Related papers: Virtual Molecular Dynamics
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
On the basis of the antisymmetrized molecular dynamics (AMD) of wave packets for the quantum system, a novel model (called AMD-V) is constructed by the stochastic incorporation of the diffusion and the deformation of wave packets which is…
Newtonian dynamics is derived from prior information codified into an appropriate statistical model. The basic assumption is that there is an irreducible uncertainty in the location of particles so that the state of a particle is defined by…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…
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…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
We show how the dynamically nonlocal formulation of classical nuclear motion in the presence of quantal electronic transitions presented many years ago by Pechukas can be localized in time using time dependent perturbation theory to give an…
We present a fully covariant transport framework for Molecular Dynamics that enables a consistent description of the evolution of relativistic N-body systems. For the first time, we derive relativistic equations of motion incorporating both…
We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Quantum geometrical molecular dynamics provides a quantum geometric picture for understanding reactive dynamics, especially excited-state conical intersection dynamics, and also a numerically exact method for strongly correlated…
Quantum dynamics for arbitrary system are traditionally realized by time evolutions of wave functions in Hilbert space and/or density operators in Liouville space. However, the traditional simulations may occasionally turn out to be…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
A generalized formalism of the so-called non-adiabatic quantum molecular dynamics is presented, which applies for atomic many-body systems in external laser fields. The theory treats the nuclear dynamics and electronic transitions…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…