Recent Changes - Search:



PENN|SEAS|BE|CBE


OUR FEATURE STORIES

Commentary in PNAS, 2010
Research @ Penn, 2010
Rethinking "Pseudo": Science Signaling, 2010
First Computational Oncology Workshop
Social Media: Biophysical Society's BLOG/Tweet, 2011
Social Media: Integrative Biology's BLOG , 2011

Social Media: Integrative Biology's Tweet, 2011

Penn Engineering Magazine, Fall 2011
NSF Highlight 2012
5th Insilico Oncology Meeting
SBE ICBN Meeting
Editorial on Multiscale Cancer Modeling
Penn News 2013


COURSES


COMPUTING



PmWiki

pmwiki.org

edit SideBar

Main /

PUBLICATIONS

HOME | MEMBERS | RESEARCH SUPPORT | PUBLICATIONS | MEDIA | RESEARCH | MOBILE

Research Publications, peer reviewed

Career Citations: 2700+

h-index: 22

Pubmed Link

  1. R. Radhakrishnan and K. E. Gubbins, 1997, “Quasi-one-dimensional phase transitions in nanopores: pore-pore correlation effects”, Phys. Rev. Lett., 78 (15), 2847. PDF
  2. R. Radhakrishnan and K. E. Gubbins, 1999, “Free energy studies of freezing in slit pores: an order parameter study using Monte Carlo simulation”, Mol. Phys., 96, 1249. PDF (pre-print)
  3. R. Radhakrishnan, K. E. Gubbins, A. Watanabe and K. Kaneko, 1999, “Freezing of simple fluids in microporous activated carbon fibers: A comparative study between simulation and experiment”, J. Chem. Phys, 111 (19), 9058. PDF
  4. M. Sliwinska-Bartkowiak, J. Gras, R. Sikorski, R. Radhakrishnan, L. D. Gelb and K. E. Gubbins, 1999, “Phase transition in pores: experimental and simulation studies of melting and freezing”, Langmuir, 15 (18), 6060. PDF
  5. A. Watanabe, K. Kaneko, T. Iiyama, R. Radhakrishnan and K. E. Gubbins, 1999, “A remarkable freezing point elevation of CCl4 in graphitic micropores”, J. Phys. Chem. B, 103 (34), 7061. PDF
  6. Review Article: L. D. Gelb, K. E. Gubbins, R. Radhakrishnan and M. Sliwinska-Bartkowiak, 1999, “Phase separation in confined systems”, Reports on Progress in Physics, 62 (12), 1573; Erratum: 2000, 63 (4), 727. PDF
  7. Remarkable melting point behavior in activated carbon fibers, R. Radhakrishnan and K. E. Gubbins, 4 Pages, Proceedings of Carbon 99, Charleston, SC, 1999.
  8. R. Radhakrishnan, K. E. Gubbins and M. Sliwinska-Bartkowiak, 2000, “Effect of the fluid-wall interaction on freezing of confined fluids: Toward the development of a global phase diagram”, J. Chem. Phys, 112 (24), 11048. PDF
  9. M. Sliwinska-Bartkowiak, G. Dudziak, R. Sikorski, R. Gras, R. Radhakrishnan, K. E. Gubbins, 2000, “Melting/freezing behavior of a fluid confined in porous glasses and MCM-41”, J. Chem. Phys., 114 (2) 950. PDF
  10. M. Sliwinska-Bartkowiak, G. Dudziak, R. Sikorski and R. Gras, R. Radhakrishnan and K. E. Gubbins, 2000, “An experimental study of the effect of fluid-wall interaction on the freezing behavior in confined fluids”, Phys. Chem. Chem. Phys., 3, 1179. PDF
  11. Understanding Freezing Behavior in Porous Materials, R. Radhakrishnan, M. Sliwinska-Bartkowiak, K.E. Gubbins, K. Kaneko, Eds. K. Kaneko, H. Kanoh, and Y. Hanzawa, Fundamentals of Adsorption 7, International Adsorption Society (IK international pub), 341, 2002.
  12. M. Sliwinska-Bartkowiak, J. Gras, R. Sikorski, G. Dudziak, R. Radhakrishnan and K. E. Gubbins, “Experimental and simulation studies of phase transitions in porous silica glasses”, June 1999, COPS-V, Heidelberg, Germany (proceedings in Studies in Surface Science and Catalysis, Elsevier, 2000).
  13. M. Sliwinska-Bartkowiak, G. Dudziak, R. Gras, R. Sikorski, R. Radhakrishnan and K. E. Gubbins, 2001, “Melting/freezing behavior of a fluid confined in pores”, Colloids and Surfaces A, 187-188, 523. PDF
