57 citations · 193 across the 14 of their papers we have counts for
14 papers
Bayesian Learning of Distance Metrics Beyond RMSD for Biomolecule Alignment, Clustering, and Domain Identification
Saumyak Mukherjee, Gerhard Hummer
Root-mean-square deviation (RMSD) is the standard metric of structural comparison in molecular dynamics (MD) simulations. In its conventional form, RMSD assigns equal weight to all…
Surface Induced Frustration of Inherent Dipolar Order in Nanoconfined Water
Sayantan Mondal, Saumyak Mukherjee, Biman Bagchi
Surface effects could play a dominant role in modifying the natural liquid order. In some cases, the effects of the surface interactions can propagate inwards, and even can interfe…
BEER: Biochemical Estimator and Explorer of Residues -- A Comprehensive Software Suite for Protein Sequence Analysis
Saumyak Mukherjee
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or…
Signatures of Surprising Diffusion-Entropy Scaling across Pressure Induced Glass Transition in Water
Saumyak Mukherjee, Biman Bagchi
Because of the negative inclination of the solid-liquid phase separation line in water, ice Ih melts on compression. On further increase in pressure the liquid water transforms int…
Origin of Multiple Infection Waves in a Pandemic: Effects of Inherent Susceptibility and External Infectivity Distributions
Saumyak Mukherjee, Sayantan Mondal, Biman Bagchi
Two factors that are often ignored but could play a crucial role in the progression of an infectious disease are the distributions of inherent susceptibility () and extern…
Attainment of Herd Immunity: Mathematical Modelling of Survival Rate
Sayantan Mondal, Saumyak Mukherjee, Biman Bagchi
We study the influence of the rate of the attainment of herd immunity (HI), in the absence of an approved vaccine, on the vulnerable population. We essentially ask the question: ho…
Dynamical Theory and Cellular Automata Simulations of Pandemic Spread: Understanding Different Temporal Patterns of Infections
Saumyak Mukherjee, Sayantan Mondal, Biman Bagchi
Here we propose and implement a generalized mathematical model to find the time evolution of population in infectious diseases and apply the model to study the recent COVID-19 pand…
Ice-water Interface: Correlation between Structure and Dynamics
Saumyak Mukherjee, Sayantan Mondal, Biman Bagchi
To comprehend the complexities of the ice-water interface, we perform a study that attempts to correlate the altered dynamics of water to its perturbed structure at, and due to, th…
In search of the origin of long-time power-law decay in DNA solvation dynamics
Saumyak Mukherjee, Sayantan Mondal, Subhajit Acharya +1
Experiments reveal that DNA solvation dynamics (SD) is characterized by multiple time scales ranging from a few ps to hundreds of ns and in some cases even up to microseconds. The…
Towards Understanding the Structure, Dynamics and Bio-activity of Diabetic Drug Metformin
Sayantan Mondal, Rudra N Samajdar, Saumyak Mukherjee +2
Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. I…
Cavity Waters Govern Insulin Association and Release: Inferences from Experimental Data and Molecular Dynamics Simulations
Saumyak Mukherjee, Sayantan Mondal, Ashish Anilrao Deshmukh +2
While a monomer of the ubiquitous hormone insulin is the biologically active form in the human body, its hexameric assembly acts as an efficient storage unit. However, the role of…
On the origin of diverse time scales in the protein hydration layer solvation dynamics: A molecular dynamics simulation study
Sayantan Mondal, Saumyak Mukherjee, Biman Bagchi
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics…
Distinguishing dynamical features of water inside protein hydration layer: Distribution reveals what is hidden behind the average
Saumyak Mukherjee, Sayantan Mondal, Biman Bagchi
Since the pioneering works of Pethig, Grant and Wuthrich on protein hydration layer, many studies have been devoted to find out if there are any general and universal characteristi…
Dynamical coupling between protein conformational fluctuation and hydration water: Heterogeneous dynamics of biological water
Sayantan Mondal, Saumyak Mukherjee, Biman Bagchi
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyro…