My email address :-
gautam@boson.bose.res.in
..
Name: GAUTAM GANGOPADHYAY
e-mail:gautam@bose.res.in FAX: (91) (33) 2335 3477
Present Status:
Working as a Senior Professor at the S N Bose National Centre
for Basic Sciences (SNBNCBS), Salt Lake City, Kolkata-700106.
Educational Qualifications:
:
Ph.D.(Science)(1993) Jadavpur University(work done at Indian Association for the Cultivation of Sciences), India
M.Sc. (Chemistry, Physical Chemistry)(1985-1987) Burdwan University, India
B.Sc.(Chemistry Hons.)(1982-1985) Burdwan University, India
Broad Research Interest:
:
i. Stochastic processes in Chemical and Biological Systems, specially interested in heterogeneous enzyme catalysis and ion-channel problems.
ii. Studies on quantum dynamics and quantum transport processes in molecular systems.
iii.Nonlinear dynamics and Reaction-diffusion systems in Chemistry and Biology.
List of Publications
110. Nonequilibrium thermodynamic Characterization of Chimeras in a Continuum Chemical Oscillator System,
P Kumar, G Gangopadhyay
Physical Review E 105 (2022) 034208
109. Limit cycle for a generalized Lienard system beyond Lienard-Levinson-Smith(LLS) theorem,
S Saha, G Gangopadhyay
Communications in Nonlinear Science and Numerical Simulation 86, (2022)
108. Universality in bio-rhythms; a perspective from nonlinear dynamics,
S. Saha, G. Gangopadhyay, D. S. Ray, Journal of Biosciences (Special issue), Springer 47 (2022) 0016.
107. Centre Manifold Analysis of 3-D nonlinear system and Kinetic stability of Protein Assembly
S Mazumdar and G Gangopadhyay
Journal of Applied Nonlinear Dynamics, 11(1) (2022) 139–152
106. Nonequilibrium thermodynamics of glycolytic traveling wave: Benjamin-Feir instability
P Kumar, G Gangopadhyay
Physical Review E 104 (2021), 014221
105. A Revisit to Turnover Kinetics of Individual Escherichia coli β-Galactosidase Molecules
P Kundu, S Saha, G Gangopadhyay
The Journal of Physical Chemistry B 125 (2021) 11793
104. 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,
Biswajit Das, Kinshuk Banerjee, and G Gangopadhyay
The Journal of Physical Chemistry B 125, (2021) 4099–4107
103. Electron-Vibration Entanglement of Resonating Dimers in Quantum Transport
Anirban Karmakar and G Gangopadhyay
The Journal of Physical Chemistry A 125, (2021), 3122–3134
102. Synchronization and metabolic energy consumption in stochastic Hodgkin-Huxley neurons: Patch size and drug blockers
K Pal, D Ghosh, G Gangopadhyay
Neurocomputing 422, (2021) 222-234
101. Kinetics of Allosteric Inhibition of Single Enzyme by Product Molecules
P Kundu, S Saha, G Gangopadhyay
The Journal of Physical Chemistry B 124 (2020) 11793
100. Parametric excitation and Hopf bifurcation analysis of a time delayed nonlinear feedback scoillator
S Saha, G Gangopadhyay, S Kumari, RK Upadhyay
International Journal of Applied and Computational Mathematics 6 (2020), 1-21
99. An Exactly Solvable Stochastic Kinetic Theory of Single-Molecule Force Experiments
P Kundu, S Saha, G Gangopadhyay
The Journal of Physical Chemistry B 124 (2020), 7735-7744
98. Suppressing birhythmicity by parametrically modulating nonlinearity in limit cycle oscillators
S Saha, S Chakraborty, G Gangopadhyay
Physica D: Nonlinear Phenomena 416, (2020) 132793
97. Stochastic Kinetic Approach to the Escape of DNA Hairpins from an α-Hemolysin Channel
P Kundu, S Saha, G Gangopadhyay
The Journal of Physical Chemistry B 124 (2020), 6575-6584
96. Termination of Action Potential Due to Site Selective Ion Channel Blockers
K Pal, G Gangopadhyay
Fluctuation and Noise Letters 19 (2020), 2050015
95. Systematic designing of bi-rhythmic and tri-rhythmic models in families of Van der Pol and Rayleigh oscillators
S Saha, G Gangopadhyay, DS Ray
Communications in Nonlinear Science and Numerical Simulation 85, (2020) 105234
94. Kinetics of escape of ssDNA molecules from α-hemolysin nanopores: a dynamic disorder study
P Kundu, S Saha, G Gangopadhyay
Journal of Statistical Mechanics: Theory and Experiment 2020 (2020), 053501
93. Mechanical Unfolding of Single Polyubiquitin Molecules Reveals Evidence of Dynamic Disorder
P Kundu, S Saha, G Gangopadhyay
ACS omega 5 (2020), 9104-9113
92. Energetic and entropic cost due to overlapping of Turing-Hopf instabilities in the presence of cross diffusion
P Kumar, G Gangopadhyay
Physical Review E 101 (2020), 042204
91. The guiding role of dissipation in kinetic proofreading networks: Implications for protein synthesis
K Banerjee, B Das, G Gangopadhyay
The Journal of Chemical Physics 152 (2020), 111102
90. MnO 2 flowery nanocomposites for efficient and fast removal of mercury (ii) from aqueous solution: a facile strategy and mechanistic interpretation
S Das, A Samanta, K Kole, G Gangopadhyay, S Jana
Dalton Transactions 49 (2020) , 6790-6800.
