Seminar schedule

We study resonant response of an oscillator with shot-noise type mass fluctuations. The model describes a nano-mechanical resonator with adsorbing and desorbing molecules. We derive an analytical expression for the spectrum of the oscillator. It applies to an arbitrary interrelation between the damping rate of the oscillator, the adsorption and desorption rates and the magnitude of frequency shift due to a single adsorption or desorption event. Depending on this interrelation the spectrum may display fine structure corresponding to variation of the number of adsorbed molecules or present a single asymmetric peak. The results can be used for high-precision fast measurements of molecular mass with nano-mechanical resonators.

Ever since the advent of Quantum Mechanics, there has been a quest for a trajectory based formulation of quantum theory that is exact. In the 1950’s, David Bohm, building on earlier work of Madelung and de Broglie, developed an exact formulation of quantum mechanics in which trajectories evolve in the presence of the usual Newtonian force plus an additional quantum force. In recent years, there has been a resurgence of interest in Bohmian Mechanics (BM) as a numerical tool because of its apparently local dynamics, which could lead to significant computational advantages for the simulation of large quantum systems. However, closer inspection of the Bohmian formulation reveals that the nonlocality of quantum mechanics has not disappeared --- it has simply been swept under the rug into the quantum force. In this work, we present a new formulation of Bohmian mechanics in which the quantum action, S, is taken to be complex. This requires the propagation of complex trajectories, but with the reward of a significantly higher degree of localization. For example, using strictly localized trajectories (no communication with their neighbors) we obtain extremely accurate quantum mechanical transmission probabilities down to 10-7. We have recently extended the formulation to include interference effects, which has been one of the major obstacles in conventional Bohmian mechanics. Applications to one- and two-dimensional transmission, thermal rate constants in one and two dimensions, the calculation of eigenvalues and nonadiabatic transitions will be presented. A variation on the method allows for the calculation of thermal rate constants and eigenvalues using just one or two zero-velocity trajectories. On the formal side, the approach is shown to be a rigorous extension of generalized Gaussian wavepacket methods to give exact quantum mechanics, and has intriguing implications for fundamental quantum mechanics.

Recent applications of experimental techniques such as second-harmonic generation and x-ray diffraction provide new information about the structure of water at interfaces and about the behavior of ions at aqueous interfaces. The picture emerging is consistent with previous and more recent molecular dynamics simulations. I will review this progress and show how it helps understand our recent theoretical work on SN2 reactions at water surfaces.

Non-specific protein adsorption is the first process in the foreign body response. Biomaterials need to provide non-fouling surfaces to prevent adsorption of blood proteins. The molecular design of surface modifiers that prevent non-specific adsorption requires the understanding of the factors that determine protein adsorption. The hierarchy of time and length scales present in the adsorption requires a multiscale approach to treat the complexity of the process. We will discuss the driving forces that determine protein adsorption and how end-grafted polymers can be used to modify the ability of the proteins to reach the surface. We will show the differences between preventing protein adsorption thermodynamically and kinetically. In particular, we will demonstrate that polymer molecular weight plays no role for the thermodynamic control while it is very important in determining the kinetics of protein adsorption. We will discuss the relevance of short time scales to understand how proteins interact with surfaces. To this end we use atomistic molecular dynamics that enable the study of a single protein in the presence of a surface and explicit water over time scales of tens of nanoseconds. For practical applications the relevant time scales are hours or days. We will show how a coarse grained molecular approach can be used to study these time scales. In particular we will show two different levels of approximations based on a molecular understanding of the adsorption process that enables, through the proper integration of degrees of freedom, to determine the kinetics of adsorption over 16 orders of magnitude in time. Comparisons with experimental observations will be presented for the cases that are available.

This talk develops mathematical models describing the evolutionary dynamics of both asexually and sexually reproducing populations of diploid unicellular organisms. The asexual and sexual life cycles are based on the asexual and sexual life cycles in Saccharomyces cerevisiae, or Baker's yeast, which normally reproduces by asexual budding, but switches to sexual reproduction when stressed. The mathematical models consider three reproduction pathways: (1) Asexual reproduction. (2) Self-fertilization (3) Sexual reproduction. We also consider two forms of genome organization. In one case, we assume that the genome consists of two multi-gene chromosomes, while in the second case we consider the opposite extreme and assume that each gene defines a separate chromosome, which we call the multi-chromosome genome. These two cases are considered in order to explore the role that recombination has on the mutation-selection balance and the selective advantage of the various reproduction strategies. We assume that the purpose of diploidy is to provide redundancy, so that damage to a gene may be repaired using the other, presumably undamaged copy (a process known as {\it homologous recombination repair}). As a result, we assume that the fitness of the organism only depends on the number of homologous gene pairs that contain at least one functional copy of a given gene. If the organism has at least one functional copy of every gene in the genome, we assume a fitness of 1 , and we assume that each homologous gene pair without a functional copy of a given gene induces a fitness penalty of alpha . However, we assume that, even among organisms with at least one functional copy of every gene, there is an effective fitness penalty for having faulty copies of genes. This fitness penalty arises as a result of the repair of a damaged functional gene when its homologue has a fixed mutation. The repair process can lead to the mutation being transferred to the functional gene, leading to the loss of functionality of both copies of a given gene. For nearly all of the reproduction strategies we consider, we find that the mean fitnesses have an upper bound of $ \max{2 e^{-N \epsilon} - 1, 0}, where N is the number of genes in the haploid set of the genome, and \epsilon is the probability that a given DNA template strand of a given gene produces a mutated daughter during replication. The only exceptions are the two- and multi-chromosome sexual reproduction pathways. These strategies are found to have a mean fitness that can exceed the mean fitness of all of the other strategies, provided that N \epsilon is sufficiently large. The critical value of N \epsilon beyond which the sexual pathways have a higher mean fitness than the other strategies decreases as \alpha approaches 1 . Furthermore, while the other reproduction strategies experience a total loss of viability due to the steady accumulation of deleterious mutations once N \epsilon $exceeds \ln 2 , the transition in the sexual pathways may be delayed to arbitrarily high values of N \epsilon provided that \alpha is sufficiently close to 1 . We explicitly allow for mitotic recombination in this work, which has been found, using previous models, to provide an identical selective advantage as sexual reproduction. With the models used in this study, we do not find any advantage for mitotic recombination over other reproduction strategies. However, sexual reproduction with random mating does have a selective advantage over other reproduction strategies. The results of this talk suggest that sex provides a selective advantage by acting on "non-essential" genes, i.e., genes that confer a fitness advantage to the organism, but are not necessary for the organism to grow and reproduce. The more "non-essential" the genes, as measured by how close \alpha is to 1 in our model, the stronger the selective advantage for sex. The results of this talk also suggest an explanation for why unicellular organisms such as Saccharomyces cerevisiae (Baker's yeast) switch to a sexual mode of reproduction when stressed. Finally, while the results of this talk are based on modeling mutation-propagation in unicellular organisms, they nevertheless suggest that, in more complex organisms with significantly larger genomes, sex is necessary to prevent the loss of viability of a population due to genetic drift.

This is more work in progress. It is based upon a series of observations of long ZnO nanoribbons by Z.L. Wang (Georgia Tech) and nanoribbons of other wurtzite materials from 2004 to present. Many explanations have been proposed for why they bend but the existing explanations are either wrong or are not consistent with observations for one reason or another. We provide a rigorous thermodynamics analysis including elasticity, surface stress, electrostatics, piezoelectric effects and charge flow in such wide bandgap semiconductors. After showing what's wrong with existing explanations, we show that the effect is the result of the coupling between a piezoelectric effect and charge flow. The results are shown to be in very good agreement with experiment.

