منابع مشابه
Coarse-Grained Simulation of DNA using LAMMPS
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of singleand double-stranded DNA. oxDNA was previously only available as standalone software, but has now been imp...
متن کاملCoarse-grained simulation of amphiphilic self-assembly.
The authors present a computer simulation study of amphiphilic self-assembly performed using a computationally efficient single-site model based on Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] and Lennard-Jones particles. Molecular dynamics simulations of these systems show that free self-assembly of micellar, bilayer, and inverse micelle arrangements can be readily achieved for a single model pa...
متن کاملCoarse-Grained Simulation of Myosin-V Movement
We describe the development of a hierarchic modelling method applied to simulating the processive movement of the myosin-V molecular motor protein along an actin filament track. In the hierarchic model, three different levels of protein structure resolution are represented: secondary structure, domain, and protein, with the level of detail changing according to the degree of interaction among t...
متن کاملPrologue Introduction to Coarse Grained Simulation
Mixing of materials by small scale turbulent motion is a critical element of many flow systems of interest in engineering, geophysics, and astrophysics. Numerical simulation plays a crucial role and turbulent mixing predictability is a major concern. Small scale resolution requirements focus typically on those of continuum fluid mechanics described by Navier–Stokes (NS) equations; different req...
متن کاملIBIsCO: A molecular dynamics simulation package for coarse-grained simulation
IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2017
ISSN: 1549-9618,1549-9626
DOI: 10.1021/acs.jctc.7b00690