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Anna Marie Pyle, and Tamar Schlick, "Challenges in RNA Structural Modeling and Design", J. Mol. Biol., 428 (5):733735, doi: 10.1016/j.jmb.2016.02.012 (2016). 
Sergei Grigoryev, Gavin Bascom, Jenna Buckwalter, Michael Schubert, Christopher Wookcock, and Tamar Schlick, "Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes", PNAS, 113(5):123843, doi: 10.1073/pnas.1518280113 (2016). 
Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jason Wang, and Tamar Schlick, "CHSalign: A Web Server That Builds upon JunctionExplorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking", PLoS ONE, 11(1):e0147097, DOI: 10.1371/journal.pone.0147097 (2016). 
Louis Petingi, and Tamar Schlick, "Partitioning RNAs into pseudonotted and pseudoknotfree regions modeled as Dual Graphs", qbio.QM,arXiv:1601.04259 (2016). 
Naoto Baba, Shereef Elmetwaly, Namhee Kim, and Tamar Schlick, "Predicting Large RNALike Topologies by a KnowledgeBased Clustering Approach", J. Mol. Biol., 428(5 Pt A): 81121, doi: 10.1016/j.jmb.2015.10.009 (2015). 
Mai Zahran, Cigdem Sevim Bayrak, Shereef Elmetwaly, and Tamar Schlick, "RAG3D: a search tool for RNA 3D substructures", Nucleic Acids Research, 43(19): 947488, doi: 10.1093/nar/gkv823 (2015). 
Rosana CollepardoGuevara, Guillem Portella, Michele Vendruscolo, Daan Frenkel, Tamar Schlick, and Modesto Orozco, "Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study", Journal of the American Chemical Society, 137:(32), 1020510215 (2015). 
Gungor Ozer, Antoni Luque, and Tamar Schlick, "The chromatin fiber: multiscale problems and approaches", Curr. Opin. Struct. Biol., 31:, 124139 (2015). 
Namhee Kim, Mai Zahran, and Tamar Schlick, "Computational Prediction of Riboswitch Tertiary Structures Including Pseudoknots by RAGTOP: A Hierarchical Graph Sampling Approach", Methods Enzymol., 553, 11535, DOI: 10.1016/bs.mie.2014.10.054 (2015). 
Gungor Ozer, Rosana CollepardoGuevara, and Tamar Schlick, "Forced unraveling of chromatin fibers with nonuniform linker DNA lengths", J. Phys.: Condens. Matter, 27(6): 064113, DOI: 10.1088/09538984/27/6/064113 (2015). 
Bret D. Freudenthal, William A. Beard, Lalith Perera, David D. Shock, Taejin Kim, Tamar Schlick, and Samuel H. Wilson, "Uncovering the polymeraseinduced cytotoxicity of an oxidized nucleotide", Nature,517, 635–639, DOI:10.1038/nature13886 (2014). 
Namhee Kim, Zhe Zheng, Shereef Elmetwaly and Tamar Schlick, "RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology", PLoS ONE, 9(9): e106074, DOI: 10.1371/journal.pone.0106074 (2014). 
Antoni Luque, Rosana CollepardoGuevara, Sergei Grigoryev and Tamar Schlick, "Dynamic condensation of linker histone Cterminal domain regulates chromatin structure", Nucleic Acids Res., 42(12): 75537560, DOI: 10.1093/nar/gku491 (2014). 
Rosana CollepardoGuevara, and Tamar Schlick, "Chromatin fiber polymorphism triggered by variations of DNA linker lengths", PNAS, DOI: 10.1073/pnas.1315872111 (2014). 
Namhee Kim, Christian Laing, Shereef Elmetwaly, Segun Jung, Jeremy Curuksu, and Tamar Schlick, "Graphbased sampling for approximating global helical topologies of RNA", PNAS, DOI: 10.1073/pnas.1318893111 (2014). 
Yunlang Li, Bret D. Freudenthal, William A. Beard, Samuel H. Wilson, and Tamar Schlick, "Optimal and Variant MetalIon Routes in DNA Polymerase β's Conformational Pathways", J. Am. Chem. Soc.,DOI: 10.1021/ja412701f (2014). 
Segun Jung and Tamar Schlick, "Interconversion between Parallel and Antiparallel Conformations of a 4H RNA junction in Domain 3 of FootandMouth Disease Virus IRES Captured by Dynamics Simulations", Biophys. J., 106(2): 447458, (2014). 
Benedetta Sampoli Benítez, Zachary R. Barbati, Karunesh Arora, Jasmina Bogdanovic, and Tamar Schlick, "How DNA Polymerase X Preferentially Accommodates Incoming dATP Opposite 8Oxoguanine on the Template", Biophys. J., 105(11): 25592568, (2013). 
Tamar Schlick, "The 2013 Nobel Prize in Chemistry Celebrates Computations in Chemistry and Biology", SIAM News, 46(10), December (2013). 
Christian Laing, Segun Jung, Namhee Kim, Shereef Elmetwaly, Mai Zahran, and Tamar Schlick, "Predicting Helical Topologies in RNA Junctions as Tree Graphs", PLoS ONE, 8(8): e71947, DOI:10.1371/journal.pone.0071947 (2013). 
Yunlang Li, and Tamar Schlick, "Gatekeeper Residues and ActiveSite Rearrangements in DNA Polymerase μ Help Discriminate Noncognate Nucleotides", PLoS Comput. Biol., 9(5), DOI:10.1371/journal.pcbi.1003074 (2013). 
