion are briefly mentioned.},
	issn = {0378-4371},
	doi = {10.1016/0378-4371(95)00117-P},
	author = {Fattal, DR and Benshaul, A.}
}
@inbook {A.~Ben-Shaul1995,
	title = {Molecular theory of chain packing, elasticity and lipid protein interaction in lipid bilayers},
	booktitle = {Structure and Dynamics of Membranes},
	volume = {1A},
	year = {1995},
	pages = {359{\textendash}402},
	publisher = {Elsevier},
	organization = {Elsevier},
	address = {Amsterdam},
	keywords = {benshaul1},
	author = {Ben-Shaul, A},
	editor = {Lipowsky, R and Sackmann, E}
}
@article { ISI:A1995TE36400043,
	title = {MONTE-CARLO AND MEAN-FIELD STUDIES OF PHASE EVOLUTION IN CONCENTRATED SURFACTANT SOLUTIONS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {103},
	year = {1995},
	month = {NOV 15},
	pages = {8764-8782},
	abstract = {A two-dimensional lattice model, originally introduced by Granek et al. [J. Chem. Phys. 101, 4331 (l994)], is used to demonstrate the intricate coupling between the intramicellar interactions that determine the optimal aggregation geometry of surfactant molecules in dilute solution, and the intermicellar interactions that govern the phase behavior at higher concentrations. Three very different scenarios of self-assembly and phase evolution are analyzed in detail, based on Monte Carlo studies and theoretical interpretations involving mean-field, Landau-Ginzburg, Bethe-Peierls, and virial expansion schemes. The basic particles in the model are {\textquoteleft}{\textquoteright}unit micelles{\textquoteright}{\textquoteright} which, due to spontaneous self-assembly or because of excluded area interactions, can fuse td form larger aggregates; These aggregates are envisaged as hat micelles composed of a bilayerlike body surrounded: by a curved semitoroidal rim. The system{\textquoteright}s Hamiltonian involves one- through four-body potentials between the unit micelles, which account for their tendency to form aggregates of different shapes, e.g., elongated vs disklike micelles. Equivalently the configurational energy of the system is a sum of micellar self-energies involving the packing free energies of the constituent molecules in the bilayer body and in rim segments of different local curvature. The rim energy is a sum of a line tension term and a 1D curvature energy which depends on the rim spontaneous curvature and bending rigidity. Different combinations of these molecular parameters imply different optimal packing geometries and hence different self-assembly and phase behaviors. The emphasis in this paper Is on systems of {\textquoteleft}{\textquoteright}curvature loving{\textquoteright}{\textquoteright} amphiphiles which, in our model, are characterized by negative line tension. The three systems studied are: (i) A dilute solution of stable disklike micelles which, upon increasing the concentration, undergoes a first-order phase transition to a continuous bilayer with isolated hole defects. An intermediate modulated {\textquoteleft}{\textquoteright}checkerboard{\textquoteright}{\textquoteright} phase appears under certain conditions at low temperatures. (ii) A system of unit micelles which in dilute solution tend to associate into Linear micelles. These micelles are rodlike gt low temperatures, becoming increasingly more flexible as the temperature increases.-Upon increasing the concentration the micelles grow and undergo (in 2D) a continuous transition into nematic and {\textquoteleft}{\textquoteright}stripe{\textquoteright}{\textquoteright} phases of long rods. At still higher concentrations the micellar stripes fuse into continuous sheets with line defects. (iii) A system in which, already in dilute solution, the micelles favor the formation of branched aggregates, analogous to the branched cylindrical micelles recently observed in certain surfactant solutions, As the concentration increases the micelles associate into networks ({\textquoteright}{\textquoteright}gels{\textquoteright}{\textquoteright}) composed of a mesh of linear micelles linked by {\textquoteleft}{\textquoteright}T-like{\textquoteright}{\textquoteright} intermicellar junctions. The network may span the entire system or phase separate and coexist with a dilute micellar phase, depending on the details of the molecular packing parameters. (C) 1995 American Institute of Physics.},
	issn = {0021-9606},
	doi = {10.1063/1.470133},
	author = {Bohbot, Y and Benshaul, A. and GRANEK, R and Gelbart, W.M.}
}
@article { ISI:A1995RT92300061,
	title = {SPONTANEOUS CURVATURE AND THERMODYNAMIC STABILITY OF MIXED AMPHIPHILIC LAYERS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {103},
	year = {1995},
	month = {SEP 1},
	pages = {3839-3848},
	abstract = {The elastic behavior of mixed bilayers composed of two amphiphilic components with different chain length (and identical head groups) is studied using two molecular level models. In both, the bilayer free energy is expressed as a sum of chain, head group and interfacial contributions as well as a mixing entropy term. The head group and interfacial terms are modeled using simple phenomenological but general expressions. The models differ in their treatment of the chain conformational free energy. In one it is calculated using a detailed mean-field molecular theory. The other is based on a simple {\textquoteleft}{\textquoteright}compression{\textquoteright}{\textquoteright} model. Both models lead to similar conclusions. Expressing the bilayer free energy as a sum of its two monolayer contributions, a thermodynamic stability analysis is performed to examine the possibility of spontaneous vesicle formation. To this end, we expand the bilayer free energy as a power series (up to second order) in terms of the monolayer curvatures, their amphiphilic compositions and the average cross sectional areas per molecule; all variables are coupled, with the molecular composition and areas treated as degrees of freedom which are allowed to relax during bending. Using reasonable molecular interaction parameters we find that a second order transition from a planar to a curved (vesicle) geometry in a randomly mixed bilayer is unlikely. Most of our analysis is devoted to calculating the spontaneous curvature and the bending rigidity of the bilayer as a function of its amphiphile chain composition. We find that adding short chain amphiphiles to a layer of long chain molecules reduces considerably its bending rigidity, as already known from calculations involving only the chain contributions. However, we find that inclusion of head group and interfacial interactions moderates the effect of the added short chains. We also find that the bending rigidity Of pure monolayers is approximately linear in chain length, as compared to the nearly cubic dependence implied by the chain free energy alone (at constant head group area). Our main result involves the calculation of the spontaneous curvature as a function of composition. We find, for different chain mixtures, that upon adding short chains to long chain monolayers, the spontaneous curvature first increases nearly Linearly with composition and then (beyond mole fraction of about 0.5) begins to saturate towards the spontaneous curvature of a pure short chain layer. Qualitative arguments are provided to explain this behavior. (C) 1995 American Institute of physics.},
	issn = {0021-9606},
	doi = {10.1063/1.470062},
	author = {May, S and Benshaul, A.}
}
@article { ISI:A1995QV07200020,
	title = {THE VESICLE MICELLE TRANSITION IN MIXED LIPID SURFACTANT SYSTEMS - A MOLECULAR-MODEL},
	journal = {LANGMUIR},
	volume = {11},
	year = {1995},
	month = {APR},
	pages = {1154-1161},
	abstract = {A molecular model is used to calculate the free energy of mixed vesicles and cylindrical micelles, composed of lipid molecules and short chain surfactants. The free energy of both aggregates (modeled as an infinite planar bilayer and an infinite cylindrical aggregate) is represented as a sum of internal free energy and mixing entropy contributions. The internal free energy is treated as a sum of chain (conformational), head group, and surface tension terms. Calculating the free energy of each aggregation geometry as a function of lipid/surfactant composition and using common tangent construction we obtain the compositions of the bilayer and the micelle at the phase transition. By varying certain molecular parameters (such as the {\textquoteleft}{\textquoteright}hard core{\textquoteright}{\textquoteright} area of the surfactant head group or the length of the surfactant tail) we study the role of molecular packing characteristics in determining the compositions at phase coexistence. We find, as expected, that upon increasing the preference of the surfactant for the micellar geometry (larger spontaneous curvature) the bilayer is solubilized at lower surfactant/lipid concentration ratios. For some typical values of the parameters used, reasonable agreement with experimental results for mixtures of egg phosphatidylcholine and octylglucoside is obtained.},
	issn = {0743-7463},
	doi = {10.1021/la00004a020},
	author = {Fattal, DR and ANDELMAN, D and Benshaul, A.}
}
@book {14518,
	title = {Micelles, Membranes, Microemulsions and Monolayers},
	year = {1994},
	pages = {608},
	publisher = {Springer},
	organization = {Springer},
	address = {New York},
	editor = {Gelbart, W.M. and Ben-Shaul, A and ROUX, D}
}
@inbook {12245,
	title = {Statistical Thermodynamics of Self-Assembly: Structure and Phase Transitions in Micellar Solutions},
	booktitle = {Micelles, Membranes, Microemulsions and Monolayers},
	year = {1994},
	pages = {1-104},
	publisher = {Springer},
	organization = {Springer},
	address = {New York},
	author = {Ben-Shaul, A and Gelbart, W.M.},
	editor = {Gelbart, W.M. and Ben-Shaul, A and ROUX, D}
}
@article { ISI:A1994PE37700006,
	title = {MEAN-FIELD CALCULATIONS OF CHAIN PACKING AND CONFORMATIONAL STATISTICS IN LIPID BILAYERS - COMPARISON WITH EXPERIMENTS AND MOLECULAR-DYNAMICS STUDIES},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {67},
	year = {1994},
	month = {SEP},
	pages = {983-995},
	abstract = {A molecular, mean-field theory of chain packing statistics in aggregates of amphiphilic molecules is applied to calculate the conformational properties of the lipid chains comprising the hydrophobic cores of dipalmitoyl-phosphatidylcholine (DPPC), dioleoyl-phosphatidylcholine (DOPC), and palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers in their fluid state. The central quantity in this theory, the probability distribution of chain conformations, is evaluated by minimizing the free energy of the bilayer assuming only that the segment density within the hydrophobic region is uniform (liquidlike). Using this distribution we calculate chain conformational properties such as bond orientational order parameters and spatial distributions of the various chain segments. The lipid chains, both the saturated palmitoyl (-(CH2)(1)4-CH3) and the unsaturated oleoyl (-(CH2)(7)-CH=CH-(CH2)(7)-CH3) chains are modeled using rotational isomeric state schemes. All possible chain conformations are enumerated and their statistical weights are determined by the self-consistency equations expressing the condition of uniform density. The hydrophobic core of the DPPC bilayer is treated as composed of single (palmitoyl) chain amphiphiles, i.e., the interactions between chains originating from the same lipid headgroup are assumed to be the same as those between chains belonging to different molecules. Similarly, the DOPC system is treated as a bilayer of oleoyl chains. The POPC bilayer is modeled as an equimolar mixture of palmitoyl and oleoyl chains. Bond orientational order parameter profiles, and segment spatial distributions are calculated for the three systems above, for several values of the bilayer thickness (or, equivalently, average area/headgroup) chosen, where possible, so as to allow for comparisons with available experimental data and/or molecular dynamics simulations. In most cases the agreement between the mean-field calculations, which are relatively easy to perform, and the experimental and simulation data is very good, supporting their use as an efficient tool for analyzing a variety of systems subject to varying conditions (e.g., bilayers of different compositions or thicknesses at different temperatures).},
	issn = {0006-3495},
	author = {Fattal, DR and Benshaul, A.}
}
@article { ISI:A1994PE11000101,
	title = {SMECTIC-A TO BILAYER EVOLUTION IN CONCENTRATED SURFACTANT SOLUTIONS - THE ROLE OF SPONTANEOUS CURVATURE},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {101},
	year = {1994},
	month = {SEP 1},
	pages = {4331-4342},