  14. M. Sliwinska-Bartkowiak, G. Dudziak, R. Sikorski, R. Gras, K. E. Gubbins, R. Radhakrishnan, K. Kaneko, 2001, “Freezing behavior in porous materials: theory and experiments”, Polish J. Chem., 75 (4), 547.
  15. M. Sliwinska-Bartkowiak, R. Radhakrishnan, and K.E. Gubbins, 2001, “Effect of confinement on melting in slit-shaped Pores: experimental and simulation study of aniline in activated carbon fibers”, Mol. Sim., 27, 323.
  16. R. Radhakrishnan, B. L. Trout, 2002, “A new approach for studying nucleation phenomena using molecular simulations: Application to CO2 hydrate clathrates”, J. Chem. Phys., 117 (4), 1786. PDF
  17. A. Demurov, R. Radhakrishnan, and B. L. Trout, 2002, “Computations of Diffusivities in ice and CO2 clathrate via molecular dynamics and Monte Carlo simulations”, J. Chem. Phys., 116 (2) 702. PDF
  18. R. Radhakrishnan, M. Sliwinska-Bartkowiak, and K. E. Gubbins, 2002, “Existence of a hexatic phase in porous media”, Phys. Rev. Lett., 89 (7), 076101. PDF. (Pubmed ID: 12190533).
  19. R. Radhakrishnan, M. Sliwinska-Bartkowiak, and K. E. Gubbins, 2002, Global Phase Diagrams for Freezing in Porous Media”, J. Chem. Phys., 116 (3), 1147. PDF
  20. R. Radhakrishnan, A. Demurov, H. J. Herzog, B. L. Trout, Modeling the dissolution of liquid CO2 in water under hydrate forming conditions, Fourth international conference on gas hydrates, Yokohama, Japan, pp262, 2002.
  21. R. Radhakrishnan, B. L. Trout, Mechanism for nucleation of CO2 hydrate clathrates studied using a Monte Carlo based approach, Fourth international conference on gas hydrates, Yokohama, Japan, pp494, 2002.
  22. R. Radhakrishnan and K. E. Gubbins, Freezing in porous materials, M. Sliwinska-Bartkowiak, 6 pages, Proceedings of COPS-VI Studies in surface science and catalysis, Elsevier, Amsterdam, 2003.
  23. Freezing/Melting in Porous Carbons, F. R. Hung, K. E. Gubbins, R. Radhakrishnan, F. Beguin and M. Sliwinska-Bartkowiak, Proceedings of the 3rd Pacific Basin Conference on Adsorption Science and Technology, ed. C-H. Lee, World Scientific, Singapore, pp. 9-16, 2003.
  24. R. Radhakrishnan, B. L. Trout, 2003, Nucleation of crystalline phases of water underhomogeneous and inhomogeneous environments, Phys. Rev. Lett., 90, 158301. PDF. (Pubmed ID: 12732077).
  25. R. Radhakrishnan, B. L. Trout, 2003, Nucleation of hexagonal ice Ih in liquid water, J. Am. Chem. Soc., 125, 7743. (Pubmed ID: 12812516).
  26. R. Radhakrishnan, A. Demurov, H. Herzog, B. L. Trout, 2003, A consistent and verifiable model for the dissolution of CO2 in water under hydrate forming conditions, Energy Conversion Management, 44, 771. PDF.
  27. C. Lo, C. A. Giurumescu, R. Radhakrishnan, B. L. Trout, 2004, Methanol coupling in the zeolite chabazite studied via first-principles molecular dynamics, Mol. Phys., 102, 281. PDF
  28. R. Radhakrishnan and T. Schlick, 2004, Biomolecular Free Energy Profiles by a Shooting/Umbrella Sampling Protocol (BOLAS), J. Chem. Phys., 121, 2436. PDF. (Pubmed ID: 15260799).
  29. R. Radhakrishnan and T. Schlick, 2004, Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta’s closing, Proc. Nat. Acad. Sci., 101, 5970. PDF; supplementary information PDF (Pubmed ID: 15069184).
  30. M. Sliwinska-Bartkowiak, G. Dudziak, M. Kempinski, W. Kempinski, R. Radhakrishnan, F. Hung, K. E. Gubbins, 2004, Melting and freezing in narrow pores: Dielectric and EPR studies, Non-linear Dielectric Phenomena in Complex liquids, Eds. S. J. Rozoska, V. P. Zhelezny, Kluwer Academic, Netherlands, pp 357-366.
