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Dr. Biswajit Das

Assistant Professor (Sr. Gr.), School of Artificial Intelligence, Coimbatore

Qualification: Doctor of Philosophy (Ph. D)
d_biswajit@cb.amrita.edu
Research Interest: Development of the field of Theoretical Biophysics and Mathematical Biology with the help of Artificial Intelligence (AI)

Bio Publications Qualification Programs Teaching Research Interest Awards Associations/Reviewers
Bio

Dr. Biswajit Das currently serves as an Assistant Professor (Sr. Gr.), School of Artificial Intelligence, Coimbatore.

He completed his B.Sc. in Chemistry from Hooghly Mohsin College, Burdwan University, and pursued his M.Sc. in Physical Chemistry from Burdwan University. He conducted his dissertation research on the stochastic dynamics of reaction network in chemical physics from S.N. Bose National Centre for Basic Sciences, Kolkata, and obtained his Ph.D. in Physical Chemistry from the University of Calcutta. Following this, he pursued post-doctoral research in Mathematical Biology at Beijing International Centre for Mathematical Research (BICMR), Peking University, China with the collaboration of Department of Mathematics, University of Washington, Seattle, USA. Before joining Amrita Vishwa Vidyapeetham, he served as a visiting scientist at BICMR for two years when he carried out research works with the collaboration of University of Pittsburgh, USA and University of Edinburgh, UK.

Dr. Das’s research interests encompass theoretical research in biophysics, and mathematical biology. He focuses on mathematical modelling and the stochastic description of reaction networks, as well as the non-equilibrium thermodynamic characterization of biophysical processes. His work also involves using machine learning to explain single molecular heterogeneous dynamics and understanding nano-scale protein dynamics through artificial intelligence (AI). Additionally, he studies the micro-hydrodynamics to understand the locomotive behaviour of microorganisms.

In his research, Dr. Das integrates equilibrium and non-equilibrium statistical mechanics with machine learning and AI concepts. At Amrita, his focus is on advancing the field of theoretical biophysics through the application of AI and machine learning.

Publications

Journal Article

Year : 2024

Elucidating the link between binding statistics and Shannon information in biological networks

Cite this Research Publication : Kinshuk Banerjee, Biswajit Das, Elucidating the link between binding statistics and Shannon information in biological networks,Journal of Chemical Physics,161, 125102, 2024.

Publisher : AIP Publishing

Year : 2024

Elucidating the link between binding statistics and Shannon information in biological cooperative networks

Cite this Research Publication : BANERJEE, KINSHUK & DAS, BISWAJIT. (2024). Elucidating the link between binding statistics and Shannon information in biological cooperative networks. 10.1101/2024.03.28.587158.

Year : 2021

On the Role of Magnesium Ions in the DNA-Scissoring Activity of the Restriction Endonuclease ApaI: Stochastic Kinetics from a Single Molecule to Mesoscopic Paradigm

Cite this Research Publication : Biswajit Das, Kinshuk Banerjee, Gautam Gangopadhyay,On the Role of Magnesium Ions in the DNA-Scissoring Activity of the Restriction Endonuclease ApaI: Stochastic Kinetics from a Single Molecule to Mesoscopic Paradigm,The Journal of Physical Chemistry B,125 (16), 4099–4107, 2021.

Year : 2021

A mechanistic model of the asymmetric torque-speed relationship of a bacterial flagellar motor

Cite this Research Publication : A mechanistic model of the asymmetric torque-speed relationship of a bacterial flagellar motor, B. Das, and H. Ge, 2021, arXiv version: arXiv:2109.01813v1 [physics.bio-ph] 4 Sep, 2021

Publisher : arXiv version

Year : 2020

The guiding role of dissipation in kinetic proofreading networks: Implications for protein synthesis

Cite this Research Publication : The guiding role of dissipation in kinetic proofreading networks: Implications for protein synthesis, K. Banerjee, B. Das, and G. Gangopadhyay, Journal of Chemical Physics (Communication),152, 111102, 2020.

