Tamar Schlick
Department of Chemistry and Courant Institute of Mathematical Sciences, New York University (NYU)
251 Mercer Street, NYC, NY 10012
Telephone: (212) 998-3116 /-3596 (sec.),
Fax: (212) 995-4152,
E-mail: schlick@nyu.edu
Group URL: monod.biomath.nyu.edu
Education
Wayne State University, Detroit, MI (B.S., Mathematics, 1982); NYU, Courant Institute of Mathematical Sciences, New York, NY (Applied
Mathematics, M.S., 1984 and Ph.D., 1987)
Previous Employment and Experience
Director of new multidepartmental Computational Biology Doctoral Program, Graduate School of Arts and Sciences, NYU (2003 - 2006);
Director of Program Development, Department of Chemistry, NYU (2003 - 2006);
Director of Graduate Studies, Department of Chemistry, NYU (2000 - 2003); Associate Investigator, Howard
Hughes Medical Institute (1994 - 2003); Affiliate, Biochemistry Department, NYU School of Medicine (1996 -);
Professor of Chemistry, Mathematics, and Computer Sciences, NYU (1996 -); Assistant (until 1992) and
Associate (until 1996) Professor of Chemistry and Mathematics, Faculty of Arts and Science and Courant Institute of Mathematical Sciences,
NYU (1989 - 1996); Weizmann Institute Postdoctoral Fellow, Weizmann Institute of Science, Rehovot, Israel
(1988); NSF Mathematical Sciences Postdoctoral Fellow in the Mathematical/Physical Sciences, Courant Institute of Mathematical Sciences, NYU (1987 - 1989)
Fellow, Honors and Awards
2005 Businesswoman of the Year (2006); American Physical Society Fellow (2005); American Association for the Advancement of Science Fellow (2004); Sri Chinmoy Lifting Up the World Oneness-Heart Award (2003); Agnes Fay Morgan Research Award in Chemistry, Iota Sigma Pi National Honor Society (2003); Burroughs
Wellcome Visiting Professor, University of North Carolina (2000 - 2001); John Simon Guggenheim
Fellow (2000 - 2001); AWIS Outstanding Woman in Science (2000); Alfred P. Sloan Research Fellow (1993 -
1995); NYU Distinguished Recent Alumna (1993); NSF Presidential Young Investigator (1991 - 1996);
Whitaker Fellow in Biomedical Engineering (1991 - 1994); Searle Scholar (1991 - 1994);
Whitehead Presidential Fellow, NYU (1991); Marie Curie American Fellow, American Association for
University Women Educational Foundation (1990 - 1991); Kurt O. Friedrichs Prize for Outstanding Dissertation
in Mathematics, Courant (1988); Jay Krakauer Prize for Outstanding Dissertation in the Sciences, NYU
(1988); NSF Mathematical Sciences Postdoctoral Fellow
(1987 - 1989); American Cancer Society Postdoctoral Fellow (declined) (1987 - 1990); Dean's Dissertation
Fellow, NYU (1986 - 1987); Phi Beta Kappa, National Honor Society, Honor Society, Graduation with Excellence
in Mathematics and French, Outstanding Leadership Award in University Programs, Wayne State
University (1982); Wayne State University Merit Scholar (Four-Year Tuition) (1978 - 1982)
TextBook
(see website for updates, reviews, etc. http://monod.biomath.nyu.edu/index/book.html)
-
T. Schlick, Molecular Modeling: An Interdisciplinary Guide, Springer-Verlag, NY (2002).
Selected Publications
(see complete list on monod.biomath.nyu.edu)
- R. Radhakrishnan and T. Schlick, Correct and Incorrect Nucleotide Incorporation Pathways in DNA Polymerase Beta, BBRC, 350: 521--529 (2006).
- R. Radhakrishnan, K. Arora, Y. Wang, W. Beard, S. Wilson, and T. Schlick, Regulation of DNA Repair Fidelity by Molecular Checkpoints: "Gates" in DNA Polymerase Beta's Substrate Selection, Biochem., 45: 15142--15156 (2006).
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G. Arya and T. Schlick, Role of Histone Tails in Chromatin Folding Revealed by a New Mesoscopic Oligonucleosome Model, Proc. Natl. Acad. Sci., 103: 16236--16241 (2006).