	abstract = {We study the two-dimensional (2-D) structural and thermodynamic changes in smectic-A/lamellar phases of self-assembling surfactant systems, in which the rim associated with a bilayer edge has a preferred curvature. This property was not considered in previous studies of 2-D aggregation, where an infinite bilayer emerges already at very low concentrations. A lattice Hamiltonian is used to describe the bending energy of the rim: An occupied lattice site corresponds to a minimum, disklike, micelle, and a bending energy penalty is associated with corners and straight edges depending on the value of the spontaneous curvature. When the spontaneous radius of curvature of the rim is small and the bending modulus is large, we find that the {\textquoteleft}{\textquoteright}condensation{\textquoteright}{\textquoteright} transition-i.e., the {\textquoteleft}{\textquoteright}collapse{\textquoteright}{\textquoteright} of the finite aggregates into a continuous bilayer-is postponed to high concentrations. At low concentrations the bending energy leads to an effective repulsive interaction between the aggregates, which in turn can result in ordered (modulated) structures for not too large ratios of thermal energy to bending energy (which is the expected situation in most systems of interest). Our model should be applicable to the systems of decylammonium chloride and cesium perflourooctanoate studied by Boden and co-workers (NMR and conductivity measurements) and Zasadzinski and co-workers (freeze fracture), where monodisperse micellar disks are observed to layer in stacked planes. In the latter system a 2-D order of disk-shaped aggregates appears within the smectic-A layers, which is also consistent with our theory. Experimental studies of the structural evolution under further condensation of the system are not yet available.},
	issn = {0021-9606},
	doi = {10.1063/1.467483},
	author = {GRANEK, R and Gelbart, W.M. and Bohbot, Y and Benshaul, A.}
}
@article { ISI:A1993MF32100011,
	title = {A MOLECULAR-MODEL FOR LIPID-PROTEIN INTERACTION IN MEMBRANES - THE ROLE OF HYDROPHOBIC MISMATCH},
	journal = {BIOPHYSICAL JOURNAL},
	volume = {65},
	year = {1993},
	month = {NOV},
	pages = {1795-1809},
	abstract = {The interaction free energy between a hydrophobic, transmembrane, protein and the surrounding lipid environment is calculated based on a microscopic model for lipid organization. The protein is treated as a rigid hydrophobic solute of thickness d(P), embedded in a lipid bilayer of unperturbed thickness d(L)o. The lipid chains in the immediate vicinity of the protein are assumed to adjust their length to that of the protein (e.g., they are stretched when d(P) \&gt; d(L)o) in order to bridge over the lipid-protein hydrophobic mismatch (d(P) - d(L)o). The bilayer{\textquoteright}s hydrophobic thickness is assumed to decay exponentially to its asymptotic, unperturbed, value. The lipid deformation free energy is represented,as a sum of chain (hydrophobic core) and interfacial (head-group region) contributions. The chain contribution is calculated using a detailed molecular theory of chain packing statistics, which allows the calculation of conformational properties and thermodynamic functions (in a mean-field approximation) of the lipid tails. The tails are treated as single chain amphiphiles, modeled using the rotational isomeric state scheme. The interfacial free energy is represented by a phenomenological expression, accounting for the opposing effects of head-group repulsions and hydrocarbon-water surface tension. The lipid deformation free energy DELTAF is calculated as a function of d(P) - d(L)o. Most calculations are for C-14 amphiphiles which, in the absence of a protein, pack at an average area per head-group a0 congruent-to 32 angstrom2 (d(L)o congruent-to 24.5 angstrom), corresponding to the fluid state of the membrane. When d(P) = d(L)o, DELTAF \&gt; 0 and is due entirely to the loss of conformational entropy experienced by the chains around the protein. When d(P) \&gt; d(L)o, the interaction free energy is further increased due to the enhanced stretching of the tails. When d(P) \&lt; d(L)o, chain flexibility (entropy) increases, but this contribution to DELTAF is overcounted by the increase in the interfacial free energy. Thus, DELTAF obtains a minimum at d(P) - d(L)o congruent-to 0. These qualitative interpretations are supported by detailed numerical calculations of the various contributions to the interaction free energy, and of chain conformational properties. The range of the perturbation of lipid order extends typically over few molecular diameters. A rather detailed comparison of our approach to other models is provided in the Discussion.},
	issn = {0006-3495},
	author = {Fattal, DR and Benshaul, A.}
}
@article { ISI:A1993KY95800002,
	title = {PHASE-TRANSITIONS IN A MONOLAYER OF INTERCONVERTING SQUARES},
	journal = {PHYSICA A},
	volume = {195},
	year = {1993},
	month = {APR 15},
	pages = {12-30},
	abstract = {The two successive fluid-fluid phase transitions in surfactant Langmuir monolayers are described using a highly simplified molecular model: a {\textquoteleft}reactive{\textquoteright} mixture of inter-converting squares of two different sizes. The model is solved by a mean-field lattice approach and by Monte Carlo simulations. The mean-field scheme involves a re-division of the original lattice into {\textquoteleft}cells{\textquoteright} which can contain either one large square representing the (projection on the lattice of) an amphiphilic molecule in a conformationally disordered ({\textquoteright}expanded{\textquoteright}) state, or clusters consisting of 1-4 small squares, each representing an ordered ({\textquoteright}stretched{\textquoteright}) molecule. This procedure circumvents some of the difficulties associated with the size disparity of the adsorbed particles. In spite of its simplicity, the model can explain some major, as well as some subtle, characteristics of experimental monolayer phase diagrams. These include the conditions under which the monolayer exhibits one phase transition, two or none; the decrease of the triple point temperature with increasing chain length, and the gradual decrease with temperature of the liquid-condensed phase density.},
	issn = {0378-4371},
	doi = {10.1016/0378-4371(93)90251-X},
	author = {Kramer, D and Benshaul, A.}
}
@article { ISI:A1992HU55700054,
	title = {FLOW-INDUCED GELATION OF LIVING (MICELLAR) POLYMERS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {96},
	year = {1992},
	month = {MAY 15},
	pages = {7710-7727},
	abstract = {We consider the effect of shear velocity gradients on the size (L) of rodlike micelles in dilute and semidilute solution. A kinetic equation is introduced for the time-dependent concentration of aggregates of length L, consisting of {\textquoteleft}{\textquoteleft}bimolecular{\textquoteright}{\textquoteright} combination processes L + L{\textquoteright} {\textendash}\&gt; (L + L{\textquoteright}) and {\textquoteleft}{\textquoteleft}unimolecular{\textquoteright}{\textquoteright} fragmentations L {\textendash}\&gt; L{\textquoteright} + (L - L{\textquoteright}). The former are described by a generalization (from spheres to rods) of the Smoluchowski mechanism for shear-induced coalescence of emulsions, and the latter by incorporating the tension-deformation effects due to flow. Steady-state solutions to the kinetic equation are obtained, with the corresponding mean micellar size (LBAR) evaluated as a function of the Peclet number P, i.e., the dimensionless ratio of flow rate-gamma and rotational diffusion coefficient D(r). For sufficiently dilute solutions, we find only a weak dependence of LBAR on P. In the semidilute regime, however, an apparent divergence in LBAR at P congruent-to 1 suggests a flow-induced first-order gelation phenomenon.},