89. Application of dynamic disorder approach to the temperature dependent non-exponential electron transfer kinetics in Rhodopseudomonas viridis
P Kundu, S Saha, G Gangopadhyay
Journal of Statistical Mechanics: Theory and Experiment 2019 (9), 093501
88. A strong enhancement in electronic current due to conical-intersection
A Karmakar, G Gangopadhyay
Physica Scripta 94 (2019), 125401
87. Reduction of Kinetic Equations to Liénard–Levinson–Smith Form: Counting Limit Cycles
S Saha, G Gangopadhyay, DS Ray
International Journal of Applied and Computational Mathematics 5 (2019), 46
86. When an oscillating center in an open system undergoes power law decay
S Saha, G Gangopadhyay
Journal of Mathematical Chemistry 57 (2019), 750-768
85. Clay-based nanocomposites as recyclable adsorbent toward Hg (II) capture: experimental and theoretical understanding
S Das, A Samanta, G Gangopadhyay, S Jana
ACS omega 3 (2018), 6283-6292
84. Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow
B Das, G Gangopadhyay
The Journal of Chemical Physics 148 (2018), 174104
83**. Reduction of kinetic equations to Liénard-Levinson-Smith Form: Counting Limit
Cycles,
S. Saha, G. Gangopadhyay and D. S. Ray,
Int. J. Appl. Comput. Math., Springer, 5(2) (2019).
82*. Diffusion Influenced Non-equilibrium Gating Processes of a Voltage-gated Potassium Ion Channel
Biswajit Das, Gangopadhyay
The Pharmaceutical and Chemical Journal, 2018, 5(2):144-166
81**. When an oscillating center in an open system undergoes power law decay,
S. Saha and G. Gangopadhyay,
J. Math. Chem. 57, 750−768 (2018).
80*. Clay-Based Nanocomposites as Recyclable Adsorbent toward Hg(II)
Capture: Experimental and Theoretical Understanding
S Das, A Samanta, G Gangopadhyay and S Jana
ACS Omega 3, 6283−6292 (2018)
79**. Large deviation theory for the kinetics and energetics of turn over of enzyme
catalysis in a chemiostatic flow
Biswajit Das and Gautam Gangopadhyay
J Chem. Phys. 148, 174104 (2018)
78*. Isochronicity and limit cycle oscillation in biochemical system,
Sandip Saha and Gautam Gangopadhyay, J. Math. Chem. 55 (3), 887-910 (2017).
77**. Nonequilibrium response of a voltage gated sodium
ion channel and biophysical characterization of dynamic hysteresis,
K Pal, B Das and G Gangopadhyay, J.Theo. Biol. 21;415:113-124 (2017).
76*. Dynamical characterization of inactivation path in
voltage-gated Na+ ion channel by non-equilibrium response spectroscopy,
Krishnendu Pal, Gautam Gangopadhyay, Channels, 10 (6): 478-497 (2016).
75**. Fermionic thermocoherent state: Efficiency of electron transport,
Anirban Karmakar and Gautam Gangopadhyay,
Phys. Rev. E 93, 022141 (2016).
74*. Kinetics and Entropy Production of Force-induced Oligomeric Enzyme
Catalysis in a Single Trajectory: Effect of Multiple Substrates,
Gangopadhyay, Biswajit Das, Kinshuk Banerjee and Gautam Gangopadhyay,
American Chemical Science Journal, 8 (4):2249-0205 (2015).
73**. Nonequilibrium thermodynamics and a fluctuation theorem for
individual reaction steps in a chemical reaction network,
Krishnendu Pal, Biswajit Das, Kinshuk Banerjee and G Gangopadhyay,
Journal of Physics: Conference Series 638 (2015) 012002.
72*. Probing kinetic drug binding mechanism in voltage-gated sodium
ion channel: open state versus inactive state blockers,
Krishnendu Pal, Gautam Gangopadhyay, Channels, 9(5):307-16 (2015).
71*. Characterization of conical intersection in a cis- trans isomerization
through nonclassicality and entanglement,
Kinshuk Banerjee, Gautam Gangopadhyay,
Journal of Math. Chem., 53 (8):1733-1749 (2015).
70*. A Noisy Nutrient Inducd Instability in Phytoplankton Blooms
T K D, A G and G Gangopadhyay
Int. J. Curr. Res. Acad. Rev. 2015 Vol. 3, 51-59
69*. Comparison of electromagnetically induced transparency in lambda, cascade and vee three-level systems
Surajit Sen, Tushar Kanti Dey, Mihir Ranjan Nath
and Gautam Gangopadhyay
Journal of Modern Optics, 2015 Vol. 62, 166–174.
68*. A fermionic bath induced antibunching and coherence in Mollow spectra
A. Karmakar and G. Gangopadhyay, Physica Scripta 89 (2014) 45001.
67. Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: Controlling single E-coli beta-galactosidase enzyme catalysis through the elementary reaction steps,
B. Das, K. Banerjee and G. Gangopadhyay,
J. Chem. Phys. 139 (2013) 244104.
66. Emission Rate, Vibronic Entanglement and Coherence in Aggregates of Conjugated Polymers,
K. Banerjee and G. Gangopadhyay, J. Phys. Chem. A 117 (2013) 8642-8650.
65. Realization of vibronic entanglement in terms
of tunneling current in an artificial molecule,
K. Banerjee and G. Gangopadhyay, J. Math. Chem. 51 (2013) 2731-2745.
64. On the estimation of cooperativity in ion channel kinetics: activation free energy and kinetic mechanism of potassium ion channel,
K Banerjee, B Das and G Gangopadhyay, J. Chem. Phys. 138,(2013) 165102.
