Schlick Group Publication List

 

 

Support Source (for Authors in our Group)
Philip Morris External Research Program
Alfred P. Sloan Foundation
American Association of University Women Educational Foundation
American Chemical Society
The Guggenheim Foundation
Howard Hughes Medical Institute
Human Frontier Science Program
National Computational Science Alliance
National Institute of General Medical Sciences
National Institutes of Health
National Science Foundation
New York University
The Searle Scholars Program
The Whitaker Foundation
Subject Category
Mathematical and physical sciences
Biological sciences
Chemical sciences
Multidisciplinary



Paper Type
Conference proceedings
Original work
Review
Others



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  1. Namhee Kim, Christian Laing, Shereef Elmetwaly, Segun Jung, Jeremy Curuksu, and Tamar Schlick, "Graph-based sampling for approximating global helical topologies of RNA",
    PNAS, DOI: 10.1073/pnas.1318893111 (2014).



  2. Yunlang Li, Bret D. Freudenthal, William A. Beard, Samuel H. Wilson, and Tamar Schlick, "Optimal and Variant Metal-Ion Routes in DNA Polymerase β's Conformational Pathways",
    J. Am. Chem. Soc.,DOI: 10.1021/ja412701f (2014).




  3. Segun Jung and Tamar Schlick, "Interconversion between Parallel and Antiparallel Conformations of a 4H RNA junction in Domain 3 of Foot-and-Mouth Disease Virus IRES Captured by Dynamics Simulations",
    Biophys. J., 106(2): 447-458, (2014).




  4. Benedetta Sampoli Benítez, Zachary R. Barbati, Karunesh Arora, Jasmina Bogdanovic, and Tamar Schlick, "How DNA Polymerase X Preferentially Accommodates Incoming dATP Opposite 8-Oxoguanine on the Template",
    Biophys. J., 105(11): 2559-2568, (2013).



  5. Tamar Schlick, "The 2013 Nobel Prize in Chemistry Celebrates Computations in Chemistry and Biology",
    SIAM News, 46(10), December (2013).




  6. 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).


  7. Yunlang Li, and Tamar Schlick, "Gate-keeper Residues and Active-Site Rearrangements in DNA Polymerase Help Discriminate Non-cognate Nucleotides", PLoS Comput. Biol., 9(5), DOI:10.1371/journal.pcbi.1003074 (2013).



  8. Rosana Collepardo-Guevara, and Tamar Schlick, "Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments",
    Biochem. Soc. Trans., 41(2): 494-500 (2013).



  9. Segun Jung, and Tamar Schlick, "Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site",
    Nucleic Acids Res., 41(3): 1483-95 (2013).



  10. Namhee Kim, Louis Petingi, and Tamar Schlick, "Network Theory Tools for RNA Modeling",
    WSEAS Transactions on Math, 12(9): 941-955 (2013).



  11. 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).



  12. Rosana Collepardo-Guevara, 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): 8803-8817 (2012).



  13. Tamar Schlick, Karunesh Arora, William A. Beard, and Samuel H. Wilson, "Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms",
    Theor Chem Acc, 131(12): 1287 (2012).



  14. Namhee Kim and Tamar Schlick, "A New Toolkit for Modeling RNA from a Pseudo-Torsional Space",
    J. Mol. Biol., doi:10.1016/j.jmb.2012.05.027 (2012).




  15. 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): 9999-10010 (2012).



  16. Tamar Schlick, "Modelers to the Rescue", In Innovations in Biomolecular Modeling and Simulations, Volume 1, T. Schlick, ed., Royal Society of Chemistry, London (2012).


  17. 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).
  18.  


    Innovations in Biomolecular Modeling and Simulations, Volume 2, T. Schlick ed., The Royal Society of Chemistry, ISBN: 978-1-84973-505-6, DOI:10.1039/9781849735056 (2012).
  19.  


    Innovations in Biomolecular Modeling and Simulations, Volume 1, T. Schlick ed., The Royal Society of Chemistry, ISBN: 978-1-84973-504-9, DOI:10.1039/9781849735049 (2012).



  20. Tamar Schlick, Jeff Hayes, and Sergei Grigoryev, "Toward Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber"
    , JBC, 287: 5183-5191 (2012).


  21. 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).



