Related papers: A Conjecture about Molecular Dynamics
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
Arithmetic dynamics is the study of number theoretic properties of dynamical systems. A relatively new field, it draws inspiration partly from dynamical analogues of theorems and conjectures in classical arithmetic geometry, and partly from…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
We have previously shown that Good-Turing statistics can be applied to molecular dynamics trajectories to estimate the probability of observing completely new (thus far unobserved) biomolecular structures, and showed that the method is…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
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,…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
It has been proposed that human physical reasoning consists largely of running "physics engines in the head" in which the future trajectory of the physical system under consideration is computed precisely using accurate scientific theories.…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
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…
The notion of microscopic state of the system at a given moment of time as a point in the phase space as well as a notion of trajectory is widely used in classical mechanics. However, it does not have an immediate physical meaning, since…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…