Research

We cherish in developing statistical mechanical models and applying them to investigate a wide range of interesting problems in physical chemistry, chemical physics, biology-inspired physics and soft condensed matter. We are also interested in fundamental aspects of statistical mechanics. We use analytical techniques and computer simulations for our research. Some of our current research interests are:

Structural Dynamics of DNA in presence of additional salt:

The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the counterions. It is well known that the structural collapse of DNA is favoured in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl₂) single stranded DNA with base sequence 5’- CGCGAATTCGCG –3’(Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. Atomistic simulations also allow us to investigate the preferential binding of Mg²⁺ to DNA backbones as compared to bases. To quantify this, we make a comparative study of the diffusion coefficients and the rotational correlation times for bulk water and that of different combinations, viz., Mg²⁺-water, water-Mg²⁺-DNA base and water-Mg²⁺-phosphate. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics. This salt induced non-monotonic dynamics of single stranded DNA is typical of multivalent salt and is absent in case of monovalent salt.

Relevant Publication(s):

1. Ion assisted structural collapse of a single stranded DNA: a molecular dynamics approach - Soumadwip Ghosh, Himanshu Dixit and Rajarshi Chakrabarti (submitted).

Transport of macromolecules through Nuclear Pore Complex (NPC):

Exchange of proteins between cell cytoplasm and nucleus takes place through nuclear pores. Each of these pores is made of proteins rich in hydrophobic amino acids. These proteins are called nucleoporins. It is believed that proteins while passing through these pores make hydrophobic contacts with the nucloporins. Recently we have developed a statistical field theory based model of transport of proteins through nuclear pores. Our formulation shows it is the vibrations of the elastic pores that actually helps in faster transport. Also a more gel like structure of the central plug of NPC would be favorable for faster transport than a brush like structure.

Very recently based on a simple polymer brush model of a cylindrical pore, mimicking NPC we show how the factors such as interaction between the tracer and the polymer chains constituting the brush can influence the diffusion. We also analyzed the effect of topology and the mobility of the brush environment on tracer transport.

Relevant Publications:

1. Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex - Rajarshi Chakrabarti, Ananya Debnath and K. L. Sebastian, Physica A: Statistical Mechanics and its Applications, 404, 65 (2014).

2. Tracer diffusion in crowded cylindrical channel - Rajarshi Chakrabarti, Stefan Kesselheim, Peter Košovan and Christian Holm, Phys. Rev. E, 87, 062709 (2013).

Loop formation in single long chain molecule:

Loop formation in long chain molecules is a primary step in polypeptide, protein folding as well as in processes like DNA transcription. We have recently looked at the effect of hydrodynamic interaction on end-to-end loop formation in flexible polymer. We have shown how hydrodynamics can actually make loop formation faster. On the other hand, in a separate study we have shown that presence of viscoelastic solvent around the chain makes looping dynamics slow. Very recently we have analyzed how internal friction can influence end-to-end looping dynamics.

Relevant Publications:

1. Looping and reconfiguration dynamics of a flexible chain with internal friction - Nairhita Samanta, Jayanta Ghosh and Rajarshi Chakrabarti, AIP Advances, 4, 067102 (2014).

2. End to end loop formation in a single polymer chain with internal friction - Nairhita Samanta and Rajarshi Chakrabarti, Chem. Phys. Letts., 582, 71 (2013).

3. Dynamics of end to end loop formation in viscoelastic fluid - Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications, 391, 5326 (2012).

4. Dynamics of end to end loop formation: A flexible chain in the presence of hydrodynamic interaction – Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications, 391, 4081 (2012).

Condensed Phase Dynamics:

Dynamical processes in chemistry and biology, e.g. chemical reactions or biological transport frequently take place in condensed phase vand microscopically can be described using theories of non equilibrium statistical mechanics. In chemical physics community a standard approach to model such processes is to use theories of Brownian motion. Based on Feynman's path integral we developed an approximate theory to calculate the rate of a chemical reaction which is modelled using a sink function in the diffusion equation. We have also worked on the barrier crossing problem of a particle subjected to color noise. Very recently we have developed a very general method to calculate the survival probability and first passage time of a Brownian particle irrespective of whether it is markovian or non-markovian or even non-Gaussian.

Relevant Publications:

1. Dynamic disorder with exponential sink – Rajarshi Chakrabarti, Chem. Phys. Letts., 495, 60 (2010).

2. A lower bound to the survival probability and an approximate first passage time distribution for Markovian and non-Markovian dynamics in phase space - Rajarshi Chakrabarti and K. L. Sebastian, J. Chem. Phys. 131, 224504 (2009).

3. Exact Analytical Evaluation of Time Dependent Transmission Coefficient from the method of reactive flux for an inverted parabolic barrier- Rajarshi Chakrabarti, J. Chem. Phys., 126 (13), 134106 (2007).

4. Rate Processes with Dynamical Disorder: A Direct Variational Approach - Ananya Debnath, Rajarshi Chakrabarti and K. L. Sebastian, J. Chem. Phys., 124 (20), 204111 (2006).

Breathing dynamics in double stranded DNA:

We have also looked at the dynamics of transient bubble known as the breathing motion in double stranded DNA. We showed how simple Rouse model could be used to describe breathing motion in double stranded DNA. Use of Rouse model also makes it possible to see the effect of chain connectivity to the breathing dynamics by going beyond a simple single reaction co-ordinate description used in earlier studies.

Relevant Publication:

1. Bubble dynamics in double stranded DNA: A Rouse chain based approach – Rajarshi Chakrabarti, Chem. Phys. Letts., 502, 107 (2011).

Statics and Dynamics of Polymer-nanoparticle mixture:

We have used integral equation theories, such as Polymer Reference Site Interaction Model (PRISM) to see the packing of polymer-nanoparticle mixture with different nano-particle shapes. We have also developed an effective one-component approach by integrating out the polymer degrees of freedom which is computationally less expensive but can semi-quantitatively predict the equilibrium structure. Also we have looked at the packing and compressibility of carbon blacks and polymer mixture and analyzed whether it would form a glass based on mode-coupling theory calculation.

Relevant Publications:

1. Packing Correlations, Collective Scattering and Compressibility of Fractal-like Aggregates in Polymer Nanocomposites and Suspensions – Rajarshi Chakrabarti, Jean-Yves Delannoy, Marc Couty and Kenneth S Schweizer, Soft Matter, 7, 5397 (2011)

2. Polymer mediated structure of nanoparticles in dense melts: transferability and effective one component approach - Rajarshi Chakrabarti and Kenneth S. Schweizer, J. Chem. Phys. 133, 144905 (2010).

Non-equilibrium Fluctuation theorem:

In recent past we showed how a system plus bath model where the system is a driven harmonic oscillator and the bath is a collection of harmonic oscillators each coupled to the system linearly can be used to verify the transient state work fluctuation theorem and Jarzynski's equality. Our formulation is equivalent to a non-markovian generalized Langevin equation description of a driven harmonic oscillator.

Relevant Publication:

1. Transient state work fluctuation theorem for a classical harmonic oscillator linearly coupled to a harmonic bath - Rajarshi Chakrabarti, Pramana – J. Phys., 72(4), 665, (2009).