63. Entropy production of a mechanically driven single oligomeric enzyme: a consequence of fluctuation theorem,
B. Das, K. Banerjee and G. Gangopadhyay, J. Math. Chem.51, (2013) 588.
62. Entropy hysteresis and nonequilibrium thermodynamic efficiency of ion conduction in a voltage-gated potassium ion-channel,
B. Das, K. Banerjee and G. Gangopadhyay,
Phys. Rev. E 86, (2012) 061915.
61. Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity,
K. Banerjee, B. Das and G. Gangopadhyay, J. Chem. Phys. 136 (2012) 154502.
60. Decoherence without dissipation due to fermionic bath,
A. Karmakar and G. Gangopadhyay, Physica Scripta 85 (2012) 045008.
59. Electronic nuclear entanglement in a conjugated polymer aggregate with a conical intersection: spectral signatures
K. Banerjee and G. Gangopadhyay, J. Phys.B 45 (2012) 045102.
58. Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study,
B. Das and G. Gangopadhyay, Chem. Phys. 393 (2012) 58.
57. Bloch space structure, the qutrit wave function and atom-field entanglement in three-level systems,
S. Sen, M. R. Nath, T. K. dey and G. Gangopadhyay, Annals of Physics 327 (2012) 224.
56. Magnetically induced variation of tunneling current and nonclassicality in a coupled quantum dot system,
K. Banerjee and G. Gangopadhyay, AIP Conf. Proc. 1384 (2011) 137.
55. Bloch equation and atom-field entanglement scenario in three-level systems,
S. Sen, M. R. Nath, T. K. dey and G. Gangopadhyay, AIP Conf. Proc. 1384 (2011) 190.
54. Role of positional disorder in the spectra of conjugated polymer
aggregates: conical intersection of potential energy surfaces
K. Banerjee and G. Gangopadhyay, J. Phys.B 43 (2010) 235104.
53. Master equation approach to single oligomeric enzyme catalysis: Mechanically controlled further catalysis,
B. Das and G. Gangopadhyay, J. Chem. Phys. 132 (2010) 135102.
52. Effect of geometry of dipolar orientations on the spectra of di and trimer chain aggregates.
K. Banerjee and G. Gangopadhyay, Phys. Rev. B 81 (2010) 035307.
51. Aggregate of a network of conjugated polymer chains: Symmetry of the excitonic states and spectral features,
K. Banerjee and G. Gangopadhyay, J. Phys.B 42 (2009) 165106.
50. Spectra of conjugated polymer aggregates: Symmetry of the interchain dressed states,
K. Banerjee and G. Gangopadhyay, J. Chem. Phys. 130 (2009) 084705.
49. Dynamical symmetry breaking of lambda and vee-type three-level systems
on quantization of the field modes,
M R Nath, S Sen, A K Sen and G. Gangopadhyay,, Pramana- J. Phys.71 (2008)77.
48. Effect of field quantization on Rabi oscillation of equidistant cascade four-level system,
M R Nath, T K Dey, S Sen and G. Gangopadhyay,, Pramana- J. Phys.70 (2008) 141.
47. Quantum electron transfer processes induced by thermocoherent state,
S. Banerjee and G. Gangopadhyay, J. Chem. Sciences 119 (2007) 1-10.
46. On the microscopic basis of Newton's law of cooling and beyond,
M R Nath, S Sen and G. Gangopadhyay, J. Chem. Phys. 127 (2007) 094505.
45. On the quantum theory of electron transfer: effect of potential surfaces of the
reactant and product,
S. Banerjee and G. Gangopadhyay, J. Chem. Phys. 126 (2007) 034102.
44. Theoretical studies of electron transfer through dendrimer architecture,
D. Rana and G. Gangopadhyay, J. Chem. Phys. 124 (2006) 044909.
43. Laser cooling of vibrational degrees of freedom of a molecular system,
S. Banerjee and G. Gangopadhyay, J. Chem. Phys. 123 (2005) 114304.
42. The absorption bandshape function of a molecule from a thermocoherent state and some associated multilinear generating-function relationships for Laguerre polynomials,
H. M. Srivastava and G. Gangopadhyay, Russ. J. Math. Phys. 11 (2004) 359-367.
41. Radiative Decay of Nonstationary System ,
S. Banerjee and G. Gangopadhyay, J. Chem. Phys. 120 (2004) 6152.
40. Born-Oppenheimer approximation: A Toy version,
G Gangopadhyay and B. Dutta-Roy, Am. J. Phys. 72 (2004) 389.
39.
Dynamics of cascade three level system interacting with the classical
and quantized field,
38. Quantum beat in pump-probe signal of molecular system,
37. Power law relaxation kinetics in reversible
enzyme-catalyzed reaction due to diffusion,
36. Power law relaxation kinetics in multistate reversible
reaction,
35. Studies on energy transfer
in Dendrimer supermolecule using classical random walk model and Eyring model,
34. Spectra of displaced distorted oscillator molecular
system ,
33. On dissipationless decoherence ,
32. Steady state spectral properties of dendrimer supermolecules
as light harvesting system,
31. An operator approach to the construction of generating
function for the product of Laguerre Polynomials: A thermal average bandshape
function of a molecule,
30. A thermal bath induced new resonances in linear and
nonlinear spectra of a two-level system,
29. A generating function for the product of Laguerre
polynomials: Franck-Condon factor for multiphoton processes,
28. Theory of non-stationary activated rate processes:
non-exponential kinetics, J Ray Chaudhuri, G Gangopadhyay and D S Ray,
J. Chem. Phys 109 (1998) 5565.
27. Quantum Theory of dissipation of a harmonic oscillator
coupled to a non-equilibrium bath; Wigner-Weisskopf decay and Physical
Spectra, J Ray Chaudhuri, B Deb, G Gangopadhyay and D S Ray, J. Phys. B
31 (1998) 3859.
