Madhurima Jana

Associate Professor

Chemistry

 (+91) 661 246 2663 , 3663

 janam[at]nitrkl.ac.in

 Biosketch

40

Publications       

4

Sponsored Projects

0

Consultancy Projects

9

Doctoral Students

2

Continuing Education

6

PG Dissertation

 Personal Information

Prof. Madhurima Jana

Associate Professor

Chemistry

Joined in Nov 2011

 Room Number: MC-318

 Department of Chemistry, National Institute of Technology Rourkela, Sundargarh, Odisha, India - 769008

 Education Qualification

  1. Ph.D.
    Computational Biophysics
    IIT Kharagpur
  2. M.Sc
    Chemistry (Spl: Physical)
    Vidyasagar University

 Experience

Teaching Experience
  • Physical and Computational Chemistry,  NIT Rourkela,  17 Nov 2011 - present
Post Doctoral Research Experience
  • Development of carbohydrate force field,  University of Maryland, Baltimore,  03 Dec 2013 - 05 Dec 2014
  • Proton transfer reaction in formic acid dimer,  Pontificia Universtded Catolica de Chile, Santiago,  01 May 2012 - 30 Jun 2012
Laboratory Development
  • Molecular Simulation Laboratory,  NIT Rourkela,  Computational laboratory equipped with servers, workstations and high performance computing cluster to carry on atomistic simulations of materials and biological macromolecules.

 Expertise Information

Research Group
Physical Chemistry
Areas of Interest
Computational biophysical chemistry - Effects of additives/cosolvent on protein structure and dynamics , Protein folding-unfolding , Structural aspects of Glycans and their interactions with Proteins, Membrane-sugar interactions , Carbohydrate Force Field development , Computer-aided drug design, Host-guest interaction in confined media , Reaction mechanism , Hydration properties of biomolecules. Visit us @ https://sites.google.com/view/madhurimajana

 Projects

Analyzing saccharide effects on lipid bilayers under alcohol induced stress: A computer simulation approach.

 Science & Engineering Research Board(SERB)

 Principal Investigator

 36 months

 Running

Sponsored

Microscopic investigation of the stability of proteins in Amino Acid solutions

 SERB

 Principal Investigator

 36 months

 Completed

Sponsored

In silico studies of structural diversity of glycosaminoglycans and their interactions with protein

 BRNS

 Principal Investigator

 36 months

 Completed

Sponsored

Effects of Alcohols on Proteins: A Molecular Dynamics Simulation Approach

 SERB

 Principal Investigator

 36 months

 Completed

Sponsored

 Continuing Education

Biomolecular Dynamics: Experimental and Theoretical Perspectives (BDETP-2017)

