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Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Wetting and drying of a rigid substrate by a Lennard-Jones fluid in molecular dynamics simulations is reported. The size of the substrate particles, being smaller than the fluid particles in former simulations, is now taken to be equal to,…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
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…
Transport properties of liquid methanol and ethanol are predicted by molecular dynamics simulation. The molecular models for the alcohols are rigid, non-polarizable and of united-atom type. They were developed in preceding work using…
Due to the improvement of computer power and the development of efficient algorithms it is now possible to combine high-dimensional quantum dynamical calculations of the dissociative adsorption of molecular beams with reliable ab-initio…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
We have simulated the dynamics of a 2D gas of hard needles by event-oriented molecular dynamics. Various quantities namely translational and rotational diffusion constants and intermediate self scattering function have been explored and…
We study equilibrium properties of polymer films and droplets on a solid substrate employing particle-based simulation techniques (Molecular Dynamics) and a continuum description. Parameter-passing techniques are explored that facilitate a…
We propose a model to study symmetric binary fluids, based in the mesoscopic molecular simulation technique known as multiparticle collision, where space and state variables are continuous while time is discrete. We include a repulsion rule…
Dissipative particle dynamics (DPD) does not conserve energy and this precludes its use in the study of thermal processes in complex fluids. We present here a generalization of DPD that incorporates an internal energy and a temperature…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
We present, in a unifying way, the main components of three asynchronous event-driven algorithms for simulating physical systems of interacting particles. The first example, hard-particle molecular dynamics, is well-known. We also present a…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…