  31. Invited Contribution: R. Radhakrishnan, B. L. Trout, 2005, Order parameters in molecular simulations, Handbook of Materials Modeling, Ed. S. Yip, Chapter 6, Kluwer Academic Publishers, Dordrecht, pp 1613-1626. PDF
  32. R. Radhakrishnan and T. Schlick, 2005, Fidelity Discrimination in DNA polymerase b: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair, J. Am. Chem. Soc., 127, 13245-13252. (Pubmed ID: 16173754).
  33. C. Lo, R. Radhakrishnan, B. L. Trout, 2005, Application of Transition Path Sampling Methods in Catalysis: A New Mechanism for C-C Bond Formation in the Methanol Coupling Reaction in Chabazite, Catal. Today, 105, 93. PDF
  34. F. R. Hung, K. E. Gubbins, R. Radhakrishnan, K. Szostak, F. Beguin, G. Dudziak, M. Sliwinska-Bartkowiak, 2005, Melting-Freezing of Lennard Jones in Carbon Nanotubes, Applied Physics Letters, 86, 103110.
  35. Review Article: C. Alba-Simionesco, B. Coasne, G. Dosseh, G. Dudziak, K. E. Gubbins, R. Radhakrishnan and M. Sliwinska-Bartkowiak, 2006, Effect of confinement on freezing and melting, J. Phys.: Cond. Matter, 18, R15-R68. PDF
  36. R. Radhakrishnan*, T. Schlick, 2006, Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta, Biochem. and Biophys. Res. Communications, 350, 521-529; *corresponding author (Pubmed ID: 17022941).
  37. R. Radhakrishnan, K. Arora, Y. Wang, W. A. Beard, S. H. Wilson, T. Schlick, Regulation of DNA repair fidelity by molecular checkpoints: gates in DNA polymerase beta's substrate selection, 2006, Biochemistry, 45, 15142-15156. (Pubmed ID: 17176036)
  38. J. Weinstein, R. Radhakrishnan, KMC-TDGL, a coarse-grained methodology for simulating interfacial dynamics in complex fluids: application to protein-mediated membrane processes, 2006, Mol. Phys., 104, 3653–3666, 2006. PDF
  39. Y. Liu§, J. Purvis§, A. Shih, J. Weinstein, N. Agrawal, R. Radhakrishnan, A multiscale computational approach to dissect early events in the Erb family receptor mediated activation, preferential signaling, and relevance to oncogenic transformations, 2007, Annals of Biomedical Engineering, 35, 1012-1025; § these authors contributed equally. PDF (Pubmed ID: 17273938).
  40. R. Radhakrishnan, Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage, 2007, Biophys J., 93, 2191-2399. PDF (Pubmed ID: 17545240).
  41. J. Purvis, Y. Liu, V. Ilango, and R. Radhakrishnan, Efficacy of tyrosine kinase inhibitors in the mutants of the epidermal growth factor receptor through a multiscale molecular/ systems model for phosphorylation and inhibition, 2007, Proceedings of Foundations in Systems Biology and Engineering II, Ed. F. Algower, M. Reuss, Fraunhofer IRB Verlag Stuttgart, pp 289-294. ISBN 978-3-8167-7436-5. PDF
  42. B. J. Anderson, R. Radhakrishnan, B. Peters, G. P. Borghi, J. W. Tester, and B. L. Trout, 2007, Molecular simulations of ice and gas hydrate nucleation, Physics and Chemistry of Ice, Molecular simulations of ice and gas hydrate nucleation, Physics and Chemistry of Ice, Royal Society of Chemistry, Eds. Werner Kuhs, Cambridge, England, 3-13. ISBN (print): 978-0-85404-350-7, DOI: 10.1039/9781847557773.
  43. R.Venkatramani and R. Radhakrishnan, The effect of oxidatively damaged DNA on the active site pre-organization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus, 2007, Proteins: structure, function, bioinformatics, 71, 1360-1372. PDF (Pubmed ID: 18058909).
