CURRICULUM VITAE
1. Name: DEBAPRASAD GIRI
2. DOB: September 01, 1966
3. Address:
Department of Physics
Indian Institute of Technology
(Banaras Hindu University)
Varanasi 221005
Telephone : +91 542 6701917 (office)
Mobile: 9839885243;
E-mail: dgiri.app@iitbhu.ac.in, dgiri99@yahoo.com
4. Education:
• B. Sc. 1987, Calcutta University,
Subject: Physics
• M. Sc. 1989, IIT, Kharagpur,
Subject: Physics (Specialization: Condensed Matter Physics)
• Ph. D. 1997, Institute of Physics, Bhubaneswar
Subject: Condensed Matter Physics
5. Present Status: Professor, Department of Physics, IIT (Banaras Hindu University), Varanasi (Since
September, 2015).
6. Previous Positions, Teaching & Research Experience:
• Professor, Department of Physics, IIT (Banaras Hindu University), Varanasi (Since September, 2015).
• Associate Professor, Department of Physics, IIT (Banaras Hindu University), Varanasi (October,
2010 - August, 2015).
• Reader, Department of Applied Physics, IT, Banaras Hindu University, Varanasi, (October, 2007 October, 2010)
• Lecturer, Physics Section, MMV, Banaras Hindu University, Varanasi (June, 2004 - October, 2007)
• Principal Investigator, DST-FAST Track Project at CTS, IIT, Kharagpur (April, 2002 - May, 2004).
• Post Doctoral Fellow / Research Associate, CTS, IIT, Kharagpur (April, 2000 - March, 2002).
• Post Doctoral Fellow / Research Associate, Department of Physics, BHU, Varanasi (March, 1998 March, 2000).
• Post Doctoral Fellow / Research Associate, Department of Physics, IIT, Mumbai (January, 1997 December, 1998).
7. Academic Profile:
(a) Area of Research : Statistical Physics, Soft Condensed Matter Physics, Computational Bio-Physics.
(b) Awards/Scholarship :
• (1981 - 1986)
National Scholarship of West Bengal Government.
• (1987 - 1989)
Merit Cum Mean Scholarship of IIT, Kharagpur for Master’s degree.
(c) Academic Recognitions : Nominated as Category-A speaker under TPSC Program of DST: 1996-97,
2000-2002, 2004-2006.
(d) Courses Taken :
• Mathematical Physics (Ph.D. Course Work); Statistical Physics, Advanced Electromagnetic Theory (IMD Engineering Physics, part III; Quantum Electronics (IMD Engineering Physics, part-IV);
Electromagnetic Theory and Optics / Introduction to Engineering Electromagnetics(B. Tech part I).
• Mathematical Physics, Statistical Physics (B.Sc (Hons) part III); Electromagnetic Theory (B.Sc
(Hons) part II); Scientific Computing (B.Sc (Hons) Part II); Mechanics ((B.Sc (Hons) Part I)).
• Physics Lab (B. Sc Part I and Part III, B. Tech Part I); Computer Lab (Part II).
8. Research Projects :
• “Linear polymer in confined geometry”, FAST Track project, DST, New Delhi, (2002-2005).
• “ Statistical Mechanics of short DNA hairpins and its melting profile”, UGC, New Delhi, (2006-2009).
9. Supervision (M.Tech Project / Dissertation & Ph.D Thesis) :
• M. Tech (4th Year) Project : 06
• M. Tech (Final Year) Dissertation : 05
• Ph. D : 02 (completed); 03 (ongoing)
10. Publications :
•
• In Journals /Preprint: 34 • Conference Proceedings: 14
LIST OF PUBLICATIONS: (IN REFERRED JOURNALS / PREPRINTS)
1. Statistical Mechanics of unfolding of polymer in presence of Molecular Crowding, Sanjiv Kumar, A. R. Singh,
D. Giri, and S. Kumar, Preprint (2016).
2. Grafted Polymer under shear flow, Sanjiv Kumar, D. P. Foster, D. Giri, and S. Kumar, Preprint (2015).
3. On the rupture of DNA Molecule, R. K. Mishra, T. Modi, D. Giri, and S. Kumar, J. Chem. Phys. 142,
174910 (2015).
4. Single polymer gating of channels under a salt gradient, Sheshnath, D. P. Foster,D. Giri, and S. Kumar, Phys.
Rev. E88, 054601 (2013).
