相关论文: Reaction rate calculation by parallel path swappin…

Parameterized artificial neural networks (ANNs) can be very expressive ansatzes for variational algorithms, reaching state-of-the-art energies on many quantum many-body Hamiltonians. Nevertheless, the training of the ANN can be slow and…

The transition interface sampling (TIS) technique allows to overcome large free energy barriers within reasonable simulation time, which is impossible for straightforward molecular dynamics. Still, the method does not impose an artificial…

Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…

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.…

Diffusion models are powerful generative models but suffer from slow sampling, often taking 1000 sequential denoising steps for one sample. As a result, considerable efforts have been directed toward reducing the number of denoising steps,…

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of…

Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-called rare events that are characterized by transitions between metastable states separated by sizeable free energy barriers. Their…

Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not…

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…

Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…

We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular…

A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…

Recent advances in powerful pre-trained diffusion models encourage the development of methods to improve the sampling performance under well-trained diffusion models. This paper introduces Diffusion Rejection Sampling (DiffRS), which uses a…

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 Schr\"{o}dinger equation for the solute atoms in…

Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…

We present a time dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off variational path sampling methodology…

We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…

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…

Simulation of surface processes is a key part of computational chemistry that offers atomic-scale insights into mechanisms of heterogeneous catalysis, diffusion dynamics, as well as quantum tunneling phenomena. The most common theoretical…

Stochastic reaction networks that exhibit bistability are common in many fields such as systems biology and materials science. Sampling of the stationary distribution is crucial for understanding and characterizing the long term dynamics of…