human serum albumin (hsa) is the most abundant protein in the blood plasma. drug binding to hsa is crucial to study the absorption, distribution, metabolism, efficiency and bioavailability of drug molecules. in this study, isothermal titration calorimetry and molecular dynamics simulation of hsa and its complex with indometacin (im) were performed to investigate thermodynamics parameters and th...

A general statistical approach is described to couple the continuum with molecular dynamics in fluid simulation. Arbitrary thermodynamic field boundary conditions can be imposed on an MD system while minimally disturbing the particle dynamics of the system. The importance of incorporating a higher order single-particle distribution function in light of the Chapman–Enskog development is demonstr...

Advances in computational power have greatly facilitated the successful implementation of large-scale computer simulations of biological assemblies and complex condensed phases. Researchers have developed numerous simulation techniques, but many of these share, at their core, the so-called molecular dynamics (MD) paradigm to simulate such systems. (See the “Molecular Dynamics in a Nutshell” sid...

Density Functional Theory (DFT) which is based on quantum mechanics theory has been broadly used to compute the energy and the structure of molecules and solids. However, the DFT method is limited when running calculations for a large system and only thousands of atoms can be solved. Alternatively, Molecular Dynamics (MD) simulation can be used to investigate the properties of the atomic system...

Modeling of phenomena is increasingly being used to obtain an understanding of important physical events as well as to predict properties that can be directly tied to experimental data. For systems with relatively low densities of particles, the Direct Simulation Monte Carlo (DSMC) method is well suited for modeling gases with non-equilibrium distributions, coupled gasdynamic and reaction effec...