Soft Matter theory and Simulation

Main areas of research

Our main research is centered around multiscale simulation method development and application to the materials which includes,

• Properties of liquids of simple and complex molecules

• Polymers, block copolymers, polymer networks in bulk, solution on surface and in confinement

• Biological materials like proteins and lipid bilayers

• Clusters, nanotubes, nanowires of metals, semiconductor materials

Our goal is to predict properties of these materials from simulations in different lengths (sub nanometer to micro) and time scale (pico to milli sceond) with a quantatively and in some cases qualitative accuracy to elucidate the macroscopic properties from molecular and mesoscopic scale.

• Molecular structure, mesoscopic morphology

• Liquid structure, solvation cell dynamics, hydrogen bond network

• Thermodynamical properties

• Interfacial tension, adhesion, surface coverage

• Conformation of proteins oligomers

• Structural and electronic properties of materials

We develop new methods for simulations and analysis according to the need of the systems.

• Multiscale method development, systematic development and parameter transfer methods from quantum chemical calculations to classical molecular dynamics simulations to coarse gained and mesoscale dissipative particle dynamics simulations

• Force field development and optimization for new systems for molecular dynamics simulations

 

Composites

  • Polycarbonate and carbon nanotube composites
  • Polymer composites are known for their improved mechanical and structural properties. Wide and diverse application of polymer composites makes it a vibrant field of study nowadays. It has become essential to investigate the change in dynamical and structural properties of polymer mixed with fillers like carbon nanotubes, nanoparticles, nanorods etc. and look into the interactions between various types of atoms at the interface in details so as to understand the basic factors which drives the change in properties. Molecular dynamics is a powerful tool to study such systems and quite useful to dig into for understanding the properties and behaviour of such composite systems.
  • Polycarbonate is a widely used polymer and while embedded with fillers it exhibits change in mechanical, thermal, electrical properties. For our study, we have taken the system of monomer and trimer of polycarbonate and single wall carbon nanotube as filler. Different percentages of mixers have been taken for the study of structural and dynamical properties. Moreover we are investigating the energetics of aggregation of nanotubes in the polymer matrix.

References

  • Souvik Chakraborty, S.Roy, Structural, Dynamical, and Thermodynamical Properties of Carbon Nanotube Polycarbonate, J. Phys. Chem B, 116 (2012), 3083–3091


Bio-Membrane

DPPC-Water Interface - water insertion mechanism

  • Lipids are amphiphilic molecules with hydrophilic head groups and hydrophobic tails. Lipids, self assembled as bilayers form the basic structure of cell membranes. DPPC is a phospholipid. Phospholipids are the most abundant class of lipids in the biological system. We study the interactions between DPPC bilayer and water using classical molecular dynamics simulations. We have proposed that water molecules get inserted deep into the DPPC bilayer- water interface, which is aided by NMe3 group present at the head group of DPPC. We also study the structuring and hydrogen bonding dynamics of the interfacial water molecules.

Refereces

  • P.R.Pandey, S.Roy, Head group mediated water insertion in DPPC bilayer, J. Phys. Chem. B, 115(2011), 3155–3163




Peptide and Protein

Early stage unwinding mechanism of homo and co-poly peptides

  • An α-helix is the most important secondary structure among the secondary structures found in proteins and peptides. Also understanding the unwinding mechanism of homopolymeric peptides can help in gaining useful insight in designing stable helical peptides and a priori knowledge of unwinding position in an α-helix made up of various amino acids. Thus, we study the unwinding mechanisms of α-helical homopolymeric peptides under ambient conditions using classical molecular dynamics simulations. In addition to this we are trying to gain insight into the unwinding mechanism of α-helical block copolymers made by various combination of amino acids.

Refereces

  • P.R.Pandey, S.Roy, Distinctions in Early Stage Unwinding Mechanisms of Zwitterionic, Capped and Neutral Forms of Different α-Helical Homopolymeric Peptides, J. Phys. Chem. B, 116 (2012), 4731-4740
  • P.R.Pandey, S.Roy, Early stages of unwinding of zwitterionic alpha-helical homopolymeric peptides, Chem. Phys. Lett., 514 (2011) 330–335