The control of electronic dynamics in the neutral electronic states of LiH before the onset of significant nuclei motion is investigated using a negative-neutral-positive (NeNePo) ultrafast IR pump-attoescond pulse train (APT) probe scheme. Starting from the ground state of the anion (LiH-), multiphoton ultrafast electron detachment and subsequent excitation of the neutral by a few femtosecond intense IR pulse produces a non-equilibrium electronic density in neutral LiH. The coherent electronic wave packet is then probed by angularly resolved photoionization to the cation by an APT generated from a replica of the pump IR pulse at several time delays. Realistic parameters for the pump and the APT are used. Several NeNePo schemes are simulated using different IR carrier frequencies, showing that the delay between the successive attosecond pulses in the train can be used as a filter to probe the different pairs of states present in the coherent electronic wave packet produced by the pump pulse. The dynamical simulations include the pump and the probe pulses to all orders by solving the time-dependent Schrodinger equation using a coupled equation scheme for the manifolds of the anion, neutral, and cation subspaces. We show that an incomplete molecular orientation of the molecule in the laboratory frame does not prevent probing the electronic density localization by angularly resolved photoelectron maps.

In nature, post-transcriptional alternative splicing processes expand the proteome biodiversity providing means to synthesize various protein isoforms. We describe the input-guided assembly of a DNAzyme-based full-adder computing system, which mimics functions of the natural processes by increasing the diversity of logic elements by the reconfiguration of the inputs. The full-adder comprises the simultaneous operation of three inputs that yield two different output signals, acting as sum and carry bits. The DNAzyme-based full-adder system consists of a library of Mg2+-dependent DNAzyme subunits and their substrates that are modified by two different fluorophore/quencher pairs that encode the sum and carry outputs. The input-guided assembly of DNAzyme subunits, formed by three inputs composed of nucleic acid hairpin structures, leads to computing modules that yield the sum and carry outputs of the full-adder. In the presence of a single input the DNAzyme computing module yields the sum fluorescence output. In the presence of two of the inputs, the reconfiguration of the input structures proceeds, leading to an input-guided computing module that yields the carry fluorescence output. By introducing all the three inputs the sequential inter-input hybridization leads to the reconfiguration of the inputs into polymer wires. These include binding sites for two types of DNAzyme and their substrates leading to the carry and sum fluorescence outputs. The advantages of the simultaneous three-input operation of the full-adder and the possibilities to implement DNAzyme-based computing modules for cascading full-adders are discussed.

Nitrogen isotopic distributions in the solar system extend across an enormous range, from -400 parts per thousand, in the solar wind and Jovian atmosphere, to about 5,000 parts per thousand in organic matter in carbonaceous chondrites. Distributions such as these require complex processing of nitrogen reservoirs and extraordinary isotope effects. While theoretical models invoke ion-neutral exchange reactions outside the protoplanetary disk and photochemical self-shielding on the disk surface to explain the variations, there are no experiments to substantiate these models. Experimental results of N-2 photolysis at vacuum UV wavelengths in the presence of hydrogen are presented here, which show a wide range of enriched delta N-15 values from 648 parts per thousand to 13,412 parts per thousand in product NH3, depending upon photodissociation wavelength. The measured enrichment range in photodissociation of N-2, plausibly explains the range of delta N-15 in extraterrestrial materials. This study suggests the importance of photochemical processing of the nitrogen reservoirs within the solar nebula.

The epithelial-to-mesenchymal transition (EMT) initiates the invasive and metastatic behavior of many epithelial cancers. Mechanisms underlying EMT are not fully known. Surprisal analysis of mRNA time course data from lung and pancreatic cancer cells stimulated to undergo TGF-beta 1-induced EMT identifies two phenotypes. Examination of the time course for these phenotypes reveals that EMT reprogramming is a multistep process characterized by initiation, maturation, and stabilization stages that correlate with changes in cell metabolism. Surprisal analysis characterizes the free energy time course of the expression levels throughout the transition in terms of two state variables. The landscape of the free energy changes during the EMT for the lung cancer cells shows a stable intermediate state. Existing data suggest this is the previously proposed maturation stage. Using a single-cell ATP assay, we demonstrate that the TGF-beta 1-induced EMT for lung cancer cells, particularly during the maturation stage, coincides with a metabolic shift resulting in increased cytosolic ATP levels. Surprisal analysis also characterizes the absolute expression levels of the mRNAs and thereby examines the homeostasis of the transcription system during EMT.

