Research Output 1960 2019

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1998

Some failures and successes of long-timestep approaches to biomolecular simulations

Schlick, T., 1998, Algorithms for macromolecular modelling. Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A., Skeel, R. D. & Reich, S. (eds.). Springer-Verlag, p. 227-262 (Lecture Notes in Computational Science and Engineering; vol. 4).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

The construction of an RNA knot and its role in demonstrating that E. coli DNA topoisomerase III is an RNA topoisomerase

Wang, H., Di Gate, R. J. & Seeman, N., 1998, Structure, motion, interaction and expression of biological macromolecules. Sarma, R. H. & Sarma, M. H. (eds.). New York: Adenine Press, p. 103-116

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

The perils of polynucleotides: The experimental gap between the design and assembly of unusual DNA structures

Seeman, N., Wang, H., Liu, B., Qi, J., Li, X., Yang, X., Liu, F., Sun, W., Shen, Z., Wang, Y., Sha, R., Mao, C., Zhang, S., Fu, T. J., Du, S. M., Mueller, J. E., Zhang, Y. & Chen, J., 1998, DNA based computers II. Landweber, L. F. & Baum, E. B. (eds.). Providence: American Mathematical Society, p. 215-233

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Tripodal coordination complexes as scaffolds for molecular recognition and catalysis

Canary, J., Allen, C. S., Castagnetto, J. M., Chuang, C. L., Lajmi, A. R., dos Santos, O. & Xu, X., 1998, Molecular recognition and inclusion. Coleman, AW. (ed.). Amsterdam: Kluwer Academic Publishers, p. 179-184

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Universal computation via self-assembly of DNA: Some theory and experiements

Winfree, E., Yang, X. & Seeman, N., 1998, DNA based computers II. Landweber, L. F. & Baum, E. B. (eds.). Providence: American Mathematical Society, p. 191-213

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Vibration-rotation-tunneling dynamics of (HF)2 and (HCI)from full dimensional quantum bound state calculations

Bacic, Z. & Qui, Y., 1998, Advances in molecular vibrations and collision dynamics, volume III. Bowman, J. M. & Bacic, Z. (eds.). Greenwhich, Connecticut: JAI Press, Vol. III. p. 183-204

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1997

A separating framework for increasing the timestep in molecular dynamics

Barth, E., Mandziuk, M. & Schlick, T., 1997, Computer simulation of biomolecular systems. van Gunsteren, W., Weiner, P. & Wilkinson, T. (eds.). Leiden, The Netherlands: ESCOM Science Publishers, Vol. 3. p. 97-121

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Control of structure and topology in DNA nanotechnology

Seeman, N., Chen, J., Zhang, Y., Fu, T-J., Li, X., Yang, X., Wang, Y., Qi, J., Liu, B. & Liu, F., 1997, Molecular nanotechnology: Biological approaches and novel applications. Minden, S. A. (ed.). Southborough, MA: IBC Libraries, 31 p. Chapter 2.2

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Directing nucleation and growth of molecular crystals on ordered substrates: The role of epitaxial interactions

Bonafede, S. J., Hillier, A. C. & Ward, M., 1997, Proceedings of the NATO Advanced Research Workshop on Modular Chemistry (held September 9 - 12 1995. Estes Park, Colorado). Michl, J. (ed.). Boston: Kluwer, p. 637

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Molecular self-assembly of hydrogen-bonded crystalline networks

Russell, V. A. & Ward, M., 1997, Proceedings of the NATO Advanced Research Workshop on Modular Chemistry (held September 9 - 12 1995. Estes Park, Colorado). Michl, J. (ed.). Boston: Kluwer, p. 397

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Peptidomimetic inhibitors of farnesyltransferase: An approach to new antitumor agents

Qian, Y., Sebti, S. M. & Hamilton, A., 1997, Advances in peptidomimetic chemistry. Abell, A. (ed.). JAI Press, Vol. 1. p. 165-192

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

The control of DNA structure: From topological modules to geometrical modules

Seeman, N., Qi, J., Li, X., Yang, X., Leontis, N. B., Liu, B., Zhang, Y., Du, S. M. & Chen, J., 1997, Modular chemistry. Michl, J. (ed.). Kluwer, p. 95-104

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1996

Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model

Ramachandran, G. & Schlick, T., 1996, Global minimization of nonconvex energy functions: Molecular conformation and protein folding. Pardalos, P., Shalloway, D. & Xue, G. (eds.). Providence, Rhode Island: American Mathematical Society, p. 215-231 (DIMACS Series in Discrete Mathematics and Theoretical Computer Science; vol. 23).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

CD spectroscopy and the helix-coil transition in peptides and polypeptides

Kallenbach, N., Lyu, P. C. & Zhou, H. X., 1996, Circular dichroism and the conformational analysis of biomolecules. Fasman, G. D. (ed.). NY: Plenum Press, p. 201-259

