49 citations · 169 across the 11 of their papers we have counts for
11 papers
Polyformer: a generative framework for thermodynamic modeling of polymeric molecules
Alessio Valentini, David Pekker, Chungwen Liang +2
The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biolog…
Machine Learning 1- and 2-electron reduced density matrices of polymeric molecules
David Pekker, Chungwen Liang, Sankha Pattanayak +1
Encoding the electronic structure of molecules using 2-electron reduced density matrices (2RDMs) as opposed to many-body wave functions has been a decades-long quest as the 2RDM co…
What does the Allen Gene Expression Atlas tell us about mouse brain evolution?
Swagatam Mukhopadhyay, Pascal Grange, Anirvan M. Sengupta +1
We use the Allen Gene Expression Atlas (AGEA) and the OMA ortholog dataset to investigate the evolution of mouse-brain neuroanatomy from the standpoint of the molecular evolution o…
The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state
Swagatam Mukhopadhyay, Anirvan M. Sengupta
We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic ma…
Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators
Swagatam Mukhopadhyay, Paul D. Schedl, Vasily M. Studitsky +1
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these lon…
Anomalous diffusion and stretched exponentials in heterogeneous glass-forming liquids: Low-temperature behavior
J. S. Langer, S. Mukhopadhyay
We propose a model of a heterogeneous glass forming liquid and compute the low-temperature behavior of a tagged molecule moving within it. This model exhibits stretched-exponential…