The theory of open quantum systems deals with systems coupled to an external, uncontrollable environment. One attempts to deduce a reduced dynamical description for the system alone.
In this talk I will report on the solution of two problems in the theory of open systems:

1. The derivation of a master equation for the system density matrix that explicitly includes bath-memory effects ("post-Markovian"), is analytically and numerically tractable, and satisfies the important constraint known as "complete positivity" (http://xxx.lanl.gov/abs/quant-ph/0404077, submitted).
2. The generalization of the adiabatic theorem of closed quantum systems to the general open systems case (http://xxx.lanl.gov/abs/quant-ph/0404147, in press Phys. Rev. A).

Consider a driven quantum system, such as a small conducting particle driven by an electromagnetic radiation, or a mesoscopic ring driven by an electromotive force. The common practice is to calculate the response (rate of energy bsorption,
conductance) using the Kubo Formula. We argue that this may lead to a huge over-estimate. In general it is essential to take into account the structure of the perturbation matrix, which may imply percolation-like dynamics. These structures are determined by both semiclassical and random matrix theory consideration, and cannot be ignored.

Cooling matter to temperatures below 1 mK has paved the way to studying the extreme quantum limit. The internal degrees of ultracold molecules offer a realm of new applications ranging from molecular Bose-Einstein condensates to 'super' chemistry. Direct cooling methods of molecules have not yet reached the ultracold regime. An alternative route has therefore been the cooling of atoms and subsequent assembly of the atoms to molecules by interaction with external fields. For this second step, magnetic fields and CW lasers have successfully been employed. However, both approaches have shortcomings which will be addressed in my talk: Association by a magnetic field requires the presence of a hyperfine manifold of the atoms, i..e. it is not a general technique. Photoassociation with CW lasers relies on spontaneous emission to yield molecules in their electronic ground state.
Hence its efficiency is limited, and in case of atomic Bose-Einstein condensate the coherence is destroyed. I will discuss in the first part of the talk, how the idea of a so-called magnetic Feshbach resonance to create molecules can be translated to optical transitions which are more generally available. In the second part, a coherent photoassociation scheme will be introduced by employing short laser pulses. I will present calculations for the example of creating rubidium dimer molecules, and I will discuss the experimental feasibility of both schemes.

Actin is a small protein that can polymerize in the cell to form long and stiff filaments. This process consumes ATP, and is nucleated and controlled by a variety of other proteins. The cell is using actin polymerization to drive shape deformations of its outer membrane, that are involved in motility and adhesion. We present a dynamical model that accounts for some of the rich variety of membrane structures and motion observed in real cells. This model shows how in the living cells non-quilibrium and equilibrium processes are combined.

The presentation traces the evolution of our experimental and modeling progress in the somewhat unorthodox use of highly concentrated sunlight for three diverse applications:

1. Power generation with advanced multi-junction semiconductor devices and new high-flux optics.
2. Medical surgical procedures.
3. The synthesis of lucrative nanomaterials

The Jahn-Teller Effect is one of the most fascinating phenomena in modern physics and chemistry. Recently it inspired the Nobel-Prize discovery of high-temperature superconductivity. The inspirational power of this effect is very high as it provides a general approach to understanding the origin of properties of molecules and crystals, and prediction of new properties (for a review see the new book at http://www.cambridge.org/uk/0521822122). The seminar talk includes a general introduction to the subject and applications to the origin and mechanism of all the (structural) symmetry breakings in molecular systems and condensed matter as due to the Jahn-Teller Effect. Together with analogous results from elementary particle theory we can conclude that degeneracy or pseudodegeneracy is the driving force of all symmetry breakings in Nature beginning with the Big Bang.

The reactions of atmospheric molecules, their mechanisms and dynamics are a major current interest of atmospheric chemistry. In this presentation the spectroscopy and the dynamics of atmospheric species are presented. Potentials from electronic structure theory and classical trajectory methods are combined to unravel the mechanism of photochemical reactions and to predict new intermediate species and possible products. The results focus on photochemistry following overtone excitations of molecules such as HNO3, H2SO4, HNO3-H2O and H2SO4-H2O. One of the interesting results is a prediction of a rapid intramolecular hopping of the hydrogen atom induced by the excitation. In addition, the efficient occurrence of dissociation of H2SO4 into SO3 + H2O is demonstrated. This reaction as induced by overtones differs in behavior from the corresponding thermal reaction. Further interesting result is the prediction of a new weakly bound species HOON in the photoexcitation of HONO.

It is proposed that theoretical simulations using electronic structure potential in "on-the-fly" dynamics calculations can be a powerful tool in the exploration of atmospheric processes.

Single photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.

I shall discuss how the formation of ultracold molecules can be optimized by use of pulsed lasers. In a recent theoretical paper [E. Luc-Koenig, R. Kosloff, M. Vatasescu and . M.-S., PRA 70, 033414] numerical calculations for photoassociation of ultracold cesium atoms with a chirped laser pulse show an important population transfer to _ 15 vibrational levels in the external well of the excited 0-g (6s + 6p3/2) potential. Such levels lie in the energy range swept by the instantaneous frequency of the pulse, thus defining a "photoassociation window". Levels outside this window may be significantly populated during the pulse, but no population remains there finally. In contrast, the population transfer to the last vibrational levels of the ground a3_+ u (6s + 6s) potential is significant, making stable molecules by sweeping an optical Feshbach resonance. The results are interpreted as an adiabatic population inversion mechanism, efficient only within the photoassociation window. The large value found for the photoassociation rate suggests promising applications. In an atomic condensate, the treatment of photoassociation and optical Feshbach resonances depends upon short range correlation effects. We have developed a model [P. Naidon, F. Masnou-Seeuws, PRA 68 033612 (2003) and preprint (2005)] where the finite size of the interatomic potentials is explicitly taken into account, introducing realistic numerical potentials. Two different approaches, the reduced pair wave function and the first-order cumulant approximations are discussed. The two methods are checked by computing the depletion of a sodium condensate in the presence of a CW photoassociation laser, under conditions similar to the NIST experiment of McKenzie et al [PRL 88, 120403 (2002)]. Their results are equivalent at low intensities I, and close to the prediction of a mean field model. In contrast they differ quantitatively for I >10 kW/cm2. Both methods show qualitative agreement on two effects: first, they predict production of correlated pairs of atoms when a high-intensity laser is rapidly switched on; second, they predict a significant reduction of the photoassociation rate at high intensities, clearly due to short range correlation effects.

Cell crawling is an important biological phenomenon underlying coordinated cell movements in morphogenesis, cancer, and wound healing. In recent decades the process of cell crawling has been experimentally and theoretically dissected into further subprocesses: protrusion of the cell at its leading edge, retraction of the cell body, and graded adhesion.
A number of one-dimensional (1-D) models explain successfully a proximal-distal organization and movement of the motile cell. However, more adequate two-dimensional (2-D) models are lacking. We propose a multiscale 2-D computational model of the lamellipodium (motile appendage) of a simply shaped, rapidly crawling ?sh keratocyte cell.
We couple submodels of (i) protrusion and adhesion at the leading edge, (ii) the elastic 2-D lamellipodial actin network, (iii) the actin-myosin contractile bundle at the rear edge, and (iv) the convection-reaction-diffusion actin transport on the free boundary lamellipodial domain. We simulate the combined model numerically using a ?nite element approach. The simulations reproduce observed cell shapes, forces, and movements and explain some experimental results on perturbations of the actin machinery. This novel 2-D model of the crawling cell makes testable predictions and posits questions to be answered by future modeling.

The high mobility of valence electrons along the backbone of a molecular chain like polyacetylene leads to an ultra-fast, very large and very directional electrical response in the linear and nonlinear regime. A detailed understanding of the microscopic processes governing the electronic response, as well as guidance in the search for new molecular assemblies with large nonlinear response properties, can and should come from theory.

Unfortunately, this electrical response is dramatically overestimated by density functional theory (DFT) with either local or semilocal density functional approximations. Here, we show that DFT does yield accurate linear and nonlinear polarizabilities when the exact exchange energy is employed together with the corresponding exact Kohn-Sham potential. We further show that approximations that are very accurate for the ground-state energy can nevertheless fail badly for the response because of potential barriers that have little effect on the ground-state energy but strongly affect the electron mobility.