To describe the time course of cellular systems, we integrate ideas from thermodynamics and information theory to discuss the work needed to change the state of the cell. The biological example analyzed is experimental microarray transcription level oscillations of yeast in the different phases as characterized by oxygen consumption. Surprisal analysis was applied to identify groups of transcripts that oscillate in concert and thereby to compute changes in free energy with time. Three dominant transcript groups were identified by surprisal analysis. The groups correspond to the respiratory, early, and late reductive phases. Genes involved in ribosome biogenesis peaked at the respiratory phase. The work to prepare the state is shown to be the sum of the contributions of these groups. We paid particular attention to work requirements during ribosomal building, and the correlation with ATP levels and dissolved oxygen. The suggestion that cells in the respiratory phase likely build ribosomes, an energy intensive process, in preparation for protein production during the S phase of the cell cycle is validated by an experiment. Surprisal analysis thereby provided a useful tool for determining the synchronization of transcription events and energetics in a cell in real time.

Hypoxia is a near-universal feature of cancer, promoting glycolysis, cellular proliferation, and angiogenesis. The molecular mechanisms of hypoxic signaling have been intensively studied, but the impact of changes in oxygen partial pressure (pO(2)) on the state of signaling networks is less clear. In a glioblastoma multiforme (GBM) cancer cell model, we examined the response of signaling networks to targeted pathway inhibition between 21% and 1% pO(2). We used a microchip technology that facilitates quantification of a panel of functional proteins from statistical numbers of single cells. We find that near 1.5% pO(2), the signaling network associated with mammalian target of rapamycin (mTOR) complex 1 (mTORC1)-a critical component of hypoxic signaling and a compelling cancer drug target-is deregulated in a manner such that it will be unresponsive to mTOR kinase inhibitors near 1.5% pO(2), but will respond at higher or lower pO(2) values. These predictions were validated through experiments on bulk GBM cell line cultures and on neurosphere cultures of a human-origin GBM xenograft tumor. We attempt to understand this behavior through the use of a quantitative version of Le Chatelier's principle, as well as through a steady-state kinetic model of protein interactions, both of which indicate that hypoxia can influence mTORC1 signaling as a switch. The Le Chatelier approach also indicates that this switch may be thought of as a type of phase transition. Our analysis indicates that certain biologically complex cell behaviors may be understood using fundamental, thermodynamics-motivated principles.

Toward identifying a cancer-specific gene signature we applied surprisal analysis to the RNAs expression behavior for a large cohort of breast, lung, ovarian, and prostate carcinoma patients. We characterize the cancer phenotypic state as a shared response of a set of mRNA or microRNAs (miRNAs) in cancer patients versus noncancer controls. The resulting signature is robust with respect to individual patient variability and distinguishes with high fidelity between cancer and noncancer patients. The mRNAs and miRNAs that are implicated in the signature are correlated and are known to contribute to the regulation of cancer-signaling pathways. The miRNA and mRNA networks are common to the noncancer and cancer patients, but the disease modulates the strength of the connectivities. Furthermore, we experimentally assessed the cancer-specific signatures as possible therapeutic targets. Specifically we restructured a single dominant connectivity in the cancer-specific gene network in vitro. We find a deflection from the cancer phenotype, significantly reducing cancer cell proliferation and altering cancer cellular physiology. Our approach is grounded in thermodynamics augmented by information theory. The thermodynamic reasoning is demonstrated to ensure that the derived signature is bias-free and shows that the most significant redistribution of free energy occurs in programming a system between the noncancer and cancer states. This paper introduces a platform that can elucidate miRNA and mRNA behavior on a systems level and provides a comprehensive systematic view of both the energetics of the expression levels of RNAs and of their changes during tumorigenicity.

The outcome of a light-matter interaction depends on both the state of matter and the state of light. It is thus a natural setting for implementing bilinear classical logic. A description of the state of a time-varying system requires measuring an (ideally complete) set of time-dependent observables. Typically, this is prohibitive, but in weak-field spectroscopy we can move toward this goal because only a finite number of levels are accessible. Recent progress in nonlinear spectroscopies means that nontrivial measurements can be implemented and thereby give rise to interesting logic schemes where the outputs are functions of the observables. Lie algebra offers a natural tool for generating the outcome of the bilinear light-matter interaction. We show how to synthesize these ideas by explicitly discussing three-photon spectroscopy of a bichromophoric molecule for which there are four accessible states. Switching logic would use the on-off occupancies of these four states as outcomes. Here, we explore the use of all 16 observables that define the time-evolving state of the bichromophoric system. The bilinear laser-system interaction with the three pulses of the setup of a 2D photon echo spectroscopy experiment can be used to generate a rich parallel logic that corresponds to the implementation of a molecular decision tree. Our simulations allow relaxation by weak coupling to the environment, which adds to the complexity of the logic operations.

