Research Output 1960 2017

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2017

Designed 3D DNA crystals

Seeman, N. C., Sha, R., Birktoft, J., Zheng, J., Liu, W., Wang, T. & Mao, C. 2017 Methods in Molecular Biology. Humana Press Inc., Vol. 1500, p. 3-10 8 p. (Methods in Molecular Biology; vol. 1500)

Research output: ResearchChapter

Nucleotide Motifs
DNA

Modeling and design of peptidomimetics to modulate protein–protein interactions

Watkins, A. M., Bonneau, R. & Arora, P. S. 2017 Methods in Molecular Biology. Humana Press Inc., Vol. 1561, p. 291-307 17 p. (Methods in Molecular Biology; vol. 1561)

Research output: ResearchChapter

Peptidomimetics
Proteins
Secondary Protein Structure
Tertiary Protein Structure
Software
2016

DNA in a material world

Seeman, N. C. Jan 1 2016 50 Years of DNA. Palgrave Macmillan, p. 113-117 5 p.

Research output: ResearchChapter

Material World
Nanotechnology
Exploitation
Molecules
History

Force field development with density-based energy decomposition analysis

Zhou, N., Wu, Q. & Zhang, Y. Mar 14 2016 Many-Body Effects and Electrostatics in Biomolecules. Pan Stanford Publishing Pte. Ltd., p. 121-145 25 p.

Research output: ResearchChapter

2015

Gibbs and Amistad

Kahr, B. Jan 1 2015 Culture of Chemistry: The Best Articles on the Human Side of 20th-Century Chemistry from the Archives of the Chemical Intelligencer. Hargittai, B. & Hargittai, I. (eds.). Springer US, p. 249-256 8 p.

Research output: ResearchChapter

Molecular craftwork with DNA

Seeman, N. C. Jan 1 2015 Culture of Chemistry: The Best Articles on the Human Side of 20th-Century Chemistry from the Archives of the Chemical Intelligencer. Springer US, p. 141-152 12 p.

Research output: ResearchChapter

Supramolecular Polymers

Elacqua, E., Ten Brummelhuis, N. & Weck, M. Jan 1 2015 Volume 3: Polymer Synthesis. wiley, Vol. 3-3, p. 71-92 22 p.

Research output: ResearchChapter

Polymers
Self assembly
Rotaxanes
Ring opening polymerization
Alkenes
2014

Chemical exchange saturation transfer contrast by glycosaminoglycans and its application for monitoring knee joint repair

Lee, J. S., Xia, D., Parasoglou, P., Chang, G., Jerschow, A. & Regatte, R. R. Jan 1 2014 Advanced Quantitative Imaging of Knee Joint Repair. World Scientific Publishing Co., p. 249-271 23 p.

Research output: ResearchChapter

Oxidation Adjacent to C X Bonds by Dehydrogenation

Stahl, S. S. & Diao, T. Feb 2014 Comprehensive Organic Synthesis: Second Edition. Elsevier Ltd., Vol. 7, p. 178-212 35 p.

Research output: ResearchChapter

Dehydrogenation
Oxidation
Carbonyl compounds
Halogenation
Selenium

Polarizing Films

Kahr, B. & Knowles, K. M. Nov 24 2014 Iodine Chemistry and Applications. Wiley Blackwell, p. 479-488 10 p.

Research output: ResearchChapter

Iodine
Light polarization
Wave interference
Wave transmission
Calcite

Time-dependent treatment of SVRT model for polyatom-polyatom reaction

Zhang, J. Z. H. 2014 Reaction Rate Constant Computations. p. 337-351 15 p. (RSC Theoretical and Computational Chemistry Series)

Research output: ResearchChapter

2013

Another important 60th anniversary

Seeman, N. C. 2013 Hierarchical Macromolecular Structures: 60 Years After The Staudinger Nobel Prize I. Vol. 261, p. 217-228 12 p. (Advances in Polymer Science; vol. 261)

Research output: ResearchChapter

DNA
Molecules
Nanotechnology
Crystal lattices
Crystals

Constrained peptide helices

Mahon, A. B. & Arora, P. S. Oct 1 2013 Understanding and Exploiting Protein-Protein Interactions as Drug Targets. Future Medicine Ltd., p. 63-73 11 p.

