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Modal methods are a long-standing approach to physical modelling synthesis. Extensions to nonlinear problems are possible, leading to coupled nonlinear systems of ordinary differential equations. Recent work in scalar auxiliary variable…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
Understanding thermal fluctuations yields insights into a wide range of behaviors in many-body systems. In this work, we analyze the dynamical adaptation of two-dimensional crystalline lattice system under harmonic interaction in response…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Causal discovery for dynamical systems poses a major challenge in fields where active interventions are infeasible. Most methods used to investigate these systems and their associated benchmarks are tailored to deterministic,…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
We study theoretically and numerically a family of multi-point dynamic susceptibilities that quantify the strength and characteristic lengthscales of dynamic heterogeneities in glass-forming materials. We use general theoretical arguments…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
Learning an effective policy to control high-dimensional, overactuated systems is a significant challenge for deep reinforcement learning algorithms. Such control scenarios are often observed in the neural control of vertebrate…
From flocks of birds to biomolecular assemblies, systems in which many individual components independently consume energy to perform mechanical work exhibit a wide array of striking behaviors. Methods to quantify the dynamics of these so…
We introduce a method of exploring potential energy contours in complex dynamical systems based on potentiostatic kinematics wherein the systems are evolved with minimal changes to their potential energy. We construct a simple iterative…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
The dynamics of quasicrystals is characterized by the existence of phason excitations in addition to the usual phonon modes. In order to investigate their interplay on an elementary level we resort to various one-dimensional model systems.…
Kinetic approaches, i.e., methods based on the lattice Boltzmann equations, have long been recognized as an appealing alternative for solving incompressible Navier-Stokes equations in computational fluid dynamics. However, such approaches…
Cytoskeletal active nematics exhibit striking non-equilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…