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

DNA nanotechnology and topology

Seeman, N., Wang, H., Qi, J., Li, X., Yang, X., Wang, Y., Qiu, H., Liu, B., Shen, Z., Sun, W., Liu, F., Molenda, J. J., Du, S. M., Chen, J., Mueller, J. E., Zhang, Y., Fu, T. J. & Zhang, S., 1996, Biological structure and dynamics. Sarma, R. H. & Sarma, M. H. (eds.). New York: Adenine Press, Vol. 2. p. 319-341

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Hydrogen bonding control of molecular self-assembly: Recent advances in design, synthesis, and analysis

Fredericks, J. & Hamilton, A., 1996, Comprehensive supramolecular chemistry. Sauvage, J. P. & Hosseini, M. W. (eds.). Oxford: Pergamon Press, Vol. 9. p. 565-594

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Metal template control of self-assembly in supramolecular chemistry

Fredericks, J. & Hamilton, A., 1996, Perspectives in supramolecular chemistry. John Wiley and Sons, Vol. 3. p. 1-39

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Photodissociation of HF in ArnHF (n=1-14,54)

Schroder, T., Schinke, R., Liu, S., Bacic, Z. & Moskowitz, W., 1996, Femtochemistry . Chergui, M. (ed.). Singapore: World Scientific, p. 277-280

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Pursuing Laplace's vision on modern computers

Schlick, T., 1996, Proceedings of the IMA program in mathematical biology. Mesirov, J., Schulten, K. & Sumners, D. W. (eds.). New York: Springer-Verlag, p. 219-247 (IMA Volumes in Mathematics and its Applications; vol. 82).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Scanning tunneling and atomic force microscopy of electrochemical interfaces

Ward, M. D. & White, H. S., 1996, Modern techniques in electroanalysis. Vanysek, P. (ed.). New York: Wiley, Vol. 139. p. 107-149 43 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Atomic force microscopy
Scanning

Self-assembly as a strategy for artificial receptor design

Linton, B., Goodman, M. S., Jubian, V. & Hamilton, A., 1996, Self-assembly in synthetic chemistry. Wuest, J. (ed.). Kluwer

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Time-dependent quantum dynamics for gas-phase and gas-surface reactions

Zhang, D. H. & Zhang, J., 1996, Dynamics of molecules and chemical reactions. Wyatt, RE. & Zhang, JZH. (eds.). New York: Marcel Dekker, p. 231

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1995

Bound states of strongly coupled multidemensional molecular Hamiltonians by discrete variable representation approach

Bacic, Z., 1995, Domain-based parallelism and problem decomposition methods in computational science and engineering. Keyes, D. E., Saad, Y. & Truhlar, D. G. (eds.). Philadelphia: SIAM, p. 263-277

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Construction of DNA polyhedra and knots through symmetry minimization

Seeman, N., Zhang, Y., Du, S. M. & Chen, J., 1995, Supramolecular stereochemistry. Siegel, J. (ed.). Dordrecht: Kluwer, p. 27-32 (NATO Advanced Research Workshop Series).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Diastereospecific recognition of triarylmethane dyes by K2So4 crystals: A case of plundered stereochemistry in postwar Europe

Kahr, B. & Kelley, M. P., 1995, Supramolecular Stereochemistry. Siegal, J. S. (ed.). Kluwer, Dordrecht, p. 203-227 (NATO ASI Series).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Hydrogen bonding control of molecular self-assembly

Yang, J., Merendaz, J. L., Zafar, A., Geib, S. J. & Hamilton, A., 1995, Supramolecular stereochemistry. Siegel, J. (ed.). Kluwer, Vol. 473. p. 141-146

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Molecular engineering of crystals by electrostatic templating

Fagan, PJ. & Ward, M., 1995, Perspectives in supramolecular chemistry. Desiraju, GR. (ed.). New York: John Wiley

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Principles and applications of the electrochemical quartz crystal microbalance

Ward, M., 1995, Monographs in electroanalytical chemistry and electrochemistry: Physical electrochemistry, principles, methods, and applications. Rubinstein, I. (ed.). New York: Marcel Dekker

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1994

Dicyclohexylcarbodiimide

Albert, J. S. & Hamilton, A., 1994, Encyclopedia of reagents for organic synthesis. Pearson, A. J. & Paquette, L. (eds.). Chichester: John Wiley and Sons

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Dicyclohexylcarbodiimide-4-dimethylaminopyridine

Albert, J. S. & Hamilton, A., 1994, Encyclopedia of reagents for organic synthesis. Pearson, A. J. & Paquette, L. (eds.). Chichester: John Wiley and Sons

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Intra- and intermolecular hydrogen bonding control of supramolecular structure

Hamilton, A., Hamuro, Y., Yang, J., Geib, S. J. & Fan, E., 1994, Computational problems in supramolecular chemistry. Wipff, G. (ed.). Kluwer, Vol. 426. p. 101-108

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Mathematical optimization

Schlick, T. & Parks, G., 1994, DOE computational sciences education project (e-book): http://csep1.phy.ornl.gov/csep.html.

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Nucleation and growth of molecular crystals on molecular interfaces

Carter, PW., Frostman, LM., Hillier, AC. & Ward, M., 1994, ACS Symposium Series. Vol. 561.

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Structural control and engineering of nucleic acids

Seeman, N., 1994, Concepts in protein engineering and design. Wrede, P. & Schneider, G. (eds.). Berlin: Walter-de-Gruyter, p. 319-343

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1992

Controlled formation & properties of responsive polymers

Weber, S. G., Wise, E. T., Hamilton, A., Fan, E., Vincent, C., Garcia-Tellado, F. & Geib, S. J., 1992, Active materials and adaptive structures. Knowles, G. J. (ed.). Institute of Physics Publishing, p. 33-38

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Directed hydrogen bonding in the design of new receptors for complexation and catalysis

Hamilton, A., 1992, Chemical and biochemical aspects of molecular recognition II. London: Royal Society of London, Vol. 111. p. 75-82

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Electrocrystallization of low-dimensional molecular solids

Ward, M., 1992, Supramolecular architecture. p. 231 (ACS Symposium Series 499).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Optimization methods in computational chemistry

Schlick, T., 1992, Reviews in Computational Chemistry. Lipkowitz, K. B. & Boyd, D. B. (eds.). New York: VCH Publishers, Vol. 3. p. 1-71 Chapter 1

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1991

Immobile junctions suggest new features of the structural chemistry of recombination

Seeman, N., Mueller, J. E., Chen, J., Kallenbach, N., Chruchill, M. E. A. & Kimball, A., 1991, Structure and method: Proceedings of the 6th Conversation in Biomolecular Stereodynamics. Vol. 1. p. 137-156

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Synthetic studies on molecular recognition

Hamilton, A., 1991, Frontiers in bioorganic chemistry. Dugas, D. H. (ed.). Berlin: Springer-Verlag, Vol. 2. p. 115-174

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1990

How to simulate the quantum-mechanical suppression of high-frequency modes in classical molecular dynamics computations

Peskin, C. & Schlick, T., 1990, Biomedical Engineering: Opening New Doors: Proceedings of the Fall 1990 Annual Meeting of the Biomedical Engineering Society. Mikulecky, D. C. & Clarke, A. M. (eds.). New York: NYU Press, p. 57-58

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Hydrogen bonding in biological and artificial molecular recognition

Hamilton, A., 1990, Advances in supramolecular chemistry. Gokel, G. (ed.). JAI Press, Vol. 1. p. 1-64

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Molecular recognition by macrocyclic receptors

Hamilton, A., 1990, Inclusion phenomena and molecular recognition. Atwood, J. L. (ed.). New York: Plenum Press, p. 57-64

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Search strategies, minimization algorithms, and molecular dynamics simulations for exploring conformational spaces of nuclear acids

Overton, M., Schlick, T., Hingerty, B. E., Peskin, C. & Broyde, S., 1990, Theoretical biochemistry and molecular biophysics, Volume 1: DNA. Beveridge, D. L. & Lavery, R. (eds.). Guilderland, New York: Adenine Press, p. 39-58

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1989

A new pair of algorithms for potential energy minimization and molecular dynamics simulations

Schlick, T., Peskin, C. & Overton, M., 1989, Book of abstracts of the sixth conversation in biomolecular stereodynamics. Sarma, R. H. (ed.). State University of New York, Albany

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Design of artificial receptors for biochemically interesting substrates

Hamilton, A., Chang, S. K., Goswami, S., Muehldorf, A. & Van Engen, D., 1989, Chemical and biochemical aspects of molecular recognition. London: Royal Society of London, Vol. 78. p. 234-242

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Nanoscale assembly and manipulation of branched DNA: A biological starting point for nanotechnology

Seeman, N., 1989, NANOCON Proceedings. Lewis, J. & Quel, J. L. (eds.). Bellevue, WA: NANOCON, p. 101-123

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Nucleotide recognition by macrocyclic receptors

Hamilton, A., Muehldorf, A., Chang, S. K., Pant, N., Goswami, S. & Van Engen, D., 1989, Advances in inclusion chemistry. Gokel, G. & Koga, K. (eds.). Amsterdam: Kluwer

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

1988

Mathematical frontiers in computational chemical physics

Kouri, DJ., Sun, Y., Mowrey, RC., Zhang, J., Truhlar, D. G., Haug, K. & Schwenke, D. W., 1988, Proceedings of the Workshop on Atomic and Molecular Structure and Dynamics. Truhlar, DG. (ed.). New York: Springer, p. 207-243

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Nucleic acid junctions: A successful experiment in macromolecular design

Seeman, N. & Kallenbach, N., 1988, Molecular structure: Chemical reactivity and biological activity.

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)