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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

Exploitation
Nanotechnology
Molecules
Material world

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: Chapter in Book/Report/Conference proceedingChapter

Decomposition
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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

Surgical Hemostasis
Aldosterone
Lutheran Blood-Group System
Erysipeloid
Cetomacrogol
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: Chapter in Book/Report/Conference proceedingChapter

Knee Joint
Glycosaminoglycans

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: Chapter in Book/Report/Conference proceedingChapter

Dehydrogenation
Ephemeral Fever
Carbonyl compounds
Oxidation
Avian Leukosis

Polarizing Films

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

Research output: Chapter in Book/Report/Conference proceedingChapter

Iodine
Arthroscopy
Light polarization
Intracranial Aneurysm
Wave interference

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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

Peptides

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: Chapter in Book/Report/Conference proceedingChapter

src Homology Domains
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: Chapter in Book/Report/Conference proceedingChapter

Artificial Organs
Molecules
Avian Leukosis
Birth Injuries
Fasciola

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: Chapter in Book/Report/Conference proceedingChapter

Molecular dynamics
Semiconductor materials

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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

Imaging techniques
Crystals

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: Chapter in Book/Report/Conference proceedingChapter

Stereochemistry
Organic compounds
Spectroscopy

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: Chapter in Book/Report/Conference proceedingChapter

Isotope Labeling
Membrane Proteins
Magnetic Resonance Spectroscopy
Butylene Glycols
Dapsone

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: Chapter in Book/Report/Conference proceedingChapter

Proteins
Drug Discovery
Drug Design
Tertiary Protein Structure
Biological Availability

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: Chapter in Book/Report/Conference proceedingChapter

Membrane Proteins
Magnetic Resonance Spectroscopy
Dapsone
Butylene Glycols
Spectrum Analysis
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: Chapter in Book/Report/Conference proceedingChapter

Dendrimers
Amino acids

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: Chapter in Book/Report/Conference proceedingChapter

Estuaries
DNA Adducts
Aromatic Polycyclic 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: Chapter in Book/Report/Conference proceedingChapter

DNA-Directed DNA Polymerase

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: Chapter in Book/Report/Conference proceedingChapter

Glycomics
Glycosylation
Lectins
Polysaccharides
Intrauterine Devices

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: Chapter in Book/Report/Conference proceedingChapter

Nanoparticles
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: Chapter in Book/Report/Conference proceedingChapter

DNA

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: Chapter in Book/Report/Conference proceedingChapter

Knee Joint

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: Chapter in Book/Report/Conference proceedingChapter

Peptides
Proteins

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: Chapter in Book/Report/Conference proceedingChapter

DNA Damage

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: Chapter in Book/Report/Conference proceedingChapter

DNA Repair
DNA

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: Chapter in Book/Report/Conference proceedingChapter

DNA Damage
Free Radicals
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: Chapter in Book/Report/Conference proceedingChapter

Crown Ethers
Crown ethers

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: Chapter in Book/Report/Conference proceedingChapter

Fiber
Model
Chromatin
Compaction
Folding

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: Chapter in Book/Report/Conference proceedingChapter

Carbonates
DNA
Negative ions
Nitrogen
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: Chapter in Book/Report/Conference proceedingChapter

Chlorophyll
Fluorescence
Membranes
Chloroplasts
Carotenoids

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: Chapter in Book/Report/Conference proceedingChapter

Proteins

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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

Functional materials

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: Chapter in Book/Report/Conference proceedingChapter

Supramolecular chemistry
Self assembly
Metals

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: Chapter in Book/Report/Conference proceedingChapter

Electrostatics
Crystals

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: Chapter in Book/Report/Conference proceedingChapter

Bibliography of Medicine
Cortodoxone
Catalysis
Afferent Loop Syndrome
Bile Pigments

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: Chapter in Book/Report/Conference proceedingChapter

Topology
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: Chapter in Book/Report/Conference proceedingChapter

Drug Discovery

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: Chapter in Book/Report/Conference proceedingChapter

Gels
Gelation
X ray diffraction
Molecular recognition
Molecular mass

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: Chapter in Book/Report/Conference proceedingChapter

molecular dynamics
polypeptides
paradoxes
statistical mechanics
free energy

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: Chapter in Book/Report/Conference proceedingChapter

Genome
Molecules
Cell
RNA
Protein

RNA: The cousin left behind becomes a star

Schlick, T. 2006 Computational Studies of RNA and DNA. Springer Netherlands, p. 259-281 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA
Graph theory
Bioinformatics
Gene expression
Stars