 Chemistry

 Coordinator

 18 Dec 2017 - 20 Dec 2017

Conference

Molecular Modeling of Materials and Biological Macromolecules

 Chemistry

 Coordinator

 22 Sep 2020 - 26 Sep 2020

Workshop

 Publications

11

Google Scholar h-index

13

Google Scholar i10-index

8

Scopus h-index

Total Publications: 40
S. Sarmah, S. Dhurua, V., S. Lyndem, M. Jana, and A. Roy, "Combined spectroscopic and computational approaches for the recognition of bioactive flavonoid 6-hydroxyflavone by human serum albumin: Effects of non-enzymatic glycation in the binding.", Journal of Molecular Liquids, vol.346, pp.118288, Elsevier 2022, 10.1016/j.molliq.2021.118288 Article
S. Santra and M. Jana, "Conformational Flexibilities and Solvation Properties of Insulin in Aromatic Amino Acid Solutions: A Molecular Dynamics Study Using CHARMM Drude Polarizable Model.", J. Comput. Biophys. Chem, vol.21, pp.391-404, World Scientific 2022, 10.1142/S2737416521420011 Article
S. Santra and M. Jana, "Influence of Aqueous Arginine Solution on Regulating Conformational Stability and Hydration Properties of the Secondary Structural Segments of a Protein at Elevated Temperatures: A Molecular Dynamics Study", J. Phys. Chem. B, vol.126, pp.1462-1476, American Chemical Society 2022, 10.1021/acs.jpcb.1c09583 Article
R. Parida, S. Pahari, and M. Jana, "Potency of New Boron-Based Heterocyclic Anion Receptor Additives to Regulate the Solvation and Transport Properties of Li-ions in Ethylene Carbonate Electrolyte of Li-Ion Battery: An Atomistic Molecular Dynamics Study", J. Power Sources, vol.521, pp.230962, Elsevier 2022, 10.1016/j.jpowsour.2021.230962 Article
S. Santra and M. Jana, "Predicting the evolution of number of native contacts of a small protein by using deep learning approach.", Comput. Biol. Chem., vol.97, pp.107625, Elsevier 2022, 10.1016/j.compbiolchem.2022.107625 Article

Show All Publications(+)

