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Peer Reviewed Papers, Books, Chapters

Year Title Citation Authors
1. 2011 GPU algorithms for molecular modeling Scientific Computing with Multicore and Accelerators, chapter 16, pp. 351-371. Chapman & Hall/CRC Press, 2011
2. 2011 The effect of correlated bath fluctuations on exciton transfer Journal of Chemical Physics, 134:095102, 2011.
3. 2011 Fîrster energy transfer theory as reflected in the structures of photosynthetic light harvesting systems. ChemPhysChem, 12:518-531, 2011.
4. 2011 Introduction to a quantum biological device, the light harvesting apparatus in purple photosynthetic bacteria. In Benoit Roux, editor, Molecular Machines. World Scientific Press, 2011. In press.
5. 2011 Quest for spatially correlated fluctuations in the FMO light-harvesting complex Journal of Physical Chemistry B, 115:758-764, 2011. (NIHMS: 258259)
6. 2011 Cytoplasmic domain filter function in the mechanosensitive channel of small conductance. Biophysical Journal, 2011. In press
7. 2011 Stereochemical errors and their implications for molecular dynamics simulations. BMC Bioinformatics, 2011. In press
8. 2011 Extension of a three-helix bundle domain of myosin VI and key role of calmodulins Biophysical Journal, 2011. In press
9. 2011 Theoretical and computational investigation of flagellin translocation and bacterial flagellum growth Biophysical Journal, 2011. In press
10. 2011 Free energy of nascent-chain folding in the translocon. Journal of the American Chemical Society, 2011. In press. (NIHMS: 292450)
11. 2011 Domain motion of individual F1-ATPase b-subunits during unbiased molecular dynamics simulations Journal of Physical Chemistry, 2011. In press. (NIHMS: 285390)
12. 2011 Modulating LOV domain photodynamics with a residue alteration outside the chromophore binding site Biochemistry, 50:2411-2423, 2011.
13. 2011 A chemical compass for bird navigation. Plenio, editors, Quantum Effects in Biology, chapter 10. Cambridge University Press, 2011. To be published
14. 2011 Quantum biology of retinal proteins Plenio, editors, Quantum Effects in Biology. Cambridge University Press, 2011. To be published
15. 2011 The effect of correlated bath fluctuations on exciton transfer. Journal of Chemical Physics, 134:095102, 2011. (9 pages). (PMC: 3064689)
16. 2011 Implementation of accelerated molecular dynamics in NAMD Computational Science & Discovery, 4:015002, 2011. (11 pages). (NIHMS: 283990)
17. 2011 Structural insights into cognate vs. near-cognate discrimination during decoding EMBO Journal, 30:1497-1507, 2011.
18. 2011 Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nature Structural & Molecular Biology, 18:614-621, 2011.
19. 2011 3rd generation DNA sequencing with a nanopore. Nanopores: Sensing and Fundamental Biological Interactions. Springer, Berlin, 2011. In press
20. 2011 Improved resolution of tertiary structure elasticity in muscle protein Biophysical Journal, 100:L22-L24, 2011. (PMC: 3037604)
21. 2011 Free-energy cost for translocon-assisted insertion of membrane proteins. Proceedings of the National Academy of Sciences, USA, 108:3596-3601, 2011. (PMC: 3048118)
22. 2011 Förster energy transfer theory as reflected in the structures of photosynthetic light harvesting systems ChemPhysChem, 12:518-531, 2011. (NIHMS: 285267)
23. 2011 Molecular dynamics simulations of forced unbending of integrin aVb3 PLoS Comput. Biol., 7(2):e1001086, 2011. (PMC: 3040657)
24. 2011 High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. Journal of Physical Chemistry Letters, 2:87-92, 2011
25. 2011 Molecular dynamics of EF-G during translocation. PROTEINS: Structure, Function, and Bioinformatics, 79:1478-1486, 2011.
26. 2011 Molecular origin of the hierarchical elasticity of titin: simulation, experiment and theory Annual Review of Biophysics, 40:187-203, 2011
27. 2011 Introduction to a quantum biological device, the light harvesting apparatus in purple photosynthetic bacteria In Benoit Roux, editor, Molecular Machines, chapter 2, pp. 19-48. World Scientific Press, 2011.
