Related papers: Peptide Conformational Equilibria Computed via a S…
We apply a recently developed method, multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, Met-enkephalin is studied and the…
Multiple equilibrium states arise in many physical systems, including various types of liquid crystal structures. Having the ability to reliably compute such states enables more accurate physical analysis and understanding of experimental…
The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J.…
We consider the problem of matching two shapes assuming these shapes are related by an elastic deformation. Using linearized elasticity theory and the finite element method we seek an elastic deformation that is caused by simple external…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
The correctness problem for reactive systems has been thoroughly explored and is well understood. Meanwhile, the efficiency problem for reactive systems has not received the same attention. Indeed, one correct system may be less fit than…
We deal with a system of two coupled differential equations, describing the evolution of a first order phase transition. In particular, we have two non-linear parabolic equations: the first one is deduced from a balance law for entropy and…
In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context…
We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…
We study the problem of a cholesteric liquid crystal confined to an elliptical channel. The system is geometrically frustrated because the cholesteric prefers to adopt a uniform rate of twist deformation, but the elliptical domain precludes…
We consider an isolated point defect embedded in a homogeneous crystalline solid. We show that, in the harmonic approximation, a periodic supercell approximation of the formation free energy as well as of the transition rate between two…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
In this paper we present a procedure to integrate, up to quadratures, the matching conditions of the energy shaping method. We do that in the context of underactuated Hamiltonian systems defined by simple Hamiltonian functions. For such…
Optimization problems associated with the interaction of linked particles are at the heart of polymer science, protein folding and other important problems in the physical sciences. In this review we explain how to recast these problems as…
What is meant by continuum lowering and ionization potential depression (IPD) in a Coulomb system depends upon precisely what question is being asked. It is shown that equilibrium (equation-of-state) phenomena and non-equilibrium dynamical…
This report details an approach to improve the accuracy and precision of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable lambda) and its application to…
In this paper, we discuss adaptive approximations of an elliptic eigenvalue optimization problem in a phase-field setting by a conforming finite element method. An adaptive algorithm is proposed and implemented in several two dimensional…