S. Lyndem, R. Gazi, M. Jana, V. K. Belwal, and A. S. Roy, "Molecular recognition of two bioactive coumarin derivatives 7-hydroxycoumarin and 4-methyl-7-hydroxycoumarin by hen egg white lysozyme: Exploring the binding mechanism, thermodynamic parameters and structural changes using multispectroscopic and computational approaches", Journal of Biomolecular Structure and Dynamics, Taylor & Francis, November 2021, https://doi.org/10.1080/07391102.2021.1995499 Article
L. Satish, S. Santra, M. Tsurkan, C. Werner, M. Jana, and H. Sahoo, "Conformational changes of GDNF-derived peptide induced by heparin, heparan sulfate, and sulfated hyaluronic acid – Analysis by circular dichroism spectroscopy and molecular dynamics simulation", International Journal of Biological Macromolecules, vol.182, pp.2144-2150, Elsevier, July 2021, 10.1016/j.ijbiomac.2021.05.194 Article
S. Santra, S. Dhurua, and M. Jana, "Analyzing the driving forces of insulin stability in the basic amino acid solutions: A perspective from hydration dynamics.", J. Chem. Phys, vol.154, pp.084901, AIP 2021, 10.1063/5.0038305 Article
L. Satish, S. Santra, M. Tsurkan, C. Werner, M. Jana, and H. Sahoo, "Conformational changes of GDNF-derived peptide induced by heparin, heparan sulfate, and sulfated hyaluronic acid – Analysis by circular dichroism spectroscopy and molecular dynamics simulation", International Journal of Biological Macromolecules 2021, 10.1016/j.ijbiomac.2021.05.194 Article
S. Dhurua, R. Parida, and M. Jana, "In-silico investigation of the conformational properties of the disaccharide units of chondroitin, dermatan and heparan sulphate in aqueous medium", Journal of the Indian Chemical Society, vol.98, no.5, pp.100064, Elsevier 2021, 10.1016/j.jics.2021.100064 Article
A. Das, S. Dey, S. Chakraborty, A. Barman, R., R. Gazi, M. Jana, and M., "Metal-Free One-Pot Synthesis of 2-(2-Hydrazinyl) Thiazole Derivatives Using Graphene Oxide in a Green Solvent and Molecular Docking Studies.", ChemistrySelect, vol.6, pp.9552-9558, Willey 2021, 10.1002/slct.202102642 Article
S. Sarmah, S. Pahari, S. Das, V., M. Jana, and A. Roy, "Non-enzymatic glycation of human serum albumin modulates its binding efficacy towards bioactive flavonoid chrysin: A detailed study using multi-spectroscopic and computational methods.", Journal of Biomolecular Structure and Dynamics, vol.32, no.2, pp.476-492, Taylor & Francis 2021, 10.1080/07391102.2019.1711196 Article
S. Santra, S. Giri, and M. Jana, "Unraveling the Origin of Interactions of Hydroxychloroquine with the Receptor-Binding Domain of SARS-CoV-2 in Aqueous Medium.", Chem. Phys. Lett., vol.764, pp.138280, Elsevier 2021, 10.1016/j.cplett.2020.138280 Article
G. N. Reddy, R. Parida, A. Munoz, M. Jana, and S. Giri, "Doped deltahedral organo-Zintl superalkali cations", Chem. Phys. Lett., vol.759, pp.137952, Elsevier 2020, https://doi.org/10.1016/j.cplett.2020.137952 Article
S. Sarmah,, S. Pahari, V. K. Belwal, M. Jana, and A. Roy, "Elucidation of molecular interaction of bioactive flavonoid luteolin with human serum albumin and its glycated analogue using multi-spectroscopic and computational studies", Journal of Molecular Liquids, vol.318, pp.114147, Elsevier 2020, https://doi.org/10.1016/j.molliq.2020.114147 Article
M. Jana and S. Santra, "Insights into the sensitivity of arginine concentration to preserve the folded form of insulin monomer under thermal stress", Journal of Chemical Information and Modeling, vol.60, no.6, pp.3105–3119, ACS Publications 2020, 10.1021/acs.jcim.0c00006 Article
S. Santra and M. Jana, "Insights into the Sensitivity of Arginine Concentration to Preserve the Folded Form of Insulin Monomer Under Thermal Stress.", J. Chem. Inf. Model., vol.60, no.6, pp.3105–3119, ACS 2020, 10.1021/acs.jcim.0c00006 Article
G. N. Reddy, R. Parida, P. Jena, M. Jana, and S. Giri, "Superhalogens as building blocks of super lewis acids", ChemPhysChem, vol.20, no.12, pp.1607-1612, Wiley, June 2019, 10.1002/cphc.201900267 Article
S. Das, S. Pahari, S. Sarmah, M. A. Rohman, D. Paul, M. Jana, and A. S. Roy, "Lysozyme–luteolin binding: molecular insights into the complexation process and the inhibitory effects of luteolin towards protein modification", Physical Chemistry Chemical Physics, vol.21, no.23, pp.12649-12666, Royal Society of Chemistry, May 2019, 10.1039/C9CP01128E Article
R. Parida, G. N. Reddy, A. Chakraborty, S. Giri, and M. Jana, "A new class of superhalogen based anion receptor in Li-ion battery electrolytes", Journal of Chemical Information and Modeling, vol.59, no.5, pp.2159-2164, American Chemical Society, February 2019, 10.1021/acs.jcim.9b00035 Article
A. Chakraborty, G. N. Reddy, M. Jana, and S. Giri, "[8] Cyclo-1, 4-naphthylene: a possible new member in hole transport family", Chemical Physics Letters, vol.715, pp.153-159, Elsevier, January 2019, 10.1016/j.cplett.2018.11.008 Article
D. Paul, S. Santra, and M. Jana, "Interactions between CD44 and HA16: an investigation on multiple binding modes of the complex by using molecular dynamics simulation studies", Journal of Indian Chemical Society, vol.96, pp.851-861, Indian Chemical Society 2019 Article
S. Das, S. Santra, M. A. Rohman, M. Ray, M. Jana, and A. Roy, "An insight into the binding of 6-hydroxyflavone with hen egg white lysozyme: a combined approach of multi-spectroscopic and computational studies", Journal of Biomolecular Structure and Dynamics, Taylor & Francis, December 2018, 10.1080/07391102.2018.1535451 Article
D. Mohanta and M. Jana, "Effects of ethanol on the secondary structure specific hydration properties of chymotrypsin Inhibitor 2 in its folded and unfolded forms", Molecular Simulation, Taylor & Francis, July 2018, 10.1080/08927022.2018.1496246 Article
D. Mohanta and M. Jana, "Can 2,2,2-trifluoroethanol be an efficient protein denaturant than methanol and ethanol under thermal stress?", Physical Chemistry Chemical Physics, vol.20, no.15, pp.9886-9896, Royal Society of Chemistry, March 2018, 10.1039/C8CP01222A Article
S. Biswas, S. Santra, S. Yesylevskyy, J. Maiti, M. Jana, and R. Das, "Picosecond solvation dynamics in nanoconfinement : Role of water and host-guest complexation", The Journal of Physical Chemistry B, vol.122, no.14, pp.3996-4005, American Chemical Society, March 2018, 10.1021/acs.jpcb.7b10376 Article
S. Santra, T. Kundu, and M. Jana, "Microscopic investigation on empirical force-field model dependent structure and dynamical properties of amino acids in aqueous medium", Journal of Indian Chemical Society, vol.95, pp.1617-1630, Scientific Publisher 2018 Article
S. Giri, R. Inostroza, and M. Jana, "The beckmann rearrangement in the framework of reaction electronic flux", Theoretical Chemistry Accounts, vol.136, no.1, pp.9, Springer, January 2017, 10.1007/s00214-016-2025-3 Article
D. Mohanta, S. Santra, and M. Jana, "Conformational disorder and solvation properties of the key-residues of a protein in water-ethanol mixed solutions", Physical Chemistry Chemical Physics, vol.19, no.48, pp.32636-32646, Royal Society of Chemistry 2017, 10.1039/c7cp06022j Article
S. Giri, R. Parida, M. Jana, S. Gutiérrez, and A. Toro, "Insights into the mechanism of ground and excited state double proton transfer reaction in formic acid dimer", The Journal of Physical Chemistry, vol.121, no.49, pp.9531–9543, American Chemical Society 2017, 10.1021/acs.jpca.7b09819 Article
D. Mohanta, S. Santra, G. N. Reddy, S. Giri, and M. Jana, "Residue specific interaction of an unfolded protein with solvents in mixed water-ethanol solutions: a combined molecular dynamics and ONIOM study", Journal of Physical Chemistry A, vol.121, no.32, pp.6172–6186, ACS 2017, 10.1021/acs.jpca.7b05955 Article
D. Mohanta and M. Jana, "Effect of ethanol concentrations on temperature driven structural changes of chymotrypsin inhibitor 2", Journal of Chemical Physics, vol.144, no.16, pp.165101, American Institute of Physics, April 2016, 10.1063/1.4947239 Article
M. Yang, T. A. D’ortoli, E. Sawen, M. Jana, G. Widmalm, and A., "Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations", Physical Chemistry Chemical Physics, vol.18, no.28, pp.18776-18794, Royal Society of Chemistry 2016, 10.1039/c6cp02970a Article
M. Jana and M. D. A, "CHARMM drude polarizable force field for aldopentofuranoses and methyl-aldopentofuranosides", Journal of Physical Chemistry B, vol.119, no.25, pp.7846-7859, American Chemical Society, May 2015, 10.1021/acs.jpcb.5b01767 Article
S. K. Sinha, M. Jana, K. Chakraborty, and S. Bandyopadhyay, "In silico studies of the properties of water hydrating a small protein", The Journal of chemical physics, vol.141, no.22, pp.22d502, American Institute of Physics, August 2014, 10.1063/1.4895533 Article
M. Jana and S. Bandyopadhyay, "Molecular dynamics study of ß-cyclodextrin-phenylalanine (1:1) inclusion complex in aqueous medium", Journal of Physical Chemistry B, vol.117, no.31, pp.9280-9287, ACS, August 2013, 10.1021/jp404348u Article
M. Jana and S. Bandyopadhyay, "Low-Frequency Vibrational Spectrum of Water around Cyclodextrin and Its Methyl-Substituted Derivatives", Langmuir, vol.26, no.17, pp.14097-14102, ACS 2012, 10.1021/la101927g Article
M. Jana and S. Bandyopadhyay, "Hydration Properties of a-, ß-, and ?-Cyclodextrins from Molecular Dynamics Simulations", The Journal of Physical Chemistry B, vol.115, no.19, pp.6347-6357, ACS 2011, 10.1021/jp2013946 Article
M. Jana and S. Bandyopadhyay, "Kinetics of hydrogen bonds in aqueous solutions of cyclodextrin and its methyl-substituted forms", J. Chem. Phys, vol.134, pp.025103, AIP 2011, 10.1063/1.3530781 Article
M. Jana and S. Bandyopadhyay, "Microscopic investigation of the hydration properties of cyclodextrin and its substituted forms", Langmuir, vol.25, no.22, pp.13084-13091., ACS 2009, 10.1021/la902003y Article