We discuss the implications of these findings to further development of orbital-dependent functionals as a means of attacking problems traditionally considered as 'too difficult for DFT'.

We present a computer model which captures the self-assembly of cationic liposomes complexed with DNA - a promising synthetically based nonviral carrier of DNA for gene therapy. The model is a full molecular description that allows the study of molecular self-assembly from structural disorder. Computational simplifications necessary for efficiency are introduced through a coarse-grained representation of the intra-molecular atomic details. The inter-molecular potentials are designed to mimic the hydrophobic effect without the explicit presence of solvent. Thus, the approach carefully balances the need for molecular detail with computational practicality in a manner that allows for solvent-free simulations of complex self-assembly over long enough time scales to address experimental reality. In addition to showing spontaneous self-assembly of cationic lipid-DNA complexes, the broad utility of the model (which extends a coarse-grained lipid bilayer model) is illustrated by demonstrating excellent agreement with X-ray diffraction experimental data for the dependence of the interaxial distance between DNA chains on the fraction of charged lipids. At high concentrations of charged lipids, the large electrostatic pressure induce the formation of pores in the membranes through which the DNA molecules may escape the complex. We suggest that this is the origin of recently observed enhanced transfection efficiency of lamellar CL-DNA complexes at high charge densities. We also find that the presence of multivalent cationic lipids tends to stabilize the system by inducing attractive interactions between the DNA rods.

The main cytoskeleton biopolymers, microtubules and actin, are known to support various cellular processes, among which we can count: cell-shape maintenance and division, cell motility, trafficking of cell organelles, neurite branching and outgrowth, and more. Despite the fact that both macromolecules have special electromagnetic properties, their potential function as electrical signal conductors is largely overlooked.

In this talk I shall discuss experimental evidence and theoretical modeling results that support a biophysical framework in which the cytoskeleton employs networks of interconnected microtubules and actin filaments to function as a sub-cellular platform for electrical signal propagation. We hypothesize that the nature of this electrical signal is based on nonlinear ionic wave propagation along the biopolymers. These signals may be utilized to control various membrane properties, for example, the transition rate of ion channel opening and closing, local membrane conductivity, mRNA transport via motor proteins, and so on. In the realm of neural activity, a direct regulation of ion channels by actin and associated cytoskeletal structures may take part in controlling and modifying the electrical response of the neuron.

References:

• Tuszynski, J. A., Portet, S., Dixon, J. M., Luxford, C., and Cantiello, H. F. (2004). Ionic wave propagation along actin filaments. Biophys. J. 86, 1890-1903.
• Priel, A., Tuszynski, J. A., and Woolf, N. (2005). Transitions in microtubule C-termini conformations as a possible dendritic signaling phenomenon. Eur. Biophys. J. 35, 40-52.
• Priel, A., Ramos, A. J., Tuszynski, J. A., and Cantiello, H. F. (2006). A bio-polymer transistor: Electrical amplification by microtubules Biophy J. 90:4639-4643.

The exchange of protons from carbon atoms in aqueous solution is known to be a very slow process. However, many enzymes have evolved to perform these proton abstraction reactions with surprising ease and specificity. In this presentation, I will focus on two different enzymes catalyzing seemingly simple C?-deprotonation reactions, both through the use of enzyme cofactors. The first enzyme, alanine racemase (AlaR), employs the cofactor pyridoxal L-phosphate (PLP) to catalyze the isomerization of L-Ala to D-Ala. This reaction is an essential step in the synthesis of the peptidoglycan layer of bacterial cell walls, making AlaR an attractive target for drug design. The second enzyme reaction involves nitroalkane oxidase (NAO), which catalyzes the oxidation of primary nitroalkanes to the corresponding aldehydes, employing flavin adenosine diphosphate (FAD) as a cofactor. The first step in this reaction is a rate limiting proton abstraction.

To elucidate the catalytic power of these two enzymes, molecular dynamics simulations, using highly accurate, yet efficient combined quantum mechanics/molecular mechanics (QM/MM) potentials, were employed to obtain free energy profiles for the enzymatic reactions as well as for model reactions in the aqueous solution phase. Both the PLP and FAD cofactors are found to play crucial yet different roles in the enhancement of the rate constants in the enzymes. Moreover, to probe the importance of nuclear quantum mechanical effects (NQE) such as zero-point energy and tunneling in these reactions, novel path-integral simulations as well as multidimensional tunneling calculations were performed. In both AlaR and NAO it is essential to include NQE to accurately predict the reaction barrier. However, whereas in AlaR tunneling plays only a minor role, in NAO tunneling is found to be important. Moreover, the tunneling in NAO is considerably enhanced compared to that in a model reaction in aqueous solution, implying that NAO has evolved to enhance tunneling.

References:
Major, D. T.; Nam, K.; Gao, J. L. J. Am. Chem. Soc. 2006, 128, 8114-8115.
Major, D.T.; York, D. M.; Gao, J. J. Am. Chem. Soc. 2005, 127, 16374-16375.
Major, D. T.; Garcia-Viloca, M.; Gao, J. J. Chem. Theory Comp. 2006, 2, 236-245.

Formation of protrusions and protein segregation on the membrane is of a great importance for the functioning of the living cell. This is most evident in recent experiments that show the effects of the mechanical properties of the surrounding substrate on cell morphology.
We model the cell membrane as having a mobile but constant population of protein with a convex spontaneous curvature. Our basic assumption is that these embrane proteins represent small clusters that may include both adhesion proteins (integrins) and proteins that activate actin polymerization (WASP). We propose a continuum model based on the Helfrich's Hamiltonian for the membrane elastic energy, including the adhesion, with the actin force added to the equations of motion. Linear stability analysis shows that sufficiently strong adhesion energy and actin polymerization force, can bring about phase separation of the membrane protein and the appearance of protrusions.
Specifically this occurs when the spontaneous curvature alone does not. Different instability characteristics are calculated for the various regimes, and are compared to various types of observed protrusions.

Mechanisms of cell signaling depend on specific conformational properties and dynamics of protein association. Detailed mechanistic understanding of these processes is essential for signaling modulation and rational drug design. I will present the development and application of approaches based on sequence-based design of inhibitory peptides, flexible peptide docking and data-driven protein conformation prediction that serve in the exploration of molecular mechanisms in cell signaling. The approaches will be illustrated in the context of G-protein coupled receptors (GPCRs) signaling cascade that includes protein kinases, PDZ scaffolding domains and GPCR dimers, emphasizing the synergistic computational and experimental insights into signal transduction.

• DNA in a temperature gradient: Temperature differences across porous rocks may feed accumulation and replication of evolving molecules. Such non-equilibrium conditions near porous thermal submarine vents are pieces in the fascinating puzzle of the origin of life.
• In the RNA world of the early soup we are studying how a genetic code could originate, building an RNA ribozyme that can charge an amino acid without enzymes, a primitive tRNA. We also show that the initial code could have started with four amino acids only: valine (GUC), alanine (GCC), glycine (GGC), aspartate (GAC).
• Encapsulation of cells in a membrane is another step in this puzzle. Building an

artificial cell based on gene expression inside vesicles reveal the physical constraints

to overcome: energy exchange, osmotic pressure, sources and sinks for protein production. This cell can sustain protein production for about one week. Self reproduction will be the next step.

Indirect chemical reactions occur when the potential energy surface has a well, in which the system has enough time to reorganize its energy between all degrees of freedom. Several reactions were studied by means of Molecular Dynamics simulations, showing chaotic-like behavior of the single trajectory over the well. While the single trajectory exemplifies considerable numerical sensitivity the averaged behavior as computed over a distribution of trajectories shows remarkable stability. This surprising and unexpected phenomenon leads us to develop the Kinetic Propagator, a novel and powerful tool. Using the Kinetic Propagator, large ensembles of classical trajectories can be replaced by a single trajectory, to provide information regarding average energy, reactivity, energy distribution and more. Computational results using the kinetic propagator are validated for 1D potential energy surfaces (Harmonic potential, Morse & Lenard-Johns potentials and Eckhart potential). An extension of the use of the Kinetic Propagator for 2D potential energy surfaces is for a potential surface with either a barrier or a well. The reactivity and distribution of translational energy over LEPS potential energy surface is introduced, along with an analytical 2D potential energy surface model.

A new MD-based approach is explored to search for candidate crystal structures of molecular solids, corresponding to minima of the enthalpy.
The approach is based on observation of phase transitions in an artificial periodic system with a small unit cell, and relies on the existence of an optimal energy range for observing freezing to low-lying minima. Tests are carried out for O-structures of nine H2O-ice polymorphs. NVE trajectories for a range of pre-imposed box shapes display freezing to the different crystal polymorphs whenever the box dimensions approximate roughly the appropriate unit cell; the exception is ice II for which freezing requires unit cell dimensions close to the correct ones. In an alternate version of the algorithm, an initial box shape is picked at random and subsequently readjusted at short trajectory intervals by enthalpy minimization. Tests reveal existence of ice forms which are "difficult" and "easy" to locate in this way. The latter crystal search procedure located successfully the remaining seven ice polymorphs, including ice V, which corresponds to the most complicated structure of all ice phases, with a monoclinic cell of 28 molecules. The method is subsequently applied in a search for the elusive HCl monohydrate structure.

Impact-heated clusters are proposed as a tool that enables experimental preparation of systems in extreme conditions. A cluster undergoes ultra fast heating and intense compression during impact with a hard surface. The computational and theoretical characterization of this ultrahigh compression and its consequences are our objective.

Characterization of the compression stage requires the calculation of the transitory pressure. By extension of the virial theorem of Clausius to describe the rapidly changing, unequilibrated impact-heated cluster system, we define instantaneous pressure. By applying constraints on the cluster, using the Lagrange multipliers technique, we calculated the instantaneous pressure during and following cluster collision with the surface. We show that for rare gas clusters the pressure can reach the teraPascal range and that it scales with the initial kinetic energy and with the mass of the particles in the cluster.

Prior to fragmentation the cluster is extremely hot. Light emission is proposed as another cooling mechanism of the cluster. While the cluster is compressed, collisions between dissimilar atoms create a transient dipole moment that we show to result in IR light emission. Each collision is like a single vibration of a heteronuclear diatom molecule, only a much more energetic one. A semi-classical collision-induced emission spectrum was calculated. We show that collision-induced emission provides a thermometer for the electronic charge distribution deformation during the collision

Principles of molecular recognition will be described with a focus on a conceptual understanding of how protein surfaces are designed to achieve highly specific molecular recognition. An application to the cadherin family of cell adhesion proteins will be presented where it is shown how small differences between closely related proteins at the molecular level are translated into highly specific adhesive interactions at the cellular level. Possible evolutionary implications will be discussed.

The reactions of atmospheric molecules, their mechanisms and dynamics are a major current interest of atmospheric chemistry. In this presentation the spectroscopy and the dynamics of atmospheric species are presented. Potentials from electronic structure theory and classical trajectory methods are combined to unravel the mechanism of photochemical reactions and to predict new intermediate species and possible products. The results focus on photochemistry following overtone excitations of molecules such as HNO3, H2SO4, HNO3-H2O and H2SO4-H2O. The calculations prove that overtone transitions are sufficiently efficient important to play a role in atmospheric conditions. The main interesting results are: (1) A prediction of a rapid intramolecular hopping of the hydrogen atom in isolated HNO3, H2SO4 induced by the excitation. (2) The efficient occurrence of dissociation of H2SO4 into SO3 + H2O is demonstrated. This reaction as induced by overtones differs in behavior from the corresponding thermal reaction. (3) A prediction of a new weakly bound species HOON in the photoexcitation of HONO.
In addition, thermal processes of atmospheric systems are presented. For example, the ionization of acids of HNO3 and H2SO4 in water is a major important issue in atmospheric chemistry. Simulations of the neutralization process of H3O+ and NO3- to form HNO3 and H2O in water clusters are presented. The results show a fast timescale of the process and that the transition state is one and unique structure in all cluster sizes. It suggests that HNO3 is a weak acid in water clusters.
It is proposed that theoretical simulations using electronic structure potential in "on-the-fly" dynamics calculations can be a powerful tool in the exploration of atmospheric processes.

The resonant dynamics of a 'two-level' atom interacting with a single quantized electromagnetic mode in high Q cavity is arguably the simplest instance of a composite quantum system with fast and slow degrees of freedom, much like the electronic and nuclear degrees of freedom in the dynamics of molecules. After introducing the system and the well-known Jaynes-Cummings model that describes it, I will show how to use semiclassical phase space dynamics to study the fast Rabi oscillations between the two energy surfaces in addition to the adiabatic internal motion on each energy surface. The method will be demonstrated by concrete dynamical calculations in systems with a moderate number of cavity photons.

Computational and experimental results describing segregation of ions at surfaces of solutions of inorganic salts in polar nonaqueous solvents are presented. It is shown that liquids such as formamide, liquid ammonia, and ethylene glycol can surface-segregate large polarizable anions like iodide, albeit less efficiently than water. In the case of liquids whose surfaces are covered with hydrophobic groups (e.g. methanol), the surface-ion effect disappears. The importance of local structure of liquid surface for understanding these phenomena is discussed.

Structural changes of Cytochrome c in mass spectrometric conditions are studied by Molecular Dynamics (MD) simulations. The simulations are carried out for two main conditions. (a) Simulations of the evaporation of water from the protein surface. The main structural features of the protein are found to be unaffected till the evaporation of the last few water molecules. Following complete evaporation, dramatic structural changes of the protein are observed. (b) Simulations of the dehydrated protein are connected to NECD experiments by a simple physical model. Comparison of the predicated cleavage pattern and experimental data leads to conclusions on the protein gas phase structure.

One of the main difficulties in the study of electronic non-adiabatic effects in molecular systems is the fact that the non-adiabatic coupling terms (NACTs) responsible for the coupling between the Born-Oppenheimer states are frequently singular or, in other words, are infinitely large. Because of this frightening feature they are consistently ignored in numerical treatments, without any justification.

The purpose of the present lecture is to familiarize ourselves with the NACTs. This we do in several ways:

1. We show how to detect a NACT

2. We learn about the sources of the NACTs and discuss the fact that these sources are points of degeneracy distributed in configuration space

3. We learn about their features and how they can be derived by solving Maxwell-type equations.

The lecture is accompanied with examples obtained from realistic systems.

Many of the properties of water and aqueous solutions is attributable to the presence of and making/breaking of hydrogen bonds. The study of these solutions with particular reference to delineating the structure and dynamics of the hydrogen bonding network has been an active field. However many questions and points of ambiguity remain. Indeed, the traditional four-coordinate local structure of water has been recently challenged.

We have used the recently developed density functional theory based ab initio molecular dynamics method implemented in the QUICKSTEP code to simulate aqueous acidic solutions and water. In order to be able to unambiguously identify and quantify the hydrogen bonds, a hydrogen bond definition more in keeping with the dynamic nature of the system was employed. The results of our analysis will be shown and compared with more traditional approaches and experiment.

Understanding the underlying physics of the binding of small molecule ligands to protein active sites is a key objective of computational chemistry and biology.  When a ligand binds to a protein, the water solvating the active site is ejected into the bulk fluid.  This makes enthalpic and entropic contributions that are widely believed to be a principal, if not dominant, source of binding free energy.  Protein active sites are often characterized by molecular length scale confined regions in which the thermodynamic properties of water can vary significantly from that observed in the bulk.  Using data from molecular dynamics simulations, we introduce clustering techniques to build a map of water occupancy in the active sites of proteins and assign chemical potentials to hydration sites using inhomogeneous solvation theory.
We then construct a semi-empirical scoring function that is based on this 3-dimensional mapping that is able to accurately predict differences in binding affinity for congeneric ligand pairs.  This method of analysis also elucidates the underlying physical basis for the structure activity relationship between these pairs and helps explain the anomalously high binding affinity of the streptavidin-biotin complex.

