Molecular dynamics simulations have been performed to study the transport properties of the dilute solution of cysteine in water at different temperatures. Structural analysis of the system has been carried out using radial distribution functions between different atoms of the solvent and solute. The self-diffusion coefficients of the solute and solvent are estimated from the slope of the mean square displacement vs the time plot using Einstein’s equation and their binary diffusion coefficients from Darken’s relation. The temperature dependency of diffusion is demonstrated via Arrhenius plots. We have further extended our work to study the effects of the system size on diffusion and to calculate the viscosity coefficients of both the solvent and solution. The calculated values are in close agreement with the previously reported results available in literature.

SARS-CoV-2 virus is the serious health concern throughout the world. A comprehensive investigation of binding of SARS-CoV-2 active site with host receptor protein hACE2 is important in designing effective drugs. In the present work, the major amino acid binding partners between the virus CTD and host receptor have been studied and are compared with SARS-CoV RBD binding with hACE2. Our investigation show that some unique hydrogen bond pairs which were not reported in previous work. Along with hydrogen bonding, salt-bridges, hydrophobic interactions and contributions of electrostatic and van der Waals contacts play significant role in binding mechanism. The binding affinity of SARS-CoV-2 CTD/hACE2 is greater than SARS-CoV RBD/hACE2. This outcome is also verified from the free energy estimation by using umbrella sampling.

Diffusion, transport of mass in response to concentration and thermal energy gradient, is an important transport property, vital in material science and life science. In the present work, we have studied about the diffusion of zwitterion glycine, zwitterion diglycine and zwitterion triglycine in SPC/E model of water using classical molecular dynamics. Self and binary diffusion coefficients of aqueous solution of these molecules have been estimated using Einstein’s method. Our results agree with experimental data reported in literatures. Temperature dependency of diffusion of glycine in water has been explored using estimated values of self and binary diffusion coefficients at four different temperature. Effects of peptide bond formation in diffusion has been studied using peptide chain composed of up to three monomers of glycine. The system-size dependence of diffusion coefficient has been studied and the shear viscosity of solvent and system has been calculated. Also, the diffusion coefficient of zwitterion glycine in other water model TIP4P/2005 has been estimated. The structure of the system has been analyzed using radial distribution function of different atoms.

The study of structural conformation of Gamma-aminobutyric acid (GABA) exhibits its biological and chemical activities. The GABA molecule is responsible in neurotransmission from one neuron to another neuron and activates the ion channels to pass the chlorine and sodium ions in nerve cells. Its conformation in solid state and gas state are extremely different and it also shows five different conformations in aqueous solution. The study of its structure in such environment can reveal its activity in cellular environment. We have performed the classical molecular dynamics study of this system of GABA in aqueous medium to deal its structure. Radial distribution function (RDF) has been used to study the structural properties of the system. BIBECHANA 18 (2021) 67-74

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