 Courses Taught

  • CY101 : Chemistry {Theory}
  • CY1101 : Chemistry {Theory}
  • CY2301 : Physical Chemistry: Equilibrium and Changes {Theory}
  • CY231 : Basic Physical Chemistry I {Theory}
  • CY231 : Basic Physical Chemistry-I {Theory}
  • CY232 : Chemical Kinetics {Theory}
  • CY331 : Basic Physical Chemistry – II {Theory}
  • CY5301 : Statistical Thermodynamics {Theory}
  • CY5302 : Computational Chemistry {Theory}
  • CY533 : Statistical Thermodynamics {Theory}
  • CY534 : Computational Chemistry {Theory}
  • CY535 : Electrochemistry {Theory}
  • CY1170 : Chemistry Laboratory {Practical}
  • CY170 : Chemistry Laboratory {Practical}
  • CY4704 : Mathematical and Computational Methods in Chemistry {Practical}
  • CY571 : Computational Chemistry Laboratory – I {Practical}
  • CY572 : Computational Chemistry Laboratory – II {Practical}

 Research Scholars

Ph.D. Students [9]
Molecular Dynamics Studies Of The Effects Of Alcohols On Chymotrypsin Inhibitor 2

 Dayanidhi Mohanta

Enrolled: Jan 2013

 Graduated : May 2018

 Supervisor

In Silico Studies Of Functionalized Aromatic Heterocyclic And Zintl Ion Based Super-Atom/Alkali/Halogen

 G Naaresh Reddy

Enrolled: Jan 2016

 Graduated : Aug 2020

 Supervisor

Microscopic Investigation Of Conformational Stability Of Proteins In Amino Acid Solutions And The Properties Of Solvent Around It

 Santanu Santra

Enrolled: Jul 2016

 Graduated : May 2022

 Supervisor

Combined Density Functional Theory And Molecular Dynamics Study On The Design And Application Of Super-Alkali/Halogen And Analysis Of Reaction Mechanism