Research output: ResearchChapter

Graph applications to RNA structure and function

Kim, N., Fuhr, K. N. & Schlick, T. Jan 1 2013 Biophysics of RNA Folding. Springer New York, p. 23-51 29 p.

Research output: ResearchChapter

RNA
Topology
Untranslated RNA
Graph theory
Biological Science Disciplines

SH3 Domains as Drug Targets

Luccarelli, J., Thompson, S. & Hamilton, A. D. Feb 26 2013 Protein-Protein Interactions in Drug Discovery. Wiley-VCH Verlag, Vol. 56, p. 101-128 28 p.

Research output: ResearchChapter

2012

8.30 Spectroscopic Analysis: Chiroptical Sensors

Canary, J. W., Dai, Z. & Mortezaei, S. Sep 2012 Comprehensive Chirality. Elsevier Ltd, Vol. 8, p. 600-624 25 p.

Research output: ResearchChapter

Spectroscopic analysis
Sensors
Molecules
Solid-state sensors
Scaffolds

Ab Initio Molecular Dynamics Studies of Conjugated Dienes on Semiconductor Surfaces

Tuckerman, M. E. & Zhang, Y. Mar 20 2012 Functionalization of Semiconductor Surfaces. John Wiley and Sons, p. 233-276 44 p.

Research output: ResearchChapter

Chapter 4: Intrinsic motions of DNA polymerases underlie their remarkable specificity and selectivity and suggest a hybrid substrate binding mechanism

Foley, M. C., Arora, K. & Schlick, T. 2012 Innovations in Biomolecular Modeling and Simulations. p. 81-110 30 p. (RSC Biomolecular Sciences)

Research output: ResearchChapter

Chiroptical Imaging of Crystals

Freudenthal, J., Kaminsky, W. & Kahr, B. Jan 31 2012 Comprehensive Chiroptical Spectroscopy. John Wiley and Sons, Vol. 1, p. 325-345 21 p.

Research output: ResearchChapter

Dynamic Stereochemistry and Chiroptical Spectroscopy of Metallo-Organic Compounds

Canary, J. W. & Dai, Z. Feb 17 2012 Comprehensive Chiroptical Spectroscopy. John Wiley and Sons, Vol. 2, p. 251-287 37 p.

Research output: ResearchChapter

Isotope labeling for solution and solid-state NMR spectroscopy of membrane proteins

Verardi, R., Traaseth, N. J., Masterson, L. R., Vostrikov, V. V. & Veglia, G. 2012 Isotope labeling in Biomolecular NMR. Vol. 992, p. 35-62 28 p. (Advances in Experimental Medicine and Biology; vol. 992)

Research output: ResearchChapter

Isotopes
Labeling
Nuclear magnetic resonance spectroscopy
Membrane Proteins
Nuclear magnetic resonance

Rational design strategies for developing synthetic inhibitors of helical protein interfaces

Mahon, A. B., Miller, S. E., Joy, S. T. & Arora, P. S. 2012 Protein-protein interactions. Wendt, M. D. (ed.). Springer, Vol. 8, p. 197-230 34 p. (Topics in Medicinal Chemistry; vol. 8)

Research output: ResearchChapter

Proteins
Pharmaceutical Preparations
alpha-Helical Protein Conformation
Drug Discovery
Drug Design

The hybrid solution/solid-state NMR method for membrane protein structure determination

Veglia, G., Traaseth, N. J., Shi, L., Verardi, R., Gopinath, T. & Gustavsson, M. 2012 Comprehensive Biophysics. Elsevier Inc., Vol. 1, p. 182-198 17 p.

Research output: ResearchChapter

Solid solutions
Membrane Proteins
Nuclear magnetic resonance
Magnetic Resonance Spectroscopy
Simulated annealing
2011

Amino Acid-Based Dendrimers

Shi, Z., Zhou, C., Liu, Z., Totsingan, F. & Kallenbach, N. R. Apr 7 2011 Amino Acids, Peptides and Proteins in Organic Chemistry. Wiley-VCH, Vol. 4, p. 491-517 27 p.

