arXiv subjects

Jorge L. Rosa-Raíces

Publications and source records attributed to Jorge L. Rosa-Raíces.

5 recordsLinked to original sources

arXiv2025

Nonadiabatic force matching for alchemical free-energy estimation

We propose a method to compute free-energy differences from nonadiabatic alchemical transformations using flow-based generative models. The method, nonadiabatic force matching, hinges on estimating the dissipation along an alchemical switching process in terms of a nonadiabatic force field that can be learned through stochastic flow matching. The learned field can be used in conjunction with short-time trajectory data to evaluate upper and lower bounds on the alchemical free energy that variationally converge to the exact value if the field is optimal. Applying the method to evaluate the alchemical free energy of atomistic models shows that it can substantially reduce the simulation cost of a free-energy estimate at negligible loss of accuracy when compared with thermodynamic integration.

physics.chem-ph↗

arXiv2024

Variational time reversal for free energy estimation in nonequilibrium steady states

Studying the structure of systems in nonequilibrium steady states necessitates tools that quantify population shifts and associated deformations of equilibrium free energy landscapes under persistent currents. Within the framework of stochastic thermodynamics, we establish a variant of the Kawasaki-Crooks equality that relates nonequilibrium free energy corrections in overdamped Langevin systems to heat dissipation statistics along time-reversed relaxation trajectories computable with molecular simulation. Using stochastic control theory, we arrive at a general variational approach to evaluate the Kawasaki-Crooks equality, and use it to estimate distribution functions of order parameters in specific models of driven and active matter, attaining substantial improvement in accuracy over simple perturbative methods.

cond-mat.stat-mech↗

arXiv2020

A generalized class of strongly stable and dimension-free T-RPMD integrators

Recent work shows that strong stability and dimensionality freedom are essential for robust numerical integration of thermostatted ring-polymer molecular dynamics (T-RPMD) and path-integral molecular dynamics (PIMD), without which standard integrators exhibit non-ergodicity and other pathologies [J. Chem. Phys. 151, 124103 (2019); J. Chem. Phys. 152, 104102 (2020)]. In particular, the BCOCB scheme, obtained via Cayley modification of the standard BAOAB scheme, features a simple reparametrization of the free ring-polymer sub-step that confers strong stability and dimensionality freedom and has been shown to yield excellent numerical accuracy in condensed-phase systems with large time-steps. Here, we introduce a broader class of T-RPMD numerical integrators that exhibit strong stability and dimensionality freedom, irrespective of the Ornstein-Uhlenbeck friction schedule. In addition to considering equilibrium accuracy and time-step stability as in previous work, we evaluate the integrators on the basis of their rates of convergence to equilibrium and their efficiency at evaluating equilibrium expectation values. Within the generalized class, we find BCOCB to be superior with respect to accuracy and efficiency for various configuration-dependent observables, although other integrators within the generalized class perform better for velocity-dependent quantities. Extensive numerical evidence indicates that the stated performance guarantees hold for the strongly anharmonic case of liquid water. Both analytical and numerical results indicate that BCOCB excels over other known integrators in terms of accuracy, efficiency, and stability with respect to time-step for practical applications.

physics.chem-ph↗

arXiv2020

Dimension-free path-integral molecular dynamics without preconditioning

Convergence with respect to imaginary-time discretization is an essential part of any path-integral-based calculation. However, an unfortunate property of existing non-preconditioned numerical integration schemes for path-integral molecular dynamics (PIMD) - including ring-polymer molecular dynamics (RPMD) and thermostatted RPMD (T-RPMD) - is that for a given MD timestep, the overlap between the exact ring-polymer Boltzmann-Gibbs distribution and that sampled using MD becomes zero in the infinite-bead limit. This has clear implications for hybrid Metropolis Monte-Carlo/MD sampling schemes. We show that these problems can be avoided through the introduction of "dimension-free" numerical integration schemes for which the sampled ring-polymer position distribution has non-zero overlap with the exact distribution in the infinite-bead limit for the case of a harmonic potential. We show that dimension freedom can be achieved via mollification of the forces from the physical potential and with the BCOCB integration scheme. The dimension-free numerical integration schemes yield finite error bounds for a given MD timestep as the number of beads is taken to infinity; these conclusions are proven for harmonic potential and borne out numerically for anharmonic systems, including water. The numerical results for BCOCB are particularly striking, allowing for three-fold increases in the stable timestep for liquid water with respect to the Bussi-Parrinello (OBABO) and Leimkuhler (BAOAB) integrators while introducing negligible errors in the statistical properties and absorption spectrum. Importantly, the dimension-free, non-preconditioned integration schemes introduced here preserve ergodicity and global second-order accuracy, and they remain simple, black-box methods that avoid additional computational costs, tunable parameters, or system-specific implementations.

physics.chem-ph↗

arXiv2019

Path-accelerated molecular dynamics: Parallel-in-time integration using path integrals

Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of distributed computing to reduce the wall-clock time of MD simulation via parallelization with respect to MD timesteps. The marginal distribution for the time evolution of a system is expressed in terms of a path integral, enabling the use of path sampling techniques to numerically integrate MD trajectories. By parallelizing the evaluation of the path action with respect to time and by initializing the path configurations from a non-equilibrium distribution, the algorithm enables significant speedups in terms of the length of MD trajectories that can be integrated in a given amount of wall-clock time. The method is demonstrated for Brownian dynamics, although it is generalizable to other stochastic equations of motion including open systems. We apply the method to two simple systems, a harmonic oscillator and a Lennard-Jones liquid, and we show that in comparison to the conventional Euler integration scheme for Brownian dynamics, the new method can reduce the wall-clock time for integrating trajectories of a given length by more than three orders of magnitude in the former system and more than two in the latter. This new method for parallelizing MD in the dimension of time can be trivially combined with algorithms for parallelizing the MD force evaluation to achieve further speedup.

physics.comp-ph↗