Publications

2018
Allolio, Christoph, Amir Haluts, and Daniel Harries. “A local instantaneous surface method for extracting membrane elastic moduli from simulation: Comparison with other strategies.” Chemical Physics (2018). Publisher's VersionAbstract

Advances over the past decade have made it possible to extract elastic constants of lipid assemblies from molecular dynamics simulations. We summarize existing strategies for obtaining membrane elastic moduli and clarify the differences in the underlying approaches. We analyze these strategies in depth, including several important advantages and limitations. By addressing these limitations, we obtain a newly formulated spatially local methodology for extracting bending and tilt moduli: The Real Space Instantaneous Surface Method (ReSIS). With its freely available implementation, this method is designed for highly dynamic systems with arbitrary interface geometries. We demonstrate how the method provides consistent results for membranes of arbitrary size. In addition, we describe alternative implementations of various Fourier-space methods, and use these to compare the results from the different available methods and from published computational data. We specifically focus on the tilt modulus, where very large differences between Fourier and real-space based methods are observed, including those derived using ReSIS. These discrepancies are likely due to the known difference between model moduli and thermodynamic moduli that are derived from the corresponding response functions. In addition, we reexamine the issue of angular degeneracy and its effect on conformational ensembles. Finally, a van ’t Hoff analysis of the tilt and bending moduli reveals that both modes act as entropic springs and that enthalpy favors nonzero tilt, perhaps heralding the spontaneous lipid chain tilt of the gel phase at lower temperatures.

Additional information and implementation available here

Ben-Abu, Natalie, Daniel Harries, Hillary Voet, and Masha Y. Niv. “The taste of KCl - what a difference a sugar makes.” Food Chemistry 255 (2018): 165-173. Publisher's VersionAbstract

Dramatic increase in NaCl consumption lead to sodium intake beyond health guidelines. KCl substitution helps reduce sodium intake but results in a bitter-metallic off-taste. Two disaccharides, trehalose and sucrose, were tested in order to untangle the chemical (increase in effective concentraion of KCl due to sugar addition) from the sensory effects. The bitter-metallic taste of KCl was reduced by these sugars, while saltiness was enhanced or unaltered. The perceived sweetness of sugar, regardless of its type and concentration, was an important factor in KCl taste modulation. Though KCl was previously shown to increase the chemical activity of trehalose but not of sucrose, we found that it suppressed the perceived sweetness of both sugars. Therefore, sensory integration was the dominant factor in the tested KCl-sugar combinations.

2017
TMAO mediates effective attraction between lipid membranes by partitioning unevenly between bulk and lipid domain
Sukenik, Shahar, Shaked Dunsky, Avishai Barnoy, Ilan Shumilin, and Daniel Harries. “TMAO mediates effective attraction between lipid membranes by partitioning unevenly between bulk and lipid domain.” Physical Chemistry Chemical Physics 19 (2017): 29862-29871. Publisher's VersionAbstract

Under environmental duress, many organisms accumulate large amounts of osmolytes – molecularly small organic solutes. Osmolytes are known to counteract stress, driving proteins to their compact native states by their exclusion from protein surfaces. In contrast, the effect of osmolytes on lipid membranes is poorly understood and widely debated. Many fully membrane-permeable osmolytes exert an apparent attractive force between lipid membranes, yet all proposed models fail to fully account for the origin of this force. We follow the quintessential osmolyte trimethylamine N-oxide (TMAO) and its interaction with dimyristoyl phosphatidylcholine (DMPC) membranes in aqueous solution. We find that by partitioning away from the inter-bilayer space, TMAO pushes adjacent membranes closer together. Experiments and simulations further show that the partitioning of TMAO away from the volume between bilayers stems from its exclusion from the lipid–water interface, similar to the mechanism of protein stabilization by osmolytes. We extend our analysis to show that the preferential interaction of other physiologically relevant solutes (including sugars and DMSO) also correlates with their effect on membrane bilayer interactions. Our study resolves a long-standing puzzle, explaining how osmolytes can increase membrane– membrane attraction or repulsion depending on their preferential interactions with lipids.

