Publications
Li, Q, Kim, G., Jing, L. Ji, X. Elmore, D.E., and Radhakrishnan, M.L. "Electrostatics-Based Computational Design and Experimental Analysis of Buforin II Antimicrobial Peptide Variants with Increased DNA Affinities." ACS Omega, 8:33701-33711, 2023.
Illingworth, S. and Radhakrishnan, M.L. "'I am here because I wanted to shine': how poetry can be used to better understand undergraduate students’ first-year chemistry or related course experiences." Chem. Res. Educ. Prac., 24:868-881, 2023.
Radhakrishnan, M.L. “How to Model for a Living: The CSGF as a Catalyst for Supermodels,” Comp. Sci. Eng., 23:34-41, 2021.
Beers, M. A.+, Hall, M. L.+, Matthew, A.G.W, Elmore D.E., Oakes, E.S.C., Goss, J.W., and Radhakrishnan, M.L. “A Fully-Integrated, Undergraduate Introductory Biology and Chemistry Course with a Community-Based Focus: I. Vision, Design, Implementation, and Development,” Biochem. Mol. Biol. Ed., 49:859-869, 2021.
Pociask, S.+, Weerapana, A.+, Taylor, P. Radhakrishnan, M.L., Oakes, E.S.C., Matthews,A.G.W., Elmore, D.E. “A Fully-Integrated, Undergraduate Introductory Biology and Chemistry Course with a Community-Based Focus: II. Assessment of Course Effectiveness,” Biochem. Mol. Biol. Ed., 49: 737-747, 2021.
Kim, R. and Radhakrishnan, M.L. “Macromolecular Crowding Effects on Electrostatic Binding Affinity: Fundamental Insights from Theoretical, Idealized Models.” J. Chem. Phys. 154, 225101, 2021.
Perez, C.P., Elmore, D.E., and Radhakrishnan, M.L. "Computationally modeling electrostatic binding energetics in a crowded, dynamic environment: Physical insights from a peptide-DNA system." J. Phys. Chem. B, 123:10718-10734, 2019.
Fernandez, O.E. and Radhakrishnan, M.L. "The Quantum Mechanics of a Rolling Moleceular 'Nanocar.'" Scientific Reports, 8:14878, 2018.
Radhakrishnan, M.L. “Perspectives: The chemistry between us.” Chemical & Engineering News, 95:30, 2017.
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. (Click to download source code and coordinate files)
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. (Click to download dataset and readme files)
Publications From Work That Had Started Prior to Mala Radhakrishnan's Arrival At Wellesley College
Radhakrishnan M.L, Tidor B. "Cellular-level models as tools for cytokine design." Biotechnol. Prog.2 6:919-937, 2010.
Zhang Y.L.*, Radhakrishnan M.L.*, Lu, X.H., Gross, A.W., Tidor B. "Symmetric signaling by an asymmetric 1 erythropoietin:2 erythropoitein receptor complex." Mol. Cell, 33:266-274, 2009.
Flaherty P, Radhakrishnan M.L., Dinh T., Rebres R.A., Roach T.I., Jordan, M.I. and Arkin A.P. "A dual receptor crosstalk model of G-protein-coupled signal transduction." PLOS Comp. Bio. 4:e1000185, 2008.
Radhakrishnan M.L., 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 M.L., 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 M.L., Su S.L. "Dead-end elimination as a heuristic for min-cut image segmentation." Proceedings of the International Conference on Image Processing, 2006.
Ahn J.S., Radhakrishnan M.L., Mapelli M., Choi S., Tidor B., Cuny G.D., Musacchio A., Yeh, L., Kosik K.S.. "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 Y.Y., Radhakrishnan M.L., Fast P.L., Cramer C.J., Truhlar D.G. "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.