5. Statistical Mechanics of DNA Rupture: Theory and Simulations, S. Nath, T. Modi, R. K. Mishra, D. Giri, B.
P. Mandal and S. Kumar, J. Chem. Phys.139, 165101 (2013).
6. Scaling of hysteresis loop of interacting polymers under a periodic force, R. K. Mishra, G. Mishra, D. Giri,
and S. Kumar, J. Chem. Phys. 138, 244905 (2013).
7. Statistical mechanics of stretching of biopolymers, A. R. Singh, D. Giri and S. Kumar, Jr. of Stat. Mech.(Theory
& Experiment), P05019 (2011).
8. Role of loop entropy in the force induced melting of DNA hairpin, Garima Mishra, D. Giri, M. S. Li, and
Sanjay Kumar, J. Chem. Phys. 135, 035102 (2011).
9. Force induced melting of the constrained DNA, A. R. Singh, D. Giri and S. Kumar, J. Chem. Phys. 132,
235105 (2010).
10. Force induced unfolding of biopolymers in a cellular environment: A model study, A. R. Singh , D. Giri and
S. Kumar, J. Chem. Phys. 131, 065103 (2009).
11. Role of pulling direction in understanding the anisotropy of the resistance of proteins to force-induced mechanical unfolding, I. Jensen, D. Giri and S. Kumar, Mod. Phys. Lett.B 24, 379 (2010).
12. Effects of molecular crowding on stretching of polymers in poor solvent, A. R. Singh , D. Giri and S. Kumar,
Phys. Rev. E 79, 051801 (2009).
13. Stretching of a single stranded DNA: Evidence for structural transitionr, Garima Mishra, D. Giri and Sanjay
Kumar, Phys. Rev. E 79, 031930 (2009).
14. Role of pulling direction in understanding the energy landscape of proteins, R. Rajesh, D. Giri, I. Jensen and
S. Kumar,Phys. Rev. E 78, 021905 (2008).
15. Conformational properties of polymers, A. R. Singh, D. Giri and S. Kumar, Pramana (2008).
16. Does changing the pulling direction give better insight of bio-molecules?, Sanjay Kumar and D. Giri, Phys.
Rev. Lett. 98, 048101 (2007).
17. Probability distribution analysis of force induced unzipping of DNA, Sanjay Kumar and D. Giri, J. Chem
Phys. 125, 044905 (2006).
18. Effects of Eye-phase in DNA unzipping, D. Giri, Sanjay Kumar, Phys. Rev. E73, 050903(R) (2006).
19. Force induced conformational transition in a system of interacting stiff polymer: Application to unfolding,
Sanjay Kumar, D. Giri, Phys. Rev. E72, 052901 (2005).
20. Force induced triple point for interacting polymers, Sanjay Kumar, D. Giri, S. M. Bhattacharjee, 71 051804
(2005).
21. Statistical mechanics of coil-hairpin transition in a single stranded DNA oligomer, Sanjay Kumar, D. Giri and
Yashwant Singh, Euro. Phys. Lett.70, 15 (2005).
22. Critical behavior of stiff polymer near the surface, D. Giri, P. K. Mishra and Sanjay Kumar, Ind. Jr. of Phys,
77A 561 (2003).
23. Does surface attached globule phase exists?, P. K. Mishra, D. Giri, Sanjay Kumar, and Yashwant Singh,
Physica A 318 171 (2003).
24. Adsorption and collapse Transitions in a linear polymer chain near an attractive wall, R. Rajesh, D. Dhar,
D. Giri, Sanjay Kumar, and Yashwant Singh, Phys. Rev. E65, 056124 (2002).
25. Crossover of a polymer chain from bulk to surface states, Yashwant Singh, D. Giri and Sanjay Kumar, J.
Phys. A:Math and Gen. 34, L67 (2001).
26. Multifractal behavior of n-simplex lattice, Sanjay Kumar, D. Giri and Sujata Krishna, Pramana 54, 863
(2000).
27. Surface adsorption and collapse transition of polymer chains in three dimensions, Yashwant Singh, Sanjay
Kumar and D. Giri, J. Phys. A:Math and Gen. 32, L407 (1999).