Research output: ResearchChapter

Covalent polycyclic aromatic hydrocarbon-DNA adducts: Carcinogenicity, structure, and function

Broyde, S., Wang, L., Cai, Y., Jia, L., Shapiro, R., Patel, D. J. & Geacintov, N. E. 2011 Chemical Carcinogenesis. Vol. 6, p. 181-207 27 p. (Current Cancer Research; vol. 6)

Research output: ResearchChapter

Estuaries
DNA Adducts
Polycyclic Aromatic Hydrocarbons
DNA Repair
Neoplasms

DNA polymerases structure, function, and modeling

Schlick, T. Jan 1 2011 Molecular Machines. World Scientific Publishing Co., p. 49-66 18 p.

Research output: ResearchChapter

Lectin microarrays: Simple tools for the analysis of complex glycans

Krishnamoorthy, L. & Mahal, L. K. 2011 Functional and Structural Proteomics of Glycoproteins. Springer Netherlands, p. 91-102 12 p.

Research output: ResearchChapter

Glycosylation
Microarrays
Lectins
Polysaccharides
Proteins

The Exploration of Biomedical Multimodality in Small Solid Core Nanoparticles

Walters, M. Jul 18 2011 Hybrid Nanomaterials: Synthesis, Characterization, and Applications. John Wiley and Sons, p. 199-218 20 p.

Research output: ResearchChapter

2010

Elucidating Structure-Function Relationships in Bulky DNA Lesions: From Solution Structures to Polymerases

Broyde, S., Wang, L., Patel, D. J. & Geacintov, N. E. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 331-352 22 p.

Research output: ResearchChapter

Functional imaging of the knee joint

Blumenkrantz, G., Li, X., Regatte, R. R., Jerschow, A. & Majumdar, S. Jan 1 2010 Advances in MRI of the Knee for Osteoarthritis. World Scientific Publishing Co., p. 185-233 49 p.

Research output: ResearchChapter

Inhibition of Protein-Protein Interactions by Peptide Mimics

Becerril, J., Rodriguez, J. M., Wyrembak, P. N. & Hamilton, A. D. Nov 30 2010 Protein Surface Recognition: Approaches for Drug Discovery. John Wiley and Sons, p. 105-131 27 p.

Research output: ResearchChapter

Introduction and Perspectives on the Chemistry and Biology of DNA Damage

Geacintov, N. E. & Broyde, S. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 1-20 20 p.

Research output: ResearchChapter

Recognition and Removal of Bulky DNA Lesions by the Nucleotide Excision Repair System

Cai, Y., Kropachev, K., Kolbanovskiy, M., Kolbanovskiy, A., Broyde, S., Patel, D. J. & Geacintov, N. E. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 261-298 38 p.

Research output: ResearchChapter

Role of Free Radical Reactions in the Formation of DNA Damage

Shafirovich, V. & Geacintov, N. E. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 81-104 24 p.

Research output: ResearchChapter

2009

Crown Ethers and Cryptands

Hamilton, A. D. Sep 1 2009 Comprehensive Heterocyclic Chemistry. Elsevier Inc., Vol. 7-7, p. 731-761 31 p.

Research output: ResearchChapter

From Macroscopic to Mesoscopic Models of Chromatin Folding

Schlick, T. Oct 1 2009 Multiscale Methods: Bridging the Scales in Science and Engineering. Oxford University Press

Research output: ResearchChapter

Chromatin
Folding
Fiber
Model
Compaction

Reactions of Reactive Nitrogen Species and Carbonate Radical Anions with DNA

Shafirovich, V., Crean, C. & Geacintov, N. E. Sep 28 2009 Radical and Radical Ion Reactivity in Nucleic Acid Chemistry. John Wiley & Sons, Inc., p. 325-355 31 p.