The Effective Fragment Potential (EFP) is a general approach to simulating intermolecular interactions. An EFP consists of interaction terms that represent Coulomb, induction, exchange repulsion, dispersion, and charge transfer potentials. Each term is derived from first principles without the use of parameters that are fitted to experiment. Consequently, an EFP can be generated simply by performing the appropriate electronic structure calculation on the monomer of interest. Following an introduction to the EFP method, several applications will illustrate the breadth of its applicability.

Reporting extensions of a recently developed approach to density functional theory with correct long-range behavior (Phys. Rev. Lett. 94, 043002 (2005)). The central quantities are a splitting functional Y[n] and a complementary exchange-correlation functional E^YXC[n]. We give a practical method for determining the value of Y in molecules, assuming an approximation for E^YXC[n] is given. The resulting theory shows good ability to reproduce the ionization potentials for various molecules. However it is not of sufficient accuracy for forming a satisfactory framework for studying molecular properties. A somewhat different approach is then adopted, which depends on a density-independent Y and an additional parameter w eliminating part of the local exchange functional. The values of these two parameters are obtained by best-fitting to experimental atomization energies and bond-lengths of the molecules in the G2(1) database. The optimized values are Y=0.5a₀^-1 and w=0.1. We then examine the performance of this slightly semi-empirical functional for a variety of molecular properties, comparing to related works and to experiment. We show that this approach can be used for describing in a satisfactory manner a broad range of molecular properties, be they static or dynamic. Most satisfactory is the ability to describe valence, Rydberg and inter-molecular charge-transfer excitations.

Vibrational spectroscopy is an extremely important tool for probing molecular properties. However, calculations required for the analysis of such experiments at an adequate level (including anharmonic effects) are a major challenge. The problem is, to a large extent, open. This lecture presents progress on this problem, with applications to biological molecules and to the characterization of their potential energy surfaces. The Vibrational Self-Consistent Field (VSCF) algorithms developed by our group include anharmonic coupling between modes, and are directly applicable to potential energy surface points from electronic structure methods, include ab initio and DFT methods.

Topics dicussed include:

1. The relative performance of ab initio and DFT for spectroscopy of biological molecules;
2. Progress toward calculations of peptides and small proteins, using electronic structure potential and with anharmonic effects;.
3. Theory versus high-resolution experiments for biological molecules in gas phase;
4. Theory versus experiment for the spectroscopy of the Photoactive Yellow Protein.

Enzymes speed the rate of chemical reactions by 12 orders of magnitude or more compared to the equivalent solution phase reaction. Though intensely studied for many decades, there is still no agreement on how enzymes actually accomplish this immense rate enhancement while still providing for biological control and specificity. The earliest, and still most popular view of this effect is the transition state binding view of Pauling. In this talk we will examine using theoretical methods, the echanism of action of a number of enzymes. We will show that the enzyme functions as a hemical machine, directly coupling vibrations of the protein ackbone to the reaction coordinate. These vibrations are highly non-isotropic - they have been selected for by evolution; and when disrupted, chemistry is interrupted.

This talk is about ions going where they are not supposed to go: to the air-water and membrane-water interfaces.

The conventional wisdom for most of the last century is that simple inorganic ions (e.g. alkali metal cations and halide anions) are repelled from the air-water interface. I will review the experimental and theoretical basis for this conclusion. Experiments performed a few years ago in the context of atmospheric chemistry hinted that there might actually be ions on the surface of aqueous atmospheric aerosols, and we subsequently predicted that, indeed, there are, using computer simulations. I will present results from these simulations, and relate them to spectroscopic experiments performed afterward that confirmed out predictions.

Lipid bilayers form the matrix of biological membranes. Membrane lipids are amphiphilic molecules, with polar headgroups and long, nonpolar (hydrocarbon) chains. The conventional wisdom is that the interior of biological membranes is a forbidden zone for charges because of the high energetic barrier to moving a charge from a medium with a high dielectric constant to one with a low dielectric constant. Once again, computer simulations show that this may not always be the case. I will present simulations that show how guanidinium ions are accommodated in phospholipid bilayers, and discuss the results in the context of the structure and function of voltage-gated potassium and proton channels.

Recognition of electrolyte solutions as central to the regulation of chemical and biological processes goes back more than a century, starting with Hofmeister's experiments on the ability of different ions to precipitate proteins. This regulation is a result of modulations in the solvent induced interactions. In this talk we will present results on the ability of different type of salts to modify the strength of the solvent induced interactions between large hydrophobic plates. The results show that amplification of the hydrophobic interaction (salting-out) is a purely entropic effect and is induced by high charge density ions that exhibit preferential exclusion. In contrast, a reduction of the hydrophobic interaction (salting-in) is induced by low charge density ions that exhibit preferential binding, the effect being either entropic or enthalpic. By analyzing changes in the enthalpy and entropy differences upon hydrophobic collapse (in salt solutions relative to pure water) we propose the mechanisms by which salting-in and salting-out take place. In addition, we will present results on changes of the solvent induced interactions between small hydrophobic particles. In this case, we do not observe a monotonic relationship between the degree of preferential binding/exclusion and changes in magnitude of the hydrophobic interaction. In particular, we find that at low salt/cosolute concentrations, salts with low charge density ions increase the solvent mediated attractions by forming a `micelle-like' structure. Our findings are relevant to phenomena long studied in solution chemistry, as we demonstrate the significant, yet subtle, effects of electrolytes on hydrophobic aggregation and collapse.

Electron dynamics in metallic clusters are examined using a time-dependent density functional theory beyond the adiabatic local density approximation (ALDA). We include temporal non-local correlations (memory) and molecular dynamics (MD). Using a known frequency-dependent exchange-correlation (XC) kernel we construct a translationally invariant memory action that yields an XC memory potential term which obeys some exact conditions. Using this framework, we study memory effects on electron dynamics in spherical Jellium “gold clusters” at zero temperature and some atomic sodium clusters at nonzero temperatures. For the gold clusters we find: (i) memory significantly broadens the surface plasmon absorption line, yet less than measured in real gold clusters, attributed to the inadequacy of the Jellium model, (ii) Two-dimensional pump-probe spectroscopy is used to study the temporal decay profile of the plasmon, finding a fast decay followed by slower tail, (iii) we examine memory effects on high harmonic generation, finding memory narrows emission lines. For the sodium clusters we find that: a comparison to the experimental absorption spectra shows that our ALDA+memory+MD and ALDA+MD models agree with the experimental results. Means, that thermal (inhomogeneous) broadening rather than the electron-electron dephasing (homogeneous broadening) is dominant. Also, we demonstrate the essence of preserving basic symmetries by the XC memory potential.

Ionization of clusters by ultraintense (10¹⁵-10²⁰ Wcm^-2) and ultrashort Gaussian laser pulses (temporal FWHM 10-100 fs) is a complex compound process, which is qualitatively different from the ionization of isolated atoms. In a first step, termed inner ionization, the laser electric field removes electrons from the atoms by classical barrier suppression ionization (BSI). The stripped electrons together with their parent ions form a nanoplasma, which has a lifetime up to several hundreds of femtoseconds. The response of the nanoplasma electrons to the laser electric field gives rise to electron impact ionizations (EII) which constitute a second inner ionization channel. In case of heavier atoms, inner ionizations leads to highly charged ions, e.g. Xe³⁶⁺ at 10²⁰ Wcm^-2. The laser electric field removes the nanoplasma electrons partly or completely from the cluster ("outer ionization"). The highly ionized cluster is unstable and expands in space ("Coulomb explosion"), accelerating the ions to very high kinetic energies.