	issn = {0021-9606},
	doi = {10.1063/1.462371},
	author = {BRUINSMA, R and Gelbart, W.M. and Benshaul, A.}
}
@article { ISI:A1992HC61000063,
	title = {MONTE-CARLO AND MEAN-FIELD STUDIES OF SUCCESSIVE PHASE-TRANSITIONS IN ROD MONOLAYERS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {96},
	year = {1992},
	month = {FEB 1},
	pages = {2236-2252},
	abstract = {In this paper we present a rigid-rod model (involving a restricted set of orientations) which is solved first with mean-field theory and then by Monte Carlo simulation. It is shown that both interparticle attractions and anisotropic adsorption energies are necessary in order for two successive fluid-fluid transitions to occur. The first is basically a gas-liquid condensation of {\textquoteleft}{\textquoteleft}lying down{\textquoteright}{\textquoteright} rods in the plane of the surface, and the second involves a {\textquoteleft}{\textquoteleft}standing up{\textquoteright}{\textquoteright} of the particles. A close qualitative correspondence is established between the results obtained in the mean-field and Monte Carlo descriptions. The role of biaxial states, i.e., in-plane orientational ordering, is also discussed in both contexts. To this end, we develop an analogy between our one-component rod monolayer and a bidisperse system of interconverting isotropic particles.},
	issn = {0021-9606},
	doi = {10.1063/1.462074},
	author = {Kramer, D and Benshaul, A. and CHEN, ZY and Gelbart, W.M.}
}
@article { ISI:A1991EY07000074,
	title = {CURVATURE DEFECTS IN LAMELLAR PHASES OF AMPHIPHILE WATER-SYSTEMS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {94},
	year = {1991},
	month = {FEB 15},
	pages = {3030-3041},
	abstract = {Within the framework of two complementary models, we show that the densities and patterns of defects in amphiphile-water systems with lamellar organization are coupled to the strength of the bilayer-bilayer interactions and hence to the overall surfactant concentration. We consider defects which introduce curvature (i.e., larger head-group area per molecule) while preserving the integrity of stacked bilayers at surfactant volume fractions of several tenths. These features are favored if the molecules comprising the lamellae are preferentially packed with a nonplanar aggregate-water interface: curvature defects lower the local free energy in systems constrained by aggregate-aggregate interactions to lamellar geometry. As the amphiphile volume fraction is increased-and the bilayer-bilayer spacing thereby decreased-we predict phase transitions between lamellar phases of different defect patterns on the bilayer surface, with concurrent decrease in the defect area fraction per bilayer. Specifically, there is a progression from a stripe-like pattern of parallel channels to a random network of line defects to a pore phase, with the latter appearing at the highest amphiphile concentrations but characterized by the lowest density of defects. Connection is made with experimental work which has recently suggested various departures from classical lamellar structure.},
	issn = {0021-9606},
	doi = {10.1063/1.459826},
	author = {Bagdassarian, CK and ROUX, D and Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1991FR75600039,
	title = {REACTANT SEGREGATION IN THE STEADY-STATE A+B-]0 REACTION ON SURFACES},
	journal = {ISRAEL JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {95},
	year = {1991},
	month = {JUN 13},
	pages = {4803-4810},
	abstract = {The steady-state bimolecular annihilation reaction A + B {\textendash}\&gt; 0 on two-dimensional surfaces is studied via computer simulations. In the simulations A and B are randomly adsorbed on vacant sites, and reaction takes place whenever A and B reach nearest-neighbor sites, either directly following adsorption or through diffusion. It is found that both with and without diffusion the reactants segregate into separate islands of A{\textquoteright}s and B{\textquoteright}s. The islands vary in size and exhibit highly ramified shapes. Moreover, the islands are self-similar with a fractal dimension D = 1.89 (similar to percolation, but also other clusters). D is found to be independent of the diffusion rate K. Other fractal dimensions, e.g., of the {\textquoteleft}{\textquoteleft}hull{\textquoteright}{\textquoteright} differ from those of percolating clusters. The steady-state coverage theta* = theta*A + theta*B decreases with K, as expected (theta*A = theta*B, corresponding to equal fluxes of A and B is the only physical solution). For systems with immobile particles (K = 0) we find theta* congruent-to 0.59 and theta* congruent-to 0.49 for the square and the triangular lattices, respectively, similar to the percolation thresholds on these lattices. The long-time characteristics of the system (D, theta*, etc.) are independent of the initial conditions of the simulation, indicating that the system reaches a stable steady state. Furthermore, for the large systems simulated (typically 500 x 500 lattice sites) it was found that the long-time behavior is independent of the input mode. Namely, the same results are obtained for conserved (i.e., exactly balanced) and nonconserved (statistically balanced) A,B input mechanisms, indicating that on the time scale of the simulations (approximately 10(4) Monte Carlo steps) the apparent steady state (for nonconserved input) is essentially identical with the true steady state (for the conserved input).},
	issn = {0022-3654},
	doi = {10.1021/j100165a039},
	author = {BECKER, OM and Ben-Nun, M and Ben-Shaul, A}
}
@article { ISI:A1991GG38300066,
	title = {STATISTICAL THERMODYNAMICS OF MOLECULAR-ORGANIZATION IN THE INVERSE HEXAGONAL PHASE},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {95},
	year = {1991},
	month = {SEP 19},
	pages = {7477-7483},
	abstract = {A mean field theory of chain packing in amphiphilic aggregates is used to calculate conformational and thermodynamic properties of the inverse hexagonal phase. These properties are compared with those for planar bilayers and curved monolayers. Calculated bond order parameters reveal that chains packed in the hexagonal arrangement have more conformational freedom than chains packed in a bilayer. The calculated order parameters are in good agreement with recent experimental results. Free energy calculations are also presented. It is found that for small areas per head group the packing free energy of amphiphiles in a bilayer is considerably higher than in the hexagonal phase.},
