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arXiv1995

Application of A Distributed Nucleus Approximation In Grid Based Minimization of the Kohn-Sham Energy Functional

In the distributed nucleus approximation we represent the singular nucleus as smeared over a smallportion of a Cartesian grid. Delocalizing the nucleus allows us to solve the Poisson equation for theoverall electrostatic potential using a linear scaling multigrid algorithm.This work is done in the context of minimizing the Kohn-Sham energy functionaldirectly in real space with a multiscale approach. The efficacy of the approximation is illustrated bylocating the ground state density of simple one electron atoms and moleculesand more complicated multiorbital systems.

chem-ph↗

arXiv1996

Studies of an Off-Lattice Model for Protein Folding: Sequence Dependence and Improved Sampling at Finite Temperature

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level spectra of chains with different types of behavior are compared. Furthermore, we use this model as a testbed for two improved Monte Carlo algorithms. Both algorithms are based on letting some parameter of the model become a dynamical variable; one of the algorithms uses a fluctuating temperature and the other a fluctuating monomer sequence. We find that by these algorithms one gains large factors in efficiency in comparison with conventional methods.

chem-ph↗

arXiv1995

Solid-to-solid isostructural transition in the hard sphere/attractive Yukawa system

A thermodynamically consistent density functional-perturbation theory is used to study the isostructural solid-to-solid transition which takes place in the hard sphere/attractive Yukawa system when the Yukawa tail is sufficiently short-ranged. A comparison with results for the square well potential allows us to study the effect of the attractive potential form on the solid-solid transition. Reasonable agreement with simulations is found for the main transition properties as well as for the phase diagram evolution with the the range of the attractive potential.

cond-mat↗

arXiv1995

How Accurate Must Potentials Be for Successful Modeling of Protein Folding?

Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,'' or ``optimal energy'' of the desirable target conformation over all possible sequences, such that the ``design'' of the sequence is governed by the interactions between monomers. With replica mean field theory, we examine the possibility to reconstruct the renaturation, or freezing transition, of the ``designed'' heteropolymer given the inevitable errors in the determination of interaction energies, that is, the difference between sets (matrices) of interactions governing chain design and conformations, respectively. We find that the possibility of folding to the designed conformation is controlled by the correlations of the elements of the design and renaturation interaction matrices; unlike random heteropolymers, the ground state of designed heteropolymers is sufficiently stable, such that even a substantial error in the interaction energy should still yield correct renaturation.

cond-mat↗

arXiv1996

Dynamics of Proton Transfer in Mesoscopic Clusters

Proton transfer rates and mechanisms are studied in mesoscopic, liquid-state, molecular clusters. The proton transfer occurs in a proton-ion complex solvated by polar molecules comprising the cluster environment. The rates and mechanisms of the reaction are studied using both adiabatic and non-adiabatic molecular dynamics. For large molecular clusters, the proton-ion complex resides primarily on the surface of the cluster or one layer of solvent molecules inside the surface. The proton transfer occurs as the complex undergoes orientational fluctuations on the cluster surface or penetrates one solvent layer into the cluster leading to solvent configurations that favor the transfer. For smaller clusters the complex resides mostly on the surface of the cluster and proton transfer is observed only when the complex penetrates the cluster and solvent configurations that favor the proton transfer are achieved. Quantitative information on the cluster reaction rate constants is also presented.

chem-ph↗

arXiv1996

Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels

The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo simulations of a 27-mer, 3 letter code lattice model, which corresponds roughly to a small helical protein. Analytic folding calculations, using simple diffusive rate theory, agree extremely well with the full simulation results. Folding in this system is best seen as a diffusive, funnel-like process.

cond-mat↗

arXiv1996

Diffusion-annihilation dynamics in one spatial dimension

We discuss a reaction-diffusion model in one dimension subjected to an external driving force. Each lattice site may be occupied by at most one particle. The particles hop with asymmetric rates (the sum of which is one) to the right or left nearest neighbour site if it is vacant, and annihilate with rate one if it is occupied. We compute the long time behaviour of the space dependent average density in states where the initial density profiles are step functions. We also compute the exact time dependence of the particle density for uncorrelated random initial conditions. The representation of the uncorrelated random initial state and also of the step function profile in terms of free fermions allows the calculation of time-dependent higher order correlation functions. We outline the procedure using a field theoretic approach.

