Photo of a portion of the periodic table showing elements

Department of

Photo of Arnab   Mukherjee

Arnab Mukherjee


Chemistry Data Science (Joint)

Theoretical and computational chemistry, biophysics


Arnab Mukherjee did his BSc from Jadavpur university, Kolkata in 1998. He then joined Indian Institute of Science, Bangalore as an integrated PhD student in chemical sciences. He completed his PhD from S. S. C. U. department of IISc Bangalore in 2005 under the supervision of Professor Biman Bagchi. Dr. Mukherjee then went for his postdoctoral research in Ecole Normale Superierure, Paris, France from 2005 to 2007 and then to University of Colorado, Boulder from 2007 to 2009. He joined IISER Pune as an assistant professor in November, 2009. He became associate professor in 2015 and full professor in 2021.


Computational Chemistry and Computational Biophysics

The research interest of Prof. Arnab Mukherjee is computational chemistry and biophysics in various topics ranging from drug-DNA intercalation, DNA structural change, single water entropy, protein folding and protein-DNA binding, dynamical recrossing and internal friction in proteins and machine learning. He also collaborates with experimental colleagues in various projects such as synthetic ion channels, spectroscopic investigation of molecular recognition, etc.

Selected Publications

Molecular mechanism of direct proflavine-DNA intercalation: Evidence for drug-induced minimum base-stacking penalty pathway.  Wilbee D. S. and A. Mukherjee, J. Phys. Chem. B 116, 12208 (2012).

Intercalation and de-intercalation pathway of proflavine through the minor and major grooves of DNA: Role of water and entropy. Wilbee D Sasikala and Arnab Mukherjee. Phys. Chem. Chem. Phys., DOI:10.1039/C3CP50501D

Single water entropy: Hydrophobic crossover and application to drug binding. Wilbee D. Sasikala and Arnab Mukherjee. J. Phys. Chem. B B 118, 10553 (2014).

Distribution of residence time of water around DNA base pairs: Governing factors and the origin of heterogeneity. Debasis Saha, Shreyas Supekar, and Arnab Mukherjee. J. Phys. Chem. B 119, 11371 (2015).

Computational approach to explore B/A junction free energy in DNA. Mandar Kulkarni and Arnab Mukherjee. Chem. Phys. Chem. 17, 147 (2016).

Probing the viscosity dependence of rate: Internal friction or the lack of friction?  V. M. Hridya and Arnab Mukherjee, J. Phys. Chem. B 122, 9081 (2018).

Molecular mechanism of intercalation of SOX-4 protein into DNA inducing bends and kinks. Reman Kumar Singh and Arnab Mukherjee. J. Phys. Chem. B 2021, 125, 15, 3752–3762.

Accurate prediction of B-form/A-form DNA conformation propensity from primary sequence: A machine learning and free energy handshake. Abhijit Gupta, Mandar Kulkarni, and Arnab Mukherjee*, Patterns (2021).(

Atomistic de-novo inhibitor generation guided drug repurposing for SARS-CoV-2 spike protein with free energy validation by well-tempered metadynamics (