Serafim  Papadimitriou

Ravi Radhakrishnan

Associate Professor

biography

Ravi Radhakrishnan as a Associate Professor in Department of Bioengineering, University of California Berkeley. He obtained the Ph.D., degree, Cornell University, USA in 2001.From 2010-2012, Associate Professor of Chemical and Biomolecular Engineering, University of Pennsylvania School of Engineering and Applied SciencesHe was Honored in 2008, Hewlett-Packard Outstanding Young Investigator, American Chemical Society; Citation: Dynamic Coupling Machinery in DNA Polymerases, Discovering Hidden Nano-Modules in Biomolecular Function through Theory and Simulationsin 2015 Fellow of the American Institute of Medical and Biological Engineering.His Leadership Positions in Scientific and Professional Societies as Invited Member of Interagency Modeling and Analysis Group,NIH, NSF, NASA, DARPA, DOE in 2011.In 2012-Present, Insilico Oncology Consortium, Virtual Physiological Human, European Commission.

 

Area of Interest

Statistical Mechanics; Molecular Systems Biology; Multiscale Modeling, Nanobiotechnology, Insilico Oncology, Insilico and Systems Pharmacology.


top publication

1. K. S. Gajula, P. J. Huwe, C. Y. Mo, D. J. Crawford, J. T. Stivers, R. Radhakrishnan, R. M. Kohli, High-throughput mutagenesis reveals functional determinants for DNA targeting by Activation-Induced Cytidine Deaminase, Nucleic Acids Research, 2014, in press. DOI: 10.1093/nar/gku689
2. R. W. Tourdot, R. P. Bradley, N. Ramakrishnan, R. Radhakrishnan, Multiscale Computational Models in Physical Systems Biology of Intracellular Trafficking, IET Systems Biology, 2014, 8(5), 198-213, DOI:http://dx.doi.org/10.1049/iet-syb.2013.0057
3. R. W. Tourdot, N. Ramakrishnan, R. Radhakrishnan, Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers, Phys. Rev. E, 2014, 90, 022717, DOI: http://dx.doi.org/10.1103/PhysRevE.90.022717
4. N. Ramakrishnan, P. B. Sunil Kumar, R. Radhakrishnan, Mesoscale computational methods for membrane remodeling by curvature inducing proteins, Physics Reports, 2014, 543, 1-60, DOI: 10.1016/j.physrep.2014.05.001
5. J. Liu, D. M. Eckmann, P. S. Ayyaswamy, R. Radhakrishnan, Modeling of Binding Free Energy of Targeted Nanocarriers to Cell Surfaces, Heat and Mass Transfer (Springer), 2014, 50(3), 315-321. DOI: 10.1007/s00231-013-1274-0
6. Counterion-mediated pattern formation in membranes containing anionic lipids, D. R. Slochower, Y.-H. Wang, R. W. Tourdot, R. Radhakrishnan, and P. A. Janmey, Advances in Colloid and Interface Science, 2014, in press. DOI: 10.1016/j.cis.2014.01.016
7. Computational Delineation of Tyrosyl-Substrate Recognition and Catalytic Landscapes in the Epidermal Growth Factor Receptor Tyrosine Kinase Domain, Y. Liu, R. Radhakrishnan, Molecular Biosystems, 2014, in press. DOI: 10.1039/C3MB70620F
8. E. Telesco, R. Vadigepalli, R. Radhakrishnan, Molecular Modeling of the ErbB4/HER4 Kinase in the Context of the HER4 Signaling Network Helps Rationalize the Effects of Clinically Identified HER4 Somatic Mutations on the Cell Phenotype, Biotechnology Journal, 2013, 8, 1452-1464. (Selected as a “In this Issue” article). DOI: 10.1002/biot.201300022
9. D. R. Slochower, P. J. Huwe, R. Radhakrishnan, and P. A. Janmey, Quantum and all-atom molecular dynamics simulations of protonation and divalent ion binding to phosphatidylinositol 4,5-bisphosphate (PIP2), J. Phys. Chem B., 2013, 117 (28), 8322–8329. (DOI)
10. Y. Zhao, J. Liu, C. Yang, B. R. Capraro, T. Baumgart, R. P. Bradley, N. Ramakrishnan, R. Radhakrishnan, T. Svitkina, and W. Guo, Generation of Membrane Curvature by Exo70, Dev. Cell., 2013, 26, 266-278. [DOI]
11. G. S. Stamatakos, N. Graf, R. Radhakrishnan, Multiscale Cancer Modeling and In Silico Oncology: Emerging Computational Frontiers in Basic and Translational Cancer Research, J. Bioengineering and Biomed. Sci., 2013, 3(2), 1000e114. (DOI) (open access) PDF (Open Access)