26. Absorption line shape of impurity molecule driven
by a fractal noise,
25. A thermal bath induced Rabi splitting on the profile
of Mollow spectrum in single molecule spectroscopy,
24. The effect of environment induced pure dephasing in
the generalized Jaynes-Cummings model,
23. The effect of environment induced pure dephasing in
the Jaynes-Cummings model,
22. Theory of Quantum fluctuations in classically chaotic
Hamiltonian systems, S Chaudhuri, G Gangopadhyay and D S Ray, Phys. Rev
E54 (1996)53
21. Field induced quantum barrier crossing; classical
chaos and weak localization, S Chaudhuri, G Gangopadhyay and D S Ray, Phys.Letts.
A216 (1996) 53.
20. Signature of Classical chaos on field induced quantum
barrier crossing, S Chaudhuri, G Gangopadhyay and D S Ray, Special issue
on Complex systems, Indian Journal of Physics, 69B (1995)507.
19. The non-Markovian master equation for stochastically
perturbed systems; effect on spectral lineshape, G Gangopadhyay and D S
Ray, J. Mol. Struc.(Theo Chem), 361 (1996) 49.
18. Population trapping in the Jaynes-Cummings model with
a kerr nonlinear medium,
17. Fluctuation and decoherence in classical chaos: A
model study of a Kubo oscillator generated by a chaotic system, S Chaudhuri,
G Gangopadhyay and D S Ray, Phys. Rev. E52 (1995) 2262.
16. Generation of a class of arbitrary two-mode field
state in a cavity, B. Deb, G Gangopadhyay and D.S. Ray, Phys. Rev. A 51
(1995) 2651.
15. Coherent phase state and displaced phase state in
a finite dimensional basis and their light field limits,
14. Master equation in quantum optics; some generalizations,
G Gangopadhyay and D S Ray, in Advances in Multiphoton Processes, edited
by S H Lin, A A Villaeys and F Fujimura, World Scientific, Singapur, 1993.
13. Population trapping in a Raman-coupled model interacting
with a two-mode quantized cavity fields, B Deb, G Gangopadhyay and D S
Ray, Phys. Rev. A 48 (1993) 1400.
12. A fluctuation-diffusion relation in chaotic dynamics,
11. Cavity field-assisted atomic relaxation and suppression
of resonance fluorescence at high intensities,
10. Non-Markovian master equation for linear and nonlinear
systems,
9. A master equation approach to multiphoton dissociation
of Morse oscillator,
8. Master equation for nonlinear dissipative systems,
G Gangopadhyay and D S Ray, J. Chem. Phys. 96 (1992) 4693
7. Cavity QED with a single Morse oscillator, G Gangopadhyay
and D S Ray, in Quantum Optics edited by R Inguva (PlenumPress, N. Y. 1992)
6. Spectral modification of the Stokes line of a Raman-coupled
three level system in a cavity,
5. Master equation for dissipative dynamics of a two-level
atom in a superintense field; field dependent relaxation,
4. Quantum electrodynamics of a single Morse oscillator
in a cavity; spectral aspects,
3 Power spectra of light scattered from a strongly driven
Morse oscillator,
2. Spectra of four-wave mixing in a self-consistent field,
1. A global stochasticity criteria for Maxwell-Bloch equation,
Summary of research activities in last few years by Prof. Gautam Gangopadhyay
1. Research interest:
*. Nonlinear nonequilibrium dynamics in Chemical and Biological systems
*. Stochastic processes in Complex systems
*. Quantum transport in molecular and Biological processes.
2. Some highlights about most important research achievement are as follows:
(i). Exploration of the energetic and entropic cost due to Turing and Hopf instabilities
in nonlinear open system
(ii). Investigation of the role of entropy production in kinetic proof reading in chemical
network
(iii) Devising a single molecule approach to deal with the dynamic disorder in various chemical
and biological processes
3. Nature of our works on some specific projects are as follows:
a. Multiscale dynamics in open Chemical and Biological Systems:
The self-sustained chemical oscillations are regularly observed in biological world to maintain a cyclic steady state e.g., cell division, circadian oscillation, calcium oscillations and other bio-systems. Our aim in this project is to look into the physical and mathematical properties of weakly nonlinear systems containing periodic orbits by adopting various methods of multiscale perturbation analysis to cover single to multi-limit cycles which can arise in various practical situations. We have presented an unified scheme to express a class of system of equations in two variables into a Liénard - Levinson -Smith(LLS) oscillator form. We have derived the condition for limit cycle for arbitrary polynomial functions of damping and restoring force. A method is devised to determine the maximum number of limit cycles admissible for a LLS oscillator. Based on this approach we proposed a scheme for systematic designing of generalised Rayleigh and Van der Pol families of oscillators with a desired number of multiple limit cycles.
b. Dynamic disorder and conformational fluctuations in reaction kinetics:
The decay of the nonexponential kinetics at the microsecond timescale, points to the relevance of having possible influence of dynamic disorder on the reaction kinetics. To rationalize the experimental results by the microscopic dynamics of protein a molecule are described in terms of the anomalous diffusion of a Brownian particle in a harmonic potential well under the action of fractional Gaussian noise.
c. Quantum transport through molecular system:
To construct the theory of quantum transport through molecular system we have developed the formulation of quantum system coupled to a fermionic bath and the model is applied in various coherent processes. In continuation of our earlier work we have studied the electronic and nuclear entanglement with nonadiabatic effects in conical intersection regime.