  44. Invited Article: N.J. Agrawal and R. Radhakrishnan, Role of glycocalyx in mediating nanocarrier cell adhesion explored using a thermodynamic model and Monte Carlo Simulation, 2007, J. Phys. Chem. C 2007, 111, 15848 - 15856. (Pubmed ID: 19081797).
  45. N.J. Agrawal, R. Radhakrishnan, P. Purohit, Coarse-grained model for DNA curvature and flexibility in the presence of DNA-binding proteins, 2007, Biophysical J, 94:3150 (Pubmed ID: 18192346).
  46. R.Venkatramani and R. Radhakrishnan, A computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase, 2008, Physical Review Letters., 100, 088102. PDF. SUPPLEMENTARY.(Pubmed ID: 18352668)
  47. J. Purvis, V. Ilango, R. Radhakrishnan, Role of Network Branching in Eliciting Differential Short-Term Signaling Responses in the Hyper-Sensitive Epidermal Growth Factor Receptor Mutants Implicated in Lung Cancer, 2008, Biotechnology progress, 24, 540-553. PDF. (Pubmed ID: 18412405)
  48. Andrew Shih, Jeremy Purvis, R. Radhakrishnan, Molecular Systems Biology of ErbB1 Signaling: Bridging the Gap through Multiscale Modeling and High-Performance Computing, 2008, Mol. Biosystems. (A Royal Society of Chemistry Journal), 4, 1151-1159. Highlight article. PDF. (Pubmed ID: 19396377).
  49. N.J. Agrawal, J. Weinstein, R. Radhakrishnan, Landscape of Finite-Temperature Equilibrium Behavior of Curvature Inducing Proteins on a Bilayer Membrane Explored using a Linearized Elastic Free Energy Model, 2008, Molecular Physics, 106, 1913-1923. PDF. (Pubmed Central: PMC3020790)
  50. A. Suenaga, M. Hatakeyama, A. B. Kiyatkin, R. Radhakrishnan, M. Taiji, and B. N. Kholodenko, Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor, 2009, Biophysical J., 96(6), 2278-2288. PDF. (Pubmed ID: 19289054).
  51. S. E. Telesco, R. Radhakrishnan, Insights into regulatory mechanisms of the HER2 tyrosine kinase domain through molecular dynamics simulations, 2008, Biophysical J., 96(6), 2321-2334. PDF. SUPPLEMENTARY.(Pubmed ID: 19289058)
  52. J. E. Purvis, R. Radhakrishnan, S. L. Diamond, Assembling large-scale kinetic models of cellular dynamics from modular steady-state networks, 2009, PLoS: Computational Biology, 5(3) e1000298. PDF. (Pubmed: 19266013)
  53. N.J. Agrawal, R. Radhakrishnan, Calculation of Free energies Calculation of free energies in fluid membranes subject to heterogeneous curvature fields, 2009, Phys Rev E, 80, 011925. PDF. SUPPLEMENTARY.(Pubmed: 19658747)
  54. J. Purvis, A. J. Shih, Y. Liu, R. Radhakrishnan, Book Chapter: Cancer cell- linking oncogenic signaling to molecular structure, Book title: Multiscale Cancer Modeling, Editors: T. S. Deisboeck, G. Stamatakos, Chapman & Hall-CRC Mathematical and Computational Biology Series, 2011, pp31-43.
  55. R. Venkatramani, R. Radhakrishnan, Computational Delineation of the Catalytic Step of a High Fidelity DNA Polymerase, 2010, Protein Science (A Protein Society Journal), 19(4), 815-825. PDF. SUPPLEMENTARY. (Pubmed: 20162624)
  56. A. J. Shih*, S. E. Telesco*, Y. Liu, R. Venkatramani, R. Radhakrishnan, Computational methods related to reaction chemistry, Comprehensive Biomaterials, eds. P. Ducheyne, Elsevier London, 2011, vol 3, 155-169. *These authors contributed equally.
  57. S. E. Telesco, A. Shih, Y. Liu, R. Radhakrishnan, Investigating Molecular Mechanisms of Specificity in Regulation of the HER2 Receptor Tyrosine Kinase through Molecular Modeling and Simulation, HER2 and Cancer: Mechanism, Testing and Targeted Therapy, Nova Science Publishers, New York, 2011, 47-80.
