56. "Exchange frequency in replica exchange molecular dynamics." Daniel Sindhikara, Yilin Meng, Adrian E. Roitberg. J. Chem. Phys. 128, 024103 (2008)
55. "Simulating Temperature Jumps for Protein Folding". Seonah Kim, Adrian E.Roitberg. Journal of Physical Chemistry B (2008)
54. "Bond or Cage Effect: How Nitrophorins Transport and Release Nitric Oxide". Marcelo A. Marti, Mariano C. Gonzalez Lebrero, Adrian E. Roitberg, Dario A. Estrin. Journal of the American Chemical Society 130(5):1611-1618 (2008),
53. "Molecular dynamics Simulations of alkanethiol monolayers with azobenzene molecules on the au(111) surface". Sabri Alkis, Ping Jiang P, Lin-Lin Wang LL, Adrian E. Roitberg, Hai-Ping Cheng, Jeffrey L. Krause. Journal of Physical Chemistry C. 111 (40): 14743-14752 (2007)
52. "Fluorescence resonance energy transfer in dye-labeled DNA". Elena Dolghih, Adrian E. Roitberg, Jeffrey L. Krause. Journal of Photochemistry and photobiology A-Chemistry. 190(2-3):321-327 (2007)
51. "Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package". Gustavo de M.Seabra, Ross C. Walker, Marcus Elstner, David A.Case, Adrian E. Roitberg. Journal of Physical Chemistry A. 111 (26):5655-5664 (2007)
50. "Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir". Adrian E. Roitberg, Asim Okur, Carlos Simmerling. Journal of Physical Chemistry B. 111(10):2415-2418 (2007)
49. "Kinetics of internal-loop formation in polypeptide chains: a simulation study". Dana Doucet, Adrian Roitberg, Stephen J. Hagen. Biophysical Journal. 92(7):2281-9 (2007)
48. "Comparison of multiple Amber force fields and development of improved protein backbone parameters". Viktor Hornak, Robert Abel, Asim Okur, Bentley Strocbine, Adrian Roitberg, Carlos Simmerling. Proteins: Structure, Function, and Bioinformatics. 65(3):712-725 (2006)
47. "The catalytic mechanism of peptidylglycine -hydroxylating monooxygenase investigated by computer simulation". Alejandro Crespo, Marcelo A. Marti, Adrian E. Roitberg, L. Mario Amzel, Dario A. Estrin. Journal of the American Chemical Society. 128(39):12817-12828 (2006)
46. "Free Energy Calculations with Non-Equilibrium Methods: Applications of the Jarzynski Relationship". Xiong, Hui; Crespo, Alejandro; Marti, Marcelo; Estrin, Dario; Roitberg, Adrian E.. Theoretical Chemistry Accounts. 116(1-3):338-346 (2006)
45. "Theoretical Study of the Isomerization Mechanism of Azobenzene and Disubstituted Azobenzene Derivatives". Christina R. Crecca, Adrian E. Roitberg. Journal of Physical Chemistry A. 110(26):8188-8203 (2006)
44. "Structural analysis of ligand binding and catalysis in chorismate lyase". Natasha Smith, Adrian E. Roitberg, Eva Rivera, Andrew Howard, Marcia J. Holden, Martin Mayhew, Salita Kaistha, D. T. Gallagher. Archives of Biochemistry and Biophysics. 445(1):72-80 (2006)
43. "Energy Transfer in the Nanostar: The Role of Coulombic Coupling and Dynamics". Wilfredo Ortiz, Brent P. Krueger, Valeria D. Kleiman, Jeffrey L. Krauese, Adrian E. Roitberg. Journal of Physical Chemistry B. 109(23):11512-11519 (2005)
42. "Non-Equilibrium Approaches to Free Energy Calculations". Adrian E. Roitberg. Annual Reports in Computational Chemistry. 1:103-111 (2005)
41. "Multiple-Steering Molecular Dynamics QM-MM Free Energy Profiles in Enzymatic Reactions". Alejandro Crespo, Marcelo A. Marti, Dario A. Estrin, and Adrian E. Roitberg. Journal of the American Chemical Society. 127 (19):6940-6941 (2005)
40. "L166P induces H8 helix unwinding in DJ-1, a protein involved in early-onset Parkinson's Disease". Adrian G. Turjanski, Omar A. Coso and Adrian E. Roitberg. Submitted to Journal of Biological Chemistry. June 2004
39. "Protein Folding Pathways Explored in Simulations with Explicit Solvation". Bentley Strockbine, Viktor Hornak, Guanglei Cui, Melinda Layten, Niels Andersen, Adrian Roitberg and Carlos L. Simmerling. Submitted to Journal of the American Chemical Society. October 2003
38. "A New Reaction Intermediate during Trimethylindium Decomposition". Jang Y. Hwang, Adrian E. Roitberg and Tim J. Anderson. To be submitted to Chemistry of Materials. August 2004
