Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD
نویسندگان
چکیده
منابع مشابه
Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to analyze simulated trajectories, either interactively or via scripts, to derive quantities of interest and provide insight for further experiments. This paper pr...
متن کاملLeast – Squares Method For Estimating Diffusion Coefficient
Abstract: Determination of the diffusion coefficient on the base of solution of a linear inverse problem of the parameter estimation using the Least-square method is presented in this research. For this propose a set of temperature measurements at a single sensor location inside the heat conducting body was considered. The corresponding direct problem was then solved by the application of the ...
متن کاملLEAST – SQUARES METHOD FOR ESTIMATING DIFFUSION COEFFICIENT
Determining the diffusion coefficient based on the solution of the linear inverse problem of the parameter estimation by using the Least-square method is presented. A set of temperature measurements at a single sensor location inside the heat conducting body is required. The corresponding direct problem will be solved by an application of the heat fundamental solution.
متن کاملA modified diffusion coefficient technique for the convection diffusion equation
A new modified diffusi on coefficient (MDC) technique for solv ing conve ction diffusion equation is proposed. The Galerkin finite-element discretization process is applied on the modified equation rather than the original one. For a class of one-dimensional convec-tion–diffusion equations, we derive the modi fied diffusion coefficient analytically as a function of the equation coefficients and...
متن کاملComputing Diffusion Coefficients of Intrinsic Point Defects in Crystalline Silicon
The quality of crystalline silicon highly influences the quality of semiconductor devices fabricated with it. Grown-in defects, such as octahedral voids or networks of large dislocation loops can be detrimental to the functionality of devices. Both type of defects result from the interaction of intrinsic point defects, vacancies and self-interstitials during growth and subsequent annealing of t...
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 Open Source Software
سال: 2019
ISSN: 2475-9066
DOI: 10.21105/joss.01698