	issn = {0022-3654},
	doi = {10.1021/j100172a066},
	author = {STEENHUIZEN, L and Kramer, D and Benshaul, A.}
}
@article { ISI:A1991FH61200037,
	title = {STATISTICAL-THERMODYNAMIC APPROACH TO FRACTURE},
	journal = {PHYSICAL REVIEW A},
	volume = {43},
	year = {1991},
	month = {APR 15},
	pages = {4396-4400},
	abstract = {We present a statistical-thermodynamic theory that associates fracture of a solid with the approach of a spinodal upon increasing stress. This formulation is illustrated by a one-dimensional model, and the temperature dependence of the nonlinear stress-strain relation and fracture stress is obtained. A two-dimensional network model is treated by both effective-medium theory and Monte Carlo simulations, showing metastability and the nucleation of microcracks.},
	issn = {1050-2947},
	doi = {10.1103/PhysRevA.43.4396},
	author = {SELINGER, RLB and WANG, ZG and Gelbart, W.M. and Benshaul, A.}
}
@article { ISI:A1990DJ23500060,
	title = {CHAIN PACKING STATISTICS AND THERMODYNAMICS OF AMPHIPHILE MONOLAYERS},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {94},
	year = {1990},
	month = {JUN 14},
	pages = {5081-5089},
	issn = {0022-3654},
	doi = {10.1021/j100375a060},
	author = {SZLEIFER, I and Ben-Shaul, A and Gelbart, W.M.}
}
@article { ISI:A1990CW22800001,
	title = {FLOW EFFECTS ON MICELLAR SIZE DISTRIBUTION},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {94},
	year = {1990},
	month = {MAR 22},
	pages = {2219-2221},
	issn = {0022-3654},
	doi = {10.1021/j100369a001},
	author = {WANG, SQ and Gelbart, W.M. and Ben-Shaul, A}
}
@article { ISI:A1990DG24900017,
	title = {KINETICALLY CONTROLLED AGGREGATION IN REACTIVE ADSORBATE OVERLAYERS},
	journal = {ISRAEL JOURNAL OF CHEMISTRY},
	volume = {30},
	year = {1990},
	pages = {179-188},
	issn = {0021-2148},
	author = {BECKER, OM and SILVERBERG, M and Benshaul, A.}
}
@article { ISI:A1990DE14600054,
	title = {MOLECULAR THEORY OF CURVATURE ELASTICITY IN SURFACTANT FILMS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {92},
	year = {1990},
	month = {JUN 1},
	pages = {6800-6817},
	issn = {0021-9606},
	doi = {10.1063/1.458267},
	author = {SZLEIFER, I and Kramer, D and Ben-Shaul, A and Gelbart, W.M. and SAFRAN, SA}
}
@article { ISI:A1990DD60800012,
	title = {STATES OF AGGREGATION AND PHASE-TRANSFORMATIONS IN MIXTURES OF PHOSPHATIDYLCHOLINE AND OCTYL GLUCOSIDE},
	journal = {BIOCHEMISTRY},
	volume = {29},
	year = {1990},
	month = {MAY 15},
	pages = {4582-4592},
	issn = {0006-2960},
	doi = {10.1021/bi00471a012},
	author = {ALMOG, S and LITMAN, BJ and WIMLEY, W and COHEN, J and WACHTEL, EJ and Y. Barenholz and Ben-Shaul, A and LICHTENBERG, D}
}
@article { ISI:A1989U570700005,
	title = {ADSORBATE LATERAL INTERACTIONS AND ISLANDING IN SURFACE-REACTION KINETICS},
	journal = {SURFACE SCIENCE},
	volume = {214},
	year = {1989},
	month = {APR},
	pages = {17-43},
	issn = {0039-6028},
	doi = {10.1016/0039-6028(89)90406-8},
	author = {SILVERBERG, M and Ben-Shaul, A}
}
@article { ISI:A1989CC36900019,
	title = {ADSORBATE-ENHANCED CHEMISORPTION IN THE CO/RE(001) SYSTEM - EXPERIMENT AND THEORY},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {93},
	year = {1989},
	month = {NOV 30},
	pages = {8059-8067},
	issn = {0022-3654},
	doi = {10.1021/j100361a019},
	author = {BECKER, OM and CHACHAM, I and M. Asscher and Ben-Shaul, A}
}
@article { ISI:A1988N240300022,
	title = {CURVATURE ELASTICITY OF PURE AND MIXED SURFACTANT FILMS},
	journal = {PHYSICAL REVIEW LETTERS},
	volume = {60},
	year = {1988},
	month = {MAY 9},
	pages = {1966-1969},
	issn = {0031-9007},
	doi = {10.1103/PhysRevLett.60.1966},
	author = {SZLEIFER, I and Kramer, D and Ben-Shaul, A and ROUX, D and Gelbart, W.M.}
}
@article { ISI:A1988R017700004,
	title = {DYNAMIC AND THERMODYNAMIC CONSEQUENCES OF ADSORBATE LATERAL INTERACTIONS IN SURFACE-REACTION KINETICS},
	journal = {JOURNAL OF STATISTICAL PHYSICS},
	volume = {52},
	year = {1988},
	month = {SEP},
	pages = {1179-1195},
	issn = {0022-4715},
	doi = {10.1007/BF01011640},
	author = {SILVERBERG, M and Ben-Shaul, A}
}
@article { ISI:A1988R017700012,
	title = {LIQUID-CRYSTALLINE STATES OF SURFACTANT SOLUTIONS OF ISOTROPIC MICELLES},
	journal = {JOURNAL OF STATISTICAL PHYSICS},
	volume = {52},
	year = {1988},
	month = {SEP},
	pages = {1307-1313},
	issn = {0022-4715},
	doi = {10.1007/BF01011648},
	author = {BAGDASSARIAN, C and Gelbart, W.M. and Ben-Shaul, A}
}
@article { ISI:A1988Q091600013,
	title = {PHASE-TRANSITIONS IN SYSTEMS OF GRAFTED RODS},
	journal = {PHYSICAL REVIEW LETTERS},
	volume = {61},
	year = {1988},
	month = {SEP 19},
	pages = {1376-1379},
	issn = {0031-9007},
	doi = {10.1103/PhysRevLett.61.1376},
	author = {CHEN, ZY and TALBOT, J and Gelbart, W.M. and Ben-Shaul, A}
}
@article { ISI:A1988R364200010,
	title = {ROLE AND MECHANISM OF ISLAND FORMATION IN CHEMISORPTION},
	journal = {PHYSICAL REVIEW LETTERS},
	volume = {61},
	year = {1988},
	month = {DEC 19},
	pages = {2859-2862},
	issn = {0031-9007},
	doi = {10.1103/PhysRevLett.61.2859},
	author = {BECKER, OM and Ben-Shaul, A}
}
@proceedings {14023,
	title = {Chain Packing and Compressional Elasticity of Surfactant Films},
	journal = {Physics of Amphiphilic Layers},
	year = {1987},
	publisher = {Springer},
	address = {Les Houches},
	author = {Gelbart, W.M. and Ben-Shaul, A and Langevin, D and Boccara, N},
	editor = {Meunier, J}
}
@proceedings {14022,
	title = {Molecular Theory for Amphiphile Packing and Elastic Properties of Monolayers and Bilayers},
	journal = {Physics of Amphiphilic Layers},
	volume = {21},
	year = {1987},
	pages = {2-8},
	publisher = {Springer},
	address = {Les Houches},
	author = {Ben-Shaul, A and SZLEIFER, I and Gelbart, W.M.},
	editor = {Meunier, J and Langevin, D and Bocara, N}
}
@article { ISI:A1987J808000090,
	title = {ADSORBATE ISLANDING IN SURFACE-REACTIONS - A COMBINED MONTE-CARLO-LATTICE GAS APPROACH},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {87},
	year = {1987},
	month = {SEP 1},
	pages = {3178-3194},
	issn = {0021-9606},
	doi = {10.1063/1.453005},
	author = {SILVERBERG, M and Ben-Shaul, A}
}
@article { ISI:A1987G806800020,
	title = {EFFECTS OF ADSORBATE ISLANDING ON REACTION-KINETICS AND THERMAL-DESORPTION SPECTRA - A MONTE-CARLO QUASI-CHEMICAL MODEL},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {134},
	year = {1987},
	month = {MAR 13},
	pages = {491-496},
	issn = {0009-2614},
	doi = {10.1016/0009-2614(87)87179-8},
