The Berne Group

Jagannath Mondal


Ph.D. in chemistry, University of Wisconsin, Madison (2011)

M.Sc. in chemistry, I.I.T. Kanpur,India (2006)

B.Sc. in chemistry, Calcutta University, India (2004)



Research Interests

My research in the Berne group mainly involves utilizing computer simulation technique to provide key insights into various problems of biophysical interest. An interesting project in this respect is exploring, from a free energy perspective, potential role of water in the binding of a drug to a protein. In particular, we are investigating the free energy cost in the complete de-wetting of pocket relative to bulk media upon binding of a ligand to a pocket. We are also using our recently developed 'watermap' technique to characterize the thermodynamic nature of pocket-water at various ligand-pocket separation.

Another focus of my research is addressing the longstanding question on the reverse role of protecting osmolyte Trimethylamine N-oxide (TMAO) and denaturing osmolyte Urea on purely hydrophobic interaction.In this respect, I am working with G.Stirnemann to explore the collapse behavior of a model lennard-Jones polymeric chain in presence of TMAO and urea , with an ultimate goal of reconciling the molecular mechanisms behind the reverse behavior of the chain in presence of two different osmolytes.

Selected Publications

A complete list can be found on my website.

J. Mondal, M. Mahanthappa and A. Yethiraj, "Self-assembly of Gemini surfactants:A computer simulation study." Journal of Physical Chemistry B,(

J. Mondal and A. Yethiraj, "Effect of secondary structure on self-assembly of amphiphilic molecules." Journal of Chemical Physics,132, 084902 (2012).

J. Mondal and A. Yethiraj, "The driving force for the association of amphiphilic molecules." Journal of Physical Chemistry Letters,2, 2391 (2011).

J. Mondal, B. P. Bratton, Y. Li, A. Yethiraj and J. C. Weisshaar, "Entropy-based mechanism of ribosome-nucleoid segregation in E.coli cells." Biophysical Journal,100, 2605 (2011).

J. Mondal, X. Zhu, Q. Cui and A. Yethiraj, "Sequence-dependent interaction of beta-peptides with membranes." Journal of Physical Chemistry B,114, 13585 (2010).

J. Mondal, B. J. Sung and A. Yethiraj, "Sequence-dependent organization of beta-peptides in self-assembled monolayers." Journal of Physical Chemistry B,113, 9379 (2009).