Publisher : Journal of Chemical Physics (Communication)

Year : 2019

Thermodynamic versus kinetic discrimination of cooperativity of enzymatic ligand binding

Cite this Research Publication : Thermodynamic versus kinetic discrimination of cooperativity of enzymatic ligand binding, B. Das, K. Banerjee and G. Gangopadhyay, Austin Biochemistry,4 (1), 2019

Publisher : Austin Biochemistry

Year : 2018

Diffusion influenced non-equilibrium gating processes of a voltage-gated potassium channel

Cite this Research Publication : Diffusion influenced non-equilibrium gating processes of a voltage-gated potassium channel, B. Das, and G. Gangopadhyay, The Pharmaceutical and Chemical Journal, 5(2): ss1-ss23, 2018

Publisher : The Pharmaceutical and Chemical Journal

Year : 2018

Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow

Cite this Research Publication : Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow, B. Das and G. Gangopadhyay, Journal of Chemical Physics, 148, 174104, 2018

Publisher : Journal of Chemical Physics

Year : 2017

Non-equilibrium response of a voltage gated sodium ion channel and biophysical characterization of dynamic hysteresis

Cite this Research Publication : Non-equilibrium response of a voltage gated sodium ion channel and biophysical characterization of dynamic hysteresis, K. Pal, B. Das, and G. Gangopadhyay, Journal of Theoretical Biology, 415, 113, 2017

Publisher : Journal of Theoretical Biology

Year : 2015

Non-equilibrium thermodynamics and a fluctuation theorem for individual reaction steps in chemical reaction network

Cite this Research Publication : Non-equilibrium thermodynamics and a fluctuation theorem for individual reaction steps in chemical reaction network, K. Pal, B. Das, K. Banerjee, and G. Gangopadhyay, Journal of Physics: Conference Series, 638, 012002, 2015

Publisher : Journal of Physics: Conference Series

Year : 2015

Kinetics and entropy production of force-induced oligomeric enzyme catalysis in a single trajectory: Effect of multiple substrates

Cite this Research Publication : Kinetics and entropy production of force-induced oligomeric enzyme catalysis in a single trajectory: Effect of multiple substrates, A. Gangopadhyay, B. Das, K. Banerjee, and G. Gangopadhyay, Chemical Science International Journal, 8(4), 1-13, 2015

Publisher : Chemical Science International Journal

Year : 2014

Propensity approach to non-equilibrium thermodynamics of a chemical reaction network: Controlling single E-coli beta-galactosidase enzyme catalysis through the elementary reaction step

Cite this Research Publication : Propensity approach to non-equilibrium thermodynamics of a chemical reaction network: Controlling single E-coli beta-galactosidase enzyme catalysis through the elementary reaction step, B. Das, K. Banerjee, and G. Gangopadhyay, Journal of Chemical Physics, 139, 174104, 2014.

Publisher : Journal of Chemical Physics

Year : 2013

Entropy production of a mechanically driven single oligomeric enzyme: a consequence of fluctuation theorem

Cite this Research Publication : Entropy production of a mechanically driven single oligomeric enzyme: a consequence of fluctuation theorem, B. Das, K. Banerjee, and G. Gangopadhyay, Journal of Mathematical Chemistry, 51, 588, 2013

Publisher : Journal of Mathematical Chemistry

Year : 2013

On the estimation of cooperativity in ion channel kinetics: Activation free energy and kinetic mechanism of Shaker K+ channel

Cite this Research Publication : On the estimation of cooperativity in ion channel kinetics: Activation free energy and kinetic mechanism of Shaker K+ channel, K. Banerjee, B. Das, and G. Gangopadhyay, Journal of Chemical Physics, 138, 165102, 2013

Publisher : Journal of Chemical Physics

Year : 2012

Entropy hysteresis and non-equilibrium thermodynamic efficiency of ion conduction in a voltage-gated potassium ion channel

Cite this Research Publication : Entropy hysteresis and non-equilibrium thermodynamic efficiency of ion conduction in a voltage-gated potassium ion channel, B. Das, K. Banerjee, and G. Gangopadhyay, Physical Review E, 86, 061915, 2012.