37. "Foreword". Adrian E. Roitberg and Carlos L. Simmerling. Journal of Molecular Graphics and Modelling. 22:317 (2004)
36. "Molecular Dynamics of Poly(benzylphenyl ether) Dendrimers: Effects of Backfolding on Forster Energy Transfer Rates". Wilfredo Ortiz, Adrian E. Roitberg, and Jeffrey L. Krause. Journal of Physical Chemistry B. 108:8218-8225 (2004)
35. "Coherent electron transport through an azobenzene molecule: A light driven molecular approach". C. Zhang, M.-H.Du, H.-P.Cheng, X.-G.Zhang, A.E.Roitberg and J.L.Krause. Phys. Rev. Lett. 92: 158301 (2004)
34. "A DFT based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase". Alejandro Crespo, Damian A. Scherlis, Marcelo A. Marti, Pablo Ordejon, Adrian E. Roitberg, and Dario A. Estrin. Journal of Physical Chemistry B. 107 (49): 13728 -13736, 2003
33. "Kinetic isotope effects in the active site of B.subtilis chorismate mutase" Sharon E. Worthington, Adrian E. Roitberg and Morris Krauss. International Journal of Quantum Chemistry. 94: 287-292 (2003)
32. "Smaller and faster: The 20-residue Trp-cage folds in 4 microseconds". Linlin Qiu, Suzette A. Pabit, Adrian E. Roitberg and Stephen J. Hagen. Journal of the American Chemical Society. 124:12952-12953 (2002)
31. "4,5-Dehydrooctafluoro[2.2]paracyclophane: facile generation and extraordinary Diels-Alder reactivity", Merle A. Battiste, Jian-Xin Duan, Yi-An Zhai, Ion Ghiviriga, Khalil A. Abboud, Adrian E. Roitberg, G. Robert Shelton and William R. Dolbier, Jr. Tetrahedron Letters. 43(39):7047-7049 (2002)
30. "All atom structure prediction and folding simulations of a stable protein" Carlos L. Simmerling, Bentley Strockbine and Adrian E. Roitberg. Journal of the American Chemical Society. 124 (38):11258 -11259 (2002)
29. "Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A QM/MM study". Mariano C. Gonzalez Lebrero, Damian E. Bikiel, M. Dolores Elola, Dario A. Estrin and Adrian E. Roitberg. Journal of Chemical Physics. 117(6):2718-2722 (2002)
28. "Benzocycloarene hydroxylation by P450 biocatalysis". Martin P. Mayhew, Adrian E. Roitberg, Yadu Tewari, Marcia J. Holden, Dave Vanderah and Vincent L. Vilker. New Journal of Chemistry. 26:35-42 (2002)
27. "Strontium clusters: many-body potential, energetics and structural transitions". Guanming Wang, Estela Blaisten-Barojas, Adrian E. Roitberg, and T.P. Martin. Journal of Chemical Physics. 115:3640 (2001)
26. "An MD/QM study of the chorismate mutase catalyzed claisen rearrangement reaction". Sharon E. Worthington, Adrian E. Roitberg and Morris Krauss. Journal of Physical Chemistry B. 105:7087-7095 (2001)
25. "Raman and FT-IR spectroscopies of fluorescein in solution". LiLi Wang, Adrian E. Roitberg, Curt Meuse and Adolfas K.Gaigalas. Spectrochimica Acta A. 57:1781-91 (2001)
24. "The electronic spectrum of the prephenate di-anion. An experimental and theoretical (MD/QM) comparison". Adrian E. Roitberg, Sharon Worthington, Marcia J. Holden, Martin P. Mayhew and Morris Krauss. Journal of the American Chemical Society. 122:7312-7316 (2000)
23. "Molecular wire conductance: electrostatic potential spatial effects". Vladimiro Mujica, Adrian E. Roitberg and Mark A. Ratner. Journal of Chemical Physics. 112:6834-6839 (2000)
22. "Pulsed terahertz spectroscopy of biomolecules". Andrea G. Markelz, Adrian E. Roitberg and Edwin H.Heilweill. Chemical Physics Letters. 320:42-48 (2000)
21. "The injecting energy at molecule/metal interfaces: implications for conductance of molecular junctions from an ab-initio molecular description". Sophia N. Yaliraki, Adrian E. Roitberg, Carlos Gonzalez, Vladimiro Mujica and Mark A. Ratner. Journal of Chemical Physics. 111:6997-7002 (1999)
20. "Electron transfer in molecules and molecular wires; geometry dependence, coherent transport and control". Vladimiro Mujica, Abraham Nitzan, Yi Mao, William Davis, Mathieu Kemp, Adrian E. Roitberg and Mark A. Ratner. Advances in Chemical Physics. 107:403-429 (1999)