Rosana CollepardoGuevara, and Tamar Schlick, "Insights into chromatin fibre structure by in vitro and in silico singlemolecule stretching experiments", Biochem. Soc. Trans., 41(2): 494500 (2013). 
Segun Jung, and Tamar Schlick, "Candidate RNA structures for domain 3 of the footandmouthdisease virus internal ribosome entry site", Nucleic Acids Res., 41(3): 148395 (2013). 
Namhee Kim, Louis Petingi, and Tamar Schlick, "Network Theory Tools for RNA Modeling", WSEAS Transactions on Math, 12(9): 941955 (2013). 
Namhee Kim, Niccole Fuhr and Tamar Schlick, "Graph Applications to RNA Structure and Function", Chapter 3, pp. 23–51, In Biophysics of RNA Folding, Ed. R. Russel, Biophysics for the Life Sciences 3, Springer Verlag (2013). 
Rosana CollepardoGuevara, and Tamar Schlick, "Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes", Nucleic Acids Res., 40(18): 88038817 (2012). 
Tamar Schlick, Karunesh Arora, William A. Beard, and Samuel H. Wilson, "Perspective: prechemistry conformational changes in DNA polymerase mechanisms", Theor Chem Acc, 131(12): 1287 (2012). 
Namhee Kim and Tamar Schlick, "A New Toolkit for Modeling RNA from a PseudoTorsional Space", J. Mol. Biol., doi:10.1016/j.jmb.2012.05.027 (2012). 
Yunlang Li, Chelsea L. Gridley, Joachim Jaeger, Joann B. Sweasy, and Tamar Schlick, "Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme’s pathway", J. Am. Chem. Soc., 134(24): 999910010 (2012). 
Tamar Schlick, "Modelers to the Rescue", In Innovations in Biomolecular Modeling and Simulations, Volume 1, T. Schlick, ed., Royal Society of Chemistry, London (2012). 
Meredith Foley, Karunesh Arora and Tamar Schlick, "Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanism", In Innovations in Biomolecular Modeling and Simulations, Volume 2, T. Schlick, ed., Royal Society of Chemistry, London (2012). 
Innovations in Biomolecular Modeling and Simulations, Volume 2, T. Schlick ed., The Royal Society of Chemistry, ISBN: 9781849735056, DOI:10.1039/9781849735056 (2012). 
Innovations in Biomolecular Modeling and Simulations, Volume 1, T. Schlick ed., The Royal Society of Chemistry, ISBN: 9781849735049, DOI:10.1039/9781849735049 (2012). 
Tamar Schlick, Jeff Hayes, and Sergei Grigoryev, "Toward Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber", JBC, 287: 51835191 (2012). 
Giulio Quarta, Ken Sin and Tamar Schlick, "Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function", PLoS Comput Biol, 8(2): e1002368. doi:10.1371/journal.pcbi.1002368 (2012). 
Rosana CollepardoGuevara and Tamar Schlick, "The Effect of Linker Histone's Nucleosome Binding Affinity on Chromatin Unfolding Mechanisms", Biophys. J., 111(7):16701680 (2011). 
Christian Laing, Dongrong Wen, Jason T. L. Wang and Tamar Schlick, "Predicting coaxial helical stacking in RNA junctions", Nucleic Acids Research, 40(2): 487498, doi:10.1093/nar/gkr629 (2011). 
Tamar Schlick and Rosana CollepardoGuevara, "Biomolecular Modeling and Simulation: The Productive Trajectory of a Field", SIAM News, 44: 6 (2011). 
Joseph Izzo, Namhee Kim, Shereef Elmetwaly and Tamar Schlick, "RAG: an update to RNAAsGraphs resource", BMC Bioinformatics, 12: 219 (2011). 
Christian Laing and Tamar Schlick, "Computational approaches to RNA structure prediction, analysis, and design", Curr. Opin. Struct. Biol., 21: 113 (2011). 
Tamar Schlick, "DNA Polymerases: Structure, Function, and Modeling", in Molecular Machines, , B. Roux, Editor, World Scientific, (2011). 
Yunlang Li and Tamar Schlick, "Modeling DNA Polymerase μ Motions: Subtle Transitions before Chemistry", Biophys. J., 99(10): 34633472 (2010). 
Hin Hark Gan and Tamar Schlick, "Chromatin Ionic Atmosphere Analyzed by a Mesoscale Electrostatic Approach", Biophys. J., 99(8): 25872596 (2010). 
Tamar Schlick, Rosana CollepardoGuevara, Leif A. Halvorsen, Segun Jung and Xia Xiao, "Biomolecular Modeling and Simulation: A Field Coming of Age" , Q. Rev. of Biophys., 44 (2): 191228 (2011). 
Meredith Foley, Victoria Padow and T. Schlick, "Extraordinary Ability of DNA Pol λ to Stabilize Misaligned DNA" , J. Am. Chem. Soc., 132: 1340313416 (2010). 
Ognjen Perisic, Rosana CollepardoGuevara and T. Schlick, "Modeling Studies of Chromatin Fiber Structure as a Function of DNA Linker Length", J. Mol. Biol., 403: 777802 (2010). 
N. Kim, J. Izzo, S. Elmetwaly, H.H. Gan and T. Schlick, "Computational Generation and Screening of RNA Motifs in Large Nucleotide Sequence Pools", Nucleic Acids Research, doi:10.1093/nar/gkq282 (2010). 