Publisher : Physical Review E

Year : 2012

Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity

Cite this Research Publication : Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity: K. Banerjee, B. Das, and G. Gangopadhyay, Journal of Chemical Physics, 136, 154502, 2012.

Publisher : Journal of Chemical Physics

Year : 2012

Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study

Cite this Research Publication : Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study, B. Das, and G. Gangopadhyay, Chemical Physics, 393, 58, 2012

Publisher : Chemical Physics

Year : 2010

Master equation approach to single oligomeric enzyme catalysis: mechanically controlled further catalysis

Cite this Research Publication : Master equation approach to single oligomeric enzyme catalysis: Mechanically controlled further catalysis, B. Das, and G. Gangopadhyay, Journal of Chemical Physics, 132, 135102, 2010

Publisher : American Institute of Physics not PubMed

Qualification
  • Post-Doctoral Experience
    • Institute Post-Doctoral Fellow (October 2013—March 2017) Beijing International centre for Mathematical Research (BICMR), Peking University, P. R. China
    • Extended Senior Research Fellow (January 2013—September 2013) S.N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, India.
  • Experience as Visiting Scholar/ Visiting Scientist:
    • Visiting Scientist (July 2023—April 2024) Beijing International Centre for Mathematical Research (BICMR), Peking University, P. R. China.
    • Visiting Scientist (July 2022—June 2023) Beijing International Centre for Mathematical Research (BICMR) & Biomedical Pioneering Innovation Centre (BIOPIC), Peking University, P. R. China.
    • Visiting Scholar (July 2020—June 2022) Beijing International Centre for Mathematical Research (BICMR) & Biomedical Pioneering Innovation Centre (BIOPIC), Peking University, P. R. China.
    • Institute Visiting Scholar (August 2019—October 2019) S. N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, India.
    • Institute Visiting Research Scholar (July 2017—July 2018) Beijing International Centre for Mathematical Research, Peking University, P. R. China
  • PhD (Year) : 2008-2013 
    Specialization : Physical Chemistry
    Thesis title : Stochastic Approaches to Heterogeneous and Complex Reaction Kinetics
Programs

GIAN/Workshops/Short-Term Training Programs Attended

  • Presented poster and a short talk (5 min) in the workshop on System Biology Approaches to Understand Complex Cellular Dynamics, IIT-Bombay, India in February, 2024.
  • Participated in the workshop on Stochastic and Nonlinear Dynamics in Chemistry and Biology, S. N. Bose National Centre for Basic Sciences, Kolkata, India, January, 2024.
  • Presented poster in the conference held on Stochastic Physics in Biology, 2023, Gordon Research Conference, Ventura, California, USA, in January, 2023
  • Presented poster in the conference, Current Trends in Theoretical Chemistry CTTC-2020, September, 2021, Bhaba Atomic Research Centre (BARC), India.
  • Presented poster in the conference held on Stochastic Physics in Biology, Gordon Research Conference, Ventura, California, USA, in January, 2017.
  • Presented poster in the Annual meeting of Biomedical Pioneering Innovation Centre (BIOPIC) Peking University, China, in December, 2015.
  • Participated in the workshop on System Biology, Beijing International Center for Mathematical Research, Beijing, China in September, 2014.
  • Presented poster in the conference held on Current Trend in Biochemical and Biophysical modelling, S. N. Bose National Centre for Basic Sciences, Kolkata, India, in October, 2013.
  • Presented poster in the conference held on Current Trends in Theoretical Chemistry, Bhaba Atomic Research Centre, Mumbai, India, in September 2013.
  • Presented poster in the International Conference on Statistical Physics and Non-linear Dynamics, S. N. Bose National Centre for Basic Sciences, Kolkata, India, in March, 2012.
  • Presented poster in the International Symposium on Chemistry and Complexity, Indian Association for the Cultivation of Science, Kolkata, India, in December, 2011.
  • Presented poster in Theoretical Chemistry Symposium, Indian Institute of Technology, Kanpur, India, in December, 2010.
  • Participated in the School on Understanding Molecular Simulations: Theory & Applications, Indian Institute of Technology, Kanpur, India in November, 2010.