  22. Rosana Collepardo-Guevara and Tamar Schlick, "The Effect of Linker Histone's Nucleosome Binding Affinity on Chromatin Unfolding Mechanisms", Biophys. J., 111(7):1670-1680 (2011).


  23. Christian Laing, Dongrong Wen, Jason T. L. Wang and Tamar Schlick, "Predicting coaxial helical stacking in RNA junctions", Nucleic Acids Research, 40(2): 487-498, doi:10.1093/nar/gkr629 (2011).



  24. Tamar Schlick and Rosana Collepardo-Guevara, "Biomolecular Modeling and Simulation: The Productive Trajectory of a Field"
    , SIAM News, 44: 6 (2011).

  25. Joseph Izzo, Namhee Kim, Shereef Elmetwaly and Tamar Schlick, "RAG: an update to RNA-As-Graphs resource"
    , BMC Bioinformatics, 12: 219 (2011).
  26. Christian Laing and Tamar Schlick, "Computational approaches to RNA structure prediction, analysis, and design", Curr. Opin. Struct. Biol., 21: 1-13 (2011).
  27. Tamar Schlick, "DNA Polymerases: Structure, Function, and Modeling", in Molecular Machines, , B. Roux, Editor, World Scientific, (2011).


  28. Yunlang Li and Tamar Schlick, "Modeling DNA Polymerase μ Motions: Subtle Transitions before Chemistry"
    , Biophys. J., 99(10): 3463-3472 (2010).
  29. Hin Hark Gan and Tamar Schlick, "Chromatin Ionic Atmosphere Analyzed by a Mesoscale Electrostatic Approach", Biophys. J., 99(8): 2587-2596 (2010).
  30. Tamar Schlick, Rosana Collepardo-Guevara, Leif A. Halvorsen, Segun Jung and Xia Xiao, "Biomolecular Modeling and Simulation: A Field Coming of Age" , Q. Rev. of Biophys., 44 (2): 191-228 (2011).
  31. Meredith Foley, Victoria Padow and T. Schlick, "Extraordinary Ability of DNA Pol λ to Stabilize Misaligned DNA" , J. Am. Chem. Soc., 132: 13403-13416 (2010).
  32. Ognjen Perisic, Rosana Collepardo-Guevara and T. Schlick, "Modeling Studies of Chromatin Fiber Structure as a Function of DNA Linker Length", J. Mol. Biol., 403: 777-802 (2010).
  33. 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).
  34. C. Laing, and T. Schlick, "Computational Approaches to RNA 3D Modeling", J. Phys.: Condens. Matter, 22: 283101 (2010).
  35. G. Quarta, N. Kim, J. A. Izzo, and T. Schlick, "Analysis of Riboswitch Structure and Function by an Energy Landscape Framework.", J. Mol. Biol., 393:993-1003 (2009).
  36. C. Laing and T. Schlick, "Analysis of Four-Way Junctions in RNA Structures.", J. Mol. Biol., 390:547-559 (2009).
  37. Tamar Schlick, "Mathematical and Biological Scientists Assess the State-of-the-Art in RNA Science at an IMA Workshop RNA in Biology, Bioengineering and Biotechnology", Int. J. Multi. Sci. Eng., 8 (4):369-378 (2010)
  38. Tamar Schlick and Ognjen Perisic, "Mesoscale simulations of two nucleosome-repeat length oligonucleosomes.", Phys. Chem. Chem. Phys., 11:10729-10737 (2009)
  39. S. Grigoryev, G. Arya, S. Correll, C. Woodcock, and T. Schlick, "Evidence for hetromorphic chromatin fibers from analysis of nucleosome interactions.", PNAS, 106(32):13317-13322 (2009)
  40. C. Laing, S. Jung, A. Iqbal, and T. Schlick, "Tertiary motifs revealed in analyses of higher-order RNA junctions.", J. Mol. Biol., 393(1):67-82 (2009)
  41. T. Schlick, "From Macroscopic to Mesoscopic Models of Chromatin Folding." Chapter 15, pp. 514--535, Multiscale Methods: Bridging the Scales in Science and Engineering, J. Fish, Editor, Oxford University Press (2009)
  42. T. Schlick, "Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules." F1000 Biology Reports, 1-51 (2009)
  43. 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, 113:13035-13047 (2009)
  44. T. Schlick, "Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure." F1000 Biology Reports, 1-48(2009)
  45. 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, 16:4045-4059 (2009)
  46. B. A. Sampoli Benitez, K. Arora, L. Balistreri, and T. Schlick, "Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation", J. Mol. Biol., 384:1086-1097 (2008)
  47. P. Sridhar, H.H. Gan, and T. Schlick, "A computational screen for C/D box snoRNAs in the human genomic region associated with Prader-Willi and Angelman syndromes", J. Biomed. Sci., 15:697-705 (2008)
  48. K. Bebenek, M. Garcia-Diaz, M. C. Foley, L. C. Pedersen, T. Schlick, and T. A. Kunkel, "Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase λ", EMBO Rep., 9:459-464 (2008)
  49. Y. Wang and T. Schlick, "Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization", J. Am. Chem. Soc., 130:13240-13250 (2008)
  50. 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., 130:3967-3977 (2008)
  51. Y. Xin, C. Laing, N.B. Leontis, and T. Schlick, "Annotation of tertiary interactions in RNA structures reveals variations and correlations.", RNA, 14:2465-2477 (2008)
  52. Y. Xin, G. Quarta, H.H. Gan, and T. Schlick, "Estimating the fraction of noncoding RNAs in mammalian transcriptomes.", Bioinformatics and Biology Insights, 2:77-95 (2008)
