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2004 RADHAKRISHNAN RESEARCH GROUP. All Rights Reserved. CONTACT US
Updated Feb 2008
Research
Publications, peer reviewed:
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
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. 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
8. 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
9. 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
10. 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).
11. 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
12. 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.
13. 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.
14. 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
15. A. Demurov, R. Radhakrishnan, and B. L.
Trout, 2002, “Computations of Diffusivities in ice
and CO2 clathrate via molecular dynamics and
16. 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
17. 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
18. R. Radhakrishnan, B. L. Trout, 2003,
“Nucleation of crystalline phases of water underhomogeneous and inhomogeneous
environments”, Phys. Rev. Lett., 90, 158301. PDF
19. R. Radhakrishnan, B. L. Trout, 2003,
“Nucleation of hexagonal ice Ih in liquid water”, J. Am. Chem. Soc.,
125, 7743. (Copyright restrictions for providing pdf, pubmed ID: 12812516)
20. 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
21. 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
22. R. Radhakrishnan and T. Schlick, 2004,
“Biomolecular Free Energy Profiles by a Shooting/Umbrella
Sampling Protocol (BOLAS)”, J. Chem. Phys., 121, 2436. PDF
23. R. Radhakrishnan and T. Schlick, 2004, “Orchestration of cooperative events in DNA synthesis and repair
mechanism unraveled by transition path sampling of DNA polymerase b’s closing”,
Proc. Nat. Acad. Sci., 101, 5970. PDF;
supplementary information PDF
24. 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,
25. 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
26. 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. (Copyright restrictions for providing pdf, pubmed ID: 16173754)
27. 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
28. 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.
29. 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. pre-print PDF
30. R. Radhakrishnan*, T. Schlick, 2006, “Correct and incorrect nucleotide incorporation pathways in DNA polymerase
β”, Biochem. and Biophys. Res.
Communications, 350, 521-529; *corresponding author PDF
31. 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. (Copyright
restrictions for providing pdf, pubmed ID:
17176036)
32. 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
33. Invited Article: 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
34. R.
Radhakrishnan, Coupling of Fast and Slow Modes in the Reaction Pathway of the
Minimal Hammerhead Ribozyme Cleavage, 2007, Biophys J., in press. PDF
35. 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, in press. PDF
36. 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, Royal Society of
Chemistry, Cambridge, England, in press.
37. 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, in press. PDF (pubmed ID: 18058909)
38. Invited
Article: N. 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. PDF
39. N. 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).
40. 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. (Pubmed ID: 18352668)
41. 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, in press. PDF.
Research Publications,
submitted for peer-review:
42. R. Radhakrishnan, “Molecular Systems Biology: Bridging
the Gap through Multiscale Modeling and High-Performance Computing”, Molecular Biosystems, 2008, submitted as a highlight article. PDF (pre-print)
43. 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”, 2006,
submitted to Phys. Rev. B. PDF (pre-print)
44. N. Agrawal, J. Weinstein, R. Radhakrishnan, Landscape of
membrane dynamical behavior under the influence of curvature inducing proteins,
submitted, 2008
45. 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, 2008, submitted to J. Mol. Biol.
Research
Publications, in preparation:
46. A. Shih, M. A. Lemmon, R. Radhakrishnan, Structural analysis
of the activation loop conformation of Epidermal Growth Factor Receptor
Tyrosine Kinase through molecular dynamics simulations, to be submitted, 2007.
47. Y. Liu, R. Radhakrishnan, Comparing molecular docking
protocols with explicit and implicit protein flexibility: application to
tyrosine kinase inhibitor docking to the epidermal growth factor receptor, to
be submitted, 2007
48. N. Agrawal, J. Nukpezah, R. Radhakrishnan, Ginzburg-Landau
dynamics under extreme curvature: a new framework implementing local Cartesian
gauge, to be submitted, 2007.
49. R. Venkatramani, R. Radhakrishnan, Catalysis in DNA Pol 1 of Bacillus stearothermophilus, to be
submitted, 2007.
50.
R. Venkatramani, R. Radhakrishnan,
Role of the oxidative lesion in Guanine in stabilizing the active-site of
high-fidelity polymerases, to be submitted, 2007.
Research
Publications, non-peer reviewed:
51. R.
Radhakrishnan, G. Venkatraghavan, M. S. Ananth, Correlation of excess energies
of mixing, 1995, Undergraduate Project Thesis, Indian Institute of Technology.
52. R.
Radhakrishnan, Understanding phase behavior in nanoporous materials: free
energy simulation studies and experiment, 2000, PhD Thesis,
53. R. Radhakrishnan, A. Demurov, H. J. Herzog, B. L. Trout,
“Modeling the dissolution of liquid CO2 in water under hydrate
forming conditions”, 2002, Fourth international conference on gas hydrates,
Yokohama, Japan, pp262.
54. R.
Radhakrishnan, B. L. Trout, “Mechanism
for nucleation of CO2 hydrate clathrates studied using a Monte Carlo
based approach”, 2002, Fourth international conference on gas hydrates,