相关论文: Volume Determination of Globular Proteins by Molec…
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…
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…
Material properties are fundamentally dictated by multiscale phenomena, which often reach mesoscale in size. The {\mu}m mesoscale is also the size which can be observed directly under an optical microscope, bridging the atomistic…
Flow marks are common surface defects that occur in injection-molded products. Their formation may be related to the flow process of the melt in the mold. Through dimensional analysis, we have discovered that the geometric shape of the flow…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
A thin plate or slab, prepared so that opposite faces have different surface stresses, will bend as a result of the stress difference. We have developed a classical molecular dynamics (MD) formulation where (similar in spirit to…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
Industrial polymeric materials often rely on antioxidants to achieve long-term reliability. Previous studies have frequently discussed the stabilization effect in the presence of macroscopic additive migration. However, the micro- to…
We present a new approach to carry out non-adiabatic molecular dynamics to study the carrier mobility in an organic monolayer. This approach allows the calculation of a 4802 atom system for 825 fs in about three hours using 51,744 computer…
Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by Molecular Dynamics (MD) computer simulation and compared to results of Lattice Boltzmann (LB) simulations. By the…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico…
A large-scale molecular dynamics (MD) simulation of acoustic cavitation in a simple liquid was performed using the supercomputer Fugaku. The system, consisting of approximately 100 billion atoms, was subjected to ultrasonic irradiation.…