  53. N. Kim, J.S. Shin, S. Elmetwaly, H.H. Gan and T. Schlick, "RAGPOOLS: RNA-As-Graph-Pools A Web Server for Assisting the Design of Structured RNA Pools for In Vitro Selection", Bioinformatics, 23(21):2959-2960, doi:10.1093/bioinformatics/btm439 (2007)
  54. 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),11244-11252 (2007)
  55. I.L. Alberts, Y. Wang, T. Schlick, "DNA polymerase catalysis: are different mechanisms possible?" , J Am Chem Soc, 129(36):11100-10 (2007)
  56. N. Kim, H. H. Gan, and T. Schlick, "A Computational Proposal for Designing Structured RNA Pools for in Vitro Selection of RNAs", RNA, 13:478-92 (2007)
  57. 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", Biophys. J.,92:3063-3070 (2007)
  58. Y. Wang and T. Schlick, "Distinct Energetics and Closing Pathwasys for DNA Polymerase Beta with 8-oxoG Template and Different Incoming Nucleotides" BMC Structural Biology, 7:7 (2007)
  59. G. Arya and T. Schlick, "Efficient Global Biopolymer Sampling with End-Transfer Configurational Bias Monte Carlo" J. Chem. Phys., 126:044107 (2007)
  60. R. Radhakrishnan and T. Schlick, "Correct and Incorrect Nucleotide Incorporation Pathways in DNA Polymerase Betas" Biochem. Biophys. Res. Comm., 350:521-529 (2006)
  61. 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)
  62. G. Arya and T. Schlick, "Role of Histone Tails in Chromatin Folding Revealed by a New Mesoscopic Oligonucleosome Model", PNAS, 103:16236-16241 (2006)
  63. 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)
  64. G. Arya, Q. Zhang, and T. Schlick, "Flexible Histone Tails in a New Mesopscopic Model of Oligonucleosomes", Biophys. J., 91:133-150 (2006)
  65. Q. Zhang and T. Schlick, "Stereochemistry and Position-Dependent Effects of Carcinogens on TATA/TBP Binding", Biophys. J., 90:1865-1877 (2006)
  66. T. Schlick, "RNA: The Cousin Left Behind Becomes a Star", in Computational Studies of DNA and RNA, pp.259-281, J. Sponer and F. Lankas, Editors, Springer Verlag, Dordrecht, The Netherlands (2006)
  67. B. Sampoli Benitez, K. Arora, and T. Schlick, "In Silico Studies of the African Swine Fever Virus DNA Polymerase X support an Induced-fit Mechanism", Biophys. J., 90:42-56 (2006)
  68. 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., 15:135-151 (2006)
  69. K. Arora, W. A. Beard, S. H. Wilson, and T. Schlick, "Mismatch Induced Conformational Distortions in Polymerase Support an Induced-Fit Mechanism for Fidelity", Biochem., 44:13328-13341 (2005)
  70. 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)
  71. 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. 35-56, Springer-Verlag, Berlin (2005)
  72. 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)
  73. 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)
  74. J. Sun, Q. Zhang, and T. Schlick, "Electrostatic Mechanism of Nucleosomal Array Folding Revealed by Computer Simulation", PNAS, 102:8180-8185 (2005)
  75. K. Arora and T. Schlick, "Conformational Transition Pathway of Polymerase /DNA Complex Upon Binding Correct Incoming Substrate", J. Phys. Chem. B, 109:5358-5367 (2005)
  76. 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)
  77. S. Pasquali, H. H. Gan, and T. Schlick, "Modular RNA Architecture Revealed by Computational Analysis of Existing Pseudoknots and Ribosomal RNAs", Nuc. Acids Res., 33:1384-1398 (2005)
  78. N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick, "Candidates for Novel RNA Topologies", J. Mol. Biol., 341:1129-1144 (2004)
  79. R. Radhakrishnan and T. Schlick, "Biomolecular Free Energy Profiles by a Shooting/Umbrella Sampling Protocol, `BOLAS' ", J. Chem. Phys., 121:2436-2444 (2004)
  80. 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, 373-377, ACM Press (2004)
  81. 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., 101:5970-5975 (2004)
  82. 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., 126:8441-8453 (2004)
  83. K. Arora and T. Schlick, "In Silico Evidence for DNA Polymerase 's Substrate-Induced Conformational Change", Biophys. J., 87:3088-3099 (2004)
  84. K. Arora and T. Schlick, "Deoxyadenosine Sugar Puckering Pathway Simulated by the Stochastic Difference Equation Algorithm", Chem. Phys. Lett., 378:1-8 (2003)
  85. 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. Roy. Soc. Lond., Series A: Mathematical, Physical & Engineering Sciences, 362: 1479-1496 (2004)
  86. H. H. Gan, D. Fera, J. Zorn, N. Shiffeldrim, U. Laserson, N. Kim, and T. Schlick, "RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features", Bioinformatics, 20: 1285-1291 (2004)
  87. 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 (2004)
  88. 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)
  89. 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., 24:2063-2074 (2003)
  90. T. Schlick, "Engineering Teams Up with Computer-Simulation and Visualization Tools to Probe Biomolecular Mechanisms", Biophys. J., New and Notable, 85:1-4 (2003)
  91. 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 Analysis", Biophys. J., 86: 3392-3408 (2004)