In this lecture, results from relativistic molecular dynamics simulations of clusters interacting with ultraintense laser pulses are presented, focusing mainly on xenon clusters. Results for the time-resolved process, the contributions from the BSI and EII channel to ion yields and spatial ion distributions as well as possibilities for their control by the laser parameters are discussed

The nature and rate of vibrational energy flow in proteins influence reaction kinetics, allosteric transitions, and are important in maintaining protein structure during function. We discuss calculations of rates and pathways for vibrational energy flow in a number of globular proteins. Among these calculations, we compute quantum mechanically the rate of anharmonic decay of the vibrational modes. Computed rates in the amide I region match the available lifetimes measured by pump-probe spectroscopy from 10 K to 310 K. Over this temperature range the experimental amide I lifetimes are nearly independent of temperature. We find that lifetimes of most higher frequency vibrational modes of proteins vary little with temperature, consistent with a propensity that we find for localized modes of a protein close in space to be typically separated by several hundred wave numbers. We shall also discuss the anomalous diffusion of vibrational energy in proteins, and the computation of thermal transport coefficients.

We probed the limits in supersonic beams velocity distribution and showed that beams can be slowed down coherently.
This new source of slow and intense beams can be used in surface probing and matter waves interference.

Nonstationary Langevin models have been developed that are capable of capturing feedback between the long-time-scale motions of a chemical environment and the underlying molecular constructs which in turn collectively comprise the environment. Although initial justifications for this formalism were heuristic and phenomenological, in recent work we have shown that in some cases it arises as the projection of a simple model of a chemical system bilinearly coupled to a harmonic bath with a time-dependent coupling. Moreover, the stochastic model can be used to surmise the diffusion of a tagged particle in a colloidal suspension which swells or shrinks with time. Alternatively, a liquid crystal, modeled as a colloidal suspension of orientable bodies, can also exhibit driven (time-dependent) behavior by way of the rotation of a magnetic field. Once again, the diffusion of a tagged particle under such time-dependence, can be surmised by the stochastic model. Though this procedure is not an explicit projection of the mechanical system onto the nonstationary GLE, it does show that the latter correctly describes the dynamics of the projected coordinate ---viz., diffusion of the solute--- under nonequilibrium conditions. Both nonequilibrium solvent models lead to behavior reminiscent of beta-relaxation processes at packing fractions substantially below that of the glass transition

In the introduction, I will talk about basic element of protein structure, closed loops of 25-30 amino acid residues: their role in protein structure, folding, and evolution. High-throughput comparative analysis of complete genomes reveals ancient sequence prototypes of closed loops and lays a ground for deriving of the proteomic code. In the major part of the talk I will address a question what mechanisms does Nature use in her quest for thermophilic proteins? I will show that both positive and negative design play an important role: Native interactions between amino acids are strengthened in thermophilic proteins (positive design) as well as repulsions are strengthened between amino acids that are distant in native structure but may interact in the misfolded conformations (negative design). Acting together these factors broaden the energy gap between native and misfolded conformations in proteins - the main determinant of protein stability. These fundamental principles of protein design are responsible for "from both ends of hydrophobicity scale" trend observed in thermophilic adaptation, whereby proteomes of thermophilic proteins are enriched in hydrophobic and charged residues at the expense of polar ones. Hydrophobic residues contribute mostly to the positive design, while repulsion between charged residues in non-native conformations of proteins contributes to negative design. Further, these findings help to understand the origin of correlated mutations in proteins, especially involving amino acids that are not in contact in their native structures.

Drawing accurate chemical and physical properties of molecules directly out of theoretical equations is a great challenge of theoretical chemistry and condensed matter physics.

In this talk we would present two different approaches, each of them is suitable to different kinds of questions:

1. The auxiliary-field Monte Carlo (AFMC) method – a method for calculating ground state properties with high accuracy and low scale of computing effort. This method belongs to the QMC family but uses a different formalism to deal with the many-body problem, which is based on the Hubbard-Stratonovich transformation.

2. The variational grand canonical electronic structure method for open system – a method for calculating ground state properties for systems with not fixed number of electrons at different temperatures. This method uses a statistical mechanics terminology to expand the varieties of situations and systems in which electronic structure calculation can be used.

The drive toward smaller electronic devices has led to vast experimental and theoretical development in the field of molecular electronics.

Recently, a new type of pure carbon system, named graphene nanoribbons, was experimentally realized. While possessing many of the intriguing physical properties of carbon nanotubes, graphene nanoribbons can be fabricated in a controlled and reproducible manner.

Furthermore, unique edge effects may lead to novel physical phenomena which could be utilized in future spintronic devices.

Using state-of-the-art electronic structure methods, we studied the electronic properties of ultra-narrow semi-conducting ribbons.

The width of the ribbons as well as the nature of the edges, including geometry and passivation were considered as control parameters for their electronic properties.

Spectroscopic fingerprints were identified as well.

We have used our recently implemented divide and conquer approach to calculate transport across elongated graphene nanoribbon junctions.

Our preliminary results indicate that these systems present high sensitivity upon surface adsorption of molecular contaminants, suggesting their potential use as chemical nanosensors.

The dissipative dynamics of a small system coupled to nonequilibrium reservoirs may be quite different in character from the equilibrium case. In this work we study the steady state dynamics of a spin system coupled to two nonequilibrium reservoirs. We consider two variants of this model:
(i) A spin-boson model, comprising a two-level-system coupled to two phononic baths of different temperatures.
(ii) A spin-fermion model, including a spin coupled to two metal leads under an applied bias voltage.

We argue that the first model can describe heat transfer through molecular junctions, and demonstrate thermal rectification and pumping of heat at the level of the Master equation for the states population. For the fermionic counterpart we develop an exact numerical technique, an out-of-equilibrium extension of Anderson-Yuval-Hamann treatment, and study the magnetic field and voltage dependent decoherence rates.

While the equilibrium spin-boson and spin-fermion models relate one to the other by a simple mapping, it is not yet clear to what extent the nonequilibrium models are related. Another interesting question we would like to address is whether a generalized fluctuation-dissipation relation can be established in steady state.

Interatomic (intermolecular) decay is a general phenomenon having a profound effect on the dynamics of highly excited states of neutral or ionized species consisting of weakly interacting entities.

The process of interatomic decay following inner-shell ionization has been first predicted theoretically by Cederbaum et al. [1] and recently observed in a series of spectacular experiments on rare gas clusters [2]. Currently, the study of interatomic (intermolecular) decay following (single or multiple) ionization or excitation is an area of a very dynamic theoretical and experimental research. In the present talk, I will review the basic theory of interatomic decay [3], as well as the most important recent developments in the theoretical and experimental study this group of processes. In particular, I will describe our current state of knowledge of interatomic decay processes in endohedral fullerenes [4], interatomic Coulombic decay in helium droplets [5] and the recently discovered resonant interatomic Coulombic decay [6]. I will also outline the most important future directions of the theoretical research, such as the study of decay cascades in core-ionized clusters and of collective decay of multiple vacancies in clusters interacting with free electron laser radiation.

References

[1] L. S. Cederbaum, J. Zobeley, and F. Tarantelli, Phys. Rev. Lett. 79, 4778 (1997).
[2] S. Marburger et al., Phys. Rev. Lett. 90, 203401 (2003); T. Jahnke et al., Phys. Rev. Lett. 93, 163401 (2004); G. ¨Ohrwall et al., Phys. Rev. Lett. 93, 173401 (2004).
[3] V. Averbukh, I. B. M¨uller, and L. S. Cederbaum, Phys. Rev. Lett. 93, 263002 (2004); V. Averbukh and L. S. Cederbaum, J. Chem. Phys. 123, 204107 (2005).
[4] V. Averbukh and L. S. Cederbaum, Phys. Rev. Lett. 96, 053401 (2006).
[5] N. V. Kryzhevoi, V. Averbukh and L. S. Cederbaum, submitted to Phys. Rev. Lett.
[6] S. Barth et al., J. Chem. Phys. 122, 241102 (2005); T. Aoto et al., to be published in Phys. Rev. Lett.; K. Gokhberg, V. Averbukh, and L. S. Cederbaum, J. Chem. Phys. 124, 144315 (2006).