Conferences/Workshops/Webinars Organized

  • Local organizer and resource person in the conference “How do cells works as simple chemical engines?” in Amrita Vishwa Vidyapeetham, Coimbatore, India.
Teaching

Courses Taught

  • Odd Semester (2024-25): Professional elective course in MTech. (21DS708): Complex Systems in Engineering, Finance & Biology: Modelling & Analysis.
  • Odd Semester (2024-25): Core course in BTech (23MAT106): Mathematics for Intelligent Systems 1.
  • Even Semester (2024-25):  Core course in BTech (23MAT112): Mathematics for Intelligent Systems II.
Research Interest
  • Proposition of the theoretical methodologies in handling big stochastic data, especially the genomic data.
  • Exploration of the information transmission mechanism through the bio-cellular networks as well as detection of its optimal pathway of using the deep-learning techniques.
  • Application of the Singular values decomposition techniques in biophysics and mathematical biology.
  • Characterization of the non-equilibrium stochastic bio-physical processes by using machine learning and optimization techniques.
Awards

Recognition

  • Invited Speaker in the International Seminar on “Living with AI: Understanding its role in Modern Living” organized by Bengal School of Technology and Management & Bengal School of Technology on May, 2024
  • Invited lecture in Department of Mathematics, IIT-Kanpur on Mathematical modelling of the non-equilibrium dynamics of the voltage-gated ion channel in March 2024.
  • Invited lecture in Department of Physics, IIT-Madras on Regulatory role of a flagellar motor in bacterial chemotaxis: An explanation of the asymmetric torque-speed relationships and its consequences in February 2024.
  • Invited lecture inBiological Physics/Physical biology seminar series on Asymmetric torque-speed relationships provide the clutch of the bacterial flagellar motor in April 2023.
  • Invited lecture in Beijing Science and Technology University on Kinetic and energetic descriptions of some biophysical processes at single molecule level in 2018.
  • Invitedlecture in the Department of Applied Mathematics, Wuhan University, China on Non-equilibrium thermodynamic descriptions of K-ion channel kinetics in 2016.
  • Invited lecture in Beijing Satellite Meeting of STATPHYS25 held on non-equilibrium phenomena, spin glasses, and algorithms, Kavli Institute of Theoretical Physics at Chinese Academy of Sciences, China on Kinetic and non-equilibrium thermodynamic descriptions of a voltage gated shaker K- Channel in 2013.

Awards

  • Received Best poster award in the category of Experiment Driven Theoretical Investigation in the conference, Current Trends in Physical Chemistry (CTTC-2020), BARC, Mumbai, India.
  • Awarded the Best Poster Certificate in Bose fest 2011 at S.N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, India.
  • Awarded for securing the first position in school in Higher Secondary examination (12th exam) in 2001.
  • Awarded for securing the first position in school in Secondary examination in 1999 (Madhyamik Examination, 10th exam).

Honors

  • Senior Research Fellowship, S. N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, India in 2010.
  • Junior Research Fellowship, S. N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, India in 2008.
  • Qualified NET-Lectureship position in 2007.
  • Fellowship for higher study from State Government of India (West Bengal Government) for two years after Madhyamik Examination (10-th Class Exam).
Associations/Reviewers

Membership/Associations

  • Associated with the community of the “Stochastic Physics in Biology,” Gordon Research Conference, USA.
  • Associated with the International seminar series, “Biological Physics/Physical biology (BPPB)”

Reviewers (National/International Journals; Conferences)
International Journals

  • Journal of Chemical Physics
  • Chaos: An interdisciplinary Journal of non-linear science.
  • Journal of applied physics
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