Metabolic engineering seeks to redirect metabolic pathways through the modification of specific biochemical reactions or the introduction of new ones with the use of recombinant technology. Many of the chemicals synthesized via introduction of product-specific enzymes or the reconstruction of entire metabolic pathways into engineered hosts that can sustain production and can synthesize high yields of the desired product as yields of natural product-derived compounds are frequently low, and chemical processes can be both energy and material expensive; current endeavors have focused on using biologically derived processes as alternatives to chemical synthesis. Such economically favorable manufacturing processes pursue goals related to sustainable development and ``green chemistry''. Metabolic engineering is a multidisciplinary approach, involving chemical engineering, molecular biology, biochemistry, and analytical chemistry. Recent advances in molecular biology, genome-scale models, theoretical understanding, and kinetic modeling has increased interest in using metabolic engineering to redirect metabolic fluxes for industrial and therapeutic purposes. The use of metabolic engineering has increased the productivity of industrially pertinent small molecules, alcohol-based biofuels, and biodiesel. Here, we highlight developments in the practical and theoretical strategies and technologies available for the metabolic engineering of simple systems and address current limitations.

The ultrafast migratory dynamics of the nonstationary hole resulting from a sudden ionization of the small tetrapeptides, Trp-(Leu)(3) and Tyr-(Ala)(3), is studied using as input a high level quantum chemistry description of the electronic structure for extended conformers computed for frozen nuclei. The sudden ionization process prepares a localized electronic wavepacket that is a superposition of a few stationary states of the cation that are energetically allowed. The superposition evolves field-free until a second ionization to the dication. The wavelength and polarization of the first ultrashort VUV ionizing pulse can be used to tailor the amplitudes on the states of the cation and the initial localization of the hole. For these molecular chains that extend over 15 angstrom, the most efficient mechanism for charge migration is sequential, involving coherent transitions between neighbor and next neighbor amino-acid subunits. The migration of the hole is probed by a second sudden ionization leading to a dication peptide. Its time scale is in the range of a few to a dozen of femtoseconds depending on the initial state of the cation built by the ionization process. The computed angular distributions provide a clear signature of the field-free dynamics between the two sudden ionization processes. Our results are consistent with the experimental observation that the charge transfer is activated, meaning that an excess energy above the ionization potential of the cation is required for facile migration of charge.

Towards a reliable identification of the onset in time of a cancer phenotype, changes in transcription levels in cell models were tested. Surprisal analysis, an information-theoretic approach grounded in thermodynamics, was used to characterize the expression level of mRNAs as time changed. Surprisal Analysis provides a very compact representation for the measured expression levels of many thousands of mRNAs in terms of very few - three, four - transcription patterns. The patterns, that are a collection of transcripts that respond together, can be assigned definite biological phenotypic role. We identify a transcription pattern that is a clear marker of eventual malignancy. The weight of each transcription pattern is determined by surprisal analysis. The weight of this pattern changes with time; it is never strictly zero but it is very low at early times and then rises rather suddenly. We suggest that the low weights at early time points are primarily due to experimental noise. We develop the necessary formalism to determine at what point in time the value of that pattern becomes reliable. Beyond the point in time when a pattern is deemed reliable the data shows that the pattern remain reliable. We suggest that this allows a determination of the presence of a cancer forewarning. We apply the same formalism to the weight of the transcription patterns that account for healthy cell pathways, such as apoptosis, that need to be switched off in cancer cells. We show that their weight eventually falls below the threshold. Lastly we discuss patient heterogeneity as an additional source of fluctuation and show how to incorporate it within the developed formalism.

Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like transcripts vary greatly, even among tumors of the same type from different individuals. Two distinguishable classes could be identified within the hardware-like component: those transcripts that are highly expressed and stable and an adaptable subset with lower expression that respond to external stimuli. Importantly, we demonstrate that this structure is conserved across organisms. Deletions of transcripts from the highly stable core are predicted to result in cell mortality. The approach provides a conceptual thermodynamic-like framework for the analysis of gene-expression levels and networks and their variations in diseased cells.

