Related papers: Shadow Molecular Dynamics for Flexible Multipole M…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations provide a rigorous physical basis for studying these dynamics,…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…
The aim of this paper is to provide a construction of stationary discrete solitons in an extended one-dimensional Discrete NLS model with non-nearest neighbour interactions. These models, models of the type with long-range interactions were…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
This article reports about a novel extension of dissipative particle dynamics (DPD) that allows the study of the collective dynamics of complex chemical and structural systems in a spatially resolved manner with a combinatorially complex…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Electrostatic theory preserves charges, but allows dipolar excitations. Elasticity theory preserves dipoles, but allows quadrupolar (Eshelby like) plastic events. Charged amorphous granular systems are interesting in their own right; here…
In this article we examine the dynamics of a colloidal particle driven by a modulated force over a sinusoidal optical potential energy landscape. Coupling between the competing frequencies of the modulated drive and that of particle motion…
To study discrete dynamical systems of different types --- deterministic, statistical and quantum --- we develop various approaches. We introduce the concept of a system of discrete relations on an abstract simplicial complex and develop…
Dusty plasma medium turns out to be an ideal system for studying the strongly coupled behavior of matter. The large size and slow response make their dynamics suitable to be captured through simple diagnostic tools. Furthermore, as the…
With the recent production of polar molecules in the quantum regime, long-range dipolar interactions are expected to facilitate the understanding of strongly interacting many-body quantum systems and to realize lattice spin models for…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
The glass transition of a hard sphere system is investigated within the framework of the density functional theory (DFT). Molecular dynamics (MD) simulations are performed to study dynamical behavior of the system on the one hand and to…
This paper extends the Lorentz-Abraham model of an electron (i.e. the equations of motion for a small spherical shell of charge, which is rigid in its proper frame) to treat a small spherically symmetric charge distribution, allowing for…
Interacting dark energy models have been suggested as alternatives to the standard cosmological model, $\Lambda$CDM. We focus on a phenomenologically interesting class of dark scattering models that is characterised by pure momentum…
Atom-centered electric multipole moments can be extremely useful in chemistry as they enable the systematic mapping of a complex electrostatic problem to a simpler model. However, since they do not correspond to physical observables, there…
An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is…
We consider the nuclear shadowing in deep-inelastic scattering corresponding to kinematic regions accessible by future experiments at electron-ion colliders. The gluon distribution at small $x$ is obtained using an improved dipole model…