12. R. P. Bradley, R. Radhakrishnan, Models for protein-cell membrane interaction, Special Issue on Multiscale Simulations in Soft Matter, Polymers (ISSN 2073-4360), 2013, 5, 890-936. [DOI]
13. B. J. Zern, A-M. Chacko, J. Liu, C. F. Greineder, E. R. Blankemeyer, R. Radhakrishnan, V. R. Muzykantov, Reduction of nanoparticle avidity enhances the selectivity of vascular targeting and PET detection of pulmonary inflammation, ACS Nano, 2013, 7(3):2461-2469. (Pubmed ID: 23383962).
14. P. S. Ayyaswamy, V. Muzykantov, D. M. Eckmann, R. Radhakrishnan, Nanocarrier Hydrodynamics and Binding in Targeted Drug Delivery: Challenges in Numerical Modeling and Experimental Validation, J. Nanotechnology for Engineering and Medicine, 2013, 4, 010101. [DOI: 10.1115/1.4024004]
15. Y. Liu, N. J. Agrawal, R. Radhakrishnan, A molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK3, and CDK2 protein kinases, J. Molecular Modeling, 2013, 19, 371-382. (DOI).
16. P. J. Huwe, and R. Radhakrishnan, Computational Methodology for Mechanistic Profiling of Kinase Domain Mutations in Cancers, Proceedings of the IEEE, 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, 2013, pp:1-4. Open access version of the article is also available through ICCS and through VPH Institute.
17. R. Radhakrishnan, B. Uma, J. Liu, P. S. Ayyaswamy, D. M. Eckmann, Temporal multiscale approach for nanocarrier motion with simultaneous adhesion and hydrodynamic interactions in targeted drug delivery , J. Computational Physics, 2012, 244, 252-263. (DOI).
18. J. H. Park1, Y. Liu1, M. A. Lemmon*, R. Radhakrishnan*, Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain, Biochem J., 2012, 448(3), 417-423; 1. Equal contribution, * co-corresponding authors. (Pubmed ID: 23101586) (DOI).
19. R. P. Bradley, R. Radhakrishnan, modeling of membrane curvature driven by epsin, Bioengineering Conference (NEBEC), IEEE Proceedings of the Bioengineering Conference (NEBEC), 38th Annual Northeast Meeting, 2012, 317-318. ISSN: 2160-7001, Print ISBN: 978-1-4673-1141-0. 10.1109/NEBC.2012.6207092. (Available at IEEE Explore)
20. R. Tourdot, J. Liu, R. Radhakrishnan, Mesoscale simulations of curvature inducing protein partitioning in the presence of mean curvature gradients, IEEE Proceedings of the Bioengineering Conference (NEBEC), 38th Annual Northeast Meeting, 2012, 366-367. ISSN: 2160-7001, Print ISBN: 978-1-4673-1141-0. DOI: 10.1109/NEBC.2012.6207116. (Available at IEEE Explore)
21. B. Uma, R. Radhakrishnan, D. M. Eckmann, P. S. Ayyaswamy, Nanocarrier-cell surface adhesive and hydrodynamic interactions: ligand-receptor bond sensitivity study, ASME Journal of Nanotechnology for Medicine and Engineering, 2012, 3, 031009.
22. B. Uma, P.S. Ayyaswamy, R. Radhakrishnan, D.M. Eckmann, Fluctuating Hydrodynamics Approach for the Simulation of Nanoparticle Brownian Motion in a Newtonian Fluid, Int. J. Micro-Nano Scale Transport, 2012, 3(1+2), 13-20.
23. B. Uma, D. M. Eckmann, R. Radhakrishnan, P. S. Ayyaswamy, Hybrid scheme combining fluctuating hydrodynamics and generalized Langevin dynamics for nearly neutrally buoyant particle in stationary medium, ASME Journal of Heat Transfer, 2013, 135, 011011.
24. R. Radhakrishnan, Roles for Thermodynamics and Catalysis in Systems Biology: Case and Point, Editorial in Journal of Thermodynamics and Catalysis, OMICS Publishing Group, 2012, 3:e102. doi:10.4172/2157- 7544.1000e102. (Open Access).
25. B.Uma, R.Radhakrishnan, D.M.Eckmann and P.S.Ayyaswamy, Fluctuating hydrodynamics approach for the simulation of nanoparticle Brownian motion in a Newtonian fluid, Proceedings of the 21st National and 10th ISHMT-ASME Heat and Mass Transfer conference, 2012.