Related papers: Coarse Grained Molecular Dynamics with Normalizing…
Subject of this paper is the simplification of Markov chain Monte Carlo sampling as used in Bayesian statistical inference by means of normalising flows, a machine learning method which is able to construct an invertible and differentiable…
Sampling from high-dimensional Gibbs measures poses a challenge when the energy landscape consists of multiple metastable states. Enhanced-sampling methods mitigate this difficulty by introducing adaptive biasing potentials to facilitate…
We propose using Normalizing Flows as a trainable kernel within the molecular dynamics update of Hamiltonian Monte Carlo (HMC). By learning (invertible) transformations that simplify our dynamics, we can outperform traditional methods at…
Machine learning techniques not only offer efficient tools for modelling dynamical systems from data, but can also be employed as frontline investigative instruments for the underlying physics. Nontrivial information about the original…
One of the most widely used samplers in practice is the component-wise Metropolis-Hastings (CMH) sampler that updates in turn the components of a vector valued Markov chain using accept-reject moves generated from a proposal distribution.…
We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility…
Monte Carlo sampling of the canonical distribution presents a formidable challenge when the potential energy landscape is characterized by a large number of local minima separated by high barriers. The principal observation of this work is…
Considering molecular dynamic simulations as a stochastic method, we investigate the possibility of time coarse graining the simulations. Similarly to Boltzmann inversion method in spatial coarse graining, which begins with a free energy…
A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single…
Modeling a high-dimensional Hamiltonian system in reduced dimensions with respect to coarse-grained (CG) variables can greatly reduce computational cost and enable efficient bottom-up prediction of main features of the system for many…
Small-scale turbulence can be comprehensively described in terms of velocity gradients, which makes them an appealing starting point for low-dimensional modeling. Typical models consist of stochastic equations based on closures for…
In the past few years, deep generative models, such as generative adversarial networks \autocite{GAN}, variational autoencoders \autocite{vaepaper}, and their variants, have seen wide adoption for the task of modelling complex data…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
In this paper, we suggest a novel sampling method for Monte Carlo molecular simulations. In order to perform efficient sampling of molecular systems, it is advantageous to avoid extremely high energy configurations while also retaining the…
Recently, through a unified gradient flow perspective of Markov chain Monte Carlo (MCMC) and variational inference (VI), particle-based variational inference methods (ParVIs) have been proposed that tend to combine the best of both worlds.…
We introduce a statistical mechanics formalism for the study of constrained graph evolution as a Markovian stochastic process, in analogy with that available for spin systems, deriving its basic properties and highlighting the role of the…
We develop a renormalization group (RG) procedure that includes important system-specific features. The key ingredient is to systematize the coarse graining procedure that generates the RG flow. The coarse graining technology comes from…
Recent advances in machine learning have led to the development of new methods for enhancing Monte Carlo methods such as Markov chain Monte Carlo (MCMC) and importance sampling (IS). One such method is normalizing flows, which use a neural…
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent,…