A. Area of research and descriptions of problems:
1. Molecular quantum Dynamics and Quantum transport:
To construct the theory of quantum transport through molecular system we have developed the formulation of quantum system coupled to a fermionic bath and the model is applied in various coherent processes. In continuation of our earlier work we have studied the electronic and nuclear entanglement with nonadiabatic effects.
On the fermionic thermocoherent state: efficiency of electron transport
On the basis of the fermionic coherent state of Cahill and Glauber[(1999), Phys. Rev. A, we have introduced here fermionic thermocoherent state in terms of the quasiprobability distribution which shows the appropriate thermal and coherent limits as in the bosonic case or Glauber-Lachs state. It is shown that the fermionic thermocoherent state can be realised as a displaced thermal state of fermions. Its relation with the fermionic displaced number state and fermion-added coherent state are explored in the spirit of bosonic case. We have investigated the nature of the average current and the suppression of noise due to thermocoherent character of the source. The theory is applied to the problem of electronic conduction. A modification of Landauer conductance formula is suggested which reflects the role of nonzero coherence of the source in electron transport.
Electron transport through molecular system: a master equation approach
Based on the formulation of quantum master equation for fermionic bath, we have estimated electron transport through a molecular system which is coupled to two electron leads with a vibrational manifold. The molecular current is studied as a function of external and internal bias and the differential conductance is studied against the external bias. We have also calculated the Fano factor as a measure of current noise. Numerical results for pyridine molecule as a system shows that electron-phonon coupling can be an indicator of current noise which can suppress molecular current. An additional electron transport channel through electron-phonon coupling gives rise to a vibration induced Coulomb blockade which can be used as a marker of vibrational modes of the system.
In a similar context we have shown a strong enhancement in electronic current due to conical-intersection in the molecular system undergoing a cis-trans isomerization.
Publications: 68*. A fermionic bath induced antibunching and coherence in Mollow spectra
A. Karmakar and G. Gangopadhyay, Physica Scripta 89 (2014) 45001.
72*. Characterization of conical intersection in a cis- trans isomerization
through nonclassicality and entanglement,
Kinshuk Banerjee, Gautam Gangopadhyay,
Journal of Math. Chem., 53 (8):1733-1749 (2015).
75**. Fermionic thermocoherent state: Efficiency of electron transport,
Anirban Karmakar and Gautam Gangopadhyay,
Phys. Rev. E 93, 022141 (2016).
86**. A strong enhancement in electronic current due to conical-intersection
Anirban Karmakar and Gautam Gangopadhyay
Physica Scripta(Accepted)
92*. Electron transport through molecular system: a master equation approach
Anirban Karmakar and Gautam Gangopadhyay (submitted)
2. Multiscale nonlinear dynamics in open Chemical and Biological Systems
Chemical oscillations show non-linear dynamical phenomenon which can be understood in terms of the stability of non-equilibrium steady state of a reaction within far away from equilibrium condition. Experimentally such open systems like, Bray, BZ and glycolytic reactions are studied extensively in a continuously flowing stirred tank reactor and the nature of the oscillatory kinetics of two intermediates gave reliable dynamical models of limit cycle. The self-sustained chemical oscillations are also regularly observed in biological world to maintain a cyclic steady state e.g., cell division[, circadian oscillation, calcium oscillations and other bio-systems. The generic feature of such diverse nature of non-linear oscillations are due to auto-catalysis and various feedback mechanisms into the system which are basically controlled by a few slow time scales of the overall process. Such periodic orbits can be isochronous or the frequency may depend on their amplitude of which the most common examples of periodic orbits of open systems are limit cycle and in some special cases they become center like in a harmonic oscillator. The ubiquity of limit cycle in dynamical system described by a pair of ordinary differential equations are quite characterised mathematically, however, a general prescription of shape, size and the number of stable limit cycles in a given system are not yet well established. From the physical point of view the response properties of a limit cycle due to an external driving field is also ill understood unlike ordinary oscillations in various physical processes. On the one hand there is a challenge in dealing with limit cycles in a strongly nonlinear systems inspite of several developments of various multiscale perturbation techniques like, Krylov-Boguliobov(K-B) method, Poincare-Linstedt method[, Renormalization Group(RG) method etc. On the other hand a limit cycle in a given dynamical system of phenomenological importance can be a great tool as the nature is playing through various stable limit cycles to regulate its self organized processes which need to be understood.
Our aim in this project is to look into the physical and mathematical properties of weakly nonlinear systems containing periodic orbits by adopting various methods of multiscale perturbation analysis to cover single to multi-limit cycles which can arise in various practical situations. More specifically we consider a class of open natural dynamical systems in the form of an oscillator of generalised Liénard equation which is utilised to study the chacterisation of various periodic orbits. In order to understand the response properties of limit cycle under external perturbation we have investigated subharmonic resonances. As the multiple limit cycle in a given system is an important issue here we have explored on the counting of limit cycles and its application in systematic construction of birhythmic and tri-rhythmic oscillators from a simple limit cycle system. As the diffusion is an integral part of the most dynamical systems in chemical and biological context we have studied reaction-diffusion systems which effectively creates a spatial inhomogeneity by adding a slower time scale in the system dynamics. In presence of diffusion, for a system of limit cycle we have investigated the diffusion driven instability through the construction of amplitude and phase equations in spatio-temporal pattern.