	author = {SILVERBERG, M and Ben-Shaul, A}
}
@article { ISI:A1987K120400047,
	title = {SCALING PROPERTIES OF CHAIN INTERACTIONS IN AMPHIPHILIC AGGREGATES},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {87},
	year = {1987},
	month = {OCT 1},
	pages = {4114-4125},
	issn = {0021-9606},
	doi = {10.1063/1.452916},
	author = {VIOVY, JL and Gelbart, W.M. and Ben-Shaul, A}
}
@article { ISI:A1987H766500061,
	title = {STATISTICAL THERMODYNAMICS OF MOLECULAR-ORGANIZATION IN MIXED MICELLES AND BILAYERS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {86},
	year = {1987},
	month = {JUN 15},
	pages = {7094-7109},
	issn = {0021-9606},
	doi = {10.1063/1.452359},
	author = {SZLEIFER, I and Ben-Shaul, A and Gelbart, W.M.}
}
@inbook {14527,
	title = {Statistical-Thermodynamic Theory of Surfactant Organization in Micelles and Bilayers},
	booktitle = {Surfactants in Solution},
	volume = {4},
	year = {1986},
	pages = {35-44},
	publisher = {Plenum},
	organization = {Plenum},
	address = {New York},
	author = {Ben-Shaul, A and SZLEIFER, I and Gelbart, W.M.},
	editor = {Mittal, K.L. and Bothorel, P}
}
@inbook {14528,
	title = {On the Theory of Micellar Size in Isotropic and Nematic Solutions},
	booktitle = {Surfactants in Solution},
	volume = {4},
	year = {1986},
	pages = {429-438},
	publisher = {Plenum},
	organization = {Plenum},
	address = {New York},
	author = {Gelbart, W.M. and McMullen, W.E. and Ben-Shaul, A},
	editor = {Mittal, K.L. and Bothorel, P}
}
@article { ISI:A1986E517600079,
	title = {CHAIN STATISTICS IN MICELLES AND BILAYERS - EFFECTS OF SURFACE-ROUGHNESS AND INTERNAL ENERGY},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {85},
	year = {1986},
	month = {NOV 1},
	pages = {5345-5358},
	issn = {0021-9606},
	doi = {10.1063/1.451679},
	author = {SZLEIFER, I and Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1986E347100076,
	title = {SIZE DISTRIBUTION OF MIXED MICELLES - RODLIKE SURFACTANT ALCOHOL AGGREGATES},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {90},
	year = {1986},
	month = {OCT 9},
	pages = {5277-5286},
	issn = {0022-3654},
	doi = {10.1021/j100412a076},
	author = {Ben-Shaul, A and RORMAN, DH and HARTLAND, GV and Gelbart, W.M.}
}
@article { ISI:A1986A149000010,
	title = {THEORY OF MICELLAR STABILITY IN ISOTROPIC AND NEMATIC PHASES},
	journal = {MOLECULAR CRYSTALS AND LIQUID CRYSTALS},
	volume = {132},
	year = {1986},
	pages = {325-337},
	issn = {0140-6566},
	doi = {10.1080/00268948608079551},
	author = {Gelbart, W.M. and McMullen, W.E. and Benshaul, A.}
}
@inbook {14524,
	title = {Amphiphile Chain Organization in Micelles of Different Geometries},
	booktitle = {Physics of Amphiphiles, Micelles, Vesicles and Microemulsions},
	year = {1985},
	pages = {404-426},
	publisher = {North-Holland},
	organization = {North-Holland},
	address = {Amsterdam},
	author = {Ben-Shaul, A and SZLEIFER, I and Gelbart, W.M.},
	editor = {Degiorgio, V and Corti, M}
}
@inbook {14525,
	title = {Effects of Inter-Aggregate Forces on Micellar Size},
	booktitle = {Physics of Amphiphiles, Micelles, Vesicles and Microemulsions},
	year = {1985},
	pages = {394-403},
	publisher = {North-Holland},
	organization = {North-Holland},
	address = {Amsterdam},
	author = {Gelbart, W.M. and Ben-Shaul, A and Masters, A.J. and McMullen, W.E.},
	editor = {Degiorigio, V and Corti, M}
}
@article { ISI:A1985AQW3100048,
	title = {CHAIN ORGANIZATION AND THERMODYNAMICS IN MICELLES AND BILAYERS .1. THEORY},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {83},
	year = {1985},
	pages = {3597-3611},
	issn = {0021-9606},
	doi = {10.1063/1.449166},
	author = {Ben-Shaul, A and SZLEIFER, I and Gelbart, W.M.}
}
@article { ISI:A1985AQW3100049,
	title = {CHAIN ORGANIZATION AND THERMODYNAMICS IN MICELLES AND BILAYERS .2. MODEL-CALCULATIONS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {83},
	year = {1985},
	pages = {3612-3620},
	issn = {0021-9606},
	doi = {10.1063/1.449167},
	author = {SZLEIFER, I and Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1985AVY0800058,
	title = {ON THE EFFECTS OF ADSORBATE AGGREGATION ON THE KINETICS OF SURFACE-REACTIONS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {83},
	year = {1985},
	pages = {6501-6513},
	issn = {0021-9606},
	doi = {10.1063/1.449550},
	author = {SILVERBERG, M and Benshaul, A. and Rebentrost, F.}
}
@article { ISI:A1985AKS8500038,
	title = {ISOTROPIC NEMATIC TRANSITION IN MICELLIZED SOLUTIONS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {82},
	year = {1985},
	pages = {5616-5623},
	issn = {0021-9606},
	doi = {10.1063/1.448597},
	author = {McMullen, W.E. and Gelbart, W.M. and Benshaul, A.}
}
@article { ISI:A1985ALU7200010,
	title = {NEMATIC STABILITY AND THE ALIGNMENT-INDUCED GROWTH OF ANISOTROPIC MICELLES},
	journal = {JOURNAL DE PHYSIQUE},
	volume = {46},
	year = {1985},
	pages = {1137-1144},
	issn = {0302-0738},
	doi = {10.1051/jphys:019850046070113700},
	author = {Gelbart, W.M. and McMullen, W.E. and Benshaul, A.}
}
@article { ISI:A1985AEQ4200016,
	title = {ON THE PARTITIONING OF COSURFACTANT IN MIXED MICELLES - SIZE ENHANCEMENT AND NEMATIC STABILITY},
	journal = {LANGMUIR},
	volume = {1},
	year = {1985},
	pages = {101-103},
	issn = {0743-7463},
	doi = {10.1021/la00061a016},
	author = {Gelbart, W.M. and McMullen, W.E. and Masters, A. and Benshaul, A.}
}
@article { ISI:A1985ATK7100008,
	title = {THEORY OF CHAIN PACKING IN AMPHIPHILIC AGGREGATES},
	journal = {ANNUAL REVIEW OF PHYSICAL CHEMISTRY},
	volume = {36},
	year = {1985},
	pages = {179-211},
	issn = {0066-426X},
	doi = {10.1146/annurev.physchem.36.1.179},
	author = {Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1984SG65500008,
	title = {MICELLAR GROWTH DUE TO INTERAGGREGATE INTERACTIONS},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {88},
	year = {1984},
	pages = {861-866},
	issn = {0022-3654},
	doi = {10.1021/j150649a008},
	author = {Gelbart, W.M. and Benshaul, A. and McMullen, W.E. and Masters, A.}
}
@article { ISI:A1984SM28100025,
	title = {ROD DISK COEXISTENCE IN DILUTE SOAP SOLUTIONS},
	journal = {JOURNAL OF COLLOID AND INTERFACE SCIENCE},
	volume = {98},
	year = {1984},
	pages = {523-536},
	issn = {0021-9797},
	author = {McMullen, W.E. and Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1984TC99800001,
	title = {STATISTICAL THERMODYNAMICS OF AMPHIPHILE CHAINS IN MICELLES},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-PHYSICAL SCIENCES},
	volume = {81},
	year = {1984},
	pages = {4601-4605},
	issn = {0027-8424},
	doi = {10.1073/pnas.81.14.4601},
	author = {Benshaul, A. and SZLEIFER, I and Gelbart, W.M.}
}
@article { ISI:A1984TZ31000028,
	title = {TRANSLATIONAL AND ROTATIONAL CONTRIBUTIONS TO THE SIZE OF MICELLES IN DILUTE SURFACTANT SOLUTIONS},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {88},