  58. F. Shi, S. E. Telesco, Y. Liu, R. Radhakrishnan*, M. A. Lemmon*, The ErbB3/HER3 Intracellular Domain is Competent to Bind ATP and Catalyze Autophosphorylation, 2010, Proceedings of the National Academy of Sciences, 107, 7692-7697. *Co-corresponding authors. (Pubmed: 20351256) SUPPLEMENTARY
  59. N.J. Agrawal, J. Nukpezah, R. Radhakrishnan, Minimal Mesoscale Model for Protein-Mediated Vesiculation in Clathrin-Dependent Endocytosis, 2010, Plos: Computational Biology, , 6(9) e1000926, 2010. doi:10.1371/journal.pcbi.1000926. (Pubmed: 20838575) SUPPLEMENTARY
  60. J. Liu, G. E. R. Weller, B. Zern, P. S. Ayyaswamy, D. M. Eckmann, V. Muzykantov, R. Radhakrishnan, A Computational Model for Nanocarrier Binding to Endothelium Validated Using In Vivo, In Vitro, and Atomic Force Microscopy Experiments, 2010, Proceedings of the National Academy of Sciences, 107(38), 16530-16535. (Pubmed: 20823256) SUPPLEMENTARY
  61. A. J. Shih, S. E. Telesco, S. H. Choi, M. A. Lemmon, R. Radhakrishnan, Molecular Dynamics Analysis of Conserved Hydrophobic and Hydrophilic Bond Interaction Networks in ErbB Family Kinases, 2011, Biochemical Journal, 436, 241-251. (Pubmed: 21426301)
  62. S. E. Telesco, A. Shih, Y. Liu, R. Radhakrishnan, Investigating Molecular Mechanisms of Activation and Mutation of the HER2 Receptor Tyrosine Kinase through Computational Modeling and Simulation, 2011, Cancer Research Journal, 4(4), 1-35.
  63. A. J. Shih, S. E. Telesco, R. Radhakrishnan, Analysis of Somatic Mutations in Cancer: Molecular Mechanisms of Activation in the ErbB family of Receptor Tyrosine Kinases, Cancers, 2011, 3(1), 1195-1231; doi:10.3390/cancers3011195 (open access). (Pubmed: 21701703)
  64. T. N. Swaminathan, B. Uma, J. Liu, R. Radhakrishnan, P. S. Ayyaswamy, D. M. Eckmann, Dynamic factors controlling carrier anchoring on vascular cells, IUBMB Life, 2011, 63(8):640-647. (Pubmed: 21721099)
  65. S. E. Telesco, A. J. Shih, F. Jia, R. Radhakrishnan, A Multiscale Modeling Approach to Investigate Molecular Mechanisms of Pseudokinase Activation and Drug Resistance in the HER3/ErbB3 Receptor Tyrosine Kinase Signaling Network, Molecular Biosystems, 2011, 7(6), 2066-2080. DOI: 10.1039/c0mb00345j. (Pubmed: 21509365)
  66. V. Muzykantov, R. Radhakrishnan, D. M. Eckmann, Dynamic factors controlling targeting nanocarriers to vascular endothelium, Current Drug Metabolism, 2012, 113, 70. (Pubmed ID: 22292809)
  67. J. Liu, R. P. Bradley, D. M. Eckmann, P. S. Ayyaswamy, R. Radhakrishnan, Multiscale Modeling of Functionalized Nanocarriers in Targeted Drug Delivery, Current Nanoscience, 2011, 7(5): 727-735. (Pubmed ID: 22116782)
  68. J. Liu, N. J. Agrawal, A. Calderon, P. S. Ayyaswamy, D. M. Eckmann, R. Radhakrishnan, Multivalent binding of nanocarrier to endothelial cells under shear flow, Biophysical J., 2011, 101(2):319-326. (Pubmed ID: 21767483).
  69. V. Ramanan, N. J. Agrawal, J. Liu, S. Engles, R. Toy, R. Radhakrishnan, Systems Biology and Physical Biology of Clathrin-Mediated Endocytosis: An Integrative Experimental and Theoretical Perspective, Integrative Biology (RSC Journal), 2011, 3(8), 803-815. DOI: 10.1039/c1ib00036e; (Pubmed ID: 21792431).
  70. B. Uma, T. N. Swaminathan, R. Radhakrishnan, D. M. Eckmann, and P. S. Ayyaswamy, Nanoparticle Brownian motion and hydrodynamic interactions in the presence of flow fields, Phys. Fluids, 2011, 23, 073602. doi:10.1063/1.3611026
  71. J. Liu, N. J. Agrawal, D. M. Eckmann, P. S. Ayyaswamy, R. Radhakrishnan, Top-down Mesoscale Models and Free Energy Calculations of Multivalent Protein-Protein and Protein-Membrane Interactions in Nanocarrier Adhesion and Receptor Trafficking, Innovations in Biomolecular Modeling, Royal Society of Chemistry Publishing, 2012, chapter 11, pp272-287. ISBN-10: 1849734100; ISBN-13: 978-1849734103