-
Y. Wang, S. Reddy, W. Beard, S. Wilson, and T. Schlick, Differing Conformational Pathways Before and After Chemistry for Insertion of dATP vs. dCTP Opposite 8-oxoG in DNA Polymerase Beta, In Press (2006).
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T. Schlick, RNA --- The Cousin Left Behind Becomes a Star, in Computational Studies of DNA and RNA, J. Sponer and F. Lankas, Editors, in Challenges and Advances in Computational Chemistry and Physics, Vol. 2 (ISBN-10: 1-4020-4794-0), Springer- Dordrecht, The Netherlands (2006).
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M. Foley, K. Arora, and T. Schlick, Sequential Side-Chain Residue Motions Transform the Binary into the Ternary State of DNA Polymerase Lambda, Biophys. J., 91: 3182--3195 (2006).
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G. Arya, Q. Zhang, and T. Schlick, Flexible Histone Tails in a New Mesoscopic Oligonucleosome Model, Biophys. J., 91: 133--150 (2006). [Figure featured on journal cover].
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Q. Zhang and T. Schlick, Stereochemistry and Position-Dependent Effects of Carcinogens on TATA/TBP
Binding, Biophys. J., 90: 1865--1877 (2006).
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Y. Wang, K. Arora, and T. Schlick, Subtle but Variable Conformational Rearrangements in the Replication
Cycle of Sulfolobus solfataricus P2 DNA Polymerase IV May Accommodate Lesion Bypass, Prot. Sci., 15: 135--151 (2006).
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B. A. Sampoli Benitez, K. Arora, and T. Schlick, Induced-Fit Mechanism for the Interaction of the African
Swine Fever Virus DNA Polymerase X with Its Target DNA, Biophys. J., 90: 42--56 (2006). [Figure featured on journal cover].
-
U. Laserson, H. H. Gan and T. Schlick, Predicting Candidate Genomic Sequences that Correspond to Synthetic Functional RNA Motifs, Nuc. Acids Res. 33: 6057--6069 (2005).
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U. Laserson, H. H. Gan, and T. Schlick, Exploring the Connection Between Synthetic and Natural RNAs in
Genomes Via a Novel Computational Approach, in New Algorithms for Macromolecular Simulation, Proceedings of the Fourth International Workshop on Algorithms for Macromolecular Modelling, Leicester, UK,
August 2004'', B. Leimkuhler, C. Chipot, R. Elber, A. Laaksonen, A. Mark, T. Schlick, C. Schuette, R.D.
Skeel, Editors, Lecture Notes in Computational Science and Engineering, Vol. 49 (ISBN 3540255427),
Springer-Verlag, Berlin (2005).
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R. Radhakrishnan and T. Schlick, Fidelity Discrimination in DNA Polymerase
: Differing Closing Profiles for a Mismatched (G:A) Versus Matched (G:C) Base Pair, J. Amer. Chem. Soc. 127: 13245--13252 (2005).
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K. Arora, W. A. Beard, S. H. Wilson, and T. Schlick, Mismatch Induced Conformational Distortions in Polymerase
Support an InducedFit Mechanism for Fidelity, Biochem. 44: 13328--13341 (2005).
-
J. Gevertz, H. H. Gan, and T. Schlick, In Vitro RNA Random Pools are Not Structurally Diverse: A Computational Analysis, RNA 11: 853--863 (2005).
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J. Sun, Q. Zhang, and T. Schlick, Electrostatic Mechanism of Nucleosomal Array Folding Revealed by Computer Simulation, Proc. Natl. Acad. Sci. 102: 8180--8185 (2005).
-
K. Arora and T. Schlick, Conformational Transition Pathway of Polymerase
/DNA upon Binding Correct Incoming Substrate, J. Phys. Chem. B 109: 5358--5367 (2005).
-
T. Schlick, The Critical Collaboration Between Art and Science: Applying An Experiment on a Bird in an
Air Pump to the Ramifications of Genomics on Society, Leonardo 38(4): 323--329 (2005).
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S. Pasquali, H. H. Gan and T. Schlick, Modular RNA Architecture Revealed by Computational Analaysis of
Existing Pseudoknots and Ribosomal RNAs, Nuc. Acids Res. 33: 1384--1398 (2005).
-
D. Fera, N. Kim, N. Shiffeldrim, J. Zorn, U. Laserson, H.H. Gan, and T. Schlick, RAG: RNA-As-Graphs
Web Resource, BMC Bioinformatics 5: 88--97 (2004). (http://www.biomedcentral.com/14712105/5/88).