Multi-cellular migration is of great significance in many biological processes, such as wound-healing, morphogenesis and embryogenesis. We present here a physical model for the dynamics of such cell migration during the wound healing response. Recent experiments demonstrate that an initially uniform cell-culture monolayer expands in a non-uniform manner, developing finger-like shapes, composed of columns of cells that move collectively. We propose a physical model to explain this phenomenon, based on the notion of dynamic instability, similar to the classic instability of fluids and crystal growth of solids. In this model we treat the outer contour of the cell culture as a continuous membrane, with the usual curvature and surface-tension elasticity. The internal motility of the cells provides the driving force for the outwards normal motion of the contour. We find in this model a dynamic instability which we then compare to the dynamic patterns observed in the wound healing experiments. Our model may be relevant for describing other phenomena involving large-scale motions of cell cultures, where there is spontaneous pattern formation.

The talk will present an overview of matrix isolation studies of the radiation-induced transformations of organic molecules carried out in our laboratory in recent years. A common matrix isolation approach is based on the concept of "rigid cage" for storage of frozen reactive species. However, as revealed in our studies, in fact, a chemically simple and seemingly inert matrix may control the radiation-induced chemical processes, tune the reactivity of primary species and even make new unusual chemical bonds. The following aspects will be outlined:

• charge transfer and excess energy relaxation of ionized organic molecules in solid noble gas matrices;
• selective matrix-assisted reactions at low temperatures;
• model studies of trapping and dynamics of hydrogen atoms;
• formation of unusual noble-gas molecules.

Abstract: Electronic structure calculations have become an indispensable tool for chemical research and development. I will illustrate scope and limitations of present-day electronic structure theory by a number of recent applications performed in my group. Topics will include structure and dimensionality crossover in gold nanoclusters, circular dichroism of cephams, Raman spectra of fullerenes, and chiral cooperativity in [2.2]paracyclophane ligands for asymmetric catalysis.

Abstract: Liquid water is an important liquid for life as we know it and has many unusual properties. In the last few years we have been using simulation to study the properties of liquids made with a range of intermolecular potentials in order to try to understand the relative importance of molecular size, the existence of a tetrahedral network and the hydrogen bond strength for both the anomalous properties of pure water and its characteristics as a solvent. The properties of water can be described reasonably well by simple model intermolecular potentials with site charges and a Lennard-Jones centre. By modifying the potential parameters one can make families of liquids with weaker hydrogen bonds, or with altered network structures, or isotropic molecules with the same 2-body correlations. Teresa Head-Gordon, Pablo Debenedetti, Jose Alejandre and I have been studying properties of these liquids. We find some surprises - for example hydrophobic solutes are more soluble in water than in liquids with weaker hydrogen bonds and the dielectric constants increase as the geometry of the network structure is changed.

Abstract: Density functional theory and time-dependent density functional theory have become popular methods for investigating the structure and response properties of electronic systems. This success is largely based on the fact that the theory frequently allows for the prediction of electronic properties with useful accuracy at a moderate computational cost. Its computational attractiveness stems from the fact that it replaces the complicated many-electron wavefunction by the electron density, which is a much simpler variable. However, there is a price to pay for this simplification, and this price is the fact that the effective potential of density functional theory is a complicated object which is non-local in space and non-local in time. These non-localities are at the heart of prominent failures of density functional theory: The incorrect description of charge-transfer and the incorrect description of electronic dynamics in strong laser fields. This talk will explain the basic concepts of (time-dependent) density functional theory and, with the help of paradigm examples of charge-transfer and strong-field excitations, shed light on its problems and possibilities to overcome them.

Coherent control provides an efficient method of generating elecrical currents in ideal systems (e.g. quantum dots) by using symmetry breaking incident light. We will introduce this approach, and discuss the feasibility of current generation in realistic molecules where electron-phononcoupling serves to decohere the necessary quantum effects. The work raises a number of fundamental issues, such as the classical limit of such control, and leads to a highly efficient method for generating femtosecond currents in polyacetylene wires.

A computational approach is used and developed to study electron transport through molecular and nano scale devices. New models and methods to describe transient electron conductance through molecular systems under the influence of time dependent perturbations are used to study quantum interference effects affecting the conductance. We will describe several studies on molecular scale system and provide insight into mechanisms underlying electronic-transport switching properties. Several recent high-profile experimental studies achieving molecular scale conductance are considered. This involves metal recognition properties of short peptides or fabricated molecular sockets based on surface confined terpyridine ligands. If time allows we will also describe: Spin-dependent electronic transport through a Porphyrin ring ligating an Fe(II) atom, and contact geometry and orientation effects of conjugated molecular field-effect transistors.

The vibrational energy relaxation and multi-dimensional infrared spectra of a vibrational mode strongly coupled to its environment are considered. The analysis is performed within the context of the hydrogen-stretch of a moderately-strong hydrogen-bonded complex dissolved in a dipolar liquid. The molecular dynamics of this system is modeled within the framework of the mixed quantum-classical Liouville method which treats the hydrogen quantum-mechanically, while the remaining degrees of freedom are treated classically. The vibrational energy relaxation is described as a multi-step process involving solvation on the excited and ground adiabatic surfaces and nonadiabatic transitions between them. The IR spectra are calculated within the framework of an adiabatic mixed quantum-classical approach. It is shown that while the commonly employed equilibrium dynamics, Condon and second-order cumulant approximation predict extremely broad and rather structureless spectra, the corresponding non-equilibrium and non-Condon spectra consist of several relatively narrow bands that can be traced back to subsets of bath configurations with large transition dipole moments. Thus, although the equilibrium dynamics, Condon and cumulant approximations can capture some general qualitative spectral trends and are able to reproduce some highly averaged quantities such as the photon-echo peak shift, they fail to reproduce many other important features of the spectra. We show that the great sensitivity of the transition dipole moment to the bath configuration provides new means for decongesting the spectra, probing statistically unfavorable bath configurations and obtaining unique information on ground and excited state solvation processes.

Surfaces of aqueous solutions are traditionally viewed as devoid of inorganic ions. Molecular simulations and surface selective spectroscopic techniques show, however, that large polarizable anions and hydronium cations can be found (and even enhanced) at the surface and are involved in chemistry at the air/water interface. Here, we present recent studies of ions at the water/vapor interface and compare from this perspective more complex aqueous interfaces, such as those of hydrated proteins. We critically examine the suitability of dielectric models for the description of the protein/water interface in analogy to the water/vapor interface. Little correlation is found between these two interfaces in terms of ion segregation. Therefore, a local picture of pairing of ions from the solution with charged and polar groups at the protein surface is advocated and combined with a model for segregation of large soft ions at hydrophobic patches of the protein surface.

Many molecular species that control genetic regulatory networks are present in low concentrations. The resulting fluctuations in reaction rates may cause large random variations in the instantaneous intracellular concentrations of molecular species which, in their turn, may have important consequences in biological functioning. The regulation mechanism in such networks is often via negative feedback of inhibiting (signal) molecules. In this work we report a previously unexplored dramatic impact that the noise in the signal molecules can have on the persistence of the regulated component in a prototypical biochemical regulatory network. We consider a minimal two-component copy number control (CNC) model of bacterial plasmids. We find that the discrete noise of the signal molecules can greatly delay the extinction of the plasmids. In addition, we determine the probability distribution function of the plasmids and show that deterministic reaction rate equations may fail in predicting the average number of plasmids even when this number is large, and the time is short compared to the mean extinction time of the plasmids.
1 Michael Assaf and Baruch Meerson, Phys. Rev. Lett. 100, 058105 (2008).

