arXiv subjects

Jeremy Schofield

Publications and source records attributed to Jeremy Schofield.

33 records · Page 2Linked to original sources

arXiv2008

Quantum free energy differences from non-equilibrium path integrals: I. Methods and numerical application

The imaginary-time path integral representation of the canonical partition function of a quantum system and non-equilibrium work fluctuation relations are combined to yield methods for computing free energy differences in quantum systems using non-equilibrium processes. The path integral representation is isomorphic to the configurational partition function of a classical field theory, to which a natural but fictitious Hamiltonian dynamics is associated. It is shown that if this system is prepared in an equilibrium state, after which a control parameter in the fictitious Hamiltonian is changed in a finite time, then formally the Jarzynski non-equilibrium work relation and the Crooks fluctuation relation are shown to hold, where work is defined as the change in the energy as given by the fictitious Hamiltonian. Since the energy diverges for the classical field theory in canonical equilibrium, two regularization methods are introduced which limit the number of degrees of freedom to be finite. The numerical applicability of the methods is demonstrated for a quartic double-well potential with varying asymmetry. A general parameter-free smoothing procedure for the work distribution functions is useful in this context.

cond-mat.stat-mech↗

arXiv2008

Quantum free energy differences from non-equilibrium path integrals: II. Convergence properties for the harmonic oscillator

Non-equilibrium path integral methods for computing quantum free energy differences are applied to a quantum particle trapped in a harmonic well of uniformly changing strength with the purpose of establishing the convergence properties of the work distribution and free energy as the number of degrees of freedom M in the regularized path integrals goes to infinity. The work distribution is found to converge when M tends to infinity regardless of the switching speed, leading to finite results for the free energy difference when the Jarzynski non-equilibrium work relation or the Crooks fluctuation relation are used. The nature of the convergence depends on the regularization method. For the Fourier method, the convergence of the free energy difference and work distribution go as 1/M, while both quantities converge as 1/M^2 when the bead regularization procedure is used. The implications of these results to more general systems are discussed.

cond-mat.stat-mech↗

arXiv2008

Efficient algorithms for rigid body integration using optimized splitting methods and exact free rotational motion

Hamiltonian splitting methods are an established technique to derive stable and accurate integration schemes in molecular dynamics, in which additional accuracy can be gained using force gradients. For rigid bodies, a tradition exists in the literature to further split up the kinetic part of the Hamiltonian, which lowers the accuracy. The goal of this note is to comment on the best combination of optimized splitting and gradient methods that avoids splitting the kinetic energy. These schemes are generally applicable, but the optimal scheme depends on the desired level of accuracy. For simulations of liquid water it is found that the velocity Verlet scheme is only optimal for crude simulations with accuracies larger than 1.5%, while surprisingly a modified Verlet scheme (HOA) is optimal up to accuracies of 0.4% and a fourth order gradient scheme (GIER4) is optimal for even higher accuracies.

cond-mat.stat-mech↗

arXiv2007

Event-Driven Dynamics of Rigid Bodies Interacting via Discretized Potentials

A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The scheme is based on a discretization of an underlying continuous potential that effectively determines the times at which interaction energies change. As in most event-driven approaches, the method consists of specifying a means of computing the free motion, evaluating the times at which interactions occur, and determining the consequences of interactions on subsequent motion for the terraced-potential. The latter two aspects are shown to be simply expressible in terms of the underlying smooth potential. Within this context, algorithms for computing the times of interaction events and carrying out efficient event-driven simulations are discussed. The method is illustrated on system composed of rigid rods in which the constituents interact via a terraced potential that depends on the relative orientations of the rods.

cond-mat.soft↗

arXiv2007

Symplectic algorithms for simulations of rigid body systems using the exact solution of free motion

Elegant integration schemes of second and fourth order for simulations of rigid body systems are presented which treat translational and rotational motion on the same footing. This is made possible by a recent implementation of the exact solution of free rigid body motion. The two schemes are time-reversible, symplectic, and exactly respect conservation principles for both the total linear and angular momentum vectors. Simulations of simple test systems show that the second order scheme is stable and conserves all constants of the motion to high precision. Furthermore, the schemes are demonstrated to be more accurate and efficient than existing methods, except for high densities, in which case the second order scheme performs at least as well, showing their general applicability. Finally, it is demonstrated that the fourth order scheme is more efficient than the second order scheme provided the time step is smaller than a system-dependent threshold value.