	year = {1984},
	pages = {6649-6654},
	issn = {0022-3654},
	doi = {10.1021/j150670a029},
	author = {McMullen, W.E. and Gelbart, W.M. and Benshaul, A.}
}
@article { ISI:A1983QG96300116,
	title = {ON THE STRETCHING OF ALKYL CHAINS BY NEMATICS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {78},
	year = {1983},
	pages = {4303-4308},
	issn = {0021-9606},
	doi = {10.1063/1.445108},
	author = {Benshaul, A. and RABIN, Y and Gelbart, W.M.}
}
@article { ISI:A1982NA42100004,
	title = {EFFECT OF INTER-AGGREGATE FORCES ON THE SIZE DISTRIBUTION OF MICELLES},
	journal = {JOURNAL OF PHYSICAL CHEMISTRY},
	volume = {86},
	year = {1982},
	pages = {316-318},
	issn = {0022-3654},
	doi = {10.1021/j100392a004},
	author = {Benshaul, A. and Gelbart, W.M.}
}
@article { ISI:A1982NY11900038,
	title = {MOLECULAR THEORY OF CURVATURE ELASTICITY IN NEMATIC LIQUIDS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {77},
	year = {1982},
	pages = {916-933},
	issn = {0021-9606},
	doi = {10.1063/1.443867},
	author = {Gelbart, W.M. and Benshaul, A.}
}
@book {14521,
	title = {Lasers and Chemical Change},
	year = {1981},
	pages = {497},
	publisher = {Springer series in Chemical Physics Vo. 10},
	organization = {Springer series in Chemical Physics Vo. 10},
	address = {Heidelberg},
	author = {Ben-Shaul, A and Haas, Y. and KOMPA, KL and LEVINE, RD}
}
@article { ISI:A1981LJ34700021,
	title = {ON THE FRAGMENTATION OF BENZENE BY MULTIPHOTOIONIZATION},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {74},
	year = {1981},
	pages = {3255-3264},
	issn = {0021-9606},
	doi = {10.1063/1.441530},
	author = {Rebentrost, F. and Benshaul, A.}
}
@article { ISI:A1981LA63700037,
	title = {A STATISTICAL-MODEL FOR THE FRAGMENTATION OF BENZENE BY MULTIPHOTOIONIZATION},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {77},
	year = {1981},
	pages = {394-398},
	issn = {0009-2614},
	doi = {10.1016/0009-2614(81)80172-8},
	author = {Rebentrost, F. and KOMPA, KL and Benshaul, A.}
}
@inbook {14520,
	title = {Chemical Laser Kinetics},
	booktitle = {Photosensitive Chemistry, in Advances in Chemical Physics},
	volume = {XLVII},
	year = {1980},
	pages = {55-83},
	publisher = {Wiley},
	organization = {Wiley},
	address = {New York},
	author = {Ben-Shaul, A},
	editor = {Jortner, J. and RICE, SA and LEVINE, RD}
}
@article { ISI:A1980JF79800023,
	title = {KINETIC MODELING OF ROTATIONAL NON-EQUILIBRIUM IN CHEMICAL-LASERS - COMPARISON OF 3 MODELS APPLIED TO THE CL2-HI-HE SYSTEM},
	journal = {JOURNAL OF APPLIED PHYSICS},
	volume = {51},
	year = {1980},
	pages = {130-141},
	issn = {0021-8979},
	doi = {10.1063/1.327406},
	author = {REUVEN, Y and Benshaul, A. and BAER, M}
}
@article { ISI:A1980KU25600045,
	title = {MULTI-PHOTON INDUCED ISOMERIZATION - DYNAMICS AND THERMODYNAMICS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {73},
	year = {1980},
	pages = {5107-5114},
	issn = {0021-9606},
	doi = {10.1063/1.439988},
	author = {Benshaul, A. and Haas, Y.}
}
@article { ISI:A1980KD62500014,
	title = {THE ROLE OF REAGENT INTERNAL EXCITATION IN COLLISION EXPERIMENTS},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {73},
	year = {1980},
	pages = {263-268},
	issn = {0009-2614},
	doi = {10.1016/0009-2614(80)80369-1},
	author = {Ben-Shaul, A and LEVINE, RD}
}
@proceedings {14517,
	title = {The HF Laser as an Irreversible Heat Engine},
	journal = {GCL-Gas Flow and Chemical Lasers},
	year = {1979},
	pages = {337-342},
	publisher = {von Karman, McGraw Hill,},
	address = {Brussels},
	author = {Kafri, O and Ben-Shaul, A},
	editor = {J.F. Wendt}
}
@proceedings {14519,
	title = {Time Dependent Kinetic-Thermodynamic Analysis of a Non-Equilibrium Molecular System: The HF Chemical Laser},
	journal = {Laser Induced Processes in Molecules},
	year = {1979},
	pages = {22-25},
	publisher = {Springer, Berlin},
	address = {Edinburgh},
	author = {Ben-Shaul, A and Kafri, O and LEVINE, RD},
	editor = {KOMPA, KL and S.M. Smith}
}
@article { ISI:A1979GN30200035,
	title = {EQUILIBRIUM DISTRIBUTIONS AND DETAILED BALANCE RELATIONS IN NONISOTHERMAL SYSTEMS},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {61},
	year = {1979},
	pages = {571-576},
	issn = {0009-2614},
	author = {Ben-Shaul, A and TABOR, M}
}
@article { ISI:A1979GM33600011,
	title = {MICROSCOPIC AND MACROSCOPIC ANALYSIS OF NONLINEAR MASTER EQUATIONS - VIBRATIONAL-RELAXATION OF DIATOMIC-MOLECULES},
	journal = {MOLECULAR PHYSICS},
	volume = {37},
	year = {1979},
	pages = {141-158},
	issn = {0026-8976},
	doi = {10.1080/00268977900100121},
	author = {TABOR, M and LEVINE, RD and Ben-Shaul, A and STEINFELD, JI}
}
@article { ISI:A1979HW53600003,
	title = {MOLECULAR CONSTRAINTS IMPLIED BY KINETIC COUPLING SCHEMES AND MAXIMAL WORK IN CHEMICAL-LASERS},
	journal = {JOURNAL OF NON-EQUILIBRIUM THERMODYNAMICS},
	volume = {4},
	year = {1979},
	pages = {363-376},
	issn = {0340-0204},
	doi = {10.1515/jnet.1979.4.6.363},
	author = {Ben-Shaul, A and LEVINE, RD}
}
@article { ISI:A1979JA44700001,
	title = {PRODUCT ROTATIONAL DISTRIBUTIONS, RELAXATION RATES AND CHEMICAL-LASER THRESHOLD TIMES},
	journal = {CHEMICAL PHYSICS},
	volume = {44},
	year = {1979},
	pages = {303-308},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(79)85214-3},
	author = {BRENNER, D and Ben-Shaul, A}
}
@article { ISI:A1979HD76600022,
	title = {ROTATIONAL AND VIBRATIONAL-RELAXATION OF DIATOMIC-MOLECULES AND A QUASI-CLASSICAL MODEL FOR ROTATIONAL RELAXATION},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {64},
	year = {1979},
	pages = {286-290},
	issn = {0009-2614},
	doi = {10.1016/0009-2614(79)80514-X},
	author = {FELDMANN, T and Ben-Shaul, A}
}
@article { ISI:A1979GM19700001,
	title = {TIME EVOLUTION OF THE PULSED HF CHEMICAL-LASER SYSTEM .1. KINETIC MODELING - ROTATIONAL NON-EQUILIBRIUM},
	journal = {CHEMICAL PHYSICS},
	volume = {36},
	year = {1979},
	pages = {291-305},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(79)85014-4},
	author = {Ben-Shaul, A and Felix, S and Kafri, O}
}
@article { ISI:A1979GM19700002,
	title = {TIME EVOLUTION OF THE PULSED HF CHEMICAL-LASER SYSTEM .2. IRREVERSIBLE THERMODYNAMIC ANALYSIS},
	journal = {CHEMICAL PHYSICS},
	volume = {36},
	year = {1979},
	pages = {307-322},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(79)85015-6},
	author = {Ben-Shaul, A and Kafri, O}
}
@article { ISI:A1978FB79300039,
	title = {NOTE ON QUASIEQUILIBRIUM VIBRATIONAL DISTRIBUTIONS OF POLYATOMIC-MOLECULES},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {55},
	year = {1978},
	pages = {560-564},
	issn = {0009-2614},
	doi = {10.1016/0009-2614(78)84038-X},
	author = {Ben-Shaul, A and KOMPA, KL}
}
@inbook {14516,
