Research Output 1960 2019

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2018

Afterglow solid-state NMR spectroscopy

Abramov, G. & Traaseth, N., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., Vol. 1688. p. 55-66 12 p. (Methods in Molecular Biology; vol. 1688).

Research output: Chapter in Book/Report/Conference proceedingChapter

Magnetic Resonance Spectroscopy
Membrane Transport Proteins
Multiple Drug Resistance
Spectrum Analysis
Membrane Proteins

DNA nanotechnology: From the pub to information-based chemistry

Seeman, N., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 1-9 9 p. (Methods in Molecular Biology; vol. 1811).

Research output: Chapter in Book/Report/Conference proceedingChapter

Nanotechnology
Parturition
DNA
Research

NMR spectroscopy approach to study the structure, orientation, and mechanism of the multidrug exporter EmrE

Leninger, M. & Traaseth, N., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., Vol. 1700. p. 83-96 14 p. (Methods in Molecular Biology; vol. 1700).

Research output: Chapter in Book/Report/Conference proceedingChapter

Multiple Drug Resistance
Magnetic Resonance Spectroscopy
Membrane Proteins
Cytoplasm
Anti-Bacterial Agents
2017

Designed 3D DNA crystals

Seeman, N., 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

Metal Complexes in Reverse Micelles

Walters, M., Nov 27 2017, Novel Nanoscale Hybrids. wiley, p. 301-322 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Coordination Complexes
Micelles

MFCC-Based Fragmentation Methods for Biomolecules

Liu, J., Zhu, T., He, X. & Zhang, J., Jun 21 2017, Fragmentation: Toward Accurate Calculations on Complex Molecular Systems. wiley, p. 323-348 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biomolecules
Fractionation
Proteins
Molecular mechanics
Solvation

Modeling and design of peptidomimetics to modulate protein–protein interactions

Watkins, A. M., Bonneau, R. & Arora, P., 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
Secondary Protein Structure
Tertiary Protein Structure
Software
Databases
2016

Chiroptical Sensors

Canary, J., Duan, X. & Liu, X., Dec 9 2016, Encyclopedia of Spectroscopy and Spectrometry. Elsevier Inc., p. 203-210 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Circular dichroism spectroscopy
Molecules
sensors
Sensors
Complexation

DNA in a material world

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

Research output: Chapter in Book/Report/Conference proceedingChapter

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: Chapter in Book/Report/Conference proceedingChapter

field theory (physics)
Decomposition
decomposition
energy
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., 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

DNA
Craftwork

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

Polymers
Self assembly
Rotaxanes
Ring opening polymerization
Alkenes
2014

1,3-Cyclohexadiene Formation Reactions: 6π and Higher-Order Electrocyclizations

Trauner, D. & Webster, R., Feb 2014, Comprehensive Organic Synthesis: Second Edition. Elsevier Ltd., Vol. 5. p. 783-826 44 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biological Products
Carbon
1,3-cyclohexadiene

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
Carbonyl compounds
Oxidation
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: Chapter in Book/Report/Conference proceedingChapter

Iodine
Light polarization
Wave interference
Calcium Carbonate
Wave transmission

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

Zhang, J., 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

A 1H NMR Assay for measuring the photostationary states of photoswitchable ligands

Banghart, M. R. & Trauner, D., 2013, Chemical Neurobiology: Methods and Protocols. Vol. 995. p. 107-120 14 p. (Methods in Molecular Biology; vol. 995).

Research output: Chapter in Book/Report/Conference proceedingChapter

Lighting
Ligands
Optical Fibers
Ion Channels
Protons

Another important 60th anniversary

Seeman, N., 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

Challenges and opportunities for optochemical genetics

Isacoff, E. Y., Kramer, R. H. & Trauner, D., Aug 28 2013, Optogenetics. Walter de Gruyter GmbH, p. 35-45 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Constrained peptide helices

Mahon, A. B. & Arora, P., 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

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: Chapter in Book/Report/Conference proceedingChapter

RNA
Topology
Untranslated RNA
Biological Science Disciplines
Graph theory

SH3 Domains as Drug Targets

Luccarelli, J., Thompson, S. & Hamilton, A., 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
Pharmaceutical Preparations
2012

2.19 Selected Diastereoselective Reactions: Electrocyclizations

Myers, E. L. & Trauner, D., Sep 2012, Comprehensive Chirality. Elsevier Ltd, Vol. 2. p. 563-606 44 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Photochemical reactions
Conservation
Carbon
Substrates
Hot Temperature

8.30 Spectroscopic Analysis: Chiroptical Sensors

Canary, J., 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

Spectroscopic analysis
Sensors
Solid-state sensors
Molecules
Scaffolds

Ab Initio Molecular Dynamics Studies of Conjugated Dienes on Semiconductor Surfaces

Tuckerman, M. & 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

DNA-Directed DNA Polymerase
Substrates

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. & 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

Organometallic Compounds
Stereochemistry
Spectroscopy

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

Verardi, R., Traaseth, N., 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
Isotopes
Labeling
Nuclear magnetic resonance spectroscopy
Membrane Proteins

Pharmacology of bacterial and mycobacterial infections: Cell wall synthesis

Lupoli, T., Hooper, D. C., Arnaout, R. A., Kahne, D. & Walker, S., Oct 31 2012, Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy: Third Edition. Wolters Kluwer (UK) Ltd., p. 1280-1314 35 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bacterial Infections
Cell Wall
Pharmacology

Rational design strategies for developing synthetic inhibitors of helical protein interfaces

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

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins
Pharmaceutical Preparations
Drug Discovery
Drug Design
Biological Availability

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

Veglia, G., Traaseth, N., 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

Solid solutions
Membrane Proteins
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
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: 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
Polycyclic Aromatic Hydrocarbons
Polycyclic Aromatic Hydrocarbon Bay-Region
DNA Repair

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., 2011, Functional and Structural Proteomics of Glycoproteins. Springer Netherlands, p. 91-102 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Glycomics
Glycosylation
Microarrays
Lectins
Polysaccharides

Switchable Proteins and Channels

Volgraf, M., Banghart, M. & Trauner, D., Aug 29 2011, Molecular Switches, Second Edition. Wiley-VCH, Vol. 1. p. 563-593 31 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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: 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

Mutagenesis
Computer Simulation
Carcinogenesis
DNA
Computer simulation

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., 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

Reactive Nitrogen Species
Chemotherapy
DNA Repair
DNA Damage
Reactive Oxygen Species

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

Nucleic Acid Conformation
DNA Adducts
Benzo(a)pyrene
DNA sequences
DNA Repair

Role of Free Radical Reactions in the Formation of DNA Damage

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

Research output: Chapter in Book/Report/Conference proceedingChapter

Free radical reactions
Nucleophiles
DNA Adducts
DNA Damage
Free Radicals
2009

Crown Ethers and Cryptands

Hamilton, A., 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

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

Chromatin
Folding
Fiber
Compaction
Tail

Reactions of Reactive Nitrogen Species and Carbonate Radical Anions with DNA

Shafirovich, V., Crean, C. & Geacintov, N., 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

Reactive Nitrogen Species
Carbonates
Anions
DNA
2008

Chlorophyll Orientation and Exciton Migration in the Photosynthetic Membrane

Breton, J. & Geacintov, N., 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
Chloroplasts
Fluorescence
fluorescence
wavelengths