28. Surface adsorption and collapse transition of linear polymer chains, Yashwant Singh, Sanjay Kumar and
D. Giri, Pramana 53, 37 (1999).
29. Sandpile Model with Activity Inhibition, S. S. Manna and D. Giri, Phys. Rev. E 56, R4914 (1997).
30. Possibility of polaronic structure in polyaniline lattice: A semiemperical quantum chemical approach, D.Giri,
Kalyan Kundu, D. Majumdar and S. P. Bhattacharyya, J. Mol. Struc. (Theo chem) 417, 175 (1997).
31. A Study of one dimensional correlated disordered system using invariant measure method, K. Kundu, D. Giri
and K. Ray, J. Phys. A Math. Gen 29, 5699 (1996).
32. Evolution of the electronic structure of cyclic polythiophene upon bipolaron doping, K. Kundu, D. Giri, J.
Chem Phys. 105, 11075 (1996).
33. Theoretical study of the evolution of electronic band structure of polythiophene due to bipolaron doping,
D.Giri and Kalyan Kundu, Phys. Rev. B 53, 4340 (1996).
34. Electronic Properties of the random trimer model with degenerate resonances, D.Giri, P. K. Datta and K.
Kundu, Physica B 210, 26 (1995).
35. Nature of States in a Random Dimer Model : Band Width Scaling Analysis, P. K. Datta, D.Giri and K.
Kundu, Phys. Rev. B48 16347 (1993).
36. Tuning of Resonances in the Generalized random Trimer Model, D.Giri, P. K. Datta and K. Kundu, Phys.
Rev. B48 14113 (1993).
37. Nonscattered States in Random Dimer Model, P. K. Datta, D.Giri and K. Kundu, Phys. Rev. B47 10727
(1993).
(II) WORKSHOP/CONFERENCE/SYMPOSIUM PROCEEDINGS:
1. The Propagation of Excitation In a Linear Mass - Spring System In the Presence of an Extra harmonic
Potential, D. Giri and Kalyan Kundu, DAE Solid State Physics Symposium, BHU, Varanasi (INDIA),
1991.
2. Transmission Coefficient Analysis for Random Dimer Model, P. K. Datta, D. Giri and Kalyan Kundu,
Workshop on “Ordering disorder : Prospect and Retrospect in Condensed Matter Physics”; held at
Hyderabad (INDIA), 1993.
3. Tunable resonances in the one dimensional correlated random disordered system, D. Giri, P. K. Datta
and Kalyan Kundu. DAE Solid State Physics Symposium, BARC, Bombay (INDIA), 1994.
4. Analytic studies of the generalized random trimer model, K. Ray, D. Giri, and Kalyan Kundu, DAE
Solid State Physics Symposium, BARC, Bombay (INDIA), 1994.
5. Nature of states in correlated disordered system : Band width scaling analysis, P. K. Datta and D.
Giri. DAE Solid State Physics Symposium, BARC, Bombay (INDIA), 1994.
6. Nature of states in the random trimer model with degenerate resonances, D. Giri, P. K. Datta and
Kalyan Kundu, DAE Solid State Physics Symposium, Jaipur (INDIA), 1994.
7. A systematic study of the structure of polyaniline oligomers, D. Giri, Kalyan Kundu, D. Majumdar
and S. P. Bhattacharyya, DAE Solid State Physics Symposium, Jaipur (INDIA), 1994.
8. Self-Organizing Random Walk, S. S. Manna and D. Giri, DAE Solid State Physics Symposium,
Cochin (INDIA), 1997.
9. Internal Avalanches in a Granular medium, S. S. Manna and D. Giri, DAE Solid State Physics
Symposium, Cochin (INDIA), 1997.
10. Surface adsorption and collapse transition of linear polymer chains, Yashwant Singh, Sanjay Kumar,
D. Giri, Golden Jubilee Discussion meeting on “Liquid Crystals and Other Soft Materials”, RRI,
Bangalore (INDIA), 1998.
11. Criticality of SAWs on n-Simplex Lattices, Sanjay Kumar and Debaprasad Giri, National Conference
on “Nonlinear Systems and Dynamics”, IIT, Kharagpur (INDIA), 2003.
11. Academic / Administrative Responsibilities:
• Head, Department of Physics (since August, 2013).
• Member, Senate of IIT (BHU) since July, 2012.
• Member, Senate Election Committee, since 2012.
• Member of PPC( BHU), DRC (BHU), DFAC of the Department.
• Member, UG-CRC monitoring committee.
• Member, Institute Annual Report Committee.
• Member, High Performance Computing Specification Committee.
12. BRIEF ACCOUNT OF RESEARCH WORK DONE AND RECENT INTEREST:
A. Work done in the area of polymer physics
A1. Adsorption and collapse transitions of a linear polymer chain near an attractive wall.
We have studied the critical behavior of linear polymer chain interacting with impenetrable surface on
regular lattices and the possible phase diagram associated with it [J. Phys. A: Math Gen. 32, L407 (1999);
ibid 34, L67 (2001); Phys. Rev. E 65, 056124 (2002); Physica A 318, 171 (2003)].
When the polymer is close to or even attached to a surface its critical properties may change because
of subtle gain in internal energy and corresponding loss of entropy. When the temperature is lowered the
excluded volume effects becomes negligible and monomer-monomer attraction becomes more prominent
than the monomer-solvent interaction. This self interaction, which is attractive, leads at low enough
temperatures to a “collapse” of polymer.
We studied adsorption transition, collapse transition and simultaneous adsorption and collapse transition and determined the conformational properties of a surface-interacting long flexible polymer chain in
a two-dimensional (2D) poor solvent (where the possibility of collapse only in bulk exists) and in threedimensional (3D) (where the possibility of collapse in both bulk and surface exists).
A simple lattice model for a linear polymer in a poor solvent is a self avoiding walk (SAW) on a regular
lattice with an attractive interaction energy u between pairs of sites of the walk which are unit distance
apart but not joined by an step of the walk. The adsorbing surface is modeled by restricting the walk to
lie in a upper half plane and by associating an attractive energy s with each monomer [site of the walk]
lying on the surface. Let CN,Ns ,Np be the number of SAWs with N monomers, having Ns (≤ N ) monomers
on the surface and Np nearest neighbors. We have obtained CN,Ns ,Np for N ≤ 30 for square lattice and for
N ≤ 20 for cubic lattice by exact enumeration method and analysed the series through ratio method with
associated Neville table.
The partition function of the attached chain is
ZN (ω, u) =
X
CN,Ns ,Np ω Ns uNp
(1)
Ns ,Np
where ω = e−s /kT and u = e−p /kT are reduced variables or Boltzmann factor. Reduced free energy for
the chain can be written as
1
log ZN (ω, u)
(2)
G(ω, u) = lim
N →∞ N
ZN (ω, u) is calculated from the data of CN,Ns ,Np using equation (1) for a given ω and u and free energy is
calculated using suitable extrapolation scheme (like ratio method, Pade approximation, Partial differential
approximation etc).
For fixed u, we identify the position of the phase boundary separating the desorbed phase from the
si
adsorbed or attached phases as that value of ω at which ∂hN
∂s is a maximum. Similarly for fixed ω, we
identify the position of the phase boundary separating the extended phase from the collapsed phase as
ui
that value of u at which ∂hN
∂u is a maximum.
The phase diagram [for 2D] shows the region of existence of the four phases (i) desorbed expanded
(DE), (ii) desorbed collapsed (DC), (iii) adsorbed expanded (AE) and (iv) surface attached globule (SAG).
We have found a new state, though it may not correspond to a new thermodynamic phase, but a surface
transition only.
In case of cubic lattice, surface is a plane (2D) and walk starts from the middle of the plane surface.
Enumerated results were used to calculate the phase diagrams and critical exponents.
In earlier case for 2D, we find four phases which meet at the multicritical point. In case of 3D two
different classes of phase diagrams are found. When the surface condition is such that it cannot have
adsorbed collapsed phase, the phase diagram is similar to that of 2D except that the phase boundary
separating the DE and DC phases which is straight in case of 2D shows bend towards higher values of
monomer-monomer attraction near the special adsorption line. In case the surface can have the adsorbed
collapsed (AC) phase we find five phases, namely, (i) DE, (ii) DC, (iii) AE, (iv) AC and (v) SAG, and two
multicritical points. On the one multicritical point the phases DE, AE, DC and SAG meet whereas on the
other phases AE, AC and SAG meet. The SAG phase exists between these two multicritical points.
To understand the insight of these different phases, we studied the distribution of monomers in different
domain and calculated the most probable configurations of the partition function. From this we have found
that in SAG state, compact globule sticks to the surface in same way as a droplet may lie on a partially
wetting surface.
We have also deduced the qualitative phase diagram [Phys. Rev. E 65, 056124 (2002)] described
above (for three dimensional case) using phenomenological arguments. In the case of a partially directed
polymer in two dimensions, we have analytically determined the exact phase diagram of the SAG phase.
In this case, the polymer has different behaviour depending on whether it is near the wall perpendicular
to the preferred direction (we call it as SAG1) or the wall parallel to the preferred direction (we call it as
SAG2). We determine the phase boundaries of SAG1 and SAG2 phases by calculating their orientation
dependent surface energy. We also determine the transition between SAG1 and SAG2 phases when both
walls are present. Both the numerical as well as analytical results corroborate the proposed qualitative
phase diagram.
A2. Collapse of stiff polymer: Application to unfolding
We have studied the semi-flexible polymer chain in poor solvent and studied the complete phase diagram
[Phys. Rev. E (2005)]. The phase diagram consists of many universality domain. We have shown that
by varying the stiffness parameter, polymer undergoes from the globule state to the folded state. The
transition from the folded to the globule appears to be first order. The conformation of folded state looks
similar to β-sheet. Therefore, it is possible to mimic the titin kind of molecule which has conformation
like β-sheet in a folded state. We also observed that there is an enhancement in θ-temperature with the
rise of stiffness parameter. We further propose that the internal information about the frozen structure of
polymer can be read from the distribution of end-to-end distance which shows saw-tooth like behaviour.
A3. Force induced unzipping of interacting polymers and possible existence of triple point.
We have considered two linear polymer chains which are mutually attracting and self-avoiding in nature
to model a double stranded DNA molecules. We have studied [Phys. Rev. E71 051804 (2005)] two different
models namely A and B which differ in the nature of the mutual interaction of the two strands.
We allow an attractive interaction between monomers or bases only if they are of opposite strands and
are nearest neighbours on the lattice. The nearest neighbour interaction mimics the short range nature
of the hydrogen bonds. In model A, any monomer of one strand can interact with any monomer of the
other strand. In model B, monomer i of one strand can interact only with the ith monomer of the other
strand. This model is similar to the models of DNA studied earlier by Poland and Scheraga [J. Chem.
Phys. 45, 1464 (1966)]. Model A is also equivalent to a diblock copolymer model [Phys. Rev. Lett. 84,
294 (2000); Phys. Rev. E 63, 041801 (2001)] which has two phase transitions with increasing temperature.
The polymers go from a compact spiral-like phase to a zipped phase which then melts at a still higher
temperature. It is this intermediate phase that is of interest to us. In view of the simple ground state in
models B, no such intermediate phases are expected or known. We applied force at one end of the chain
and studied the phase diagram in force-temperature plane. We have shown the existence of a force induced
triple point in an interacting polymer problem that allows two zero-force thermal phase transitions (model
A), but not in model B. A general phase diagram with multicritical points in an extended parameter space
is also proposed for the first time.
B. Work done in the area of Computational Statistical Physics: Sandpile model, Granular System and
Self-organized Criticality.
We have used extensive computer simulation to study [ Phys. Rev. E (rapid Commn.) 56, R4914
(1997)] the sandpile model in which bonds of the system are inhibited for activity after a certain number of
transmission of grains. This condition impels an unstable sand coloumn to distribute grains only to those
neighbours that have toppled less than m times. In this non-abelian model grains effectively move faster
than the ordinary diffusion (super-diffusion). A system size dependent crossover from Abelian sandpile
behaviour to a new critical behaviour is observed for all values of the parameter m.