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K. Arora and T. Schlick, In Silico Evidence for DNA Polymerase
's Substrate-Induced Conformational
Change, Biophys. J. 87: 3088--3099 (2004).
-
Q. Zhang, S. Broyde, and T. Schlick, Deformations of Promoter DNA Bound to Carcinogens Help Interpret Effects on TATA-Element Structure and Activity, Phil. Trans. Royal Soc. Lond., Series A: Mathematical, Physical & Engineering Sciences 362: 1479--1496 (Special Volume on Mechanics of DNA) (2004).
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R. Radhakrishnan and T. Schlick, Biomolecular Free Energy Profiles by a Shooting/Umbrella Sampling Protocol, "BOLAS", J. Chem. Phys. 121: 2436--2444 (2004).
-
L. Yang, W. A. Beard, S. H. Wilson, S. Broyde, and T. Schlick, Highly Organized but Pliant Active Site of
DNA Polymerase
: Compensatory Mechanisms in Mutant Enzymes Revealed by Dynamics Simulations and Energy Analyses, Biophys. J. 86: 3392--3408 (2004).
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J. Zorn, H. H. Gan, N. Shiffeldrim, and T. Schlick, Structural Motifs in Ribosomal RNAs: Implications for
RNA Design and Genomics, Biopolymers 73: 340--347 (2004).
-
N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick,
Candidates for Novel RNA Topologies,
J. Mol. Biol. 341: 1129--1144 (2004).
-
L. Yang, K. Arora, W. A. Beard, S. H. Wilson, and T. Schlick,
The Critical Role of Magnesium Ions in DNA Polymerase Beta's Closing and Active Site Assembly, J. Amer. Chem. Soc. 126: 8441--8453 (2004).
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U. Laserson, H. H. Gan, and T. Schlick, Searching for 2D RNA Geometries in Bacterial
Genomes, Proceedings of the Twentieth Annual ACM Symposium on Computational Geometry, June 9--11, New York, pp. 373--377, ACM Press (2004)
(http://doi.acm.org/10.1145/997817.997819).
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H. H. Gan, D. Fera, J. Zorn, M. Tang, N. Shiffeldrim, U. Laserson, N. Kim, and
T. Schlick, RAG: RNA-As-Graphs Database --
Concepts, Analysis, and Features, Bioinformatics 20: 1285--1291 (2004).
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R. Radhakrishnan and T. Schlick,
Orchestration of Cooperative Events in DNA Synthesis and Repair Mechanism
Unraveled by Transition Path Sampling of DNA Polymerase
's Closing,
Proc. Natl. Acad. Sci. USA 101: 5970--5975 (2004).
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T. Schlick,
Engineering Teams Up with Computer-Simulation and Visualization Tools
to Probe Biomolecular Mechanisms,
Biophys. J. 85: 1--4 (Invited New & Notable article)
(2003). [Figure featured on journal cover].
-
J. Huang, Q. Zhang, and T. Schlick, Effect of DNA
Superhelicity and Bound Proteins on Mechanistic Aspects of the Hin-mediated and Fis-enhanced Inversion, Biophys. J. 85: 804--817 (2003).
-
H. H. Gan, S. Pasquali, and T. Schlick, A Survey of Existing RNAs Using Graph Theory with Implications
to RNA Analysis and Design, Nuc. Acids. Res. 31: 2926--2943 (2003).
-
L. Yang, W. A. Beard, S. H. Wilson, B. Roux, S. Broyde, and T. Schlick, Local Deformations Revealed
by Dynamics Simulations of DNA Polymerase
with DNA Mismatches at the Primer Terminus, J. Mol.
Biol. 321: 459--478 (2002).
-
X. Qian and T. Schlick, Efficient Multiple Timestep Integrators with Distance-Based Force Splitting for
Particle-Mesh Ewald Molecular Dynamics Simulations, J. Chem. Phys. 116: 5971--5983 (2002).
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L. Yang, W. A. Beard, S. H. Wilson, S. Broyde, and T. Schlick, Polymerase
Simulations Reveal that
Arg258 Rotation is a Slow Step Rather than Large Subdomain Motions Per Se, J. Mol. Biol. 317: 651--671 (2002).
