Influence of different cryo-protectants for cryo-preservation of protein

Pair hydrophobic interaction between two nonpolar solutes in water is known to be decreased by reduction of temperature. This is often connected with the cold denaturation of a protein due to the destabilization of the protein’s hydrophobic core at low temperature. Glycerol is known to be a very efficient protein stabilizer which can prevents the cold denaturation. Here, we ask whether glycerol can stabilize a hydrophobic core by reducing the cooling effect of the pair hydrophobic interaction in water. Using a molecular simulation study we have found that glycerol increases pair hydrophobicity in water and at the highest glycerol concentration, studied here, the hydrophobicity does not decrease appreciably with decreasing temperature. Therefore, the above results indirectly put forward a mechanism of protein’s stabilization by glycerol at low temperature. 

 

Presentation1.jpg
images.jpg

Jump translational dynamics of supercooled water

 

Some experiments have witnessed gradual decoupling of viscosity from the translational self-diffusion of supercooled water with decreasing temperature. This indicates the breakdown of the Stokes-Einstein (SE) equation in supercooled water. While some theoretical and computer simulation studies indicated the jump translation of the molecules as a probable origin of the above decoupling, direct quantitative evidence is still lacking. Through a molecular dynamics (MD) simulation study, along with careful consideration of translational jump motion, we have found the most definite proof of increasing relevance of translational jump diffusion in the above decoupling phenomena. By separating the jump-only diffusion contribution from the overall diffusion of the water, we obtain the residual diffusion coefficient, which remains strongly coupled to the viscosity of the medium at the supercooled regime. These new findings can help to elucidate many experimental studies featuring molecular transport properties, where strong diffusion-viscosity decoupling is present.

 

Jump translational dynamics of supercooled water

 

Some experiments have witnessed gradual decoupling of viscosity from the translational self-diffusion of supercooled water with decreasing temperature. This indicates the breakdown of the Stokes-Einstein (SE) equation in supercooled water. While some theoretical and computer simulation studies indicated the jump translation of the molecules as a probable origin of the above decoupling, direct quantitative evidence is still lacking. Through a molecular dynamics (MD) simulation study, along with careful consideration of translational jump motion, we have found the most definite proof of increasing relevance of translational jump diffusion in the above decoupling phenomena. By separating the jump-only diffusion contribution from the overall diffusion of the water, we obtain the residual diffusion coefficient, which remains strongly coupled to the viscosity of the medium at the supercooled regime. These new findings can help to elucidate many experimental studies featuring molecular transport properties, where strong diffusion-viscosity decoupling is present.

 

1-s2.0-S0009261417307613-fx1.jpg

Jump translational dynamics of supercooled water

 

Some experiments have witnessed gradual decoupling of viscosity from the translational self-diffusion of supercooled water with decreasing temperature. This indicates the breakdown of the Stokes-Einstein (SE) equation in supercooled water. While some theoretical and computer simulation studies indicated the jump translation of the molecules as a probable origin of the above decoupling, direct quantitative evidence is still lacking. Through a molecular dynamics (MD) simulation study, along with careful consideration of translational jump motion, we have found the most definite proof of increasing relevance of translational jump diffusion in the above decoupling phenomena. By separating the jump-only diffusion contribution from the overall diffusion of the water, we obtain the residual diffusion coefficient, which remains strongly coupled to the viscosity of the medium at the supercooled regime. These new findings can help to elucidate many experimental studies featuring molecular transport properties, where strong diffusion-viscosity decoupling is present.

 

Studies on biophysical systems

We are studying the structure and dynamics of different biomolecules. Our primary focus is on molecular level understanding of various important physical behavior of the different class of biomolecular systems (e.g. lipid bilayer, proteins, etc.). Currently, we are working on the permeation of various entities (e.g water, drug molecules, nanomaterials etc.) across the lipid membrane. We use classical molecular dynamics simulation technique for  the above studies. 

 

untitled-1.gif

Discotic liquid crystal on the water-vapour interface

We simulate discotic liquid crystal molecules on the water-vapour interface and study various physical properties. These works are done in a close collaboration with experimental work. We predict properties, such as e surface pressure (π) - area per molecule isotherms, orientation of molecules, and their strength of hydrogen bonding. Understanding the intermolecular interactions governing self-assembly is important to engineer molecular packing that controls the charge transport in discotic liquid crystal-based organic electronics

vmdscene-sn1.png

Molecular Dynamics Simulation Group We try to think like a molecule