C. Laing, and T. Schlick, "Computational Approaches to RNA 3D Modeling", J. Phys.: Condens. Matter, 22: 283101 (2010). 
G. Quarta, N. Kim, J. A. Izzo, and T. Schlick, "Analysis of Riboswitch Structure and Function by an Energy Landscape Framework.", J. Mol. Biol., 393:9931003 (2009). 
C. Laing and T. Schlick, "Analysis of FourWay Junctions in RNA Structures.", J. Mol. Biol., 390:547559 (2009). 
Tamar Schlick, "Mathematical and Biological Scientists Assess the StateoftheArt in RNA Science at an IMA Workshop RNA in Biology, Bioengineering and Biotechnology", Int. J. Multi. Sci. Eng., 8 (4):369378 (2010) 
Tamar Schlick and Ognjen Perisic, "Mesoscale simulations of two nucleosomerepeat length oligonucleosomes.", Phys. Chem. Chem. Phys., 11:1072910737 (2009) 
S. Grigoryev, G. Arya, S. Correll, C. Woodcock, and T. Schlick, "Evidence for hetromorphic chromatin fibers from analysis of nucleosome interactions.", PNAS, 106(32):1331713322 (2009) 
C. Laing, S. Jung, A. Iqbal, and T. Schlick, "Tertiary motifs revealed in analyses of higherorder RNA junctions.", J. Mol. Biol., 393(1):6782 (2009) 
T. Schlick, "From Macroscopic to Mesoscopic Models of Chromatin Folding." Chapter 15, pp. 514535, Multiscale Methods: Bridging the Scales in Science and Engineering, J. Fish, Editor, Oxford University Press (2009) 
T. Schlick, "Molecular dynamicsbased approaches for enhanced sampling of longtime, largescale conformational changes in biomolecules." F1000 Biology Reports, 151 (2009) 
M.C. Foley and T. Schlick, "Relationship Between Conformational Changes in Pol λ Active Site Upon Binding Incorrect Nucleotides and Mismatch Incorporation Rates" J. Phys. Chem. B, 113:1303513047 (2009) 
T. Schlick, "Monte Carlo, harmonic approximation, and coarsegraining approaches for enhanced sampling of biomolecular structure." F1000 Biology Reports, 148(2009) 
G. Arya and T. Schlick, "A Tale of Tails: How Histone Tails Mediate Chromatin Compaction in Different Salt and Linker Histone Environments" J. Phys. Chem. A, 16:40454059 (2009) 
B. A. Sampoli Benitez, K. Arora, L. Balistreri, and T. Schlick, "Mismatched basepair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation", J. Mol. Biol., 384:10861097 (2008) 
P. Sridhar, H.H. Gan, and T. Schlick, "A computational screen for C/D box snoRNAs in the human genomic region associated with PraderWilli and Angelman syndromes", J. Biomed. Sci., 15:697705 (2008) 
K. Bebenek, M. GarciaDiaz, M. C. Foley, L. C. Pedersen, T. Schlick, and T. A. Kunkel, "Substrateinduced DNA strand misalignment during catalytic cycling by DNA polymerase λ", EMBO Rep., 9:459464 (2008) 
Y. Wang and T. Schlick, "Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals waterdependent pathways and requirements for active site reorganization", J. Am. Chem. Soc., 130:1324013250 (2008) 
M. C. Foley and T. Schlick, "Simulations of DNA pol λ R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin", J. Am. Chem. Soc., 130:39673977 (2008) 
Y. Xin, C. Laing, N.B. Leontis, and T. Schlick, "Annotation of tertiary interactions in RNA structures reveals variations and correlations.", RNA, 14:24652477 (2008) 
Y. Xin, G. Quarta, H.H. Gan, and T. Schlick, "Estimating the fraction of noncoding RNAs in mammalian transcriptomes.", Bioinformatics and Biology Insights, 2:7795 (2008) 
N. Kim, J.S. Shin, S. Elmetwaly, H.H. Gan and T. Schlick, "RAGPOOLS: RNAAsGraphPools A Web Server for Assisting the Design of Structured RNA Pools for In Vitro Selection", Bioinformatics, 23(21):29592960, doi:10.1093/bioinformatics/btm439 (2007) 
M.D. Bojin and T. Schlick, "A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase ", J. Phys. Chem. B, 111(38),1124411252 (2007) 
I.L. Alberts, Y. Wang, T. Schlick, "DNA polymerase catalysis: are different mechanisms possible?" , J Am Chem Soc, 129(36):1110010 (2007) 
N. Kim, H. H. Gan, and T. Schlick, "A Computational Proposal for Designing Structured RNA Pools for in Vitro Selection of RNAs", RNA, 13:47892 (2007) 
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 8oxoG in DNA Polymerase Beta", Biophys. J.,92:30633070 (2007) 
Y. Wang and T. Schlick, "Distinct Energetics and Closing Pathwasys for DNA Polymerase Beta with 8oxoG Template and Different Incoming Nucleotides" BMC Structural Biology, 7:7 (2007) 
G. Arya and T. Schlick, "Efficient Global Biopolymer Sampling with EndTransfer Configurational Bias Monte Carlo" J. Chem. Phys., 126:044107 (2007) 
R. Radhakrishnan and T. Schlick, "Correct and Incorrect Nucleotide Incorporation Pathways in DNA Polymerase Betas" Biochem. Biophys. Res. Comm., 350:521529 (2006) 