28. 2011 Viewing the mechanisms of translation through the computational microscope In Joachim Frank, editor, Molecular Machine in Biology. Cambridge University Press, 2011. In press
29. 2011 Quest for spatially correlated fluctuations in the FMO light-harvesting complex Journal of Physical Chemistry B, 115:758-764, 2011. (NIHMS: 258259)
30. 2011 Applications of the molecular dynamics flexible fitting method. Journal of Structural Biology, 173:420-427, 2011. (PMC: 20932910)
31. 2011 Fast molecular electrostatics algorithms on GPUs In Wen-Mei Hwu, editor, GPU Computing Gems, chapter 4, pp. 43-58. Morgan Kaufmann Publishers, 2011.
32. 2011 GPU-accelerated computation and interactive display of molecular orbitals In Wen-Mei Hwu, editor, GPU Computing Gems, chapter 1, pp. 5-18. Morgan Kaufmann Publishers, 2011
33. 2010 Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance Biochemistry, 49:9190-9198, 2010. (NIHMS: 264222)
34. 2010 Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza PLoS Currents: Influenza, 2009 Aug 27:RRN1015, 2010. (9 pages). (PMC: 2762416)
35. 2010 Tertiary and secondary structure elasticity of a six-Ig titin chain Biophysical Journal, 98:1085-1095, 2010. (PMC: 2849065)
36. 2010 Multi-scale simulations of membrane sculpting by N-BAR domains Molecular Simulations and Biomembranes: From Biophysics to Function, chapter 6, pp. 146-176. Royal Society of Chemistry, 2010.
37. 2010 Probing a structural model of the nuclear pore complex channel through molecular dynamics Biophysical Journal, 98:1658-1667, 2010. (PMC: 2865169)
38. 2010 Self-assembly of photosynthetic membranes. ChemPhysChem, 11:1154-1159, 2010. (NIHMS: 285262)
39. 2010 Recognition of the regulatory nascent chain TnaC by the ribosome Structure, 18:627-637, 2010. (NIHMS: 224560)
40. 2010 Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel Biophysical Journal, 98:2189-2198, 2010. (PMC: 2872222)
41. 2010 Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding PLoS One, 5:e9890, 2010. (12 pages). (PMC: 2855342)
42. 2010 Acuity of a cryptochrome and vision based magnetoreception system in birds Biophysical Journal, 99:40-49, 2010. (PMC: 2895366)
43. 2010 Photosynthetic vesicle architecture and constraints on efficient energy harvesting Biophysical Journal, 99:67-75, 2010. (PMC: 2895385)
44. 2010 How birds and other animals orient in the Earth magnetic field Physik Journal, 9:23-28, 2010. (article in German only). (NIHMS: 280922)
45. 2010 Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases PLoS Comput. Biol., 5:e1000939, 2010. (13 pages). (PMC: 2944783)
46. 2010 Challenges in protein folding simulations: Force field, timescale, sampling, and analysis Nature Physics, 6:751-758, 2010. (PMC: 3032381)
47. 2010 Flow-induced b-hairpin folding of the glycoprotein Iba b-switch Biophysical Journal, 99:1182-1191, 2010. (PMC: 2920744)
48. 2010 Squeezing protein shells: how continuum elastic models, molecular dynamics simulations and experiments coalesce at the nanoscale. Biophysical Journal, 99:1175-1181, 2010. (PMC: 2920642)
49. 2010 O2-reactivity of flavoproteins: Dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase Journal of Biological Chemistry, 285:24439-24446, 2010. (PMC: 2915680)
50. 2010 Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane New Journal of Physics, 12:085005, 2010. (19 pages). (PMC: 2997751)
51. 2010 Computational microscopy of the role of protonable surface residues in nanoprecipitation oscillations. ACS Nano, 4:4463-4474, 2010. (PMC: 2927718)
52. 2010 GPU-accelerated molecular modeling coming of age Journal of Molecular Graphics and Modelling, 29:116-125, 2010. (PMC: 2934899)
53. 2010 Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain. Structure, 18:1443-1449, 2010. (PMC: 3027149)
54. 2010 The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. Journal of Molecular Biology, 402:741-760, 2010. (PMC: 2967302)
55. 2010  Immersive molecular visualization and interactive modeling with commodity hardware. Lecture Notes in Computer Science, 6454:382-393, 2010. (PMC: 3032211)
56. 2010 Self-assembly of photosynthetic membranes ChemPhysChem, 11:1154-1159, 2010.
