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Biomechanical biofeedback may enhance rehabilitation and provide clinicians with more objective task evaluation. These feedbacks often rely on expensive motion capture systems, which restricts their widespread use, leading to the…
Kinetic equations are crucial for modeling non-equilibrium phenomena, but their computational complexity is a challenge. This paper presents a data-driven approach using reduced order models (ROM) to efficiently model non-equilibrium flows…
Run-and-Tumble Particles (RTPs) are a key model of active matter. They are characterized by alternating phases of linear travel and random direction reshuffling. By this dynamic behavior, they break time reversibility and energy…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…
A hierarchical (triple scale) simulation methodology is presented for the prediction of the dynamical and rheological properties of high molecular weight entangled polymer melts. The methodology consists of atomistic, moderately…
We present a fast and feature-complete differentiable physics engine, Nimble (nimblephysics.org), that supports Lagrangian dynamics and hard contact constraints for articulated rigid body simulation. Our differentiable physics engine offers…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…
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…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
The extended Lagrangian molecular dynamics (XLMD) method provides a useful framework for reducing the computational cost of a class of molecular dynamics simulations with constrained latent variables. The XLMD method relaxes the constraints…
Active plasma resonance spectroscopy (APRS) refers to a class of plasma diagnostic methods that use the ability of plasma to resonate at or near the electron plasma frequency for diagnostic purposes. The planar multipole resonance probe…
We discuss a theoretical approach that employs machine learning potential energy surfaces (ML-PESs) in the nonadiabatic dynamics simulation of polyatomic systems by taking 6-aminopyrimidine as a typical example. The Zhu-Nakamura theory is…
In this paper, we address the modeling issues of cell movement and division with a special focus on the phenomenon of volume exclusion in a lattice-based, exact stochastic simulation framework. We propose a new exact method, called Reduced…
We present an inference scheme of long timescale, non-exponential kinetics from Molecular Dynamics simulations accelerated by stochastic resetting. Standard simulations provide valuable insight into chemical processes but are limited to…
Feynman path integrals (PIs) have found many uses in approximate quantum dynamics methods that are able to efficiently calculate real-time quantum correlation functions. The PIs typically take the form of discrete imaginary time slices over…
Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…
Plasmas with varying collisionalities occur in many applications, such as tokamak edge regions, where the flows are characterized by significant variations in density and temperature. While a kinetic model is necessary for…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…