Related papers: Best practices for nonadiabatic molecular dynamics…
A novel method of coherent manipulation of the electron tunneling in quantum-dots is proposed, which utilizes the quantum interference in nonadiabatic double-crossing of the discrete energy levels. In this method, we need only a smoothly…
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 study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Quantum computing has the potential to reduce the computational cost required for quantum dynamics simulations. However, existing quantum algorithms for coupled electron-nuclear dynamics simulation either require fault-tolerant devices, or…
Dynamics of neutral atoms in nonuniform magnetic fields, typical of quadrupole magnetic traps, is considered by applying an accurate method for solving nonlinear systems of differential equations. This method is more general than the…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
Mixed quantum-classical mechanics descriptions are critical to modeling coupled electron-nuclear dynamics, i.e. non-adiabatic molecular dynamics, relevant to photochemical and photophysical processes. We argue that, for polyatomic…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Nonadiabatic effects that arise from the concerted motion of electrons and atoms at comparable energy and time scales are omnipresent in thermal and light-driven chemistry at metal surfaces. Excited (hot) electrons can measurably affect…
The interaction between electronic and vibrational degrees of freedom in single-molecule junctions may result from the dependence of the electronic energies or the electronic states of the molecular bridge on the nuclear displacement. The…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
The accurate description of large molecular systems in complex environments remains an ongoing challenge for the field of computational chemistry. This problem is even more pronounced for photo-induced processes, as multiple excited…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
Optimally-shaped electromagnetic fields have the capacity to coherently control the dynamics of quantum systems and thus offer a promising means for controlling molecular transformations relevant to chemical, biological, and materials…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…