Related papers: NVU dynamics. III. Simulating molecules at constan…
The numerical integration of the Nose-Hoover dynamics gives a deterministic method that is used to sample the canonical Gibbs measure. The Nose-Hoover dynamics extends the physical Hamiltonian dynamics by the addition of a "thermostat"…
Fast and accurate structural dynamics analysis is important for structural design and damage assessment. Structural dynamics analysis leveraging machine learning techniques has become a popular research focus in recent years. Although the…
We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is a collision-resolution algorithm that overcomes the numerical constraints arising from particle…
We describe recent developments in the hybrid atomistic/continuum modelling of dense fluids. We discuss the general implementation of mass, momentum and energy transfers between a region described by molecular dynamics and the neighbouring…
In this work, we develop a neural-physics solver based on finite volume method (FVM), namely NeuralFVM, for turbulent flows by implementing the standard $k$-$\omega$ model designed for efficient Graphics Processing Unit (GPU) execution. The…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
We write down and apply the linearized fluid and gravitational equations consistent with pseudo-Newtonian simulations, whereby Newtonian hydrodynamics is used with a pseudo-Newtonian monopole and standard Newtonian gravity for higher…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis, with a focus on the coupling between chemical reactions and mechanical dynamics. Extending the classical Toner-Tu framework,…
The presented paper is an attempt to investigate the dynamical states of an hydrodynamical isothermal turbulent self-gravitating system using some powerful tools of the classical thermodynamics. Our main assumption, inspired by the work of…
A conservative finite-volume framework, based on a collocated variable arrangement, for the simulation of flows at all speeds, applicable to incompressible, ideal-gas and real-gas fluids is proposed in conjunction with a fully-coupled…
Learning-based methods have made significant progress in physics simulation, typically approximating dynamics with a monolithic end-to-end optimized neural network. Although these models offer an effective way to simulation, they may lose…
We develop data-driven models to predict the dynamics of a freely settling sphere in a quiescent Newtonian fluid using experimentally obtained trajectories. Particle tracking velocimetry was used to obtain a comprehensive dataset of…
In 2001, Bertalmio et. al. drew an analogy between the image intensity function for the image inpainting problem and the stream function in a two-dimensional (2D) incompressible fluid. An approximate solution to the inpainting problem is…
To simulate plasma phenomena, large-scale computational resources have been employed in developing high-precision and high-resolution plasma simulations. One of the main obstacles in plasma simulations is the requirement of computational…
Data-driven modeling techniques have been explored in the spatial-temporal modeling of complex dynamical systems for many engineering applications. However, a systematic approach is still lacking to leverage the information from different…
We continue our investigation of finite deformation linear viscoelastodynamics by focusing on constructing accurate and reliable numerical schemes. The concrete thermomechanical foundation developed in the previous study paves the way for…
Using molecular dynamics simulations and integral equations (Rogers-Young, Percus-Yevick and hypernetted chain closures) we investigate the thermodynamic of particles interacting with continuous core-softened intermolecular potential.…