Research interests
- Simulation studies of liquid-liquid phase separation in membraneless organelles
- Single molecular properties of Intrinsically disordered protein (IDP) and their bindings
- Interaction and dynamics of naturally occurring Deep Eutectic Solvents (DESs) and Ionic Liquids (ILs)
Brief summary of my projects:
Liquid-Liquid Phase Separation (LLPS) in Membraneless Organelles: Recent experimental studies have revealed that membraneless organelles are multi-component viscous liquid droplets, assembled through phase separation of proteins and RNAs. These organelles are involved in many crucial biological functions. Understanding their formation and genetic basis is challenging due to the intrinsic complexity of cellular environment and multivalent nature of interactions among biomolecules. We have studied "KE" sequences using coarse-grain lattice and off-lattice simulations to understand how the phase separation propensity depends on the charge pattern of amino acids. We find that a sequence with a "blocky" charge pattern is more prone to phase separate. The study also highlights the utility and limitations of analytical theory and charge pattern parameters commonly used in the literature to predict phase separation propensity. Further modifications of force field parameters and simulations techniques are underway to study complex biological systems.
References:
1. Suman Das, Adam Eisen, Yi-Hsuan Lin and Hue Sun Chan*, A lattice model of charge-pattern-dependent polyampholyte phase separation, J. Phys. Chem. B 2018, 122, 5418-5431.
2. Suman Das, Alan Amin, Yi-Hsuan Lin and Hue Sun Chan*, Coarse-grained residue-based models of disordered protein condensates: Utility and limitations of simple charge pattern parameters, Phys. Chem. Chem. Phys. 2018, 20(45), 28558-28574.
References:
1. Suman Das, Adam Eisen, Yi-Hsuan Lin and Hue Sun Chan*, A lattice model of charge-pattern-dependent polyampholyte phase separation, J. Phys. Chem. B 2018, 122, 5418-5431.
2. Suman Das, Alan Amin, Yi-Hsuan Lin and Hue Sun Chan*, Coarse-grained residue-based models of disordered protein condensates: Utility and limitations of simple charge pattern parameters, Phys. Chem. Chem. Phys. 2018, 20(45), 28558-28574.
Reorientational Jump Dynamics of DESs and ILs: H-bond, one of the driving forces for many chemical and biological processes dominates physico-chemical properties of DESs and ILs. In order to understand how H-bond governs dynamical properties of acetamide+electrolyte DESs, we have analysed jump reorientational motion of molten acetamide. We characterise various properties associated with the jump dynamics. Next, we analyse the jump dynamics of acetamide in presence of three electrolytes: lithium bromide, lithium nitrate and lithium perchlorate. We bisect the jump dynamics into two categories: (a) acetamide-acetamide and (b) acetamide-electrolyte. A comparison of these two showcase the effect of anion dependence on jump dynamics. Further, we study the reorientational dynamics of BMIM+PF6 IL where we observed how different dynamics for cation and anion are governed by their difference in simulated jump characteristics. We propose from all these studies that reorientational jump dynamics is a "universal property" of all H-bonded liquids.
References:
1. Suman Das, Ranjit Biswas* and Biswaroop Mukherjee*, Reorientational jump dynamics and its connections to hydrogen bond relaxation in molten acetamide: An all-atom molecular dynamics simulation study, J. Phys. Chem. B 2015, 119, 274-283.
2. Suman Das, Ranjit Biswas* and Biswaroop Mukherjee*, Orientational jumps in (acetamide + electrolyte) deep eutectics: Anion dependence, J. Phys. Chem. B 2015, 119, 11157-11168.
3. Suman Das, Biswaroop Mukherjee* and Ranjit Biswas*, Orientational dynamics in a room temperature ionic liquid: Are angular jumps predominant? J. Chem. Phys. 2018, 148, 193839.
References:
1. Suman Das, Ranjit Biswas* and Biswaroop Mukherjee*, Reorientational jump dynamics and its connections to hydrogen bond relaxation in molten acetamide: An all-atom molecular dynamics simulation study, J. Phys. Chem. B 2015, 119, 274-283.
2. Suman Das, Ranjit Biswas* and Biswaroop Mukherjee*, Orientational jumps in (acetamide + electrolyte) deep eutectics: Anion dependence, J. Phys. Chem. B 2015, 119, 11157-11168.
3. Suman Das, Biswaroop Mukherjee* and Ranjit Biswas*, Orientational dynamics in a room temperature ionic liquid: Are angular jumps predominant? J. Chem. Phys. 2018, 148, 193839.
Interactions and Dynamics of (Amide+Electrolyte) DESs: DESs have gained a lot of attention in the last decade along with ILs because of their tunable physico-chemical properties that make them attractive for numerous industrial applications. However, it is imperative to understand the molecular level interactions and dynamics that effects their properties. We use all-atom molecular dynamic simulations to study various kind of interactions through radial distribution functions, cluster size distributions and lifetime distribution of clusters. Dynamical properties have been characterised via mean squared distribution, intermediate scattering functions, van-Hove correlation functions, H-bond correlations etc. We find that "heterogeneity" in acetamide+electrolyte DES is originated from the clusters formed by lithium and various anions. These clusters are embedded in acetamide solutions. Anions because of their large differences in size and shapes interact in a distinct way leading to the anion dependent heterogeneity of the solution. Our results offer new insights into the complex interplay of interactions of these complex liquids that govern their physico-chemical properties.
References
1. Anuradha Das, Suman Das and Ranjit Biswas*, Fast fluctuations in deep eutectic melts: Multi-probe fluorescence measurements and all-atom molecular dynamics simulation study, Chem. Phys. Lett. 2013, 581, 47-51.
2. Suman Das, Biswaroop Mukherjee* and Ranjit Biswas*, Microstructures and their lifetimes in acetamide/electrolyte deep eutectics: Anion dependence, J. Chem. Sci. 2017, 129, 939-951.
3. Kallol Mukherjee, Suman Das, Ejaj Tarif, Anjan Barman and Ranjit Biswas*, Dielectric relaxation in acetamide+urea deep eutectics and neat molten urea: Origin of time scales via temperature dependent measurements and computer simulations, J. Chem. Phys. 2018, 149, 124501.
References
1. Anuradha Das, Suman Das and Ranjit Biswas*, Fast fluctuations in deep eutectic melts: Multi-probe fluorescence measurements and all-atom molecular dynamics simulation study, Chem. Phys. Lett. 2013, 581, 47-51.
2. Suman Das, Biswaroop Mukherjee* and Ranjit Biswas*, Microstructures and their lifetimes in acetamide/electrolyte deep eutectics: Anion dependence, J. Chem. Sci. 2017, 129, 939-951.
3. Kallol Mukherjee, Suman Das, Ejaj Tarif, Anjan Barman and Ranjit Biswas*, Dielectric relaxation in acetamide+urea deep eutectics and neat molten urea: Origin of time scales via temperature dependent measurements and computer simulations, J. Chem. Phys. 2018, 149, 124501.