M. Foley, K. Arora, and T. Schlick, "Sequential Sidechain Residue Motions Transform the Binary into the Ternary State of DNA Polymerase Lambda" Biophys. J., 91:31823195 (2006) 
G. Arya and T. Schlick, "Role of Histone Tails in Chromatin Folding Revealed by a New Mesoscopic Oligonucleosome Model", PNAS, 103:1623616241 (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., 45:1514215156 (2006) 
G. Arya, Q. Zhang, and T. Schlick, "Flexible Histone Tails in a New Mesopscopic Model of Oligonucleosomes", Biophys. J., 91:133150 (2006) 
Q. Zhang and T. Schlick, "Stereochemistry and PositionDependent Effects of Carcinogens on TATA/TBP Binding", Biophys. J., 90:18651877 (2006) 
T. Schlick, "RNA: The Cousin Left Behind Becomes a Star", in Computational Studies of DNA and RNA, pp.259281, J. Sponer and F. Lankas, Editors, Springer Verlag, Dordrecht, The Netherlands (2006) 
B. Sampoli Benitez, K. Arora, and T. Schlick, "In Silico Studies of the African Swine Fever Virus DNA Polymerase X support an Inducedfit Mechanism", Biophys. J., 90:4256 (2006) 
Y. Wang, K. Arora, and T. Schlick, "Subtle but Variable Conformational Rearrangements in the Replication Cycle of Sulfolobus solfactarius P2 DNA polymerase IV (Dpo4) May Accommodate Lesion Bypass", Prot. Sci., 15:135151 (2006) 
K. Arora, W. A. Beard, S. H. Wilson, and T. Schlick, "Mismatch Induced Conformational Distortions in Polymerase Support an InducedFit Mechanism for Fidelity", Biochem., 44:1332813341 (2005) 
U. Laserson, H. H. Gan, and T. Schlick, "Predicting Candidate Genomic Sequences that Correspond to Synthetic Functional RNA Motifs", Nuc. Acids Res., 33:60576069 (2005) 
U. Laserson, H. H. Gan, and T. Schlick, "Exploring the Connection Between Synthetic and Natural RNAs in Genomes Via a Novel Computational Approach", in Advances in Algorithms for Macromolecular Simulation, Proceedings of the Fourth International Workshop on Algorithms for Macromolecular Modelling, Leicester, UK, August 2004, C. Chipot, R. Elber, A. Laaksonen, B. Leimkuhler, A. Mark, T. Schlick, R.D. Skeel, C. Schuette, Editors, Lecture Notes in Computational Science and Engineering, Vol. 49, pp. 3556, SpringerVerlag, Berlin (2005) 
J. Gevertz, H. H. Gan, and T. Schlick, " In Vitro RNA Random Pools are Not Structurally Diverse: A Computational Analysis", RNA, 11:853863 (2005) 
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., 127:1324513252 (2005) 
J. Sun, Q. Zhang, and T. Schlick, "Electrostatic Mechanism of Nucleosomal Array Folding Revealed by Computer Simulation", PNAS, 102:81808185 (2005) 
K. Arora and T. Schlick, "Conformational Transition Pathway of Polymerase /DNA Complex Upon Binding Correct Incoming Substrate", J. Phys. Chem. B, 109:53585367 (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):323329 (2005) 
S. Pasquali, H. H. Gan, and T. Schlick, "Modular RNA Architecture Revealed by Computational Analysis of Existing Pseudoknots and Ribosomal RNAs", Nuc. Acids Res., 33:13841398 (2005) 
N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick, "Candidates for Novel RNA Topologies", J. Mol. Biol., 341:11291144 (2004) 
R. Radhakrishnan and T. Schlick, "Biomolecular Free Energy Profiles by a Shooting/Umbrella Sampling Protocol, `BOLAS' ", J. Chem. Phys., 121:24362444 (2004) 
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 911, New York, 373377, ACM Press (2004) 
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., 101:59705975 (2004) 
L. Yang, K. Arora, W. A. Beard, S. H. Wilson, and T. Schlick, "Critical Role of Magnesium Ions in DNA Polymerase 's Closing and Active Site Assembly", J. Am. Chem. Soc., 126:84418453 (2004) 
K. Arora and T. Schlick, "In Silico Evidence for DNA Polymerase 's SubstrateInduced Conformational Change", Biophys. J., 87:30883099 (2004) 
K. Arora and T. Schlick, "Deoxyadenosine Sugar Puckering Pathway Simulated by the Stochastic Difference Equation Algorithm", Chem. Phys. Lett., 378:18 (2003) 
Q. Zhang, S. Broyde, and T. Schlick, "Deformations of Promoter DNA Bound to Carcinogens Help Interpret Effects on TATAelement Structure and Activity", Phil. Trans. Roy. Soc. Lond., Series A: Mathematical, Physical & Engineering Sciences, 362: 14791496 (2004) 
H. H. Gan, D. Fera, J. Zorn, N. Shiffeldrim, U. Laserson, N. Kim, and T. Schlick, "RAG: RNAAsGraphs Database  Concepts, Analysis, and Features", Bioinformatics, 20: 12851291 (2004) 
D. Fera, N. Kim, N. Shiffeldrim, J. Zorn, U. Laserson, H. H. Gan, and T. Schlick, "RAG: RNAAsGraphs Web Resource", BMC Bioinformatics, 5:88 (2004) 
J. Zorn, H. H. Gan, N. Shiffeldrim, and T. Schlick, "Structural Motifs in Ribosomal RNAs: Implications for RNA Design and Genomics", Biopolymers, 73: 340347 (2004) 