Publications: 78*. Isochronicity and limit cycle oscillation in biochemical system,
Sandip Saha and Gautam Gangopadhyay, J. Math. Chem. 55 (3), 887-910 (2017).
82**. When an oscillating center in an open system undergoes power law decay,
S. Saha and G. Gangopadhyay,
J. Math. Chem., 57 (3), 750−768 (2018).
83**. Reduction of kinetic equations to Liénard-Levinson-Smith Form: Counting Limit
Cycles, S. Saha, G. Gangopadhyay and D. S. Ray,
Int. J. Appl. Comput. Math., Springer, 5(2) (2019).
88*. Hopf bifurcation analysis of a time delayed nonlinear feedback oscillator,
S. Saha, G. Gangopadhyay, S. Kumari and R. K. Upadhyay. (submitted)
89*. A recipe for construction of multirhythmic models in van der Pol and Rayleigh
family of oscillators,
S. Saha and G. Gangopadhyay and D. S. Ray. (Submitted)
3. Nonequilibrium Features Of Voltage Gated Sodium Ion Channel
The research on the voltage-gated sodium ion channel draws immense attention in neuroscience as they are targeted for anesthesia and treatments for genetic diseases in brain, muscle and heart etc. The Sodium ion channel initiates the action potential, the most essential requirement for communication between cells. We have investigated the nonequilibrium kinetic and thermodynamic responses of sodium ion channel using Nonequilibrium Response Spectroscopy(NRS) where a continuous supply of energy takes place in to the system from external sources using oscillating or fluctuating or pulsed voltage protocol which forces the ion channel to stay in non equilibrium situation.
The particular works done are briefly given below:
(a) Using oscillating external voltage protocol we have studied the dynamic hysteresis at nonequilibrium steady state and its parametric dependence(e.g. frequency, amplitude, mean voltage) of external voltage protocol. The work done for overall gating dynamics is estimated by calculated the loop area of total entropy production rate. The utilization of energy and associated dissipative work done at nonequilibrium steady state is also estimated. (b) We have shown that open state drug blocking is a free energy driven process while closed state blocking is an entropy driven process. Comparing all voltage protocols we concluded that inactive state blockers are more potent channel blockers than open state blockers. (c) Next we switched our study from single channel to the whole cell Hodgkin-Huxley neuron. Modifying existing Hodgkin-Huxley model with sodium as well as potassium drug bound states and using Gillespie's exact Markov simulation technique a more realistic picture of drug binding is obtained.(d) Finally we have extended our study from one neuron to two neurons, unidirectionally coupled via electrical synapses. We have shown that the size of patch/channel number fluctuations in individual neurons have very important role in unidirectional synchronization and metabolic energy consumption. The effect of sodium, potassium blockers have very interesting and distinct effect on synchronization process and metabolic energy consumption.
Publications: 73*. Probing kinetic drug binding mechanism in voltage-gated sodium ion channel: open state versus inactive state blockers,
Krishnendu Pal, Gautam Gangopadhyay, Channels, 9(5):307-16 (2015).
76*. Dynamical characterization of inactivation path in
voltage-gated Na+ ion channel by non-equilibrium response spectroscopy,
Krishnendu Pal, Gautam Gangopadhyay, Channels, 10 (6): 478-497 (2016).
77**. Nonequilibrium response of a voltage gated sodium
ion channel and biophysical characterization of dynamic hysteresis,
Krishnendu Pal, Biswajit Das and Gautam Gangopadhyay,
J.Theo. Biol. 21;415:113-124 (2017).
81*. Diffusion Influenced Non-equilibrium Gating Processes
of a Voltage-gated Potassium Ion Channel
Biswajit Das, Gangopadhyay
The Pharmaceutical and Chemical Journal, 2018, 5(2):144-166
85*. Termination Of Action Potential Due To Site Selective Ion Channel Blockers
Krishnendu Pal and Gautam Gangopadhyay
Fluctuation and Noise Letters World Scientific(Accepted)
4. Kinetics and nonequilibrium thermodynamics of enzyme catalysis:
Large deviation theory for the kinetics and energetics of turn over of enzyme catalysis in a chemiostatic flow
In the framework of large deviation theory we have characterized nonequilibrium turn over statistics of enzyme catalysis in a chemiostatic flow with externally controllable parameters, like substrate injection rate and mechanical force. In kinetics of the process we have shown the fluctuation theorems in terms of the symmetry of the scaled cumulant generating function(SCGF) in transient and steady state regime and similar symmetry rule is reflected in large deviation rate function(LDRF) as a property of the dissipation rate through boundaries. Large deviation theory also gives the thermodynamic force of nonequilibrium steady state(NESS), as is usually recorded experimentally by single molecule technique, which plays a key role responsible for the dynamical symmetry of the SCGF and LDRF. Using some special properties of Legendre transformation here we have provided a relation between the fluctuations of fluxes and dissipation rates and among them the fluctuation of turn over rate is routinely estimated but the fluctuation in dissipation rate is yet to be characterized for small systems. Such an enzymatic reaction flow system can be a very good testing ground to systematically understand the rare events from the large deviation theory which is beyond fluctuation theorem and central limit theorem.
