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Machine learning potentials have achieved great success in accelerating atomistic simulations. Many of them relying on atom-centered local descriptors are natural for parallelization. More recent message passing neural network (MPNN) models…
A mixture of Brownian particles at different temperatures has been a useful model for studying the out-of-equilibrium properties of systems made up of microscopic components with differing levels of activity. This model was previously…
Understanding and simulating how a quantum system interacts and exchanges information or energy with its surroundings is a ubiquitous problem, one which must be carefully addressed in order to establish a coherent framework to describe the…
In this review chapter we focus on the many-body dynamics of cold polar molecules in the strongly interacting regime. In particular, we discuss a toolbox for engineering many-body Hamiltonians based on the manipulation of the electric…
Being cognizant of the abundance of multi-body interactions in various complex systems, here we investigate a possible way to incorporate multi-body interactions in dynamical networks. Adopting hypergraph as the underlying architecture aids…
We report the realization and modeling of a triple-antidot molecule hosting three interacting quantum Hall quasiparticles, with tunnel coupling between antidots tunable via the magnetic field. The measured tunneling conductance spectrum…
Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Previous…
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…
This paper addresses the problem of parallelizing computations to study non-linear dynamics in large networks of non-locally coupled oscillators using heterogeneous computing resources. The proposed approach can be applied to a variety of…
Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
We study the boundary conditions at a fluid-solid interface using molecular dynamics simulations covering a broad range of fluid-solid interactions and fluid densities, and both simple and chain-molecule fluids. The slip length is shown to…
The two and three-body contacts are central to a set of univeral relations between microscopic few-body physics within an ultracold Bose gas and its thermodynamical properties. They may also be defined in trapped few-particle systems, which…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
Virtually every biological function emerges through the organization of molecules in time and space. Consequently, a major challenge in statistical physics is to uncover the universal principles governing macromolecular self-organization…
We propose a platform for observing and controlling the interactions between atomic ions and a quantum gas of polar molecules in the ultracold regime. This approach is based on the combination of several recently developed methods in two…
Rhythmic phenomena, which are ubiquitous in biological systems, are typically modelled as systems of coupled limit cycle oscillators. Recently, there has been an increased interest in understanding the impact of higher-order interactions on…