cond-mat↗

arXiv1996

Scaling and Scale Breaking in Polyelectrolyte

We consider the thermodynamics of a uniformly charged polyelectrolyte with harmonic bonds. For such a system there is at high temperatures an approximate scaling of global properties like the end-to-end distance and the interaction energy with the chain-length divided by the temperature. This scaling is broken at low temperatures by the ultraviolet divergence of the Coulomb potential. By introducing a renormalization of the strength of the nearest- neighbour interaction the scaling is restored, making possible an efficient blocking method for emulating very large polyelectrolytes using small systems. The high temperature behaviour is well reproduced by the analytical high-$T$ expansions even for fairly low temperatures and system sizes. In addition, results from low-$T$ expansions, where the coefficients have been computed numerically, are presented. These results approximate well the corresponding Monte Carlo results at realistic temperatures. A corresponding analysis of screened chains is performed. The situation here is complicated by the appearance of an additional parameter, the screening length. A window is found in parameter space, where scaling holds for the end-to-end distance. This window corresponds to situations where the range of the potential interpolates between the bond length and the size of the chain. This scaling behaviour, which is verified by Monte Carlo results, is consistent with Flory scaling. Also for the screened chain a blocking approach can be devised, that performs well for low temperatures, whereas the low-$T$ expansion is inaccurate at realistic temperatures.

chem-ph↗

arXiv1996

Van der Waals clusters in the ultra-quantum limit: a Monte Carlo study

Bosonic van der Waals clusters of sizes three, four and five are studied by diffusion quantum Monte-Carlo techniques. In particular we study the unbinding transition, the ultra-quantum limit where the ground state ceases to exist as a bound state. We discuss the quality of trial wave functions used in the calculations, the critical behavior in the vicinity of the unbinding transition, and simple improvements of the diffusion Monte Carlo algorithm.

chem-ph↗

arXiv1996

Feynman-Kac Kernels in Markovian Representations of the Schroedinger Interpolating Dynamics

Probabilistic solutions of the so called Schrödinger boundary data problem provide for a unique Markovian interpolation between any two strictly positive probability densities designed to form the input-output statistics data for the process taking place in a finite-time interval. The key issue is to select the jointly continuous in all variables positive Feynman-Kac kernel, appropriate for the phenomenological (physical) situation. We extend the existing formulations of the problem to cases when the kernel is \it not \rm a fundamental solution of a parabolic equation, and prove the existence of a continuous Markov interpolation in this case. Next, we analyze the compatibility of this stochastic evolution with the original parabolic dynamics, while assumed to be governed by the temporally adjoint pair of (parabolic) partial differential equations, and prove that the pertinent random motion is a diffusion process. In particular, in conjunction with Born's statistical interpretation postulate in quantum theory, we consider stochastic processes which are compatible with the Schrödinger picture quantum evolution.

quant-ph↗

arXiv1995

Integral equation theory for the electrode-electrolyte interface with the central force water model. Results for an aqueous solution of sodium chloride

The structure of an aqueous solution of sodium chloride at a planar electrode is investigated by integral equation techniques. With the central force water model the aqueous electrolyte is modelled as a mixture of sodium and chloride ions and partially charged hydrogen and oxygen atoms interacting via effective spherically symmetric pair potentials. The bulk correlation functions are obtained from the Ornstein-Zernike equation. With the Wertheim-Lovett-Mou-Buff equation we have calculated the density profiles at the uncharged and charged electrode. Steric interactions between the differently sized ions and the ice-like water structure near the electrode dominates the ionic distribution. This model electrolyte also responds differently to opposite charges on the electrode.

chem-ph↗

arXiv1995

The Atomic and Electronic Structure of Liquid N- Methylformamide as Determined from Diffraction Experiments

The structure of liquid N-methylformamide (NMF) has been investigated using synchrotron radiation at 77 and 95 keV. The use of high energy photons has several advantages, in this case especially the large accessible momentum transfer range, the low absorption and the direct comparability with neutron diffraction. The range of momentum transfer covered is 0.6 Å$^{-1} <$ Q $<$24.0 Å$^{-1}$. Neutron diffraction data on the same sample in the same momentum transfer range have been published previously. In that study two differently isotope - substituted species were investigated. In order to compare neutron and photon diffraction data properly Reverse Monte Carlo (RMC-) simulations have been performed. Some modifications had to be added to the standard RMC- code introducing different constraints for inter- and intramolecular distances as these distances partly overlap in liquid NMF. RMC- simulations having only the neutron data as input were carried out in order to test the quality of the X-ray data. The photon structure factor calculated from the RMC- configurations is found to agree well with the present experimental data, while it deviates considerably from earlier X-ray work using low energy photons (17 keV). Finally we discuss whether the different interaction mechanisms of neutrons and photons can be used to directly access the electronic structure in the liquid. Evidence is presented that the elastic self scattering part of liquid NMF is changed with respect to the independent atom approximation. This modification can be accounted for by a simple charged atoms model.

chem-ph↗

arXiv1996

Optical absorption of non-interacting tight-binding electrons in a Peierls-distorted chain at half band-filling

In this first of three articles on the optical absorption of electrons in half-filled Peierls-distorted chains we present analytical results for non-interacting tight-binding electrons. We carefully derive explicit expressions for the current operator, the dipole transition matrix elements, and the optical absorption for electrons with a cosine dispersion relation of band width $W$ and dimerization parameter $δ$. New correction (``$η$''-)terms to the current operator are identified. A broad band-to-band transition is found in the frequency range $Wδ< ω< W$ whose shape is determined by the joint density of states for the upper and lower Peierls subbands and the strong momentum dependence of the transition matrix elements.

