Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective
D Chowdhury - Physics Reports, 2013 - Elsevier
A molecular motor is made of either a single macromolecule or a macromolecular complex.
Just like their macroscopic counterparts, molecular motors “transduce” input energy into …
Just like their macroscopic counterparts, molecular motors “transduce” input energy into …
Physics of collective transport and traffic phenomena in biology: progress in 20 years
D Chowdhury, A Schadschneider, K Nishinari - Physics of Life Reviews, 2024 - Elsevier
Enormous progress have been made in the last 20 years since the publication of our review
[1] in this journal on transport and traffic phenomena in biology. In this brief article we …
[1] in this journal on transport and traffic phenomena in biology. In this brief article we …
Reservoir crowding in a resource-constrained exclusion process with a dynamic defect
To understand the complicated transport processes that occur in biological and physical
systems, we investigate a constrained totally asymmetric simple exclusion process with a …
systems, we investigate a constrained totally asymmetric simple exclusion process with a …
Backtracking dynamics of RNA polymerase: pausing and error correction
Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of
such pauses is backtracking, where the RNA polymerase translocates backward with …
such pauses is backtracking, where the RNA polymerase translocates backward with …
First-passage processes on a filamentous track in a dense traffic: optimizing diffusive search for a target in crowding conditions
Several important biological processes are initiated by the binding of a protein to a specific
site on the DNA. The strategy adopted by a protein, called transcription factor (TF), for …
site on the DNA. The strategy adopted by a protein, called transcription factor (TF), for …
Dynamic blockage in an exclusion process
We study an asymmetric exclusion model with one dynamic roadblock particle. The
roadblock particle is allowed to move diffusively as well as by long-range jumps mimicking …
roadblock particle is allowed to move diffusively as well as by long-range jumps mimicking …
Cooperative RNA polymerase molecules behavior on a stochastic sequence-dependent model for transcription elongation
The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the
major component of the transcription machinery. The development of single-molecule …
major component of the transcription machinery. The development of single-molecule …
Asymmetric exclusion process with a dynamic roadblock and open boundaries
Motivated by complex transport processes occurring in nature, we study a totally asymmetric
simple exclusion process (TASEP) with a dynamic'roadblock'particle. The roadblock particle …
simple exclusion process (TASEP) with a dynamic'roadblock'particle. The roadblock particle …
Error correction during DNA replication
AK Sharma, D Chowdhury - Physical Review E—Statistical, Nonlinear, and …, 2012 - APS
DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two
different situations during DNA replication. It plays its a normal role as a polymerase …
different situations during DNA replication. It plays its a normal role as a polymerase …
Template-directed biopolymerization: Tape-copying turing machines
AK Sharma, D Chowdhury - Biophysical Reviews and Letters, 2012 - World Scientific
DNA, RNA and proteins are among the most important macromolecules in a living cell.
These molecules are polymerized by molecular machines. These natural nano-machines …
These molecules are polymerized by molecular machines. These natural nano-machines …