cond-mat.soft↗

arXiv2006

Numerical implementation of the exact dynamics of free rigid bodies

In this paper the exact analytical solution of the motion of a rigid body with arbitrary mass distribution is derived in the absence of forces or torques. The resulting expressions are cast into a form where the dependence of the motion on initial conditions is explicit and the equations governing the orientation of the body involve only real numbers. Based on these results, an efficient method to calculate the location and orientation of the rigid body at arbitrary times is presented. This implementation can be used to verify the accuracy of numerical integration schemes for rigid bodies, to serve as a building block for event-driven discontinuous molecular dynamics simulations of general rigid bodies, and for constructing symplectic integrators for rigid body dynamics.

cond-mat.stat-mech↗

arXiv2006

Discontinuous Molecular Dynamics for Semi-Flexible and Rigid Bodies

A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and interaction rules are derived from Lagrangian mechanics in the presence of constraints. This approach is most suitable when the body is composed of relatively few point masses or is semi-flexible. In the second method, the equations of rigid bodies are used to derive explicit analytical expressions for the free evolution of arbitrary rigid molecules and to construct a simple scheme for computing interaction rules. Efficient algorithms for the search for the times of interaction events are designed in this context, and the handling of missed interaction events is discussed.

cond-mat.stat-mech↗

arXiv2006

Discontinuous Molecular Dynamics for Rigid Bodies: Applications

Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous potentials are compared with simulations in which the molecules interact through standard continuous Lennard-Jones potentials. It is shown that under similar conditions of temperature and pressure, the rigid discontinuous molecular dynamics method reproduces the essential dynamical and structural features found in continuous-potential simulations at both gas and liquid densities. Moreover, the discontinuous molecular dynamics approach is demonstrated to be between 2 to 100 times more efficient than the standard molecular dynamics method depending on the specific conditions of the simulation. The rigid discontinuous molecular dynamics method is also applied to a discontinuous-potential model of a liquid composed of rigid benzene molecules, and equilibrium and dynamical properties are shown to be in qualitative agreement with more detailed continuous-potential models of benzene. Qualitative differences in the dynamics of the two models are related to the relatively crude treatment of variations in the repulsive interactions as one benzene molecule rotates by another.

cond-mat.stat-mech↗

arXiv2005

Mode-coupling theory for multiple-time correlation functions of tagged particle densities and dynamical filters designed for glassy systems

The theoretical framework for higher-order correlation functions involving multiple times and multiple points in a classical, many-body system developed by Van Zon and Schofield [Phys. Rev. E 65, 011106 (2002)] is extended here to include tagged particle densities. Such densities have found an intriguing application as proposed measures of dynamical heterogeneities in structural glasses. The theoretical formalism is based upon projection operator techniques which are used to isolate the slow time evolution of dynamical variables by expanding the slowly-evolving component of arbitrary variables in an infinite basis composed of the products of slow variables of the system. The resulting formally exact mode-coupling expressions for multiple-point and multiple-time correlation functions are made tractable by applying the so-called N-ordering method. This theory is used to derive for moderate densities the leading mode coupling expressions for indicators of relaxation type and domain relaxation, which use dynamical filters that lead to multiple-time correlations of a tagged particle density. The mode coupling expressions for higher order correlation functions are also succesfully tested against simulations of a hard sphere fluid at relatively low density.

cond-mat.stat-mech↗

arXiv2004

Glassy dynamics and domains: exact results for the East model

A general matrix-based scheme for analyzing the long-time dynamics in kinetically constrained models such as the East model is presented. The treatment developed here is motivated by the expectation that slowly-relaxing spin domains of arbitrary size govern the highly cooperative events that lead to spin relaxation at long times. To account for the role of large spin domains in the dynamics, a complete basis expressed in terms of domains of all sizes is introduced. It is first demonstrated that accounting for single domains of all possible sizes leads to a simple analytical result for the two-time single-spin correlation function in the East model that is in excellent quantitative agreement with simulation data for equilibrium spin up density values c greater or equal to 0.6. It is then shown that including also two neighboring domains leads to a closed expression that describes the slow relaxation of the system down to c approximately 0.3. Ingredients of generalizing the method to lower values of c are also provided, as well as to other models. The main advantage of this approach is that it gives explicit analytical results and that it requires neither an arbitrary closure for the memory kernel nor the construction of an irreducible memory kernel. It also allows one to calculate quantities that measure heterogeneity in the same framework, as is illustrated on the neighbor-pair correlation function and the distribution of relaxation times.