57. 2010 Photosynthetic vesicle architecture and constraints on efficient energy harvesting Biophysical Journal, 99:67-75, 2010. (PMC: 2895385)
58. 2010 Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane New Journal of Physics, 12:085005, 2010. (19 pages). (PMC: 2997751)
59. 2009 A glycophorin A-like framework for the dimerization of photosynthetic core complexes Journal of the American Chemical Society, 131:17096-17098, 2009. (PMC: 2792896)
60. 2009 Maturation of high-density lipoproteins. Journal of the Royal Society Interface, 6:863-871, 2009. (PMC: 2805102)
61. 2009 Molecular control of ionic conduction in polymer nanopores Faraday Discussion, 143:47-62, 2009. (PMC: 2907245)
62. 2009 Ligand migration and cavities within scapharca dimeric HbI: Studies by time-resolved crystallography, Xe binding, and computational analysis Structure, 17:1494-1504, 2009. (PMC: 2785043)
63. 2009 Elucidating the mechanism behind irreversible deformation of viral capsids Biophysical Journal, 97:2061-2069, 2009. (PMC: 2756377)
64. 2009 Common structural transitions in explicit-solvent simulations of villin headpiece folding Biophysical Journal, 97:2338-2347, 2009. (PMC: 2764099)
65. 2009 Membrane-bending mechanism of amphiphysin N-BAR domains Biophysical Journal, 97:2727-2735, 2009. (PMC: 2776244)
66. 2009 Discovery through the computational microscope. Structure, 17:1295-1306, 2009. (PMC: 2927212)
67. 2009 Membrane curvature induced by aggregates of LH2s and monomeric LH1s Biophysical Journal, 97:2978-2984, 2009. (PMC: 2784572)
68. 2009 Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions Journal of Chemical Theory and Computation, 5:3022-3031, 2009. (PMC: 2990227)
69. 2009 Regulation of the protein-conducting channel by a bound ribosome Structure, 17:1453-1464, 2009. (PMC: 2778611)
70. 2009 Science and engineering in the petascale era Computing in Science and Engineering, 11:28-36, 2009.
71. 2009 Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome Science, 326:1369-1373, 2009. (PMC: 2920595)
72. 2009 Structural insight into nascent polypeptide chain-mediated translational stalling Science, 326:1412-1415, 2009. (PMC: 2920484)
73. 2009 Light harvesting complex II B850 excitation dynamics Journal of Chemical Physics, 131:225101, 2009. (9 pages). (PMC: 2802260)
74. 2009 Ionic current rectification through silica nanopores Journal of Physical Chemistry C, 113:1850-1862, 2009. (PMC: 2658614)
75. 2009 Nanoelectromechanics of methylated DNA in a synthetic nanopore. Biophysical Journal, 96:L32-L34, 2009. (PMC: 2717226)
76. 2009 Photochemical reaction dynamics of the primary event of vision studied by a hybrid molecular simulation Biophysical Journal, 96:403-416, 2009. (PMC: 19167292)
77. 2009 Protein-induced membrane curvature investigated through molecular dynamics flexible fitting Biophysical Journal, 97:321-329, 2009. (PMC: 2711417)
78. 2009 A glycophorin A-like framework for the dimerization of photosynthetic core complexes Journal of the American Chemical Society, 131:17096-17098, 2009. (PMC: 2792896)
79. 2009 Light harvesting complex II B850 excitation dynamics Journal of Chemical Physics, 131:225101, 2009. (9 pages). (PMC: 2802260)
80. 2009 Molecular Dynamics Flexible Fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods, 49:174-180, 2009. (PMC: 2753685)
81. 2009 Magnetoreception through cryptochrome may involve superoxide Biophysical Journal, 96:4804-4813, 2009. (PMC: 2712043)
82. 2009 Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains Structure, 17:882-892, 2009. (PMC: 2743466)
83. 2009 Molecular dynamics simulations of membrane channels and transporters Current Opinion in Structural Biology, 19:128-137, 2009. (PMC: 2680122)
84. 2009 Force field bias in protein folding simulations. Biophysical Journal, 96:3772-3780, 2009. (PMC: 2711430)
85. 2009 Limits for reduction of effective focal volume in multiple-beam light microscopy Optics Express, 17:2861-2870, 2009
86. 2009 High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, New York, NY, USA, 2009. ACM
87. 2009 structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides Chemical Physics, 357:188-197, 2009. (PMC: 2678753)
88. 2009 Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics Structure, 17:449-459, 2009. (PMC: 2701619)
89. 2009 Elasticity and rupture of a multi-domain neural cell adhesion molecule complex. Biophysical Journal, 96:3005-3014, 2009. (PMC: 2718298)
90. 2009 Modeling transport through synthetic nanopores  IEEE Nanotechnology, 3:20-28, 2009.