  92. D. A. Beard and T. Schlick, "Unbiased Rotational Moves for Rigid-Body Dynamics", Biophys. J., 85:2973-2976 (2003)
  93.  
    H. H. Gan and T. Schlick, "Methods for Macromolecular Modeling (M3): 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 12-14, 2000, T. Schlick and H. H. Gan, eds., Lecture Notes in Computational Science and Engineering, Vol. 24, pp. 1-25, Springer Verlag, Berlin (2002)
  94. 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)
  95. J. Aishima, R. K. Gitti, J. E. Noah, H. H. Gan, T. Schlick, and C. Wolberger, "A Hoogsteen Base Pair Embedded in Undistorted B-DNA", Nuc. Acids Res., 30:5244-5252 (2002)
  96. 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., 31:2926-2943 (2003)
  97. D. Xie and T. Schlick, "A More Lenient Stopping Rule for Line Search Algorithms", Optim. Meth. Softw., 17:683-700 (2002)
  98. D. Xie, S. B. Singh, E. M. Fluder, and T. Schlick, "Principal Component Analysis Combined with Truncated-Newton Minimization for Dimensionality Reduction of Chemical Databases", Math. Program. Ser. B, 95:161-185 (2003)
  99. J. Huang and T. Schlick, "Macroscopic Modeling and Simulations of Supercoiled DNA with Bound Proteins", J. Chem. Phys., 117:8573-8586 (2002)
  100.  
    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, 19:33-48 (2003)
  101. D. Strahs, D. Barash, X. Qian, and T. Schlick, "Sequence-Dependent Solution Structure and Motions of 13 TATA/TBP Complexes", Biopolymers, 69:216-243 (2003)
  102. D. Barash, L. Yang, X. Qian, and T. Schlick, "Inherent Speedup Limitations in Multiple Timestep/ Particle Mesh Ewald Algorithms", J. Comp. Chem., 24:77-88 (2003)
  103. 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)
  104. 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)
  105. P. F. Batcho and T. Schlick, "New Splitting Formulations for Lattice Summations", J. Chem. Phys., 115:8312-8326 (2001)
  106. 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)
  107. T. Schlick, "Time-Trimming Tricks for Dynamic Simulations: Splitting Force Updates to Reduce Computational Work", Structure, 9:R45-R53 (2001)
  108. P. F. Batcho and T. Schlick, "Special Stability Advantages of Position Verlet Over Velocity Verlet in Multiple-Timestep Integration", J. Chem. Phys., 115:4019-4029 (2001)
  109. 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)
  110. 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)
  111. 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., 83:2781-2791 (2002)
  112. X. Qian, D. Strahs, and T. Schlick, "Dynamic Simulations of 13 TATA Variants Refine Kinetic Hypotheses on Sequence/Activity Relationships", J. Mol. Biol., 308:681-703 (2001)
  113. H. H. Gan, A. Tropsha, and T. Schlick, "Lattice Protein Folding with Two and Four-Body Statistical Potentials", Proteins: Struc. Func. Gen., 43: 161-174 (2001)
  114. T. Schlick and L. Yang, "Long-Timestep 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)
  115. D. A. Beard and T. Schlick, "Computational Modeling Predicts the Structure and Dynamics of Chromatin Fiber", Structure, 9:105-114, February (2001)
  116. H. H. Gan, A. Tropsha, and T. Schlick, "Generating Folded Protein Structures with a Lattice Chain Growth Algorithm", J. Chem. Phys., 113:5511-5524, October (2000)
  117. J. Huang, T. Schlick, and A. Vologodskii, "Dynamics of Site Juxtaposition in Supercoiled DNA", Proc. Natl. Acad. Sci., 98:968-973, January (2001)
  118. 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, 2:38-51, Nov/Dec (2000)
  119. D. A. Beard and T. Schlick, "Modeling Salt-Mediated Electrostatics of Macromolecules: The Discrete Surface Charge Optimization Algorithm and Its Application to the Nucleosome", Biopolymers, 58:106-115 , January (2001)
  120. D. Strahs and T. Schlick, "A-tract Bending: Insights into Experimental Structures by Computational Models", J. Mol. Biol., 301:643-663, August (2000)
  121. D. A. Beard and T. Schlick, "Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics", J. Chem. Phys., 112:7313-7322, May (2000)
  122. D. A. Beard and T. Schlick, "Inertial Stochastic Dynamics. II. Influence of Inertia on Slow Kinetic Processes of Supercoiled DNA", J. Chem. Phys., 112:7323-7338, May (2000)
  123. D. Xie and T. Schlick, "Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization", Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, Volume 40, pages 267-286, C. A. Floudas and P. M. Pardalos, eds., Kluwer Academic Publishers, Dororecht/Boston/London (2000)
  124. T. Schlick, "Computational Molecular Biophysics Today: A Confluence of Methological Advances and Complex Biomolecular Applications", J. Comp. Phys., 151:1-8, May (1999)
  125. A. Sandu and T. Schlick, "Resonance Analysis in Force Splitting Methods for Biomolecular Dynamics", J. Comp. Phys., 151:74-113, May (1999)
  126. 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., 151:9-48, May (1999)