Research output: ResearchChapter

2008

Chlorophyll Orientation and Exciton Migration in the Photosynthetic Membrane

Breton, J. & Geacintov, N. E. May 30 2008 Chlorophyll Organization and Energy Transfer in Photosynthesis. wiley, p. 217-236 20 p.

Research output: ResearchChapter

Chlorophyll
Fluorescence
Membranes
LDS 751
fluorescence

Controlling Protein-Protein Interactions: Protein Secondary Structure Mimetics as Modulators of Protein-Protein and Protein-Ligand Interactions

Yin, H. & Hamilton, A. D. Apr 21 2008 Chemical Biology: From Small Molecules to Systems Biology and Drug Design, Volume 1-3. John Wiley and Sons, Vol. 1, p. 250-269 20 p.

Research output: ResearchChapter

Noncovalent side chain modification

Nair, K. P. & Weck, M. Feb 25 2008 Molecular Recognition and Polymers: Control of Polymer Structure and Self-Assembly. John Wiley and Sons, p. 103-136 34 p.

Research output: ResearchChapter

2007

Foldamer-based Molecular Recognition

Becerril, J., Rodriguez, J. M., Saraogi, I. & Hamilton, A. D. Jun 14 2007 Foldamers: Structure, Properties, and Applications. Wiley-VCH Verlag GmbH & Co. KGaA, p. 193-228 36 p.

Research output: ResearchChapter

Functional Materials via Multiple Noncovalent Interactions

Carlisle, J. R. & Weck, M. Jan 16 2007 Functional Organic Materials: Syntheses, Strategies and Applications. John Wiley and Sons, p. 261-292 32 p.

Research output: ResearchChapter

Metal Template Control of Self-Assembly in Supramolecular Chemistry

Fredericks, J. R. & Hamilton, A. D. Mar 12 2007 Supramolecular Control of Structure and Reactivity. wiley, Vol. 3, p. 1-39 39 p.

Research output: ResearchChapter

Molecular engineering of crystals by electrostatic templating

Fagan, P. J. & Ward, M. D. Mar 12 2007 The crystal as a supramolecular entity. Wiley, Vol. 2, p. 107-135 29 p.

Research output: ResearchChapter

Stability of Supported Pincer Complex-Based Catalysts in Heck Catalysis

Sommer, W. W., Jones, C. C. & Weck, M. 2007 The Chemistry of Pincer Compounds. Elsevier, p. 385-397 13 p.

Research output: ResearchChapter

Catalysis
Catalysts
Kinetics
Catalyst poisoning
Decomposition

Synthetic DNA Topology

Seeman, N. C. Dec 30 2007 Molecular Catenanes, Rotaxanes and Knots: A Journey Through the World of Molecular Topology. wiley, p. 323-356 34 p.

Research output: ResearchChapter

2006

Alpha-Helix Mimetics in Drug Discovery

Yin, H., Lee, G. I. & Hamilton, A. D. Nov 2 2006 Drug Discovery Research: New Frontiers in the Post-Genomic Era. John Wiley & Sons, Inc., p. 281-299 19 p.

Research output: ResearchChapter

Cryo-tem, X-ray diffraction and modeling of an organic hydrogel

Estroff, L. A. & Hamilton, A. D. 2006 Molecular Gels: Materials with Self-Assembled Fibrillar Networks. Springer Netherlands, p. 721-742 22 p.

Research output: ResearchChapter

gels
diffraction
x rays
gelation
ice

Equilibrium statistical mechanics, non-hamiltonian molecular dynamics, and novel applications from resonance-free timesteps to adiabatic free energy dynamics

Abrams, J. B., Tuckerman, M. E. & Martyna, G. J. 2006 Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. Vol. 703, p. 139-192 54 p. (Lecture Notes in Physics; vol. 703)

Research output: ResearchChapter

polypeptides
statistical mechanics
free energy
molecular dynamics
paradoxes

Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach

Laserson, U., Gan, H. H. & Schlick, T. 2006 New Algorithms for Macromolecular Simulation. Vol. 49, p. 35-56 22 p. (Lecture Notes in Computational Science and Engineering; vol. 49)

Research output: ResearchChapter

Genome
Molecules
Cell
RNA
Genes