91. 2009 Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proceedings of the National Academy of Sciences, USA, 106:1063-1068, 2009. (PMC: 2613361)
92. 2009 Multilevel summation of electrostatic potentials using graphics processing units. Journal of Parallel Computing, 35:164-177, 2009. (PMC: 2743154)
93. 2009 Protein-induced membrane curvature investigated through molecular dynamics flexible fitting Biophysical Journal, 97:321-329, 2009. (PMC: 2711417)
94. 2008 Exploring the possibilities for radical pair effects in cryptochrome Plant Signaling and Behavior, 3:676-677, 2008. (PMC: 2634554)
95. 2008 Flow induced structural transition in the b-switch region of glycoprotein Ib.  Biophysical Journal, 95:1303-1313, 2008. (PMC: 2479615)
96. 2008 Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics Structure, 16:673-683, 2008. (PMC: 2430731)
97. 2008 Molecular models need to be tested: the case of a solar flares discoidal HDL model. Biophysical Journal, 94:L87-L89, 2008. (PMC: 2397337)
98. 2008 From atomic-level structure to supramolecular organization in the photosynthetic unit of purple bacteria. The Purple Phototrophic Bacteria, volume 28 of Advances in Photosynthesis and Respiration, pp. 275-294. Springer, 2008
99. 2008 The roles of pore ring and plug in the SecY protein-conducting channel.  Journal of General Physiology, 132:709-719, 2008. (PMC: 2585858)
100. 2008 Using VMD - an introductory tutorial. Current Protocols - Bioinformatics, 5:Unit 5.7, 2008.
101. 2008 Adapting a message-driven parallel application to GPU-accelerated clusters. In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, Piscataway, NJ, USA, 2008. IEEE Press
102. 2008 Ten-microsecond MD simulation of a fast-folding WW domain. Biophysical Journal, 94:L75-L77, 2008. (PMC: 2367204)
103. 2008 Length dependent optical effects in single walled carbon nanotubes. Journal of Physical Chemistry B, 112:6211-6213, 2008.
104. 2008 GPU acceleration of cutoff pair potentials for molecular modeling applications In CF'08: Proceedings of the 2008 conference on Computing Frontiers, pp. 273-282, New York, NY, USA, 2008. ACM
105. 2008 The allosteric role of the Ca++ switch in adhesion and elasticity of C-cadherin Biophysical Journal, 94:4621-4633, 2008. (PMC: 2397358)
106. 2008 Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Biophysical Journal, 95:789-803, 2008. (PMC: 2440475)
107. 2008 A structural mechanism for MscS gating in lipid bilayers Science, 321:1210-1214, 2008. (PMC: 2897165)
108. 2008 Molecular mechanisms of ligand recognition by NR3 subtype glutamate receptors. EMBO Journal, 27:2158-2170, 2008. (PMC: 2516888)
109. 2008 Four-scale description of membrane sculpting by BAR domains Biophysical Journal, 95:2806-2821, 2008. (PMC: 2527247)
110. 2008 Intrinsic curvature properties of photosynthetic proteins in chromatophores Biophysical Journal, 95:2822-2836, 2008. (PMC: 2527265)


4th Annual Pharma R&D Asia Congress
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