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P. F. Batcho, D. A. Case, and T. Schlick, Optimized Particle-Mesh Ewald/Multiple-Timestep Integration
for Molecular Dynamics Simulations, J. Chem. Phys. 115:
4003--4018 (2001).
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X. Qian, D. Strahs, and T. Schlick,
A New Program for Optimizing Periodic Boundary Models of
Solvated Biomolecules (PBCAID),
J. Comp. Chem. 22: 1843--1850 (2001).
-
X. Qian, D. Strahs, and T. Schlick,
Dynamic Simulations of 13 TATA Variants Refine Kinetic
Hypotheses of Sequence/Activity Relationships,
J. Mol. Biol. 308: 681--703 (2001).
-
D. Beard and T. Schlick,
Computational Modeling Predicts the Structure and Dynamics of the Chromatin Fiber,
Structure 9: 105--114 (2001).
-
D. Beard and T. Schlick,
Modeling Salt-Mediated Electrostatics of Macromolecules:
The Algorithm DiSCO (Discrete Surface Charge Optimization)
and Its Application to the Nucleosome, Biopolymers
58: 106--115 (2001).
[Figure featured on journal cover].
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T. Schlick, D. Beard, J. Huang,
D. Strahs, and X. Qian, Computational Challenges in Simulating Large
DNA Over Long Times, IEEE Comp. Sci. Eng. (Special
Issue on Computational Chemistry) 2: 38--51 (2000).
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D. Beard and T. Schlick, Inertial Stochastic
Dynamics: I. Long-Timestep Methods for Langevin Dynamics,
J. Chem. Phys. 112: 7313--7322 (2000).
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T. Schlick, R.D. Skeel, A.T.
Brunger, L.V. Kale, J. Hermans, K. Schulten, and J.A.
Board, Jr., Algorithmic Challenges in Computational
Molecular Biophysics, J. Comp. Phys.
151: 9--48 (1999).
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T. Schlick, Computational
Molecular Biophysics Today: A Confluence of
Methodological Advances and Complex Biomolecular
Applications, J. Comp. Phys. 151: 1--8 (1999).
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D. Xie and T. Schlick, Effiecient Implementation of the Truncated Newton Method for Large Scale
Chemistry Applications, SIAM J. Opt. 10: 132--154 (1999).
-
H. Jian, T. Schlick, and A. Vologodskii,
Internal Motion of Supercoiled DNA: Brownian Dynamics
Simulations of Site Juxtaposition,
J. Mol. Biol. 284: 287--296 (1998).
[Figure featured on journal cover].
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T. Schlick, M. Mandziuk, R. Skeel, K. Srinivas,
Nonlinear Resonance Artifacts in Molecular Dynamics,
J. Comp. Phys. 139: 1--29 (1998).
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E. Barth and T. Schlick, Overcoming Stability
Limitations in Biomolecular Dynamics: I. Combining Force
Splitting via Extrapolation with Langevin Dynamics in LN,
J. Chem. Phys. 109: 1617--1632 (1998).
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P. Derreumaux and T. Schlick, Simulation of
the Loop Opening/Closing of the Enzyme Triosephosphate
Isomerase (TIM), Biophys. J. 74: 72--81 (1998).
-
T. Schlick, Geometry
Optimization, Contributed chapter to the Encyclopedia
of Computational Chemistry (5 volumes), P. von Rague
Schleyer, Editor in Chief, and N. L. Allinger, T. Clark,
J. Gasteiger, P. A. Kollman, and H. F. Schaefer III,
eds., John Wiley & Sons, West Sussex, Vol. 2,
pp. 1136--1157 (1998).
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T. Schlick, E. Barth, and M.
Mandziuk, Biomolecular Dynamics at Long Timesteps:
Bridging the Time Scale Gap Between Simulation
and Experimentation, Annu. Rev. Biophys.
Biomol. Struct. 26: 179--220 (1997).
-
R. D. Skeel, G. Zhang, and T. Schlick, A
Family of Symplectic Integrators: Stability, Accuracy,
and Molecular Dynamics Applications, SIAM
J. Sci. Comp. 18: 203--222 (1997).
-
T. Pinou, T. Schlick, B. Li, and H. Dowling,
Addition of Darwin's Third Dimension to Evolutionary
Trees, J. Theor. Bio. 219: 505--512 (1996).
-
T. Schlick and A. Brandt, A Multigrid
Tutorial with Applications to Molecular Dynamics,
IEEE Comp. Sci. Eng. 3: 78--83 (1996).