19. "Molecular wires: charge transport, mechanisms and control". Mark A. Ratner, William Davis, Mathieu Kemp, Vladimiro Mujica, Adrian E. Roitberg and Sophia Yaliraki. Annals of the New York Academy of Sciences. 852:22-36 (1998)
18. "Binding and electron transfer between putidaredoxin and cytochrome P450cam (CYP101). Theory and experiments". Adrian E. Roitberg, Marcia Holden, Martin Mayhew, Igor Kurnikov, David Beratan and Vincent Vilker. Journal of the American Chemical Society. 120:8927-8932 (1998)
16. "Probing the interactions of putidaredoxin with redox partners in camphor P450 5-monooxygenase by mutagenesis of surface residues". Marcia Holden, Martin Mayhew, David Bunk, Adrian E. Roitberg and Vincent Vilker. Journal of Biological Chemistry. 272:21720-21725 (1997)
15. "A vibrational eigenfunction for a protein: The anharmonic Coupled-Mode Ground State of BPTI". Adrian E. Roitberg, R. Benny Gerber and Mark A. Ratner. Journal of Physical Chemistry B. 101: 1700-1706 (1997)
14. "Molecular wires: resonances, staircases, rectification, bonding and speculation". Mathieu Kemp, Vladimiro Mujica, Adrian E. Roitberg, Yi Mao and Mark A. Ratner. Atomic and Molecular Wires", NATO ASI Series E. Applied Sciences. 341:203-217. C. Joachim (Ed.). Kluwer Academic Publishers (1997)
13. "Moller-Plesset perturbation theory applied to vibrational problems". Lawrence Norris, Mark A. Ratner, Adrian E. Roitberg and R. Benny Gerber. Journal of Chemical Physics. 105:11261-11267 (1996)
12. "Molecular wires, extended couplings and disorder effects". Mathieu Kemp, Adrian E. Roitberg, Todd Wanta, Vladimiro Mujica and Mark A. Ratner. Journal of Physical Chemistry. 100:8349-8355 (1996)
11. "A model for coulomb interaction in electron transport in one-dimensional mesoscopic devices". Mujica, Vladimiro; Kemp, Mathieu; Roitberg, Adrian; Ratner, Mark. Condensed Matter Theories. 11:261-272 (1996)
10. "Current-voltage characteristics of molecular wires. Eigenvalue staircase, coulomb blockade and rectification". Vladimiro Mujica, Mathieu Kemp, Adrian E. Roitberg and Mark A. Ratner. Journal of Chemical Physics. 104:7296 (1996)
9. "Anharmonic wave functions of proteins: quantum self-consistent field calculations of BPTI". Adrian E. Roitberg, Ron Elber, R. Benny Gerber and Mark A. Ratner. Science. 268:1319-1322 (1995)
8. "MOIL: a program for simulations of macromolecules". Ron Elber, Adrian E. Roitberg, Carlos L. Simmerling, Robert Goldstein, Hy Li, Gennady Verkhiver, Chen Keasar, J. Zhang and Alex Ulitsky. Computer Physics Communications. 91:159 (1995)
7. "Resonances and interference effects on the effective electronic coupling in electron transfer". Amanda Cheong, Adrian E. Roitberg, Vladimiro Mujica and Mark A. Ratner. Journal of Photochemsitry and Photobiology: A, Chemistry. 82:81-86 (1994)
6. "A perturbed mean field approach to the decay rates of excited vibrational states in extended systems: an application to I2(Ne)n". Adrian E. Roitberg, R. Benny Gerber and Mark A. Ratner. Journal of Chemical Physics. 100:4355-4366 (1994)
5. "MOIL: A molecular dynamics program with emphasis in conformational searches and reaction path calculations". Ron Elber, Adrian E. Roitberg Carlos L. Simmerling, Robert Goldstein, Gennady Verkhivker, Hy Li and Alex Ulistky. NATO ASI Series B. Physics. 325:165-191 (1994)
4. "Modeling side-chains in peptides and proteins with the Locally Enhanced Sampling/simulated annealing method". Adrian E. Roitberg and Ron Elber. "The Protein Folding Problem and Tertiary Structure Determination". Ed K.Merz Jr. and S. Le Grand. Birkhauser Pub (1994)
2. "Conformational transitions". Ryzard Czerminski, Adrian E. Roitberg, Chyung Choi, Alex Ulistsky and Ron Elber. AIP 239. Advances in Biomolecular Simulations. 153-173 (1991)
1. "Reductive dissolution of neutron and gamma irradiated magnetite". Maria dos Santos Afonso, Cecilia Di Risio, Adrian E. Roitberg, Roberto Marques and Miguel Blesa. International Journal of Applied Instrumentation Part. C. Radiation in Physics and Chemistry. 36:3 (1990)
Copyright (c) 2003-2004 The Roitberg Group All right reserved.
Contact kim@qtp.ufl.edu for more information.