Effect of Diffusion of Substrates on the Non-Equilibrium Turnover of Single Oligomeric Enzyme Catalysis
Here we have shown how to account for the effect of substrate diffusion in single oligomeric enzyme kinetics with chemiostatic condition. We have provided a master equation based formulation of reaction-diffusion dynamics of enzyme catalysis in nonequilibrium state where the diffusion of substrates affect the conformational dynamics of oligomeric enzyme. As the nonequilibrium total entropy production rate(epr) can give the information of both the kinetic and temporal profile of energetics of the process, here we have systematically shown the results both in the reaction controlled and diffusion controlled regimes. In a similar context dynamic disorder is studied in electron transfer in single molcule enzyme and mechanical unfolding of single poly-ubiquitin molecule.
Publications: 74*. Nonequilibrium thermodynamics and a fluctuation theorem for
individual reaction steps in a chemical reaction network,
Krishnendu Pal, Biswajit Das, Kinshuk Banerjee and G Gangopadhyay,
Journal of Physics: IOP Conf. Ser. 638 (2015) 012002.
79**. Large deviation theory for the kinetics and energetics of turn over of enzyme
catalysis in a chemiostatic flow
Biswajit Das 1 and Gautam Gangopadhyay J Chem Phys. 148, 174104 (2018)
84*. Thermodynamic versus Kinetic Discrimination of Cooperativity of Enzymatic Ligand Binding, Biswajit Das, Kinshuk Banerjee and G Gangopadhyay,Austin Biochemistry - Volume 4 Issue 1 – 2019
93*. Application of dynamic disorder approach to the temperature dependent
non-exponential electron transfer kinetics in Rhodopseudomonas viridis,
Prasanta Kundu, Soma Saha and G. Gangopadhyay,
J. Stat, Mech. Theo. Expt. 1742-5468 (2019).
94*. Mechanical unfolding of single poly-ubiquitin molecules reveals evidence of dynamic disorder
Prasanta Kundu, Soma Saha, and Gautam Gangopadhyay (submitted)
Research Output
(a) Published in Peer-Reviewed Journals :
(Papers written during the tenure as Professor(2014-2019)
68*. A fermionic bath induced antibunching and coherence in Mollow spectra
A. Karmakar and G. Gangopadhyay,
Physica Scripta 89 (2014) 45001.
69*. Comparison of electromagnetically induced transparency in lambda, cascade and vee three-level systems
Surajit Sen, Tushar Kanti Dey, Mihir Ranjan Nath
and Gautam Gangopadhyay
Journal of Modern Optics, 2015 Vol. 62, 166–174.
70*. A Noisy Nutrient Inducd Instability in Phytoplankton Blooms
T K D, A G and G Gangopadhyay
Int. J. Curr. Res. Acad. Rev. 2015 Vol. 3, 51-59
71*. Characterization of conical intersection in a cis- trans isomerization
through nonclassicality and entanglement,
Kinshuk Banerjee, Gautam Gangopadhyay,
Journal of Math. Chem., 53 (8):1733-1749 (2015).
72*. Probing kinetic drug binding mechanism in voltage-gated sodium
ion channel: open state versus inactive state blockers,
Krishnendu Pal, Gautam Gangopadhyay, Channels, 9(5):307-16 (2015).
73**. Nonequilibrium thermodynamics and a fluctuation theorem for
individual reaction steps in a chemical reaction network,
Krishnendu Pal, Biswajit Das, Kinshuk Banerjee and G Gangopadhyay,
Journal of Physics: Conference Series 638 (2015) 012002.
74*. Kinetics and Entropy Production of Force-induced Oligomeric Enzyme
Catalysis in a Single Trajectory: Effect of Multiple Substrates,
Gangopadhyay, Biswajit Das, Kinshuk Banerjee and Gautam Gangopadhyay,
American Chemical Science Journal, 8 (4):2249-0205 (2015).
75**. Fermionic thermocoherent state: Efficiency of electron transport,
Anirban Karmakar and Gautam Gangopadhyay,
Phys. Rev. E 93, 022141 (2016).
76*. Dynamical characterization of inactivation path in
voltage-gated Na+ ion channel by non-equilibrium response spectroscopy,
Krishnendu Pal, Gautam Gangopadhyay, Channels, 10 (6): 478-497 (2016).
77**. Nonequilibrium response of a voltage gated sodium
ion channel and biophysical characterization of dynamic hysteresis,
K Pal, B Das and G Gangopadhyay, J.Theo. Biol. 21;415:113-124 (2017).
78*. Isochronicity and limit cycle oscillation in biochemical system,
Sandip Saha and Gautam Gangopadhyay, J. Math. Chem. 55 (3), 887-910 (2017).
79**. Large deviation theory for the kinetics and energetics of turn over of enzyme
catalysis in a chemiostatic flow
Biswajit Das and Gautam Gangopadhyay
J Chem. Phys. 148, 174104 (2018)
80*. Clay-Based Nanocomposites as Recyclable Adsorbent toward Hg(II)
Capture: Experimental and Theoretical Understanding
S Das, A Samanta, G Gangopadhyay and S Jana
ACS Omega 3, 6283−6292 (2018)
81**. When an oscillating center in an open system undergoes power law decay,
S. Saha and G. Gangopadhyay,
J. Math. Chem. 57, 750−768 (2018).
80*. Diffusion Influenced Non-equilibrium Gating Processes of a Voltage-gated Potassium Ion Channel
Biswajit Das, Gangopadhyay
The Pharmaceutical and Chemical Journal, 2018, 5(2):144-166
83**. Reduction of kinetic equations to Liénard-Levinson-Smith Form: Counting Limit
Cycles, S. Saha, G. Gangopadhyay and D. S. Ray,
Int. J. Appl. Comput. Math., Springer, 5(2) (2019).