cond-mat↗

arXiv1996

Exact results for the optical absorption of strongly correlated electrons in a half-filled Peierls-distorted chain

In this second of three articles on the optical absorption of electrons in a half-filled Peierls-distorted chain we present exact results for strongly correlated tight-binding electrons. In the limit of a strong on-site interaction $U$ we map the Hubbard model onto the Harris-Lange model which can be solved exactly in one dimension in terms of spinless fermions for the charge excitations. The exact solution allows for an interpretation of the charge dynamics in terms of parallel Hubbard bands with a free-electron dispersion of band-width $W$, separated by the Hubbard interaction $U$. The spin degrees of freedom enter the expressions for the optical absorption only via a momentum dependent but static ground state expectation value. The remaining spin problem can be traced out exactly since the eigenstates of the Harris-Lange model are spin-degenerate. This corresponds to the Hubbard model at temperatures large compared to the spin exchange energy. Explicit results are given for the optical absorption in the presence of a lattice distortion $δ$ and a nearest-neighbor interaction $V$. We find that the optical absorption for $V=0$ is dominated by a peak at $ω=U$ and broad but weak absorption bands for $| ω-U | \leq W$. For an appreciable nearest-neighbor interaction, $V>W/2$, almost all spectral weight is transferred to Simpson's exciton band which is eventually Peierls-split.

cond-mat↗

arXiv1996

Optical absorption of strongly correlated half-filled Mott-Hubbard chains

In this last of three articles on the optical absorption of electrons in a half-filled Peierls-distorted chain we address the dimerized extended Hubbard model in the limit of a large on-site interaction $U$. When the Hubbard interaction is large both compared to the band width $W$ and the nearest neighbor interaction $V$ the charge dynamics is properly described by the Harris-Lange model. This model can be exactly mapped onto a model of free spinless Fermions in parallel (Hubbard-)bands of width $W$ which are eventually Peierls-split. To determine the coherent absorption features at low temperatures we design and employ the ``no-recoil approximation'' in which we assume that the momentum transfer to the spin degrees of freedom can only be $Δq_S=0$ or $Δq_S=π/a$ during an optical excitation. We present explicit analytical results for the optical absorption in the presence of a lattice dimerization $δ$ and a nearest-neighbor interaction $V$ for the Néel and dimer state. We find that the coherent part of the optical absorption for $V=0$ is given by a single peak at $ω=U$ and broad but weak absorption bands for $Wδ\leq |ω-U| \leq W$. The central peak at $ω=U$ only vanishes for $δ=0$ in the Néel state. For an appreciable nearest neighbor interaction $V>W/2$ almost all spectral weight is transferred to the $Δq_C=0$-exciton and the $Δq_C=π/a$-exciton whose relative spectral weights very sensitively depend on both the lattice and the spin dimerization of the ground state.

cond-mat↗

arXiv1995

Corrections to scaling in 2--dimensional polymer statistics

Writing $ = AN^{2ν}(1+BN^{-Δ_1}+CN^{-1}+ ...)$ for the mean square end--to--end length $ $ of a self--avoiding polymer chain of $N$ links, we have calculated $Δ_1$ for the two--dimensional {\em continuum} case from a new {\em finite} perturbation method based on the ground state of Edwards self consistent solution which predicts the (exact) $ν=3/4$ exponent. This calculation yields $Δ_1=1/2$. A finite size scaling analysis of data generated for the continuum using a biased sampling Monte Carlo algorithm supports this value, as does a re--analysis of exact data for two--dimensional lattices.

cond-mat↗

arXiv1996

Equation of State of the Hard-Sphere Crystal

A new approach to the averaged two-particle distribution function of a crystalline phase is presented. It includes an indirect check of the merit of the Gaussian approximation for the local density and a new way to inferring values of the thermodynamic variables from simulation data. The equation of state and the compressibility of the hard-sphere FCC crystal is computed from Tarazona free energy density functional [Phys. Rev. A {\bf 31}, 2672 (1985)]. They are in excellent agreement with simulation results over the physical range of densities up to almost close packing. We also include the comparison with the results obtained by two other functional approaches which are also excellent.

cond-mat↗

arXiv1995

Entropic Barriers, Frustration and Order: Basic Ingredients in Protein Folding

We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this state is reached in a time that scales as $M^λ$, with $λ\simeq 3$. This scaling is limited by the amount of frustration which leads to the dynamical selectivity of proteins: foldable proteins are limited to $\sim 300$ monomers; and they are stable in {\it one} range of temperatures, independent of size and structure. These predictions explain generic properties of {\it in vivo} proteins.

cond-mat↗