Q. Zhang, D. A. Beard, and T. Schlick, "Constructing Irregular Surfaces to Enclose Macromolecular Complexes for Mesoscale Modeling Using the Discrete Surface Charge Optimization (DiSCO) Algorithm", J. Comp. Chem., 24:20632074 (2003) 
T. Schlick, "Engineering Teams Up with ComputerSimulation and Visualization Tools to Probe Biomolecular Mechanisms", Biophys. J., New and Notable, 85:14 (2003) 
L. Yang, W. A. Beard, S. H. Wilson, S. Broyde, and T. Schlick, "Highly Organized but Pliant Activesite of DNA Polymerase : Compensatory Mechanisms in Mutant Enzymes Revealed by Dynamics Simulations and Energy Analysis", Biophys. J., 86: 33923408 (2004) 
D. A. Beard and T. Schlick, "Unbiased Rotational Moves for RigidBody Dynamics", Biophys. J., 85:29732976 (2003) 
H. H. Gan and T. Schlick, "Methods for Macromolecular Modeling (M^{3}): Assessment of Progress and Future Perspectives", in Computational Methods for Macromolecules: Challenges and Applications  Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling, New York, October 1214, 2000, T. Schlick and H. H. Gan, eds., Lecture Notes in Computational Science and Engineering, Vol. 24, pp. 125, Springer Verlag, Berlin (2002) 
J. Huang, Q. Zhang, and T. Schlick, "Effect of DNA Superhelicity and Bound Proteins on Mechanistic Aspects of the Hinmediated and Fisenhanced Inversion", Biophys. J., 85:804817 (2003) 
J. Aishima, R. K. Gitti, J. E. Noah, H. H. Gan, T. Schlick, and C. Wolberger, "A Hoogsteen Base Pair Embedded in Undistorted BDNA", Nuc. Acids Res., 30:52445252 (2002) 
H. H. Gan, S. Pasquali, and T. Schlick, "Exploring The Repertoire of RNA Secondary Motifs Using Graph Theory with Implications for RNA Design", Nuc. Acids Res., 31:29262943 (2003) 
D. Xie and T. Schlick, "A More Lenient Stopping Rule for Line Search Algorithms", Optim. Meth. Softw., 17:683700 (2002) 
D. Xie, S. B. Singh, E. M. Fluder, and T. Schlick, "Principal Component Analysis Combined with TruncatedNewton Minimization for Dimensionality Reduction of Chemical Databases", Math. Program. Ser. B, 95:161185 (2003) 
J. Huang and T. Schlick, "Macroscopic Modeling and Simulations of Supercoiled DNA with Bound Proteins", J. Chem. Phys., 117:85738586 (2002) 
D. Barash, T. Schlick, M. Israeli, and R. Kimmel, "Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps", J. Math. Imag. Vision, 19:3348 (2003) 
D. Strahs, D. Barash, X. Qian, and T. Schlick, "SequenceDependent Solution Structure and Motions of 13 TATA/TBP Complexes", Biopolymers, 69:216243 (2003) 
D. Barash, L. Yang, X. Qian, and T. Schlick, "Inherent Speedup Limitations in Multiple Timestep/ Particle Mesh Ewald Algorithms", J. Comp. Chem., 24:7788 (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., 321:459478 (2002) 
X. Qian and T. Schlick, "Efficient Multiple Timestep Integrators with DistanceBased Force Splitting for ParticleMeshEwald Molecular Dynamics Simulations", J. Chem. Phys., 116:59715983 (2002) 
P. F. Batcho and T. Schlick, "New Splitting Formulations for Lattice Summations", J. Chem. Phys., 115:83128326 (2001) 
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., 317:651671 (2002) 
T. Schlick, "TimeTrimming Tricks for Dynamic Simulations: Splitting Force Updates to Reduce Computational Work", Structure, 9:R45R53 (2001) 
P. F. Batcho and T. Schlick, "Special Stability Advantages of Position Verlet Over Velocity Verlet in MultipleTimestep Integration", J. Chem. Phys., 115:40194029 (2001) 
P. F. Batcho, D. A. Case, and T. Schlick, "Optimized ParticleMesh Ewald/MultipleTimestep Integration for Molecular Dynamics Simulations", J. Chem. Phys., 115:40034018 (2001) 
X. Qian, D. Strahs, and T. Schlick, "A New Program for Optimizing Periodic Boundary Models of Solvated Biomolecules (PBCAID)", J. Comp. Chem., 22:18431850 (2001) 
H. H. Gan, R. A. Perlow, S. Roy, J. Ko, M. Wu, J. Huang, S. Yan, A. Nicoletta, J. Vafai, D. Sun, L. Wang, J. E. Noah, S. Pasquali, and T. Schlick, "Analysis of Protein Sequence/Structure Similarity Relationships", Biophys. J., 83:27812791 (2002) 
X. Qian, D. Strahs, and T. Schlick, "Dynamic Simulations of 13 TATA Variants Refine Kinetic Hypotheses on Sequence/Activity Relationships", J. Mol. Biol., 308:681703 (2001) 
H. H. Gan, A. Tropsha, and T. Schlick, "Lattice Protein Folding with Two and FourBody Statistical Potentials", Proteins: Struc. Func. Gen., 43: 161174 (2001) 
T. Schlick and L. Yang, "LongTimestep Biomolecular Dynamics Simulations: LN Performance on a Polymerase Beta / DNA System", in Multiscale Computational Methods in Chemistry and Physics, Vol 177, NATO Science Series: Series III Computer and Systems Sciences, A. Brandt, J. Bernholc and K. Binder, eds., IOS Press, Amsterdam (2001) 