  72. B. Uma, T. N. Swaminathan, P. S. Ayyaswamy, D. M. Eckmann, R. Radhakrishnan, Generalized Langevin dynamics of a nanoparticle using a finite element approach: Thermostating with correlated noise, J. Chem. Phys., 2011, 135, 114104. DOI: 10.1063/1.3635776; Erratum, 136, 019901, 2012.
  73. J. Liu, R. Tourdot, V. Ramanan, N. J. Agrawal, R. Radhakrishnan, Mesoscale Modeling and Simulations of Spatial Partitioning of Curvature Inducing Proteins under the Influence of Mean Curvature Fields in Bilayer Membranes, Molecular Physics, 2012, 110(11–12), 1127–1137. (DOI:10.1080/00268976.2012.664661)
  74. B. Uma, D. M. Eckmann, P. S. Ayyaswamy, R. Radhakrishnan, A hybrid formalism combining fluctuating hydrodynamics and generalized Langevin dynamics for the simulation of nanoparticle thermal motion in an incompressible fluid medium, Molecular Physics, 2012, 110(11–12), 1057–1067. (DOI: 10.1080/00268976.2012.663510)
  75. S. E. Telesco, A. Shih, Y. Liu, R. Radhakrishnan, Investigating Molecular Mechanisms of Specificity in Regulation of the HER2 Receptor Tyrosine Kinase through Molecular Modeling and Simulation, International Journal of Cancer Research and Prevention (2011), ISSN: 1554-1134, Volume 4, Number 3, 2012, pp219-252. (open access)
  76. S. E. Telesco, R. Radhakrishnan, Structural Systems Biology and Multiscale Signaling Models, Annals of Biomedical Engineering, 2012, 40(11), 2295-2306. (Pubmed ID: 22539148).
  77. B.Uma, R.Radhakrishnan, D.M.Eckmann and P.S.Ayyaswamy, Modeling of a nanoparticle motion in a Newtonian fluid: A comparison between fluctuating hydrodynamics and generalized Langevin methods, Proceedings of the ASME 3rd Micro/Nanoscale Heat and Mass Transfer International Conference, Paper No. MNHMT2012-75019, 2012.
  78. J. Liu, D. M. Eckmann, P. S. Ayyaswamy, R. Radhakrishnan,Modeling of Binding Free Energy of Targeted Nanocarriers to Cell Surfaces, The Seventh Interdisciplinary Transport Phenomena Conference, Proceedings of ITP2011, Interdisciplinary Transport Phenomena VII: Fluid, Thermal, Biological, Materials and Space Sciences, 2011, Dresden, Germany, pp6-6 to 6-11.
  79. 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.
  80. 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).
  81. 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.
  82. 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).
  83. 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.
  84. 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).
  85. 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.
  86. 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)
  87. 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)
  88. 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).
  89. 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, in press. DOI: 10.1115/1.4024004.
  90. 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).
  91. 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, 2013, 3(1+2), 13-20.
  92. 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. (open access)
  93. 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)
  94. Y. Zhao, J. Liu, C. Yang, B. R. Capraro, T. Baumgart, R. P. Bradley, N. Ramakrishnan, R. Radhakrishnan, T. Svitkina, and W. Guo, Exo70 generates membrane curvature for morphogenesis and cell migration, Dev. Cell., 2013, 26(3), 266-278. DOI.
  95. 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)

