Related papers: Mapping Variable Ring Polymer Molecular Dynamics: …
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
We present a hybrid method for the simulation of colloidal systems, that combines molecular dynamics (MD) with the Lattice-Boltzmann (LB) scheme. The LB method is used as a model for the solvent in order to take into account the…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…
Using molecular dynamics simulations, we determine the linear and nonlinear viscoelastic properties of a model polymer melt in the unentangled regime. Several approaches are compared for the computation of linear moduli, including…
Understanding the quantum dynamics of strongly coupled molecule-cavity systems remains a significant challenge in molecular polaritonics. This work develops a comprehensive self-consistent model simulating electromagnetic interactions of…
A non-intrusive model order reduction (MOR) method that combines features of the dynamic mode decomposition (DMD) and the radial basis function (RBF) network is proposed to predict the dynamics of parametric nonlinear systems. In many…
Compared to real-valued signals, complex-valued signals provide a unique and intuitive representation of the phase of real physical systems and processes, which holds fundamental significance and is widely applied across many fields of…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
Multidimensional spectroscopy unveils the interplay of nuclear and electronic dynamics, which characterizes the ultrafast dynamics of various molecular and solid-state systems. In a class of models widely used for the simulation of such…
Effective motion representation is crucial for enabling robots to imitate expressive behaviors in real time, yet existing motion controllers often ignore inherent patterns in motion. Previous efforts in representation learning do not…
Recently, fictitious identical particles have provided a promising way to overcome the fermion sign problem and have been used in path integral Monte Carlo (PIMC) to accurately simulate warm dense matter with up to 1000 electrons (T.…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
In this work, we derive a multi-fragment real-time extension of projected density matrix embedding theory (pDMET) designed to treat non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static…
The direct simulation Monte Carlo (DSMC) method is a widely used stochastic particle approach to solving the Boltzmann equation. However, its computational cost remains a major drawback, which can be attributed to statistical errors when…
We report a novel multi-scale simulation methodology to quantitatively predict the thermodynamic behaviour of polymer mixtures, that exhibit phases with broken orientational symmetry. Our system consists of a binary mixture of oligomers and…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
We propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isothermal-isobaric ensembles. We also present a symplectic algorithm in the constant normal pressure and lateral…
A parallel implementation of coupled spin-lattice dynamics in the LAMMPS molecular dynamics package is presented. The equations of motion for both spin only and coupled spin-lattice dynamics are first reviewed, including a detailed account…