	title = {Thermodynamics of Molecular Disequilibrium},
	booktitle = {Chemical and Biochemical Applications of Lasers},
	year = {1977},
	pages = {145-192},
	publisher = {Academic Press},
	organization = {Academic Press},
	address = {New York},
	author = {LEVINE, RD and Ben-Shaul, A},
	editor = {C.B. Moore}
}
@article { ISI:A1977DB53500001,
	title = {COMPUTER-SIMULATION OF PULSED CL+HBR CHEMICAL-LASER - EFFECTS OF ROTATIONAL NONEQUILIBRIUM},
	journal = {CHEMICAL PHYSICS},
	volume = {21},
	year = {1977},
	pages = {1-19},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(77)85173-2},
	author = {Keren, E. and Gerber, R. B. and Ben-Shaul, A}
}
@article { ISI:A1977DN21700001,
	title = {STATISTICAL-MODELS AND PRIOR DISTRIBUTIONS IN THEORY OF CHEMICAL-REACTIONS},
	journal = {CHEMICAL PHYSICS},
	volume = {22},
	year = {1977},
	pages = {341-366},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(77)89023-X},
	author = {Ben-Shaul, A}
}
@inbook {14515,
	title = {Statistical and Dynamical Models of Population Inversion},
	booktitle = {Handbook of Chemical Lasers},
	year = {1976},
	pages = {581-617},
	publisher = {John Wiley \& Sons, Inc.},
	organization = {John Wiley \& Sons, Inc.},
	address = {New York},
	author = {Ben-Shaul, Avinoam and G. Ludwig Hofacker and J.F. Bott},
	editor = {R.W.F. Gross}
}
@article { ISI:A1976CP55900002,
	title = {ESTIMATES OF CHEMICAL-LASER EFFICIENCY IN LIMITS OF FAST AND SLOW ROTATIONAL RELAXATION},
	journal = {CHEMICAL PHYSICS},
	volume = {18},
	year = {1976},
	pages = {13-21},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(76)87033-4},
	author = {Ben-Shaul, A}
}
@article { ISI:A1976CD89700016,
	title = {VIB-ROTATIONAL ENERGY-DISTRIBUTIONS AND RELAXATION PROCESSES IN PULSED HF CHEMICAL-LASERS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {65},
	year = {1976},
	pages = {1711-1728},
	issn = {0021-9606},
	doi = {10.1063/1.433316},
	author = {Ben-Shaul, A and KOMPA, KL and SCHMAILZL, U}
}
@article { ISI:A1975AU23700015,
	title = {CHEMICAL LASERS - THERMODYNAMIC ANALYSIS OF A SYSTEM IN DISEQUILIBRIUM},
	journal = {CHEMICAL PHYSICS},
	volume = {10},
	year = {1975},
	pages = {367-392},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(75)87050-9},
	author = {Ben-Shaul, A and Kafri, O and LEVINE, RD}
}
@article { ISI:A1974T649100010,
	title = {ENTROPIES AND TEMPERATURE PARAMETERS CHARACTERIZING PRODUCT DISTRIBUTIONS IN CHEMICAL-REACTIONS AND CORRESPONDING THERMODYNAMIC QUANTITIES},
	journal = {MOLECULAR PHYSICS},
	volume = {27},
	year = {1974},
	pages = {1585-1600},
	issn = {0026-8976},
	doi = {10.1080/00268977400101321},
	author = {Ben-Shaul, A}
}
@article { ISI:A1974V049600078,
	title = {PRIOR-EXPECTATION DISTRIBUTION FUNCTIONS FOR ENERGY DISPOSAL AND ENERGY CONSUMPTION IN REACTIVE MOLECULAR COLLISIONS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {61},
	year = {1974},
	pages = {4937-4938},
	issn = {0021-9606},
	doi = {10.1063/1.1681831},
	author = {Ben-Shaul, A and LEVINE, RD and Bernstein, RB}
}
@article { ISI:A1973R679800014,
	title = {CHARACTERIZATION OF INVERTED POPULATIONS IN CHEMICAL LASERS BY TEMPERATURE-LIKE DISTRIBUTIONS - GAIN CHARACTERISTICS IN F+H2-]HF+H SYSTEM},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {59},
	year = {1973},
	pages = {4664-4673},
	issn = {0021-9606},
	doi = {10.1063/1.1680678},
	author = {Ben-Shaul, A and HOFACKER, GL and KOMPA, KL}
}
@article { ISI:000202879800010,
	title = {Product state distribution in chemical reactions: Vibrational temperature and rotational distributions},
	journal = {CHEMICAL PHYSICS},
	volume = {1},
	year = {1973},
	month = {MAY-JUN},
	pages = {244-255},
	abstract = {The distributions of vibrational, rotational and translational energies in the products of atom-diatomic molecule reactions are studied on the basis of their {\textquoteleft}{\textquoteleft}temperature parametere{\textquoteright}. The validity of the vibrational temperature concept, which my characterize the variaous distributions, is examined from different points of view. The analysis is done on the basis of available data from chemiluminescence, chemical laser and molecular beams measurements and from classical trajectory calculations. All the reactions investigated are exothermic with exothermicities ranging between approximate to 17 kcal/mole and approximate to 85 kcal/mole. In most products a high degree of population inversion is found. An attempt is made to predict the complete vibrotational state distribution using the vibrational temperature only. This attempt is equivalent to the assumption that apart from the vibration, the other degrees of freedom have reached a (microcanonical) equilibrium. The agreement with experimental results is good.},
	issn = {0301-0104},
	doi = {10.1016/0301-0104(73)85019-0},
	author = {Ben-Shaul, A}
}
@article { ISI:A1973Q914500007,
	title = {UNIFIED TREATMENT OF MOLECULAR-INTERACTIONS AT FINITE TEMPERATURES},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {59},
	year = {1973},
	pages = {2229-2233},
	issn = {0021-9606},
	doi = {10.1063/1.1680324},
	author = {BAER, S and Ben-Shaul, A}
}
@article { ISI:A1972O219800061,
	title = {ENTROPY AND CHEMICAL CHANGE .2. ANALYSIS OF PRODUCT ENERGY-DISTRIBUTIONS - TEMPERATURE AND ENTROPY DEFICIENCY},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {57},
	year = {1972},
	pages = {5427+},
	issn = {0021-9606},
	doi = {10.1063/1.1678242},
	author = {Ben-Shaul, A and Bernstein, RB and LEVINE, RD}
}
@article { ISI:A1972L541800035,
	title = {LONG-RANGE MANY-MOLECULE INTERACTIONS IN AN EXTENDED VAN DER WAALS EQUATION OF STATE},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {56},
	year = {1972},
	pages = {1238-\&},
	issn = {0021-9606},
	doi = {10.1063/1.1677352},
	author = {BAER, S and Ben-Shaul, A}
}
@article { ISI:A1972N392600002,
	title = {PRODUCT STATE DISTRIBUTION IN EXOERGIC CHEMICAL REACTIONS AND CONCEPT OF TEMPERATURE},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {15},
	year = {1972},
	pages = {160+},
	issn = {0009-2614},
	doi = {10.1016/0009-2614(72)80141-6},
	author = {Ben-Shaul, A and Bernstein, RB and LEVINE, RD}
}
@article { ISI:A1972M268000008,
	title = {QUANTUM MECHANICAL PERTURBATION EXPANSION FOR SECOND VIRIAL-COEFFICIENT AND URSELL-MAYER FUNCTION},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {56},
	year = {1972},
	pages = {3773-\&},
	issn = {0021-9606},
	doi = {10.1063/1.1677777},
	author = {BAER, S and Ben-Shaul, A}
}
@article { ISI:A1970G762900005,
	title = {ON EFFECT OF NUCLEAR MOTION ON INTERACTION BETWEEN DIATOMIC MOLECULES},
	journal = {MOLECULAR PHYSICS},
	volume = {19},
	year = {1970},
	pages = {33-\&},
	issn = {0026-8976},
	doi = {10.1080/00268977000100981},
	author = {BAER, S and Ben-Shaul, A}
}