This article is part of the themed collection: 2017 PCCP HOT Articles

Poplinger, Michal, Ilan Shumilin, and Daniel Harries. “Impact of trehalose on the activity of sodium and potassium chloride in aqueous solutions: why trehalose is worth its salt.” Food Chemistry 237 (2017): 1209-1215. Publisher's Version
Wisdom of the crowd
Sapir, Liel, and Daniel Harries. “Wisdom of the crowd.” Bunsen-Magazin 19, no. 4 (2017): 152-162. Sapir&Harries_BM_2017.pdf
Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations
Doktorova, Milka, Daniel Harries, and George Khalashvili. “Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations.” Physical Chemistry Chemical Physics 19 (2017): 16806-16818. Publisher's Version
Revisiting hydrogen bond thermodynamics in molecular simulations
Sapir, Liel, and Daniel Harries. “Revisiting hydrogen bond thermodynamics in molecular simulations.” Journal of Chemical Theory and Computation 13, no. 6 (2017): 2851–2857. Publisher's Version
2016
Hu, Yuwei, Jason S Kahn, Weiwei Guo, Fujian Huang, Michael Fadeev, Daniel Harries, and Itamar Willner. “Reversible modulation of DNA-based hydrogel shapes by internal stress interactions.” Journal of the American Chemical Society 138, no. 49 (2016): 16112-16119. Publisher's Version
Competing processes of micellization and fibrillization in native and reduced casein proteins
Portnaya, Irina, Sharon Avni, Ellina Kesselman, Yoav Boyarski, Shahar Sukenik, Daniel Harries, Nily Dan, Uri Cogan, and Dganit Danino. “Competing processes of micellization and fibrillization in native and reduced casein proteins.” Physical Chemistry Chemical Physics 18, no. 32 (2016): 22516-22525. Publisher's Version
Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations
Johner, Niklaus, Daniel Harries, and George Khelashvili. “Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations.” BMC bioinformatics 17, no. 1 (2016): 1. Publisher's Version
Macromolecular compaction by mixed solutions: Bridging versus depletion attraction
Sapir, Liel, and Daniel Harries. “Macromolecular compaction by mixed solutions: Bridging versus depletion attraction.” Current Opinion in Colloid & Interface Science 22 (2016): 80-87. Publisher's Version
Nonclassical Crystal Growth as Explanation for the Riddle of Polarity in Centrosymmetric Glycine Crystals
Meirzadeh, Elena, Liel Sapir, Hagai Cohen, Sidney R Cohen, David Ehre, Daniel Harries, Meir Lahav, and Igor Lubomirsky. “Nonclassical Crystal Growth as Explanation for the Riddle of Polarity in Centrosymmetric Glycine Crystals.” Journal of the American Chemical Society 138, no. 44 (2016): 14756-14763. Publisher's Version
Properties of Polyvinylpyrrolidone in a Deep Eutectic Solvent
Sapir, Liel, Christopher B Stanley, and Daniel Harries. “Properties of Polyvinylpyrrolidone in a Deep Eutectic Solvent.” The Journal of Physical Chemistry A 120, no. 19 (2016): 3253-3259. Publisher's Version
2015
Kulig, Waldemar, Agnieszka Olżyńska, Piotr Jurkiewicz, Anu M Kantola, Sanna Komulainen, Moutusi Manna, Mohsen Pourmousa, et al.Cholesterol under oxidative stress—How lipid membranes sense oxidation as cholesterol is being replaced by oxysterols.” Free Radical Biology and Medicine 84 (2015): 30-41. Publisher's Version
Galanis, Jennifer, Aakriti Sood, Ron Gill, and Daniel Harries. “The contribution of capping layer dielectric properties to nanoparticle stability.” Colloids and surfaces A: Physicochemical and engineering aspects 483 (2015): 239-247. Publisher's Version
Sapir, Liel, and Daniel Harries. “Is the depletion force entropic? Molecular crowding beyond steric interactions.” Current Opinion in Colloid & Interface Science 20, no. 1 (2015): 3-10. Publisher's Version
Sapir, Liel, and Daniel Harries. “Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions.” Journal of chemical theory and computation 11, no. 7 (2015): 3478-3490. Publisher's Version
Sukenik, Shahar, Liel Sapir, and Daniel Harries. “Osmolyte induced changes in peptide conformational ensemble correlate with slower amyloid aggregation: a coarse-grained simulation study.” Journal of chemical theory and computation 11, no. 12 (2015): 5918-5928. Publisher's Version
2014
Harries, Daniel, and Uri Raviv. “1 Soft Matter Physics of Lipid Membrane–Based Assemblies.” In Liposomes, Lipid Bilayers and Model Membranes: From Basic Research to Application, edited by Georg Pabst, Norbert Kučerka, Mu-Ping Nieh, and John Katsaras, 3-26. Boca Raton: CRC Press, 2014. Publisher's Version
Johner, Niklaus, Daniel Harries, and George Khelashvili. “Curvature and lipid packing modulate the elastic properties of lipid assemblies: comparing HII and lamellar phases.” The journal of physical chemistry letters 5, no. 23 (2014): 4201-4206. Publisher's Version

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