Statistical view of Biological dynamics.
1. Understanding Mechanism of Opening and Closing of Loop of a Long Polymer Chain:Understanding the kinetics of loop formation of long chain polymer molecules has been an interesting research field both, to experimentalists and theoreticians. Loop formation is believed to be an initial step in understanding several protein events. The theories of loop formation dynamics are in general approximate. The looping dynamics of a single polymer chain having reactive end-groups hav been modeled by simplest possible option. In our model, dynamics of end-to end distance is mathematically represented by an equation for a random walking under harmonic potential. Looping process is ensured by adding a sink of arbitrary strength in that equation. We have also incorporated the effect of all other chemical reactions involving either one or both of the end-group on rate of end-to-end loop formation - to the best of our knowledge this is the first time this has been done in any analytical model. An important future direction of this research is to understand the dynamics of contact formation between different parts of a long chain molecule.
- Understanding looping kinetics of a long polymer molecule in solution. Exact solution for delta function sink model, M. Ganguly* & A. Chakraborty, Physica A, 484, 163 (2017).
- Exploring the role of relaxation time, bond length and length of the polymer looping of a long polymer chain. M. Ganguly* & A. Chakraborty, Chem. Phys. Lett. [under revision] (2017).
- Understanding looping kinetics of a long polymer molecule in solution. Exact solution for delocalized sink model, M. Ganguly* & A. Chakraborty [submitted] (2018).
- Understanding reversible looping kinetics of a long polymer molecule in solution. Exact Solution for delta function sink model, M. Ganguly* & A. Chakraborty [submitted] (2018).
- Understanding reversible looping kinetics of a long polymer molecule in solution. Exact Solution for delocalized sink model, M. Ganguly* & A. Chakraborty [in preparation] (2018).
Polymer looping problem: The fundamental understanding of loop formation of long polymer chains in solution has been an important thread of research for several theoretical and experimental studies. Loop formations are important phenomenological parameters in many important biological processes. We will perform Brownian dynamics simulation studies of looping of a single polymer chains to to see how ' shape of the sink function' decides the looping dynamics.
Molecular Ratchets: It was mentioned by R. P. Feynman that a microscopic ratchet in equilibrium with an isothermal heat bath can not have any preference in rotational direction - otherwsie the ratchet can be used to extract work from an isothermal system, which violates the second law of thermodynamics. Here we plan to vary temperature with time and use symmetric and assymetric ratchet for computer simulation.