Related papers: Data-driven molecular modeling with the generalize…
Langevin equations or generalized Langevin equations (GLEs) are popular models for describing the motion of a particle in a fluid medium in an effective manner. Here we examine particles immersed in an inherently nonequilibrium fluid, i.e.,…
Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…
Purely data driven approaches for machine learning present difficulties when data is scarce relative to the complexity of the model or when the model is forced to extrapolate. On the other hand, purely mechanistic approaches need to…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Langevin dynamics has found a large number of applications in sampling, optimization and estimation. Preconditioning the gradient in the dynamics with the covariance - an idea that originated in literature related to solving estimation and…
Given (small amounts of) time-series' data from a high-dimensional, fine-grained, multiscale dynamical system, we propose a generative framework for learning an effective, lower-dimensional, coarse-grained dynamical model that is predictive…
We develop a combined machine learning (ML) and quantum mechanics approach that enables data-efficient reconstruction of flexible molecular force fields from high-level ab initio calculations, through the consideration of fundamental…
Deep generative models have emerged as a powerful class of priors for signals in various inverse problems such as compressed sensing, phase retrieval and super-resolution. Here, we assume an unknown signal to lie in the range of some…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
This study explores the utility of a kernel in complex Langevin simulations of quantum real-time dynamics on the Schwinger-Keldysh contour. We give several examples where we use a systematic scheme to find kernels that restore correct…
Predicting the molecular friction and energy landscapes under nonequilibrium conditions is key to coarse-graining the dynamics of selective solute transport through complex, fluctuating and responsive media, e.g., polymeric materials such…
Simulating the long-timescale dynamics of biomolecules is a central challenge in computational science. While enhanced sampling methods can accelerate these simulations, they rely on pre-defined collective variables that are often difficult…
A theoretical framework which unifies the conventional Mori-Zwanzig formalism and the approximate Koopman learning is presented. In this framework, the Mori-Zwanzig formalism, developed in statistical mechanics to tackle the hard problem of…
We introduce a novel class of score-based diffusion processes that operate directly in the representation space of Lie groups. Leveraging the framework of Generalized Score Matching, we derive a class of Langevin dynamics that decomposes as…
This study explores the utility of a kernel in complex Langevin simulations of quantum real-time dynamics on the Schwinger-Keldysh contour. We give several examples where we use a systematic scheme to find kernels that restore correct…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
Deep Generative Models (DGMs) have been shown to be powerful tools for generating tabular data, as they have been increasingly able to capture the complex distributions that characterize them. However, to generate realistic synthetic data,…
The exact quantum dynamics of lattice models can be computationally intensive, especially when aiming for large system sizes and extended simulation times necessary to converge transport coefficients. By leveraging finite memory times to…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…