Mala Radhakrishnan

  • Program Years: 2004-2007
  • Academic Institution: Massachusetts Institute of Technology
  • Field of Study: Physical Chemistry
  • Academic Advisor: Bruce Tidor
  • Practicum(s):
    Lawrence Berkeley National Laboratory (2005)
  • Degree(s):
    Ph.D. Physical Chemistry, Massachusetts Institute of Technology, 2007
    A.B. Chemistry and Physics, Harvard University, 2000

Current Status


Fernandez, O.E. and Radhakrishnan, M.L. "The Quantum Mechanics of a Rolling Moleceular 'Nanocar.'" Scientific Reports, 8:14878, 2018.

Sim, S., Wang, P., Beyer, B.N., Cutrona, K.J., Radhakrishnan, M.L., Elmore, D.E. "Investigating the nucleic acid interactions of histone-derived antimicrobial peptides." FEBS Letters. 591:706-717, 2017.

Norabuena, E., Barnes Williams, S., Klureza, M., Goehring, L., Gruessner, B., Radhakrishnan, M.L., Jamieson, E., Nunez, M. "Effect of the Spiroiminodihydantoin Lesion on Nucleosome Stability and Positioning." Biochemistry 55: 2411-421, 2016.

Shen, Y., Radhakrishnan, M.L., and Tidor, B. "Molecular mechanisms and design principles for promiscuous inhibitors: Lessons learned from HIV-1 protease inhibition." Proteins: Structure, Function, and Bioinformatics. 83:351-372, 2015.

Qi, H.W., Nakka, P., Chen, C., and Radhakrishnan, M.L. "The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: A computational, implicit solvent-based study." PLoS ONE, 9(6):e98618, 2014.

Kreienkamp, A.B., Liu, L. Y. Minkara, M.S., Knepley, M.G. Bardhan, J.P., and Radhakrishnan, M.L. "Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding," special edition ("Mathematical and Computational Molecular Biology") of Molecular Based Mathematical Biology. 1:124-150, 2013.

Radhakrishnan, M.L. "Designing Electrostatic Interactions in Biological Systems via Charge Optimization or Combinatorial Approaches: Insights and Challenges with a Continuum Electrostatic Framework," Theor. Chem Acc., (Theor. Chim. Acta.), 131:1, 2012. (invited feature article)

Minkara, M. S., Davis, P. H., and Radhakrishnan, M. L. Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors and variants of HIV-1 RT.Proteins: Structure, Function, and Bioinformatics, 80:573-590, 2012.

Doherty, K. M., Nakka, P., King, B. M., Rhee, S.-Y., Holmes, S. P., Shafer, R.W., and Radhakrishnan, M.L. A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinformatics, 12:477, 2011.

Radhakrishnan ML, Tidor B. Cellular-level models as tools for cytokine design. Biotechnol. Prog.2 6:919-937, 2010.

Zhang YL*, Radhakrishnan ML*, Lu, XH, Gross, AW, Tidor B. Symmetric signaling by an asymmetric 1 erythropoietin:2 erythropoitein receptor complex.Mol. Cell, 33:266-274, 2009.

Flaherty P, Radhakrishnan ML, Dinh T, Rebres RA, Roach TI, Jordan, MI and Arkin AP. A dual receptor crosstalk model of G-protein-coupled signal transduction. PLOS Comp. Bio. 4:e1000185, 2008.

Radhakrishnan ML, Tidor B. Optimal drug cocktail design: Methods for targeting molecular ensembles and insights from theoretical model systems. J. Chem. Inf. Model. 48:1055-1073, 2008.

Radhakrishnan ML, Tidor B. Specificity in molecular design: A physical framework for probing the determinants of binding specificity and promiscuity in a biological environment. J. Phys. Chem. B 111:13419-13435, 2007.

Radhakrishnan ML, Su SL. Dead-end elmination as a heuristic for min-cut image segmentation.Proceedings of the International Conference on Image Processing, 2006.

Ahn JS, Radhakrishnan ML, Mapelli M, Choi S, Tidor B, Cuny GD, Musacchio A, Yeh, L., Kosik KS. Defining cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation. Chem. Biol. 12:811-823, 2005.

Deng T, Whitesides G, Radhakrishnan M, Zabow G, Prentiss M. Manipulation of magnetic microbeads in suspension using micromagnetic systems fabricated with soft lithography. App. Phys. Lett. 78:1775-1777, 2001.

Chuang YY, Radhakrishnan ML, Fast PL, Cramer CJ, Truhlar DG. Direct dynamics for free radical kinetics in solution: solvent effect on the rate constant for the reaction of methanol with atomic hydrogen. J. Phys. Chem. A 103:4893-4909, 1999.


2008 DOE CSGF Howes Scholar
Won honorable mention in DOE CSGF 2005 Essay Competition
Dept. of Chemistry Award for Excellence in Teaching by a Graduate Student
Robert T. Haslam Graduate Fellowhip, 2002-2003 (MIT)
Phi Beta Kappa, 2000