3 papers
cond-mat.soft2021
On the emergence of orientational order in folded proteins with implications for allostery
Debayan Chakraborty, Mauro Lorenzo Mugnai, D. Thirumalai
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully u…
cond-mat.stat-mech2018
Charge fluctuation effects on the shape of flexible polyampholytes with applications to Intrinsically disordered proteins
Himadri S. Samanta, Debayan Chakraborty, D. Thirumalai
Random polyampholytes (PAs) contain positively and negatively charged monomers that are distributed randomly along the polymer chain. The interaction between charges is assumed to…
q-bio.BM2018
Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
Debayan Chakraborty, Naoto Hori, Dave Thirumalai
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar…