Our group's research interest focuses on studying the structure and dynamics in complex environments: from single particles to giant polymers. We apply tools of non-equilibrium statistical physics to develop theoretical and computational models to study various systems in the field of Soft Matter and Biophysics. Especially we are interested in the effect of macromolecular crowding, ergodicity breaking, and self-activity on the diffusion processes of macromolecules. Shapes of polymer networks, structure and dynamics of polymers are also studied. We are also interested in the effect of epigenetics on chromatin structure and dynamics.
RESEARCH EXPERIENCE
2020-till date
Assistant Professor
NIT-Warangal, TS
2018-2019
Assistant Professor
SRM University, Chennai, TN
2016-2018
Post Doctoral Scientist
CNRS, University of Grenoble, France
2014-2016
Post Doctoral Scientist
Ecole Polytechnique, University of Paris Saclay, France
2013-2014
Post Doctoral Scientist
University of Potsdam, Germany
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2007-2013
Ph.D. (Physics)
IIT Bombay, Mumbai, India
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EDUCATION
2005-2007
M.Sc. (Physics)
IIT Bombay, Mumbai, India
2002-2005
B.Sc. (Physics(H), Mathematics, Chemistry)
Calcutta University, Ram Krishna Mission Vidyamandira Belur Math
RESEARCH HIGHLIGHT
Chromosome Conformation Capture
Predicted vs experimental HiC contact map of Drosophila 3R chromosome
Chromatin as a
block copolymer
Our work is featured on the front cover of Soft Matter Journal
Diffusion of tracer particle at different crowding environments
Chromatin folding via active loop extrusion
Schematic of the 3D tracer–obstacle system, here the tracer–obstacle binding strength was increased from left to right.
SELECTED PUBLICATIONS
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Dynamics of interior loop formation in the presence of confinement
Jaeoh Shin, Surya K. Ghosh, In preparation, (2023)
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Switching polymer translocation by the amalgamation of entropy and interaction
Vrinda Garg, Rejoy Mathew, Riyan Ibrahim, Kulveer Singh, Surya K. Ghosh, Submitted, (2023).
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Choline based deep eutectic solvent for denitrogenation of diesel oil: a molecular dynamics study
Kishant Kumar, Anand Bharati, Ajoy Kumar, Surya K. Ghosh, Amit Kumar, Accepted in Journal of Molecular Liquids, (2022).
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Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern
Pavan K Madasu, Arpita Maity, Surya K. Ghosh, Thyageshwar Chandran Journal of Biomolecular Structure and Dynamics, 5, 4, (2022)
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Amine as a bottom-line functionality on DDS surface for efficient endosomal escape and enhanced subcellular targets
S. M. Roy, Sourav Barman, Surya K. Ghosh, Subrata Pore, Arnab Basu, R. Mukherjee, A. R. Maity, Journal of Drug Delivery Science and Technology,
71, 103303, (2022)
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Kinetics of nanomedicine in tumor spheroid as an in-vitro model system for efficient tumor-targeted drug delivery with insights from mathematical modeling
S. M. Roy, Vrinda Garg, Sourav Barman, Amit Ranjan Maity, Surya K. Ghosh, Frontiers in Bioengineering and Biotechnology, 9, 2296, (2021).
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Possible negative correlation between electrical thermal conductivity in p-doped WSe2 single crystal
N Kumari, M Kalyan, Surya K. Ghosh, Amit R. Maity, R Mukherjee Materials Research Express 8 (4), 045902, (2021)
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Genome organization via loop extrusion, insights from polymer physics models
Surya K. Ghosh, and Daniel Jost Briefings in Functional Genomics (Oxford), 11, 2041-2657, (2021)
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Polymer physics approaches to loop extrusion mechanism in chromatin
Surya K. Ghosh and Daniel Jost, Briefings in Functional Genomics, Oxford, (2020)
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How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes
Surya K. Ghosh* and Daniel Jost, PLoS Comput Biol, 14(5), e1006159 (2018)
* Corresponding Author.
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Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments
Surya K. Ghosh, A. G. Cherstvy, Denis Grebenkov, R. Metzler, New J. Phys., 18, 013027 (2016)
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Interactions of rod-like particles on responsive elastic sheets
Surya K. Ghosh, Andrey Cherstvy, Eugene P. Petrov, Ralf Metzler, Soft Matter, 12, 7908 (2016)
– Cover: It has been featured on the front cover page of the Soft Matter journal.
– Highlight: Selected in the August 7th, 2016 online issue of Assembly Papers.