Ultrafast UV excitation can prepare a nonstationary coherent superposition of molecular electronic states. The purely electronic dynamics before the onset of nuclear motion can be probed by a sudden XUV ionization of the electronic wave packet. Dynamical computations at the many-electron level on the LiH and 1-azabicyclo[3.3.3]undecane (C10H19N) molecules show that molecular frame photoelectron angular distributions reflect the spatial localization and undulations of the electronic coherent superposition accessed by the initial ultrafast UV excitation. The sudden ionization is sensitive to interference effects.

The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a construction of the logically reversible Toffoli and Fredkin gates by implementing a library of predesigned Mg2+-dependent DNAzymes and their respective substrates. Although the logical reversibility, for which each set of inputs uniquely correlates to a set of outputs, is demonstrated, the systems manifest thermodynamic irreversibility originating from two quite distinct and nonrelated phenomena. (i) The physical readout of the gates is by fluorescence that depletes the population of the final state of the machine. This irreversible, heat-releasing process is needed for the generation of the output. (ii) The DNAzyme-powered logic gates are made to operate at a finite rate by invoking downhill energy-releasing processes. Even though the three bits of Toffoli's and Fredkin's logically reversible gates manifest thermodynamic irreversibility, we suggest that these gates could have important practical implication in future nanomedicine.

A methodology is developed for the analysis of multivariate data by maximal entropy and it is shown how the surprisal reduces to the more familiar bivariate and univariate forms. When multivariate data is available it is shown how the uni- or bi-variate surprisal parameters can be expressed as a sum of terms containing contributions of different pathways. But if averaging so as to reduce the number of variables is performed before the data analysis then all that one can determine is the sum but not the individual contributions: averaging completely hides essential details and correlations. The formalism is illustrated by an application to ultrafast translational equilibration that occurs when a cold rare gas cluster impacts a hard surface at a hypersonic speed.

We report on a method for quantitating the distance dependence of cell-cell interactions. We employ a microchip design that permits a multiplex, quantitative protein assay from statistical numbers of cell pairs, as a function of cell separation, with a 0.15 nL volume microchamber. We interrogate interactions between pairs of model brain cancer cells by assaying for six functional proteins associated with PI3k signaling. At short incubation times, cells do not appear to influence each other, regardless of cell separation. For 6 h incubation times, the cells exert an inhibiting influence on each other at short separations and a predominately activating influence at large separation. Protein-specific cell-cell interaction functions are extracted, and by assuming pairwise additivity of those interactions, the functions are shown to correctly predict the results from three-cell experiments carried out under the identical conditions.

The computed time evolution of excited electronic and nuclear:states:. of dinitrogen following a broad laser pulse excitation of the dipole allowed singlet Pi states is discussed. The computations use two complementary methods to solve the time-dependent Schrodinger equation of the molecule. The electronic evolution is described as spanning seven states, the three dipole-allowed singlet states (b,c,o(1)Pi(u)) and four triplet states (C,C',F,G(3)Pi(u)). Spin orbit coupling mixes states of the two manifolds. The computed dynamics includes the attosecond pulse single photon pumping from the electronic ground state. The ultrafast exit to the continuum from the bound states that are optically excited and the large isotope effect on this process are used as a probe of the electron dynamics as coupled to the Onset of the nuclear motion. For -'4N2-, prompt predissociation to the continuum of the repulsive C'(3)Pi(u) state is facilitated primarily by the b(1)Pi(u)(v=3)-C-3 Pi(u)(v = 9) coupling whereas for N-15(2) it is the b1 Pi(u) (v =4)-C-3 Pi(u)(v =10) coupling term. Predissociation from the F3 Pi u and G(3)Pi(u) stateS is important at the high energies because of their strong coupling to the continuum.

Electronic reorganization during and after excitation by an intense ultrashort pulse is computed for LiH in a many-electron multireference time-dependent approach at a fixed nuclear geometry. The electronic dipole moment is used to probe the temporal response of the charge density. Above a field-strength threshold, there is an extensive Stark shifting and Rabi broadening of levels with corresponding distortion of the charge distribution whose response at strong fields is neither adiabatic nor diabatic. A nonresonant IR pulse is more effective in inducing charge shake-up during the pulse.