Research Publications, non-peer reviewed

  1. R. Radhakrishnan, G. Venkatraghavan, M. S. Ananth, Correlation of excess energies of mixing, 1995, Undergraduate Project Thesis, Indian Institute of Technology.
  2. R. Radhakrishnan, Understanding phase behavior in nanoporous materials: free energy simulation studies and experiment, 2000, PhD Thesis, Cornell University. PDF
  3. M. Sliwinska-Bartkowiak, R. Radhakrishnan, and K. E. Gubbins, “Quasi-two-dimensional melting in porous media: effect of multi-layers and cross-over in scaling behavior”, 2008 Condensed Matter Archives, arXiv.org: arXiv:0805.4628v1 link. PDF (pre-print)
  4. J. Purvis, A Systems Approach to Cellular Signal Transduction, PhD Thesis, University of Pennsylvania, Genomics and Computational Biology Graduate Group, Advisors R. Radhakrishnan, S. L. Diamond, 2009. PDF
  5. N. J. Agrawal, Modeling the bioenergetics of protein-mediated membrane deformation, PhD Thesis, University of Pennsylvania, Chemical and Biomolecular Engineering, Advisor R. Radhakrishnan, 2009. PDF
  6. Y. Liu, Computational Modeling of Protein Kinases, PhD Thesis, University of Pennsylvania, Bioengineering, Advisor R. Radhakrishnan, 2010. PDF
  7. A. J. Shih, UNVEILING THE MOLECULAR MECHANISMS REGULATING THE ACTIVATION OF THE ERBB FAMILY RECEPTORS AT ATOMIC RESOLUTION THROUGH MOLECULAR MODELING AND SIMULATIONS, PhD Thesis, University of Pennsylvania, Bioengineering, Advisor R. Radhakrishnan, 2011. PDF
  8. S. E. Telesco, MULTISCALE MODELING OF THE ERBB RECEPTOR TYROSINE KINASE SIGNALING NETWORK THROUGH THEORY AND EXPERIMENT, PhD Thesis, University of Pennsylvania, Bioengineering, Advisor R. Radhakrishnan, 2011. PDF
  9. R. Tourdot, R. Radhakrishnan, Clathrin Mediated Endocytosis and its Role in Viral Entry. Atlas Genet Cytogenet Oncol Haematol. March 2013. URL
Edit - History - Print - Recent Changes - Search
Page last modified on August 20, 2013, at 12:41 PM