Related papers: Energy-conserving molecular dynamics is not energy…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Molecular dynamics (MD) simulations of the zeta potential are so poor that it has become common to term their predictions 'apparent'. Here we demonstrate how zeta potentials that agree with measured values can be calculated by: (1)…
Magnetic reconnection is an explosive process that accelerates particles to high energies in Earth's magnetosphere, offering a unique natural laboratory to study this phenomenon. This study investigates how well data-driven fully kinetic…
Machine learning (ML) methods are being used in almost every conceivable area of electronic structure theory and molecular simulation. In particular, ML has become firmly established in the construction of high-dimensional interatomic…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
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…
Turbulent diffuse molecular clouds can exhibit complicated morphologies caused by the interactions among radiation, chemistry, fluids, and fields. We performed full 3D simulations for turbulent diffuse molecular interstellar media,…
In this work, we analytically examine the validity of molecular dynamics for a soft potential system by considering a simple one-dimensional system with a piecewise continuous linear repulsive potential wall having a constant slope $a$. We…
A molecular dynamics (MD) simulation of planar Couette flow is presented for the minimal channel in which turbulence structures can be sustained. Evolution over a single breakdown and regeneration cycle is compared to computational fluid…
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…
Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this,…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Machine learning force fields have emerged as promising tools for molecular dynamics (MD) simulations, potentially offering quantum-mechanical accuracy with the efficiency of classical MD. Inspired by foundational large language models,…
Energy-based modeling is a promising approach to unsupervised learning, which yields many downstream applications from a single model. The main difficulty in learning energy-based models with the "contrastive approaches" is the generation…
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…
The leapfrog integrator is widely used because of its excellent stability in molecular dynamics simulation. This is recognized as being due to the existence of a discrete variational structure of the equations. We introduce a modified…
Molecular dynamics (MD) simulations are used to determine the diffusion coefficients, electrophoretic mobilities and electrical conductivity of a charged colloidal suspension in the salt-free regime as a function of the colloid charge. The…
While molecular dynamics (MD) is a very useful computational method for atomistic simulations, modeling the interatomic interactions for reliable MD simulations of real materials has been a long-standing challenge. In 2007, Behler and…