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Non-universal tracer diffusion in crowded media of non-inert obstacles
Surya K. Ghosh, Andrey G. Cherstvy, Ralf Metzler, Phys. Chem. Chem. Phys., 17, 1847 (2015)
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Deformation propagation in responsive polymer network films
Surya K. Ghosh, Andrey G. Cherstvy, Ralf Metzler, J. Chem. Phys., 141, 074903 (2014)
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Stretching force-dependent transition in single-strand DNA
Kulveer Singh, Surya K. Ghosh, Sanjay Kumar, Anirban Sain, Europhys. Lett., 100, 68004 (2012)
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From chemosensing in microorganisms to practical biosensors
Surya K. Ghosh, Tapanendu Kundu, Anirban Sain, Phys. Rev. E., 86, 051910 (2012)
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Effect of intrinsic curvature on semiflexible polymers
Surya K. Ghosh, Kulveer Singh, Anirban Sain, Phys. Rev. E., 80, 051904 (2009)
– Highlight: Selected for the Nov 15th, 2009 issue of Virtual Journal of Biological Physics.
RESEARCH
Anomalous Diffusion in Complex Environment
In biological systems, most of the time ensemble average is not available and we need to rely only on the time average quantities. A topic of intense current investigation pursues the question of how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing entities. We study the diffusion of different system ranging from tracer particles to giant polymers in the complex cellular environment. In particular we are interested the processes which shows anomalous behavior.
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To start with, we designed a continuum space between a lattice of excluded volume, immobile non-inert obstacles to mimic the complex celluar environments. In particular, we analyze how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. Motivated by recent experiments we also studied the motion of finite sized tracer particles in a heterogeneously crowded environment made up of quenched distributions of monodisperse crowders of varying sizes. For given spatial distributions of monodisperse crowders we demonstrate how anomalous diffusion with strongly non-Gaussian features arises in model systems. We investigate both biologically relevant situations of particles released either at the surface of an inner domain or at the outer boundary, exhibiting distinctly different features of the observed anomalous diffusion for heterogeneous distributions of crowders.
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We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Inter alia, our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.
Chromosome, Chromatin and Epigenetics
The chromosome architecture inside cell nuclei plays important roles in regulating cell functions. Many experimental and modeling efforts are dedicated to deciphering the mechanisms controlling such organization. There are proliferation of experimental studies which report the hierarchical structure of chromosomes but how exactly they physically organize in 3D is not fully understood. In modeling, the main challenges are
to develop adequate models and simulation methods to investigate correctly these highly dense long polymer chains. Taken into consideration the fundamental physical characteristics of chromosomes, we developed robust and numerically efficient polymer models that enabled us to explore long chromosomes over long time periods with good statistics. We applied this framework to investigate the dynamical folding of chromosome in drosophila. Accounting for the local biochemical information, we were able to reproduce the experimentally-measured contact frequencies between any pairs of genomic loci quantitatively and to track the hierarchical chromosome structure throughout the cell cycle. Our results further support the picture of a very dynamic chromosome organization driven by weak short-range interactions.
Statistical Properties of polymers
Our work on polymers concerned conformational statistics of intrinsically curved polymers (ICP), which are relevant in the biological context. Our focus was to identify unique signatures of intrinsic curvature which could distinguish it from an ordinary semiflexible polymer. We calculat the spatial correlation function of the local polymer orientation, exactly and the end-to-end distribution function, using transfer matrix method. A reliable distinguishing feature turned out to be the loop formation probability. We studied shape transitions of ICP under compressive force, analytically, in the weakly bending limit. We also developed a new model to explain the double plateau behavior in the force-extension curve of synthetic single stranded DNA like polyA. This model incorporated two transitions: a helix-coil transition and an over-stretching transition.
Hydrogel as a responsive thin film of polymer network
What are the physical laws of the mutual interactions of objects bound to cell membranes, such as various membrane proteins or elongated virus particles? We study the elastic deformations in a cross-linked polymer network film triggered by the binding of sub micron particles with a sticky surface, mimicking the interactions of viral pathogens with thin films of stimulus-responsive polymeric materials such as hydrogels. To rationalize this, investigated the mutual interactions of different types of particles such as spherical, elongated, etc, adsorbed on the surface of responsive elastic two-dimensional sheets. Specifically, we quantify sheet deformations as a response to adhesion of such filamentous particles. These attractive orientation-dependent substrate-mediated interactions between the rod-like particles on responsive sheets can drive their aggregation and self-assembly. The results of this computational study provide new insight into collective phenomena in soft polymer network films and may, in particular, be applied to applications for visual detection of pathogens such as viruses via a macroscopic response of thin films of cross-linked hydrogels.
Dr. Surya K. Ghosh
Assistant Professor
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Email:
skghosh [at] nitw.ac.in
physicsurya [at] gmail.com
Phone:
Office: +33 4 5652 0066
Mobile: +33 7 5417 5277
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Address:
Office: Room 303
National Institute of Technology,
Warangal - 506004,
TS, INDIA
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Web:
https://wsdc.nitw.ac.in/facultynew/facultyprofile/id/17031
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