D. A. Beard and T. Schlick, "Computational Modeling Predicts the Structure and Dynamics of Chromatin Fiber", Structure, 9:105114, February (2001) 
H. H. Gan, A. Tropsha, and T. Schlick, "Generating Folded Protein Structures with a Lattice Chain Growth Algorithm", J. Chem. Phys., 113:55115524, October (2000) 
J. Huang, T. Schlick, and A. Vologodskii, "Dynamics of Site Juxtaposition in Supercoiled DNA", Proc. Natl. Acad. Sci., 98:968973, January (2001) 
T. Schlick, D. A. Beard, J. Huang, D. Strahs, and X. Qian, "Computational Challenges in Simulating Large DNA over Long Times", IEEE Computing in Science & Engineering, 2:3851, Nov/Dec (2000) 
D. A. Beard and T. Schlick, "Modeling SaltMediated Electrostatics of Macromolecules: The Discrete Surface Charge Optimization Algorithm and Its Application to the Nucleosome", Biopolymers, 58:106115 , January (2001) 
D. Strahs and T. Schlick, "Atract Bending: Insights into Experimental Structures by Computational Models", J. Mol. Biol., 301:643663, August (2000) 
D. A. Beard and T. Schlick, "Inertial Stochastic Dynamics. I. Longtimestep Methods for Langevin Dynamics", J. Chem. Phys., 112:73137322, May (2000) 
D. A. Beard and T. Schlick, "Inertial Stochastic Dynamics. II. Influence of Inertia on Slow Kinetic Processes of Supercoiled DNA", J. Chem. Phys., 112:73237338, May (2000) 
D. Xie and T. Schlick, "Visualization of Chemical Databases Using the Singular Value Decomposition and TruncatedNewton Minimization", Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, Volume 40, pages 267286, C. A. Floudas and P. M. Pardalos, eds., Kluwer Academic Publishers, Dororecht/Boston/London (2000) 
T. Schlick, "Computational Molecular Biophysics Today: A Confluence of Methological Advances and Complex Biomolecular Applications", J. Comp. Phys., 151:18, May (1999) 
A. Sandu and T. Schlick, "Resonance Analysis in Force Splitting Methods for Biomolecular Dynamics", J. Comp. Phys., 151:74113, May (1999) 
T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. Hermans, K. Schulten, and J. A. Board, Jr., "Algorithmic Challenges in Computational Molecular Biophysics", J. Comp. Phys., 151:948, May (1999) 
D. Xie and T. Schlick, "Efficient Implementation of the Truncated Newton Method for Large Scale Chemistry Applications", SIAM J. Opt., 10: 132154 October (1999) 
D. Xie and T. Schlick, "Remark on the Updated Truncated Newton Minimization Package, Algorithm 702", ACM Trans. Math. Softw., 25, 108122, March (1999) 
D. Xie, L. R. Scott and T. Schlick, "Analysis of the SHAKESOR Algorithm for Constrained Molecular Dynamics Simulations", Methods and Applications of Analysis, a Special issue dedicated to Prof. Cathleen Morawetz of the Courant Institute, 7: 577590, September (2000) 
D. Xie, A. Tropsha and T. Schlick, "An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with TruncatedNewton Minimization", J. Chem. Inf. Comput. Sci., 40:167177, December (1999) 
E. Barth and T. Schlick, "I. Overcoming Stability Limitations in Biomolecular Dynamics: Combining Force Splitting via Extrapolation with Langevin Dynamics in LN", J. Chem. Phys., 109:16171632, August (1998) 
E. Barth and T. Schlick, "II. Extrapolation Versus Impulse in MultipleTimestepping Schemes: Linear Analysis and Applications to Newtonian and Langevin Dynamics", J. Chem. Phys. 109:16331642, August (1998) 
P. Derreumaux and T. Schlick, "Simulation of the Loop Opening/Closing of the Enzyme Triosephosphate Isomeraze (TIM)", Biophys. J., 74:7281, January (1998) 
H. Jian, T. Schlick, and A. Vologodskii, "Internal Motion of Supercoiled DNA: Brownian Dynamics Simulations of Site Juxtaposition", J. Mol. Biol., 284:287296, November (1998) 
T. Schlick, "Geometry Optimization", Contributed chapter to the Encyclopedia of Computational Chemistry (5 Volumes), Volume 2, pages 11361157, 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 (1998) 
T. Schlick, "Some Failures and Successes of LongTimestep Approaches to Biomolecular Simulations", in Algorithms for Macromolecular Modeling, Volume 4, pages 227262, SpringerVerlag series in "Lecture Notes in Computational Science and Engineering", P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, R. D. Skeel, and S. Reich, eds. (1998) 
T. Schlick, M. Mandziuk, R. D. Skeel, and K. Srinivas, "Nonlinear Resonance Artifacts in Molecular Dynamics", J. Comp. Phys., 139:129, February (1998) 
L. Y. Zaslavsky and T. Schlick, "An Adaptive Multigrid Technique for Evaluating LongRange Forces in Biomolecular Simulations", App. Math. Comp., 97:237250, December (1998) 