Charge mobility in organic semiconductors is the central issue for organic electronics. It has been long time debated on whether the charge transport be described as “band-like” or thermally activated hopping process. We have employed the first-principles DFT mapping to Holstein-Peierls model to calculate the temperature and pressure-dependent charge mobility for Naphthalene single crystals [1]. At the molecular level, by employing the Marcus electron transfer theory within the hopping regime, we find that the predicted mobility can justify molecular design strategies in several occasions [2]. We pointed out that the quantum nuclear tunneling effects of the intra-molecular vibration which strongly couples the charge transfer excitation can apparently clarify such controversy [3].
[1] Linjun Wang, Qian Peng, Qikai Li, Zhigang Shuai, J. Chem. Phys. 127, 044506~1-9 (2007).
[2] Xiaodi Yang, Qikai Li, and Zhigang Shuai, Nanotechnology 18, 424029 (2007); Liqiang Li, Hongxiang Li, Xiaodi Yang,Wenping Hu, Yabin Song, Zhigang Shuai, Wei Xu, Yunqi Liu and Daoben Zhu, Adv. Mater. 19, 2613-2617 (2007); Yabin Song, et al., J. Am. Chem. Soc. 128, 15940 (2006).
[3] Guangjun Nan, Xiaodi Yang, Linjun Wang, Zhigang Shuai, Yi Zhao, submitted.

I will talk about effects of quenched fixed charge disorder on effective electrostatic interactions between charged surfaces in a one-component (counterion-only) Coulomb fluid. Analytical results can be explicitly derived for two asymptotic and complementary cases: i) mean-field or Poisson-Boltzmann limit (including Gaussian-fluctuations correction), which is valid for small electrostatic coupling, and ii) strong-coupling limit, where electrostatic correlations mediated by counterions become significantly large as, for instance, realized in systems with high-valency counterions. In the particular case of two apposed and ideally polarizable planar surfaces with equal mean surface charge, the effect of the disorder is nil on the mean-field level and thus the plates repel. In the strong-coupling limit, however, the effect of charge disorder turns out to be additive in the free energy and leads to an enhanced long- range attraction between the two surfaces. The equilibrium inter- plate distance between the surfaces decreases for elevated disorder strength (i.e. for increasing mean-square deviation around the mean surface charge), and eventually tends to zero, suggesting a disorder-driven collapse transition.

The number of independent observables of a quantum system with the effective Hilbert space dimension N grows as N^2 which is a prohibitingly large number in physically interesting applications. Therefore, efficient simulation of a quantum dynamics must be oriented to simulating a small subset of observables. We propose a computational scheme using expansion of the evolving state in a certain observables-oriented time-dependent basis (the basis of the generalized coherent states (GCS) with respect to a distinguished subalgebra of observables). The propagation of the state and computation of the expectation values of the restricted set of observables can be performed efficiently, provided the number of terms in the expansion is not large. Unfortunately, a generic quantum dynamics leads to extensive branching of terms in the expansion of the evolving state. We argue that the corresponding dynamics of the restricted set of observables can still be simulated efficiently, provided a certain condition is met, which can be interpreted as a condition that the observables are "classical". The unitary evolution of "classical" observables can be simulated by an open system dynamics, resulting from the coupling of the system to a certain (fictitious) bath. This fictitious system-bath coupling should be viewed as a computational tool inducing a coarse graining of the evolving state. The resulting open system dynamics can be represented as the evolution of a mixture of quantum stochastic trajectories (unravelings), each representing an evolving superposition of a small number of the GCS. The quantum stochastic trajectories can be computed efficiently and the expectation values of the distinguished observables can be calculated efficiently for each trajectory. Averaging over the unravelings recovers the unitary evolution of the restricted set of observables. It is shown that the averaging can be performed efficiently provided the measurement of the corresponding observables in the lab can be performed efficiently.

Nonadiabatic alignment is a coherent approach to control over the spatial properties of molecules, wherein a short, moderately-intense laser pulse is applied to populate a broad rotational wavepacket with fascinating properties. In the limit of small isolated molecules, it has evolved in recent years into an active field of theoretical and experimental research with a rich variety of applications.

Following a brief review of the essential physics underlying nonadiabatic alignment, we discuss one of these applications, namely the use of high harmonics generated from aligned molecules both as a probe of the underlying electronic and rotational dynamics and as a control of the emitted light. Next, we extend the concept of alignment to dissipative environments, including dense gases and solutions. We illustrate the application of rotational wavepackets as a probe of the dissipative properties of dense media and propose a means of disentangling population relaxation from decoherence effects via strong laser alignment. We extend alignment to control the torsional motions of polyatomic molecules, and apply torsional control in solutions to manipulate charge transfer events, suggesting a potential route to light controlled molecular switches. Finally, we introduce a route to guided molecular assembly, wherein laser alignment is extended to induce long range orientational order in molecular layers, and propose an approach to control of transport through molecular junctions with coherent light.

Interferometers that operate with neutral atoms are very sensitive measurement devices. On the one hand the atoms are sensitive to any effect that is proportional to mass, while on the other hand, neutral atoms are not suffering from high sensitivity to stray electromagnetic fields. Matter interferometry has contributed to precision measurements of gravity and polarization, while exhibiting some of the most boggling quantum effects such as the Aharonov–Casher effect and the principle of equivalence. We propose a new architecture for an interferometer for sub-thermal atoms. The splitting and reflection of the beam is done by diffraction of atoms reflected from a crystal surface, which is one of the oldest evidence of de-Broglie wave nature of matter. Analysis of the performance of the proposed interferometer using helium atoms and a LiF crystal yields guidelines for its construction. It is found that the atoms should be hypothermal rather than thermal. Even et al. are building an adequate source of such atoms. Other technological requirements for constructing such an apparatus, as well as its sensitivity will be described. We calculate the throughput of the interferometer for various parameters and demonstrate the route to its optimization. The new architecture enables wide angular separation of the split beam while keeping the dimensions of the interferometer compact. We discuss this advantage and other implications of the new scheme.

Protein folding and binding is commonly depicted as a search for the minimum energy conformation. Modeling of protein complex structures by RosettaDock often results in a set of low-energy conformations near the native structure. Ensembles of low-energy conformations can appear, however, in other regions, especially when backbone movements occur upon binding. What then characterizes the energy landscape near the correct orientation? We applied a machine learning algorithm to distinguish ensembles of low-energy conformations around the native conformation from other low-energy ensembles. The resulting classifier, FunHunt, uses a restricted set of features that can teach us about the nature of native interfaces. Remarkably, the energy decrease of trajectories toward near-native orientations is significantly larger than for other orientations. This provides a possible explanation for the stability of association in the native orientation.

The fact that until now there is no common mechanism for proton diffusion in liquid water draws attention to its interest and potential. Using conditional-radial-distribution-functions (cRDF) around the hydronium we were able to show that the hydronium RDF, calculated at long time-segments, is distinctively different then the RDF calculated at short time-segments. The equilibrium RDF of the hydronium can be presented as a linear combination of the RDF calculated at long & short segments (Eigen & Zundel structures, respectively). Using time-dependent-radial-distribution-functions (TD-RDF), at consecutive times before a proton transfer, we were able to show how the hydronium starts from its Eigen state and gradually changes to its Zundel state, with the single peak of g(r) splitting into two peaks during the transition state.

Gene expression is regulated by the recognition of specific DNA binding sites by transcription factors. Specific contacts and indirect readout in which the overall shape of a DNA binding site is recognized have been described as determinants of protein-DNA binding. However, the role of subtle alterations of DNA structure in protein-DNA recognition is still not fully understood. We found a new biophysical recognition code that explains the functional specificity of a Hox protein in DNA binding. Homeodomain proteins have low DNA binding specificities, which contrast with the specific biological functions of these proteins. Although the majority of contacts between Hox proteins and DNA are located in the major groove, specificity often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor. Based on crystallographic, in-vitro, in-vivo, and computational studies, we showed that a Hox protein recognizes specific DNA binding sites via residues located in these extended regions that insert into the minor groove, but only when presented with the correct DNA sequence. The sequence dependent minor groove geometry induces an electrostatic profile that determines if argenines are attracted to intrude the minor groove. All-atom Monte Carlo simulations indicate that this local minor groove geometry is an intrinsic structural feature of the DNA binding sites.