-
B. Mishra and T. Schlick, The Notion of Error
in Langevin Dynamics: (1) Linear Analysis, J. Chem. Phys.
105: 299--318 (1996).
-
T. Schlick, Pursuing Laplace's
Vision On Modern Computers, Proceedings of the IMA
Program in Mathematical Biology, IMA Volumes in Mathematics
and its Applications, Vol. 82, pp. 219--247, J. Mesirov,
K. Schulten, and D.W. Sumners, eds., Springer-Verlag, New York
(1996).
-
T. Schlick, Modeling
Superhelical DNA: Recent Analytical and Dynamic
Approaches, Curr. Opin. Struc. Bio. 5: 245--262 (1995). Special issue on Theory and Simulation,
B. Honig, ed.
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M. Mandziuk and T. Schlick, Resonance in the
Dynamics of Chemical Systems Simulated by the Implicit Midpoint
Scheme, Chem. Phys. Lett. 237: 525--535 (1995).
-
G. Ramachandran and T. Schlick, Solvent
Effects on Supercoiled DNA Explored by Langevin Dynamics
Simulations, Phys. Rev. E 51: 6188--6203
(1995).
-
T. Schlick, B. Li, and W.K. Olson, The
Effects of Salt on Supercoiled DNA Energetics and Dynamics,
Biophys. J. 67: 2146--2166 (1994).
-
G. Zhang and T. Schlick, The
Langevin/Implicit-Euler/Normal-Mode Scheme (LIN) for
Molecular Dynamics at Large Timesteps, J. Chem. Phys.
101: 4995--5012 (1994).
-
P. Derreumaux, G. Zhang, B. Brooks, and T.
Schlick, A Truncated-Newton Method Adapted for CHARMM
and Biomolecular Applications, J. Comp. Chem.
15: 532--552 (1994).
-
G. Zhang and T. Schlick, LIN: A New Algorithm
Combining Implicit Integration and Normal Mode Techniques
for Molecular Dynamics, J. Comp. Chem. 14: 1212--1233 (1993).
-
X. Zou, I.M. Navon, M. Berger, P.K.H. Phua, T.
Schlick, and F.X. Le Dimet, Numerical Experience with
Limited-Memory and Truncated Newton Methods, SIAM
J. Opt. 3: 582--608 (1993).
-
T. Schlick, Modified Cholesky Factorizations
for Sparse Preconditioners, SIAM J. Sci. Comp. 14: 424--445 (1993).
-
T. Schlick, Optimization
Methods in Computational Chemistry, in
Reviews in Computational Chemistry, Volume 3,
Chapter 1, pp. 1--71, K.B. Lipkowitz and D.B. Boyd,
eds., VCH Publishers, New York (1992).
-
A. Nyberg and T. Schlick, On Increasing the
Time Step in Molecular Dynamics, Chem. Phys. Lett. 198: 538--546 (1992).
-
T. Schlick and W.K. Olson, Trefoil Knotting Revealed by Molecular Dynamics of Supercoiled DNA, Science 257: 1110--1115 (1992).
-
T. Schlick and A. Fogelson, TNPACK -- A
Truncated Newton Minimization Package for Large-Scale
Problems: I. Algorithm and Usage,
ACM Trans. Math. Softw. 18: 46--70 (1992).
-
T. Schlick and A. Fogelson, TNPACK -- A
Truncated Newton Minimization Package for Large-Scale
Problems: II. Implementation Examples,
ACM Trans. Math. Softw. 18: 71--111 (1992).
-
T. Schlick and W.K. Olson, Computer Simulations of Supercoiled DNA Energetics and
Dynamics, J. Mol. Biol 223: 1089-1119 (1992).
-
T. Schlick and C.S. Peskin, Can Classical Equations
Simulate Quantum-Mechanical Behavior? A Molecular
Dynamics Investigation of a Diatomic Molecule with a
Morse Potential, Comm. Pure Appl. Math. 42: 1141--1163 (1989).
-
C.S. Peskin and T. Schlick, Molecular Dynamics by
the Backward-Euler Method, Comm. Pure Appl. Math.
42: 1001--1031 (1989).
-
T. Schlick and M. Overton, A Powerful Truncated
Newton Method for Potential Energy Minimization,
J. Comp. Chem. 8: 1025--1039 (1987).
-
W.L. Hase, D.M. Ludlow, R.J. Wolf, and T. Schlick,
Translational and Vibrational Energy Dependence of the
Cross Section for H + C2H4 --->
C2H5, J. Phys. Chem. 85: 958--968 (1981).