C. Work done in the area of Correlated disordered system and conducting polymers.
• The work of Anderson [Phys. Rev. 109, 1492 (1958)] in the context of a tight binding model
(TBM) and of Mott and Twose [Adv. Phys. 10, 107 (1961)] on the electronic eigenstates of disordered
systems firmly established that all such states in one dimensional disordered systems are exponentially
localized irrespective of the strength of the disorder. Of course, this result cannot be rigorously valid in
one dimensional systems in which disorder is correlated. One of the example is the model proposed by
Dunlap, Kundu and Phillips [Phys. Rev. B40, 10999 (1989)]. However, the simplest example of correlated
disordered systems is the random dimer model (RDM) [Phys. Rev. Lett.65, 88 (1990)]. RDMs are random
binary alloys with elements of one component appearing in pairs. So, in the context of a TBH, this model
is characterized by a short range correlation in site energies. Due to this short range correlation, a set
of nonscattered states in the neighborhood of the dimer energy is obtained. Random dimer systems,
being the simplest example of the correlated disordered systems, does not offer further scope to improve
upon the width of nonscattered states. On the other hand nonscattered states are essential for disordered
systems to show anomalous transport behavior. Hence, it is necessary to study thoroughly the resonance
property of cluster of various sizes and kinds. Primarily we deal with the resonance property of a trimer
in its generalized form. A random system composed of this trimer and a host element is referred to as
Generalized Random Trimer Model (GRTM) [Phys. Rev. B48 14113 (1993)]. This model is studied
by transfer matrix formalism. It is found that such a random system can sustain nonscattered states
under variety of conditions provided structural correlation between the host element and the elements of
the trimer is introduced. We have also shown the existence of a doubly degenerate resonance. To our
knowledge this is the first time such a situation has been obtained in a disordered system. If the resonance
energy is inside the parent band, the width of the nonscattered states is found to decay as N −1/4 , where
N is the number of sites in the sample. When the resonance energy is at one of the band edges the width
goes as N −1/3 . This results is further substantiated by the numerical estimation of the width of the total
transmitting zone. A sharp transition in the width near the band edges of the parent band is also found.
Density of states (DOS) for this degenerate resonance model has been calculated. This DOS also shows
nonscattered states around the resonance energy. Band width scaling analysis [Phys. Rev. B48 16347
(1993)] has been done to discern the nature of states around the resonance energy. This analysis shows
that states around the resonance energy are indeed extended in nature provided resonance energy is inside
the parent band. If it is at one of the band edges, this analysis suggests that the states are critical like.
Mean square displacement of electrons in this system supports these results.
• In continuation, we have studied whether or not the trimer can be used to explain the anomalous
electrical conductivity in polyaniline [J. Mol. Struc. (Theo chem) 417, 175 (1997)]. There are two parts of
this work. First part consists of identifying the proper unit which can be transformed to a trimer by real
space renormalization group procedure. The next part is to substantiated the structure by appropriate
quantum mechanical calculations. We have used SCF AM1 method for this purpose.
• We have also explored the possible theoretical model [Phys. Rev.B 53, 4340 (1996)] for the conducting
polymers like Polythiophene, Polypyrrole systems. We studied theoretically the evolution of electronic
structure of polythiophene (PT) due to bipolaron doping after modifying the σ-bond compressibility model.
It is also interesting to note that all the calculations in organic conducting polymers are done with open
chains. The basic premise is that the boundary conditions will not effect the outcome. So, we have also
studied the evolution of the electronic structure of conducting polymers using periodic boundary [J. Chem
Phys. 105, 11075 (1996)].
•
Current Research Interest :
1. Conformational behaviors of DNA/RNA Hairpin loops
Our main objective is to provide a systematic theoretical and computational studies of the formation
of DNA/RNA hairpin loops and their role in thermal and force induced melting. A semi-microscopic
model for DNA, which incorporates base direction for the first time, has been used to study the
coil-hairpin transition in a single stranded DNA (ssDNA). It was shown that the rate of unzipping
of hairpin stem is proportional to exp(u) (u being the internal energy) and independent of length of
the loop and dimensionality of the space while the rate of closing varies greatly with loop length and
dimensionality of the space [Europhys. Lett. 70, 15, 2005]. It has been found experimentally that
the type of nucleotides in the loop play the major role in the stability of the hairpin, such as, loop
formed by T- type of nucleotide is less stable than the loop formed by A- type nucleotide. Therefore
it is worthwhile to understand the effect of sequence dependent rigidity of single stranded DNA/RNA
on melting profile.
2. Force induced unzipping of dsDNA: existence of Eye phase
Here we consider a semi-microscopic model of double strand DNA (dsDNA) by incorporating the
directional nature of hydrogen bond to describe the force induced unzipping transition. We have used
force as a thermodynamic parameter and obtained the global phase diagram where the existence of an
intermediate phase leads to the triple point in f-T (force-temperature) plane in a system of interacting
polymers. By applying force in the middle of the chains, we were also able to predict the existence of
an Eye phase in dsDNA, which has great significance in the understanding of transcription process
of dsDNA. [Phys. Rev. E, 71, 51804, 2005; Phys. Rev. E, 73, 50903 (R), 2006, J. Chem. Phys. 124,
44904, 2006].