E. Barth, M. Mandziuk, and T. Schlick, "A Separating Framework for Increasing the Timestep in Molecular Dynamics", contributed chapter to Computer Simulation of Biomolecular Systems, Volume 3, Chapter 4, pages 97120, W. van Gunsteren, P. Weiner and T. Wilkinson eds., ESCOM Science Publishers, Ledien, The Netherlands (1997) 
H. Jian, A. Vologodskii, and T. Schlick, "A Combined Wormlike Chain and Bead Model for Dynamic Simulations of Long DNA", J. Comp. Phys., 136:168179, September (1997) 
G. Liu, T. Schlick, A. J. Olson, and W. K. Olson, "Configurational Transitions in DNA Supercoils Represented by FourierSeries CurveFitting Techniques", Biophys. J., 73:17421762, October (1997) 
G. Ramachandran and T. Schlick, "On Buckling Transitions in Supercoiled DNA: Dependence on Elastic Constants and DNA Size", Biopolymers, 41:525, January (1997) 
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., 26:181222 (1997) 
R. D. Skeel, G. Zhang and T. Schlick, "A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications", SIAM J. Sci. Comp., 18:203222 (1997) 
B. Mishra and T. Schlick, " The Notion of Error in Langevin Dynamics: (1) Linear Analysis", J. Chem. Phys., 105:299318, July (1996) 
T. Pinou, T. Schlick, B. Li, and H. Dowling, "Addition of Darwin's Third Dimension to Evolutionary Trees", J. Theor. Bio., 219:505512, October (1996) 
G. Ramachandran and T. Schlick, "Beyond Optimization: Simulating the Dynamics of Supercoiled DNA by a Macroscopic Model", in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Volume 23, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, P. Pardalos, D. Shalloway, and G. Xue, eds., pages 215231, American Mathematical Society, Providence, Rhode Island (1996) 
T. Schlick, "Pursuing Laplace's Vison on Modern Computers", Proceedings of the IMA Program in Mathematical Biology, IMA Volumes in Mathematics and its Applications, Volume 82, pages 219247, J. Mesirov, K Schulten, and D. W. Sumners, eds., SpringerVerlag, New York (1996) 
T. Schlick and A. Brandt, "A Multigrid Tutorial with Applications to Molecular Dynamics", IEEE Comp. Sci. Eng., 3:7883, Fall (1996) 
P. Derreumaux and T. Schlick, "Long Timestep Dynamics of Peptides by the Dynamics Driver Approach", Proteins: Struc. Func., Gen., 21:282302, April (1995) 
G. Liu, W. K. Olson, and T. Schlick, "Application of Fourier Analysis to Computer Simulation of Supercoiled DNA Formation", Comp. Polymer Sci., 5:727 (1995) 
M. Mandziuk and T. Schlick, "Resonance in the Dynamics of Chemical Systems Simulated by the Implicit Midpoint Scheme", Chem. Phys. Lett., 237:525535, March (1995) 
G. Ramachandran and T. Schlick, "Solvent Effects on Supercoiled DNA Explored by Langevin Dynamics Simulations", Phys., Rev. E., 51:61886203, June (1995) 
T. Schlick, "Modeling Superhelical DNA: Recent Analytical and Dynamic Approaches", Curr. Opin. Struc. Bio., 5:245262, April (1995). Special issue on Theory and Simulation, B. Honig, ed. 
T. Schlick and C. S. Peskin, "Comment on 'Backward Euler and other methods for simulating molecular fluids'", J. Chem. Phys., 103:98889889, December (1995) 
G. Zhang and T. Schlick, "Implicit Integration Schemes for Langevin Dynamics", Mol. Phys. 84:10771098 (1995) 
V. Z. Averbukh, S. Figueroa, and T. Schlick, "Remark on Algorithm 566", ACM Trans. Math. Softw., 20:282285, September (1994) 
J. A. Board, Jr., L. V. Kalé, K. Schulten, R. D. Skeel, and T. Schlick, "Modeling Biomolecules: Larger Scales, Longer Durations", IEEE Comp. Sci. Eng., 1:1930, Winter (1994) 
P. Derreumaux, G. Zhang, B. Brooks, and T. Schlick, "A TruncatedNewton Method Adapted for CHARMM and Biomolecular Applications", J. Comp. Chem., 15:532552, April (1994) 
T. Schlick, B. Li, and M. H. Hao, "Calibration of the Timestep for Molecular Dynamics of Supercoiled DNA Modeled by BSplines", in Structural Biology, State of the Art 1993, Volume 1, Proceedings of the Eighth Conversation, M. H. Sarma and R. S. Sarma, eds., pages 157174, Adenine Press, Guiderland, New York (1994) 
T. Schlick, B. Li, and W. K. Olson, "The Influence of Salt on the Structure and Energetics of Supercoiled DNA", Biophys. J., 67:21462166, December (1994) 
T. Schlick, W. K. Olson, T. Westcott, and J. P. Greenberg, "On Higher Buckling Transition in Supercoiled DNA", Biopolymers, 34:565597, May (1994) 
G. Zhang and T. Schlick, "The Langevin/ImplicitEuler/NormalMode Scheme (LIN) for Molecular Dynamics at Large Timesteps", J. Chem. Phys., 101:49955012, September (1994) 
T. Schlick, "Modified Cholesky Factorizations for Sparse Preconditioners", SIAM J. Sci. Comp., 14:424445, March (1993) 
T. Schlick, W. K. Olson. T. Westcott, G. Liu, and J. P. Greenberg, "Supercoiled Configurations of Small DNA Rings and Their Dynamics", Abstract of the Eigth Conversation in Biomolecular Stereodynamics, J. Biomol. Struct. Dyn., 10 a170 (1993) 