Synergistic Activities
Advisory Committee Member - NIH Director's Pioneer Award Evaluator (2005,2006); HHMI-NIBIB (Howard Hughes Medical Institute - National Institute of Biomedical Imaging and Bioengineering, NIH) Initiative for Interdisciplinary Graduate Research training (2005); NIH Computational Biophysics study section (2004); New York Academy of Sciences Women Investigators Network (2004 - ); National Iota Sigma Pi Award Committee (2004); NSF with UK (EPSRC) High Speed Computing in the 21st Century, Focus on Materials and Biological Applications (2004); NYU's Center for Teaching Excellence (2004 - ); NIH Member of the Physical Biochemistry Review Study Section (2003 - 2006); The Philip Morris External Research Program Peer Review (2003); NSF's Advanced Computational Infrastructure (PACI) Resource Allocation
Committee (2002 - ); NPACI (National Partnerships for Advanced Computational Infrastructure)
Panel Review Board, NSF (2002 - ); Member-at-Large of the AAAS Section A (Mathematics) (2002 -
2005); NIH Special Focus Group (convened by Elias Zerhouni) (2002); Faculty of 1000, Structural Biology/
Theory and Simulation (2001 - ); NIH Special Study Section B, NIGMS (2001); Alumni Executive Committee, Wayne State University (2001 - ); Finance Committee, Biophysical Society (2001 - 2004); Michigan Life Sciences Corridor (MLSC) Fund Review Board, managed by The Washington Advisory Board (WAG), Purnell W. Choppin and James B. Wyngaarden, Principals (2000); NIH Site Visit panel,
Intramural Review of Computational Applications Program (SAIC), NCI (2000); NIH BBCA study section
(1999); SIAM Life Sciences Activity Group Steering Committee (1999 - ); Computational Science Program, External Advisory Board, Computational Science Program of the School of Computational Science and Information Technology (CSIT), Florida State University, Institute of Molecular Biophysics (1999 - ); NSF/NIH/DOE panel, Next
Generation Biology: the Role of Next Generation Computing (1998); Vice-Chair Nomination Committee, Theoretical Chemical Subdivision, Physical Chemistry Division, American Chemical Society (1998 - ); Advisor to Museum Exhibition: The Chemistry of Living Things, New York Hall of Science, Flushing Meadows Corona Park, New York (1997 - ); NSF Academic Research Infrastructure
Program (1996); Burroughs Wellcome Fund, Advisory Committee for Interface Program Between the
Physical and Biological Sciences (1995 - 2000); AMS-SIAM Committee on Applied Mathematics (1995 -
2000); SIAM's representative to the AMS-ASA-AWM-IMS-MAA-NCTM-SIAM Committee on Women in
the Mathematical Sciences (1994 - 2002); NIH RAC Board for the Parallel Structural Biology Project of the
San Diego Supercomputing Center and UCSD (1994 - ); NIH Board of Scientific Counselors, National Library
of Medicine (1994 - 1999); National Research Council, NAS, Report on Mathematical Challenges from
Theoretical/Computational Chemistry, (1994 - 1995); NSF Biophysics Division (1993 - 1995); NIH Special
Review Committee for Structural Biology as Applied to the Problem of Targeted Drug Design for the Treatment
of AIDS Initiative (1992); NSF Advanced Scientific Computing Postdoctoral Research Associateship
Program (1991 - 1994)
Editorial Boards - SIAM Journal on Scientific Computing (2006 - 2009); SIAM Multiscale Modeling and Simulation (2005 - 2008); Biomedical Computational Review (2005 - ); Biomolecular Engineering (2004 - ); Biophysics J. (2004 - 2007); J. Comp. Phys. (1997 - ); Springer Verlag Lecture Notes in Comp. Sci. and Engin.