 Rakesh Parida

Enrolled: Jan 2017

 Graduated : Apr 2022

 Supervisor

Computational Chemistry

 Shakuntala Dhurua

Enrolled: Jan 2019

 Continuing

 Supervisor

Computational Chemistry

 Rabiul Gazi

Enrolled: Jan 2020

 Continuing

 Supervisor

Computational Chemistry

 Piyusaranjan Giri

Enrolled: Aug 2021

 Continuing

 Supervisor

Computational Chemistry

 Sankar Maity

Enrolled: Apr 2022

 Continuing

 Supervisor

Computational Chemistry

 Susanta Kumar Sahoo

Enrolled: Jul 2022

 Continuing

 Supervisor

Executive Ph.D. Students [1]
Computational Chemistry

 Sashmita Nayak

 Continuing

 Supervisor

 Dissertations

PG Dissertation
  • Malay Raul (416CY2049), "Interaction Between CD44 and hyaluronan: A molecular dynamics simulation approach" - M.Sc.    Supervisor     2017-18 Spring
  • Sudipta Ganguly (417CY2038), "EFFECT OF LIGANDS AND SOLVENTS ON THE ALKYLATION OF ZINTL CLUSTER: A DENSITY FUNCTIONAL THEORY STUDY" - M.Sc.    Supervisor     2018-19 Spring
  • Prabir Sarkar (418CY2051), "MOLECULAR DYNAMICS STUDIES OF DMPC BILAYER WITH PYRAZINE DERIVATIVES." - M.Sc.    Supervisor     2019-20 Spring
  • Samrat Sarkar (419CY2056), "Conformational Flexibilities of Insulin Monomer in Beta-Cyclodextrin at Elevated Temperature" - M.Sc.    Supervisor     2020-21 Spring
  • Suzatra Chatterjee (418CY2035), "In-silico Study of Binding between Chondroitin Sulfate and Strontium" - M.Sc.    Supervisor     2020-21 Spring
  • Umang Hembram (420CY2029), "MOLECULAR DYNAMICS STUDY OF ANHYDROUS AND HYDRATED DMPC BILAYER IN PRESENCE AND ABSENCE OF IONS." - M.Sc.    Supervisor     2021-22 Spring
UG Dissertation
  • Motilal Chhatria (411CY5076), "Molecular Dynamics Simulation of Large Ring Cyclodextrins in Aqueous Medium" - Integrated M.Sc.    Supervisor     2015-16 Spring
  • Siddharth Kamal (411CY5084), "Molecular Dynamics Studies of Glycosaminoglycans in Aqueous Medium" - Integrated M.Sc.    Supervisor     2015-16 Spring
  • Siddharth Kamal (411CY5084), "Molecular Dynamics Studies of Glycosaminoglycans in Aqueous Medium" - Integrated M.Sc.    Supervisor     2016 Summer
  • Tathagata Kundu (412CY5049), "Systematic comparison of empirical force fields for molecular dynamics simulations of amino acid solutions" - Integrated M.Sc.    Supervisor     2017 Summer
  • Rituparnna Mishra (413CY5004), "Molecular Dynamics Studies of a-, ß- and ?- cyclodextrins in water-methanol binary mixtures" - Integrated M.Sc.    Supervisor     2017-18 Spring
  • Abhijeet Mohanty (414CY5048), "Molecular Dynamics Studies of Cyclodextrin-Amino Acid Inclusion Complexes" - Integrated M.Sc.    Supervisor     2018-19 Spring
  • Anuj Kumar Ray (414CY5082), "Molecular Dynamics Studies of DMPC Bilayer" - Integrated M.Sc.    Supervisor     2018-19 Spring
  • Sachin Ramesh Nambiar (414CY5063), "Analysis of Double Proton Transfer Reactions in the light of Conceptual Density Functional Theory" - Integrated M.Sc.    Supervisor     2018-19 Spring
  • Gautam Jha (415CY5055), "COMPUTATIONAL STUDY OF MAGNETIC CLUSTERS OF HEAVY ACTINIDES AND THEIR PROPERTIES" - Integrated M.Sc.    Supervisor     2019-20 Spring
  • Ajeet Singh (417CY5008), "DEVELOPMENT OF SIMPLE FORTRAN CODE TO READ THE BINARY TRAJECTORIES TO ANALYZE PROTEIN FLEXIBILITY" - Integrated M.Sc.    Supervisor     2021-22 Spring

 Awards and Honours

Awards and Honours
  • Fellow of Indian Chemical Society,    2019
  • BRNS-DAE Young Scientist Award,    2018
  • IUSSTF award (by United States-India Science and Technology Endowment Fund, Govt. of USA and INDIA),    2013
  • Eli-Lily Asia Outstanding Thesis Award (1st Prize),    2012
Memberships / Fellowships
  • • Community Member, American Chemical Society,    2020
  • • Life member, Indian Chemical Society,    2018
  • • Life member, Chemical Research Society of India,    2013
  • • Member, Odisha Chemical Society, India,    2013
  • • JRF through GATE ( IIT Kharagpur),    2006
  • • JRF-SRF (CSIR-UGC),    2005