G. Zhang and T. Schlick, "LIN: A New Algorithm Combining Implicit Integration and Normal Mode Techniques for Molecular Dynamics", J. Comp. Chem., 14:12121233, July (1993) 
X. Zou, I. M. Navon, M. Berger, P. K. H. Phua, T. Schlick and F. X. Le Dimet, "Numerical Experience with LimitedMemory and Truncated Newton Methods", SIAM J. Opt., 3:582608, August (1993) 
V. Z. Averbukh, S. Figueroa, and T. Schlick, "HESFCN A FORTRAN Package of Hessian Subroutines for Testing Nonlinear Optimization Software", Computer Science Technical Report, 610:143, June (1992) 
A. Nyberg and T. Schlick,"On Increasing the Time Step in Molecular Dynamics", Chem. Phys. Lett., 198:538546, October (1992) 
T. Schlick, "Optimization Methods in Computational Chemistry", in Reviews in Computational Chemistry, Volume 3 , Chapter 1, pages 171, K. B. Lipkowitz and D. B. Boyd, eds., VCH Publishers, New York (1992) 
T. Schlick and A. Fogelson, "TNPACK  A Truncated Newton Minimization Package for Large Scale Problems: I. Algorithm and Usage", ACM Trans. Math. Softw., 18:4670, March (1992) 
"T. Schlick and A. Fogelson, "TNPACK  A Truncated Newton Minimization Package for Large Scale Problems: II. Implementation Examples", ACM Trans. Math. Softw., 18:71111, March (1992) 
T. Schlick and W. K. Olson, "Computer Simulations of Supercoiled DNA Energetics and Dynamics", J. Mol. Biol., 223:10891119, February (1992) 
T. Schlick and W. K. Olson, "Trefoil Knotting Revealed by Molecular Dynamics of Supercoiled DNA", Science, 257:11101115, August (1992) 
A. Nyberg and T. Schlick, "A Computational Investigation of Dynamic Properties with the ImplicitEuler Scheme for Molecular Dynamics Situations", J. Chem. Phys., 95:49864996, October (1991) 
T. Schlick, "New Approaches to Potential Energy Minimization and Molecular Dynamics Algorithms", based on an invited presentation at the Molecular Mechanics and Molecular Dynamics Workshop , Florida State University, Tallahassee, Comput. Chem., 15:251260 (1991) 
T. Schlick, S. Figueroa, and M. Mezei, "A Molecular Dynamics Simulation of a Water Droplet by the ImplicitEuler/Langevin Scheme", J. Chem. Phys., 94:21182129, February (1991) 
T. Schlick, B. E. Hingerty, C. S. Peskin, M. L. Overton, and S. Broyde, "Search Strategies, Minimization Algorithms, and Molecular Dynamics Simulations for Exploring Conformational Spaces of Nucleic Acids", in Theoretical Biochenmistry and Molecular Biophysics, Volume 1, pages 3958, D. L. Beveridge and R. Lavery, eds., Adenine Press, Guilderland, New York (1991) 
T. Schlick, "Implementation of the Schnabel and Eskow Modified Cholesky Factorization in the Context of LargeScale Nonlinear Optimization", Computer Science Technical Report, Courant Institute 525:140, (1990) 
C. S. Peskin and T. Schlick, "Molecular Dynamics by the BackwardsEuler Method", Comm. Pure Appl. Math., 42:10011031 (1989) 
T. Schlick, "A Recipe for Evaluating and Differentiating Cos Expressions", J. Comp. Chem., 10:951956, May (1989) 
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., 42:11411163 (1989) 
T. Schlick, C. S. Peskin, and M. L. Overton, "A New Pair of Algorithms for Potential Energy Minimization and Molecular Dynamics Simulations", Book of Abstracts of the Sixth Conversation in Biomolecular Stereodynamics, Volume 151, pages 74113, R. H. Sarma, ed., State University of New York, Albany (1989) 
T. Schlick, "A Modular Strategy for Generating Starting Conformations and Data Structures of Polynucleotide Helices for Potential Energy Calculations", J. Comp. Chem., 9:861889, June (1988) 
T. Schlick, "Modeling and Minimization Techniques for Predicting ThreeDimensional Structures of Large Biological Molecules", Ph. D. Dissertation, Courant Institute, Department of Mathematics, New York University (1987). 
T. Schlick and M. Overton, "A Powerful Truncated Newton Method for Potential Energy Minimization", J. Comp. Chem., 8:10251039, May (1987) 
T. Schlick, C. Peskin, S. Broyde, and M. Overton, "An Analysis of the Structural and Energetic Properties of Deoxyribose by Potential Energy Methods" J. Comp. Chem., 8:11991224, June (1987) 
T. Schlick, C. Peskin, S. Broyde and M. Overton, "Development of a New Computational Approach for the Prediction of Nucleic Acid Structure by Potential Energy Methods: I. Deoxyribose", Computer Science Technical Report, Courant Institute, 264:160 (1986) 
W. L. Hase, D. M. Ludlow, R. J. Wolf and T. Schlick, "Translational and Vibrational Energy Dependence of the Cross Section for H + C_{2}H_{4} > C_{2}H_{5}" J. Phys. Chem., 85:958968 (1981)