84*. Thermodynamic versus Kinetic Discrimination of Cooperativity of Enzymatic Ligand Binding,
Biswajit Das, Kinshuk Banerjee and G Gangopadhyay,
Austin Biochemistry - Volume 4 Issue 1 - 20196
85*. Termination Of Action Potential Due To Site Selective Ion Channel Blockers
Krishnendu Pal and Gautam Gangopadhyay
Fluctuation and Noise Letters World Scientific(Accepted)
86**. A strong enhancement in electronic current due to conical-intersection
Anirban Karmakar and Gautam Gangopadhyay
Physica Scripta(Accepted)
Papers Communicated:
87*. Effect of Channel Noise in Synchronization and Metabolic Energy Consumption in Unidirectionally
Coupled Neurons: Drug Blocking of Sodium and Potassium Channels
Krishnendu Pal, Gautam Gangopadhyay(submitted)
arXiv:1810.04381 [physics.bio-ph]
88*. Hopf bifurcation analysis of a time delayed nonlinear feedback oscillator,
S. Saha, G. Gangopadhyay, S. Kumari and R. K. Upadhyay. (submitted)
89*. A recipe for construction of multirhythmic models in van der Pol and Rayleigh
family of oscillators,
S. Saha and G. Gangopadhyay and D. S. Ray. (Submitted)
90*. Oscillating resonances in parametrically excited limit cycle,
S. Saha, S. Chakraborty and G. Gangopadhyay.
91*. Amplitude equation for Reaction-Diffusion system and traveling waves in glycolysis,
S. Saha, P. Kumar and G. Gangopadhyay.
92*. Electron transport through molecular system: a master equation approach
Anirban Karmakar and Gautam Gangopadhyay (submitted)
93*. Application of dynamic disorder approach to the temperature dependent
non-exponential electron transfer kinetics in Rhodopseudomonas viridis,
Prasanta Kundu, Soma Saha, and Gautam Gangopadhyay
J. Stat, Mech. Theo. Expt. 1742-5468 (2019).
94*. Mechanical unfolding of single poly-ubiquitin molecules reveals
evidence of dynamic disorder
Prasanta Kundu, Soma Saha, and Gautam Gangopadhyay (submitted)
95. Energetic and entropic cost due to overlapping of Turing-Hopf instabilities in the presence of cross diffusion
Premashis Kumar and Gautam Gangopadhyay, PHYSICAL REVIEW E 101, 042204 (2020)
96. The guiding role of dissipation in kinetic
proofreading networks: Implications
for protein synthesis,
Kinshuk Banerjee, Biswajit Das and Gautam Gangopadhyay,
J. Chem. Phys. 152, 111102 (2020)
M R Nath,S Sen and G Gangopadhyay, Pramana-J. Phys. 61 (2003) 1089-1100.
S. Banerjee and G. Gangopadhyay, J. Phys. B 36 (2003) 2967.
S. Paul and G. Gangopadhyay, J. Chem. Phys. 119(2003) 3501.
S. Paul and G. Gangopadhyay, Chem. Phys. Letts.
369 (2003) 643.
D. Rana and G. Gangopadhyay, J. Chem. Phys.
118 (2003) 434.
S. Banerjee and G. Gangopadhyay, Chem. Phys. Letts.
359 (2002) 295.
G. Gangopadhyay, M. Sanjay Kumar and S. Dattagupta, J.
Phys. A 34 (2001) 5485.
D. Rana and G. Gangopadhyay, Chem. Phys. Letts. 314 (2001)
324.
G Gangopadhyay, J. Phys. A Math. & Gen. 32
(1999) L441.
G Gangopadhyay, S Ghoshal and
Y Tanimura, Chem. Phys. 242 (1999) 367.
G Gangopadhyay,
J. Phys. A Math. & Gen. 31 (1998) L771.
G Gangopadhyay and Y Tanimura, Chem. Phys. Letts. 289
(1998) 97.
G Gangopadhyay and
S Ghoshal Chem. Phys. Letts 289 (1998) 287.
G Gangopadhyay and S H Lin, Pramana-
J. Phys. 49 (1997) 399.
G Gangopadhyay and S H Lin, Physica Scripta
55 (1997) 425.
A Bandyopadhyay and G Gangopadhyay , J. Mod. Opt.
43 (1996) 487.
G Gangopadhyay,
J. Mod. Opt. Vol 41 (1994) 525.
S Chaudhuri,G Gangopadhyay and D S Ray, Phys.Rev.E 47 (1993)311
G Gangopadhyay, S Basu and
D S Ray, Phys. Rev. A 47 (1993) 1314
G Gangopadhyay and D S Ray, Phys. Rev. A 46 (1992) 1507
G Gangopadhyay and D S Ray, J. Chem. Phys. 97 (1992)
4104
G Gangopadhyay and D S Ray, Phys. Rev. A 45 (1992) 1843
G Gangopadhyay and D S Ray, Phys. Rev. A 44 (1991) 2206
G Gangopadhyay and D S Ray, Phys. Rev. A 43 (1991) 6424
G Gangopadhyay and D S Ray, Phys. Rev. A 41 (1990) 6429
G Gangopadhyay and D S Ray, Phys. Rev. A 41 (1990) 3985
G Gangopadhyay and D S Ray, Phys. Rev. A 40 (1989) 3750
Summary of research work of Gautam Gangopadhyay: Areas of Research: Chemical Physics. During the period, (2014-2019) we have worked broadly in the following four projects