  127. D. Xie and T. Schlick, "Efficient Implementation of the Truncated Newton Method for Large Scale Chemistry Applications", SIAM J. Opt., 10: 132-154 October (1999)
  128. D. Xie and T. Schlick, "Remark on the Updated Truncated Newton Minimization Package, Algorithm 702", ACM Trans. Math. Softw., 25, 108-122, March (1999)
  129. D. Xie, L. R. Scott and T. Schlick, "Analysis of the SHAKE-SOR Algorithm for Constrained Molecular Dynamics Simulations", Methods and Applications of Analysis, a Special issue dedicated to Prof. Cathleen Morawetz of the Courant Institute, 7: 577-590, September (2000)
  130. D. Xie, A. Tropsha and T. Schlick, "An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization", J. Chem. Inf. Comput. Sci., 40:167-177, December (1999)
  131. 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., 109:1617-1632, August (1998)
  132. E. Barth and T. Schlick, "II. Extrapolation Versus Impulse in Multiple-Timestepping Schemes: Linear Analysis and Applications to Newtonian and Langevin Dynamics", J. Chem. Phys. 109:1633-1642, August (1998)
  133. P. Derreumaux and T. Schlick, "Simulation of the Loop Opening/Closing of the Enzyme Triosephosphate Isomeraze (TIM)", Biophys. J., 74:72-81, January (1998)
  134. H. Jian, T. Schlick, and A. Vologodskii, "Internal Motion of Supercoiled DNA: Brownian Dynamics Simulations of Site Juxtaposition", J. Mol. Biol., 284:287-296, November (1998)
  135. T. Schlick, "Geometry Optimization", Contributed chapter to the Encyclopedia of Computational Chemistry (5 Volumes), Volume 2, pages 1136-1157, 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)
  136. T. Schlick, "Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations", in Algorithms for Macromolecular Modeling, Volume 4, pages 227-262, Springer-Verlag 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)
  137. T. Schlick, M. Mandziuk, R. D. Skeel, and K. Srinivas, "Nonlinear Resonance Artifacts in Molecular Dynamics", J. Comp. Phys., 139:1-29, February (1998)
  138. L. Y. Zaslavsky and T. Schlick, "An Adaptive Multigrid Technique for Evaluating Long-Range Forces in Biomolecular Simulations", App. Math. Comp., 97:237-250, December (1998)
  139. 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 97-120, W. van Gunsteren, P. Weiner and T. Wilkinson eds., ESCOM Science Publishers, Ledien, The Netherlands (1997)
  140. H. Jian, A. Vologodskii, and T. Schlick, "A Combined Wormlike Chain and Bead Model for Dynamic Simulations of Long DNA", J. Comp. Phys., 136:168-179, September (1997)
  141. G. Liu, T. Schlick, A. J. Olson, and W. K. Olson, "Configurational Transitions in DNA Supercoils Represented by Fourier-Series Curve-Fitting Techniques", Biophys. J., 73:1742-1762, October (1997)
  142. G. Ramachandran and T. Schlick, "On Buckling Transitions in Supercoiled DNA: Dependence on Elastic Constants and DNA Size", Biopolymers, 41:5-25, January (1997)
  143. 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., 26:181-222 (1997)
  144. 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)
  145. B. Mishra and T. Schlick, " The Notion of Error in Langevin Dynamics: (1) Linear Analysis", J. Chem. Phys., 105:299-318, July (1996)
  146. T. Pinou, T. Schlick, B. Li, and H. Dowling, "Addition of Darwin's Third Dimension to Evolutionary Trees", J. Theor. Bio., 219:505-512, October (1996)
  147. 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 215-231, American Mathematical Society, Providence, Rhode Island (1996)
  148. 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 219-247, J. Mesirov, K Schulten, and D. W. Sumners, eds., Springer-Verlag, New York (1996)
  149. T. Schlick and A. Brandt, "A Multigrid Tutorial with Applications to Molecular Dynamics", IEEE Comp. Sci. Eng., 3:78-83, Fall (1996)
  150. P. Derreumaux and T. Schlick, "Long Timestep Dynamics of Peptides by the Dynamics Driver Approach", Proteins: Struc. Func., Gen., 21:282-302, April (1995)
  151. G. Liu, W. K. Olson, and T. Schlick, "Application of Fourier Analysis to Computer Simulation of Supercoiled DNA Formation", Comp. Polymer Sci., 5:7-27 (1995)
  152. M. Mandziuk and T. Schlick, "Resonance in the Dynamics of Chemical Systems Simulated by the Implicit Midpoint Scheme", Chem. Phys. Lett., 237:525-535, March (1995)
  153. G. Ramachandran and T. Schlick, "Solvent Effects on Supercoiled DNA Explored by Langevin Dynamics Simulations", Phys., Rev. E., 51:6188-6203, June (1995)
  154. T. Schlick, "Modeling Superhelical DNA: Recent Analytical and Dynamic Approaches", Curr. Opin. Struc. Bio., 5:245-262, April (1995). Special issue on Theory and Simulation, B. Honig, ed.
  155. T. Schlick and C. S. Peskin, "Comment on 'Backward Euler and other methods for simulating molecular fluids'", J. Chem. Phys., 103:9888-9889, December (1995)
  156. G. Zhang and T. Schlick, "Implicit Integration Schemes for Langevin Dynamics", Mol. Phys. 84:1077-1098 (1995)