(1996 - ); J. Theo. Biol. (1995 - )
Organizer/Co-Organizer - IMA Special Year in Computational Chemistry, University of Minnesota, Minneapolis, MN (2008 - 2009); IMA Special Year in Mathematics of Molecular and Cellular Biology (with DeWitt Sumners and Richard James), University of Minnesota, Minneaoplis, MS (2007 - 2008); IMA Workshop on RNA Biology, Bioengineering and Nanotechnology (with Eric Westhof), Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN (2007); 2007 SIAM Conference on Mathematics for Industry (Broad theme: Mathematics for Life Sciences), (2007); Fourth International Symposium on Algorithms for Molecular Modeling, Co-Organizer, University of Leicester, England (2004); Second SIAM Life Sciences Conference (2004); Geometric and PDE Modeling
Problems in the Life Sciences, PRIMA, Hawaii (2004); Mathematical and Computational Approaches
to Biomolecular Simulations, MSRI, Berkeley (2003); Workshop on Modeling and Simulation for Materials,
Institute for Pure and Applied Mathematics (IPAM), UCLA (2002); First SIAM Life Sciences Conference,
Boston (2002); SIAM Computational Sciences Meeting, Washington, D.C. (2000); Third International Symposium
on Algorithms for Macromolecular Modeling, New York (2000); International Conference on Multiscale
Methods, Weizmann Institute (2000); DIMACS/PMMB Workshop on DNA Topology (1997); IMA
Special Year in High Performance Computing (1997); Molecular Dynamics Minisymposium, SIAM, Charlotte
(1995); Multigrid Techniques with Applications to Molecular Dynamics, Weizmann Institute (1995);
Program in Mathematical Biology, MSRI Berkeley (1992)
Recent Invited Presentations - Biomolecular Simulation 2007 - First Annual Meeting of the Collaborative Project for Biomolecular Simulation (CCPB), University of Nottingham, UK (2007); Carolina Biophysics Symposium, Durham, NC (2006); Theoretical Chemistry Seminar Series, MIT, Boston, MA (2006); 60th Birthday Celebration for Charlie Peskin Symposium, Courant Institute, NYU, New York (2006); NSF-funded workshop on developing ideas for a new mathematical biology center, Washington, D.C. (2006); Loew Meeting 2005, International Society of Quantum Biology & Pharmacology
(ISQBP), College of Staten Island (2005); Biological Society Seminar Series, New York University, New York (2005); Multi-Teraflop Computing in Biology, Materials, and Energy Science, a Workshop
organized by Brookhaven National Lab, IBM, and Stony Brook; Stony
Brook, New York (2005); Women In Science At Yale (WISAY) Group, Yale University, New Haven, CN (2005); Iota Sigma Pi National Honor Society for Women in Chemistry Triennial Convention,
Sweet Briar College, Lynchburg, VA (2005); Mathematical Issues in Molecular Dynamics Workshop,
Banff International Research Station, Banff, Canada (2005); Women at the Forefront of Biological
Physics symposium, American Physical Society of Biological Physics and the
Committee on the Status of Women in Physics, Los Angeles, CA (2005); Simulation of Biomolecules – Methods at the Boundaries, Opportunities for Physicists in Biophysics, Division of Biological Physics, American Physical Society National Meeting, Los Angeles, CA (2005); Young Researchers Workshop in Mathematical Biology, The Mathematical Biosciences
Institute, Ohio State University, Columbus, OH (2005); Duke Structural Biology
and Biophysics student seminar program, Duke University, Durham, NC (2005);
Fourth International Symposium on Algorithms for Macromolecular Modeling,
University of Leicester, UK (2004); American Chemical Society National Meeting,
Symposium on The Molecular Origin of Replication and Translation, Philadelphia,
PA (2004); Plenary Speaker, Society for Mathematical Biology and International
Society of Computational Biology annual meeting, University of Michigan, Ann
Arbor, MI (2004); Plenary Speaker, ACM Symposium on Computational Geometry, Brooklyn
Polytechnic, New York, NY (2004); Distinguished Lecture Series, Department of
Computer Science, University of Illinois, Champaign/Urbana, IL (2004); NSF
with UK (EPSRC) Joint Conference of High Speed Computing in the 21st Century,
with Focus on Materials and Biological Applications, Washington, D.C (2004);
12th Annual Bud Suddath Bioscience Symposium, Computational Biology (2004);