cond-mat.stat-mech↗

arXiv2003

Langevin equation for the extended Rayleigh model with an asymmetric bath

In this paper a one-dimensional model of two infinite gases separated by a movable heavy piston is considered. The non-linear Langevin equation for the motion of the piston is derived from first principles for the case when the thermodynamic parameters and/or the molecular masses of gas particles on left and right sides of the piston are different. Microscopic expressions involving time correlation functions of the force between bath particles and the piston are obtained for all parameters appearing in the non-linear Langevin equation. It is demonstrated that the equation has stationary solutions corresponding to directional fluctuation-induced drift in the absence of systematic forces. In the case of ideal gases interacting with the piston via a quadratic repulsive potential, the model is exactly solvable and explicit expressions for the kinetic coefficients in the non-linear Langevin equation are derived. The transient solution of the non-linear Langevin equation is analyzed perturbatively and it is demonstrated that previously obtained results for systems with the hard-wall interaction are recovered.

cond-mat.stat-mech↗

arXiv2003

An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution

In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schrödinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.

physics.chem-ph↗

arXiv2003

Langevin Equation for the Rayleigh model with finite-ranged interactions

Both linear and nonlinear Langevin equations are derived directly from the Liouville equation for an exactly solvable model consisting of a Brownian particle of mass $M$ interacting with ideal gas molecules of mass $m$ via a quadratic repulsive potential. Explicit microscopic expressions for all kinetic coefficients appearing in these equations are presented. It is shown that the range of applicability of the Langevin equation, as well as statistical properties of random force, may depend not only on the mass ratio $m/M$ but also by the parameter $Nm/M$, involving the average number $N$ of molecules in the interaction zone around the particle. For the case of a short-ranged potential, when $N\ll 1$, analysis of the Langevin equations yields previously obtained results for a hard-wall potential in which only binary collisions are considered. For the finite-ranged potential, when multiple collisions are important ($N\gg 1$), the model describes nontrivial dynamics on time scales that are on the order of the collision time, a regime that is usually beyond the scope of more phenomenological models.

cond-mat.stat-mech↗

arXiv2001

Mode coupling theory for multi-point and multi-time correlation functions

We present a theoretical framework for higher-order correlation functions involving multiple times and multiple points in a classical, many-body system. Such higher-order correlation functions have attracted much interest recently in the context of various forms of multi-dimensional spectroscopy, and have found an intriguing application as proposed measures of dynamical heterogeneities in structural glasses. The theoretical formalism is based upon projection operator techniques which are used to isolate the slow time evolution of dynamical variables by expanding the slowly-evolving component of arbitrary variables in an infinite, ``multi-linear'' basis composed of the products of slow variables of the system. Using the formalism, a formally exact mode coupling theory is derived for multi-point and multi-time correlation functions. The resulting expressions for higher-order correlation functions are made tractable by applying a rigorous perturbation scheme, called the N-ordering method, which is exact for systems with finite correlation lengths in the thermodynamic limit. The theory is contrasted with standard mode coupling theories in which the noise or fluctuating force appearing in the generalized Langevin equation is assumed to be Gaussian, and it is demonstrated that the non-Gaussian nature of the fluctuating forces leads to important contributions to higher-order correlation functions. Finally, the higher-order correlation functions are evaluated analytically for an ideal gas system for which it is shown that the mode coupling theory is exact.

cond-mat.stat-mech↗

arXiv2001

Multiple-Point and Multiple-Time Correlations Functions in a Hard-Sphere Fluid

A recent mode coupling theory of higher-order correlation functions is tested on a simple hard-sphere fluid system at intermediate densities. Multi-point and multi-time correlation functions of the densities of conserved variables are calculated in the hydrodynamic limit and compared to results obtained from event-based molecular dynamics simulations. It is demonstrated that the mode coupling theory results are in excellent agreement with the simulation results provided that dissipative couplings are included in the vertices appearing in the theory. In contrast, simplified mode coupling theories in which the densities obey Gaussian statistics neglect important contributions to both the multi-point and multi-time correlation functions on all time scales.

cond-mat.stat-mech↗