  157. V. Z. Averbukh, S. Figueroa, and T. Schlick, "Remark on Algorithm 566", ACM Trans. Math. Softw., 20:282-285, September (1994)
  158. 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., 1:19-30, Winter (1994)
  159. 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, April (1994)
  160. T. Schlick, B. Li, and M. H. Hao, "Calibration of the Timestep for Molecular Dynamics of Supercoiled DNA Modeled by B-Splines", in Structural Biology, State of the Art 1993, Volume 1, Proceedings of the Eighth Conversation, M. H. Sarma and R. S. Sarma, eds., pages 157-174, Adenine Press, Guiderland, New York (1994)
  161. T. Schlick, B. Li, and W. K. Olson, "The Influence of Salt on the Structure and Energetics of Supercoiled DNA", Biophys. J., 67:2146-2166, December (1994)
  162. T. Schlick, W. K. Olson, T. Westcott, and J. P. Greenberg, "On Higher Buckling Transition in Supercoiled DNA", Biopolymers, 34:565-597, May (1994)
  163. 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, September (1994)
  164. T. Schlick, "Modified Cholesky Factorizations for Sparse Preconditioners", SIAM J. Sci. Comp., 14:424-445, March (1993)
  165. 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)
  166. 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, July (1993)
  167. 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, August (1993)
  168. V. Z. Averbukh, S. Figueroa, and T. Schlick, "HESFCN -A FORTRAN Package of Hessian Subroutines for Testing Nonlinear Optimization Software", Computer Science Technical Report, 610:1-43, June (1992)
  169. A. Nyberg and T. Schlick,"On Increasing the Time Step in Molecular Dynamics", Chem. Phys. Lett., 198:538-546, October (1992)