Accelerating Dynamical Simulations, SIMU CECAM Workshop, Lyons, France (2004);
Biophysics Colloquium, Columbia University, New York, NY (2004); Biophysical
Society Annual Meeting, Symposium on Applied Biocomputations and Long Time
Scales, Baltimore, MD (2004); Levich Institute Seminar, IGERT Lecture Series on
Soft Materials, City College of CUNY, New York, NY (2003); Rensselaer
Polytechnic Institute, Interdisciplinary Seminar, Troy, NY (2003); New
Colloquium Series: Interdisciplinary Research in the Life Sciences, Physical
Chemistry Division of the Chemistry Department and the Molecular and
Computational Biology Division of the Department of Biological Studies,
University of Southern California, Los Angeles, CA (2003); Distinguished
Speaker, Symposium on Computing in Chemistry, The Institute for Scientific
Computing (Director William H. Hase), Wayne State University, Detroit, MI
(2003); American Society Meeting, Frontiers in DNA Research: An
Interdisciplinary Symposium, Computers in Chemistry (COMP) section with
co-sponsorship by the Biological Sciences (BIOL) and Medicinal Chemistry
(MEDI) divisions, New York, NY (2003); SciCADE03: Scientific Computing
and Differential Equations), Minisymposium on Molecular Dynamics, Trondheim,
Norway (2003); Howard Hughes Summer School Faculty Lecture, Department of
Biology, New York University, New York, NY (2003); Faculty Lecturer, NSF Summer
School on Theoretical and Computational Biophysics: Computational Approaches
for Simulation of Biological Systems Sponsored by the Theoretical and
Computational Biophysics Group (Director Klaus Schulten), University of
Illinois at Urbana-Champaign, IL (2003); Applied Mathematics Colloquium,
Courant Institute of Mathematical Sciences, New York University, New York, NY
(2003); Chemistry and Biochemistry Colloquium, City College of CUNY, New York,
NY (2003); Understanding Physical Chemistry of Biomolecular Motors,
Physical Chemistry Symposium (Q. Cui and C. Bustamante, Organizers), American
Chemical Society National Meeting, New Orleans, LA (2003); Computer in
Chemistry Division (H. Carlson, Organizer), American Chemical Society National
Meeting, New Orleans, LA (2003); Mathematical and Computational Approaches to
Biomolecular Simulations, Mathematical Sciences Research Institute, University
of California at Berkeley, Berkeley, CA (2003); Modeling and Simulation for
Material Program on Mathematics in Nanoscale Science and Engineering, Institute
for Pure and Applied Mathematics (IPAM), University of California at Los
Angeles, Los Angeles, CA (2002); New York Academy of Sciences,
Bioinformatics/Computational Biology Group, New York, NY (2002);
Computational Science and Engineering minisymposium, SIAM 50th Annual
meeting, Philadelphia, PA (2002); Dynamics of Proteins on a Continuous
Energy Landscape, CECAM workshop, Lyon, France (2002); Symposium in
Remembrance of Peter A. Kollman, American Chemical Society (ACS) Computers
in Chemistry Division, ACS National Meeting, Orlando, FL (2002); Molecular
Simulations in Structural Biology and Drug Discovery, Symposium in memory
of Peter Kollman, University of California, San Francisco, CA (2002);
Frontiers of Structural Biology, Keystone Symposium, Breckenridge, CO
(2002); Mathematics and Molecular Biology VII: Modeling Across the Scales
--- Atoms to Organisms, Program in Mathematics and Biology, Santa Fe, NM
(2002)
Postgraduate-Scholar Sponsor:
I. Alberts, G. Arya, D. Barash (University of Haifa, Israel), E. Barth (Kalamazoo
College), P. Batcho (Princeton University), D. Beard (Wisconson Medical College),
M. Bojin, P. Derreumaux (CNRS, France), H. H. Gan, J. Jaramillo, H. Jian (Citibank,
NYC), Y.-P. Liu (Western Michigan University), M. Mandziuk (Long Island University),
B. Mishra (Wall Street, NYC), X. Qian (Morgan Stanley, NYC), R. Radhakrishnan
(University of Pennsylvania), A. Sandu (Michigan Technological University), D. Strahs
(Pace University), J. Sun (Cornell), Y. Wang, D. Xie (University of Wisconsin-Milwaukee),
Y. Xin, L. Yang, L. Zaslavsky (SAIC, MD), Q. Zhang (Scripps)
Graduate Advisor: K. Arora (Scripps), S. D'Souza, M. Foley, J. Huang
(VeraChem, MA), N. Kim, S. Reddy, D. Rooklin, N. Shiffeldrim, S. Yaghmour, Q. Zhang
(Scripps)
Other Students:
J. Potter, G. Quarta, E. Sherman, J. Sofaer, N. Tran