相关论文: Accelerated sampling by infinite swapping of path …
An improved real-time quantum Monte Carlo procedure is presented and applied to describe the electronic transfer dynamics along molecular chains. The model consists of discrete electronic sites coupled to a thermal environment which is…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
Efficient sampling from ensembles of Hamiltonian cycles is critical for predicting the thermodynamic properties of compact polymers, with applications including modeling protein and RNA folding and designing soft materials. Although…
We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains.…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
For real-time multirotor kinodynamic motion planning, the efficiency of sampling-based methods is usually hindered by difficult-to-sample homotopy classes like narrow passages. In this paper, we address this issue by a hybrid scheme. We…
This paper introduces a framework for simulating finite dimensional representations of (jump) diffusion sample paths over finite intervals, without discretisation error (exactly), in such a way that the sample path can be restored at any…
Dynamics of a particle diffusing in a confinement can be seen a sequence of bulk-diffusion-mediated hops on the confinement surface. Here, we investigate the surface hopping propagator that describes the position of the diffusing particle…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Atomistic simulations of thermodynamic properties of magnetic materials rely on an accurate modelling of magnetic interactions and an efficient sampling of the high-dimensional spin space. Recent years have seen significant progress with a…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling (MSES) technique suggested by Moritsugu and coworkers (J. Chem. Phys. 133, 224105 (2010)). The basic idea of…
Interactive global illumination remains a challenge in radiometrically- and geometrically-complex scenes. Specialized sampling strategies are effective for specular and near-specular transport because the scattering has relatively low…
We derive an effective cluster model to address the transport properties of mutually interacting small polarons. We propose a decoupling scheme where the hopping dynamics of any given particle is determined by separating out explicitly the…
A new method is proposed for integrating the equations of motion of an elastic filament. In the standard finite-difference and finite-element formulations the continuum equations of motion are discretized in space and time, but it is then…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
An exact real time quantum dynamics preaveraged over imaginary time path integral is formulated for general condensed phase equilibrium ensemble. This formulation results in the well-known centroid dynamics approach upon filtering of…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…
Sampling from distributions of implicitly defined shapes enables analysis of various energy functionals used for image segmentation. Recent work describes a computationally efficient Metropolis-Hastings method for accomplishing this task.…
We implement a rare-event sampling scheme for quantifying the rate of thermally-activated nonadiabatic transitions in the condensed phase. Our QM/MM methodology uses the recently developed INAQS package to interface between an elementary…