  170. T. Schlick, "Optimization Methods in Computational Chemistry", in Reviews in Computational Chemistry, Volume 3 , Chapter 1, pages 1-71, K. B. Lipkowitz and D. B. Boyd, eds., VCH Publishers, New York (1992)
  171. 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, March (1992)
  172. "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, March (1992)
  173. T. Schlick and W. K. Olson, "Computer Simulations of Supercoiled DNA Energetics and Dynamics", J. Mol. Biol., 223:1089-1119, February (1992)
  174. T. Schlick and W. K. Olson, "Trefoil Knotting Revealed by Molecular Dynamics of Supercoiled DNA", Science, 257:1110-1115, August (1992)
  175. A. Nyberg and T. Schlick, "A Computational Investigation of Dynamic Properties with the Implicit-Euler Scheme for Molecular Dynamics Situations", J. Chem. Phys., 95:4986-4996, October (1991)
  176. 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., 15:251-260 (1991)
  177. T. Schlick, S. Figueroa, and M. Mezei, "A Molecular Dynamics Simulation of a Water Droplet by the Implicit-Euler/Langevin Scheme", J. Chem. Phys., 94:2118-2129, February (1991)
  178. 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 39-58, D. L. Beveridge and R. Lavery, eds., Adenine Press, Guilderland, New York (1991)
  179. T. Schlick, "Implementation of the Schnabel and Eskow Modified Cholesky Factorization in the Context of Large-Scale Nonlinear Optimization", Computer Science Technical Report, Courant Institute 525:1-40, (1990)
  180. C. S. Peskin and T. Schlick, "Molecular Dynamics by the Backwards-Euler Method", Comm. Pure Appl. Math., 42:1001-1031 (1989)

  181. T. Schlick, "A Recipe for Evaluating and Differentiating Cos Expressions", J. Comp. Chem., 10:951-956, May (1989)
  182. 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)
  183. 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 74-113, R. H. Sarma, ed., State University of New York, Albany (1989)
  184. T. Schlick, "A Modular Strategy for Generating Starting Conformations and Data Structures of Polynucleotide Helices for Potential Energy Calculations", J. Comp. Chem., 9:861-889, June (1988)
  185. T. Schlick, "Modeling and Minimization Techniques for Predicting Three-Dimensional Structures of Large Biological Molecules", Ph. D. Dissertation, Courant Institute, Department of Mathematics, New York University (1987).
  186. T. Schlick and M. Overton, "A Powerful Truncated Newton Method for Potential Energy Minimization", J. Comp. Chem., 8:1025-1039, May (1987)
  187. 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., 8:1199-1224, June (1987)
  188. 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, 264:1-60 (1986)
  189. 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)