3. Role of pulling direction in understanding the energy landscape of proteins
At present we are also studying the force-extension curves of flexible and semi-flexible polymers
by changing the direction of the pulling force. Anisotropy is the key issue in understanding the
mechanism of protein unfolding and change in pulling direction provides enhanced insight of such
processes. The first analytical solution of our model shows that changing the pulling direction can
change the nature of the unfolding transitions. The emergence of many new intermediate states due
to the pulling direction suggests that there may be many pathways to the unfolding of a polymer.
[Phys. Rev. Lett. 98, 048101, 2007; Phys. Rev. E, 78 021905, 2008].
4. Force induced unfolding of bio-polymers in a cellular environment
Our main aim here is to study the effect of an applied force on a polymer trapped in a random
environment. The random environment mimics the effect of crowding agents as seen in the cell. The
confinement of the polymer to a restricted portion of the phase space leads to the loss in entropy.
This model may be viewed as the simplest representation of bio-polymers in a cell. We show the
existence of intermediate states during stretching arising as a consequence of molecular crowding
[Phys. Rev. E 79, 051801 2009]. It may be noted that there are many biological events which are
rare in nature. The occurrence of such event may be because of long-tail behavior in the distribution of partition function. Therefore, at this moment of time additional numerical and experimental
works are required to understand the effect of crowding agents on unfolding processes seen in the cell.
5. Force induced melting of the constrained DNA
We have developed a simple model to study the effects of an applied force on the melting of a
double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture
and slippage like transition in a dsDNA. We show that in absence of an applied force, the melting
temperature and the melting profile of dsDNA strongly depend on the constrained imposed on the
ends of dsDNA. The nature of the phase boundary which separates the zipped and the open state for
the shearing like transition is remarkably different than the DNA unzipping [J. Chem. Phys. 132,
235105 (2010)].
6. Statistical mechanics of DNA rupture: Theory and simulations
We consider a simple model to study the effects of the shear force on the rupture mechanism on a
double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with
explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the
rupture force. We obtain a significant difference between the atomistic simulations and the existing
results in the literature based on the coarse-grained models (theory and simulations). We discuss the
possible reasons and improve the coarse-grained model by incorporating the consequences of semimicroscopic details of the nucleotides in its description. The distributions obtained by the modified
model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic
simulations [J. Chem. Phys. 139, 165101 (2013)].
7. Single polymer gating of channels under a solvent gradient
We have studied the effect of a gradient of solvent quality on the coil-globule transition for a polymer
in a narrow pore. A simple self-attracting, self-avoiding walk model of a polymer in solution shows
that the variation in the strength of the interaction across the pore leads the system to go from one
regime (good solvent) to the other (poor solvent) across the channel. This may be thought to be
analogous to thermophoresis, where the polymer goes from the hot region to the cold region under
the temperature gradient. The behavior of short chains is studied using exact enumeration while the
behavior of long chains is studied using transfer matrix techniques. The distribution of the monomer
density across the layer suggests that a gate-like effect can be created, with potential applications as
a sensor [Phys. Rev. E88, 054601 (2013)].
•
FUTURE PLAN :
The field of bio-polymer was mostly studied by biologist, chemist, biochemist etc. Development of
some very sensitive and sophisticated experimental setup such as optical tweezer, atomic force microscope,
FRET etc which can probe the biological molecules at the level of single molecule have revolutionized
the field of biological physics. From these studies it revealed that simple interaction is inadequate in
describing the structural and conformational behavior of bio-polymers e.g DNA and protein. There are
many interesting results from the recent experiments at the single molecule level. However, there are very
few theoretical attempts to explain these findings at molecular level. Hence, there is a clear need for
theoretical understanding of these results. At present we have been doing these problems through different
techniques (like exact enumeration technique, transfer matrix technique, Monte Carlo simulation method,
coarse-grained MD etc.). We also intend to study those using all atom simulation method (Molecular
Dynamics). We expect our studies will provide better insight of the conformational properties of biopolymers and resolve some of the issues related to DNA/RNA and proteins.