Research Output 1949 2019

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Review article
2019

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

Bevilacqua, P. C., Harris, M. E., Piccirilli, J. A., Gaines, C., Ganguly, A., Kostenbader, K., Ekesan, Ş. & York, D. M., Jun 21 2019, In : ACS chemical biology. 14, 6, p. 1068-1076 9 p.

Research output: Contribution to journalReview article

RNA Cleavage
Catalytic RNA
Ontology
RNA
Enzymes
1 Citation (Scopus)

Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II

Lee, J., Crickard, J. B., Reese, J. C. & Lee, T., Apr 15 2019, In : Methods. 159-160, p. 51-58 8 p.

Research output: Contribution to journalReview article

Nucleosomes
RNA Polymerase II
Transcription
Elongation
Molecules
2018
31 Citations (Scopus)

Best Practices for Reporting Electrocatalytic Performance of Nanomaterials

Voiry, D., Chhowalla, M., Gogotsi, Y., Kotov, N. A., Li, Y., Penner, R. M., Schaak, R. E. & Weiss, P. S., Oct 23 2018, In : ACS nano. 12, 10, p. 9635-9638 4 p.

Research output: Contribution to journalReview article

Nanostructured materials
5 Citations (Scopus)

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles

Frankel, E. A. & Bevilacqua, P. C., Feb 6 2018, In : Biochemistry. 57, 5, p. 483-488 6 p.

Research output: Contribution to journalReview article

Catalytic RNA
Catalysis
RNA
Protons
Protonation
4 Citations (Scopus)

Engineered control of enzyme structural dynamics and function

Boehr, D. D., D'Amico, R. N. & O'Rourke, K. F., Apr 1 2018, In : Protein Science. 27, 4, p. 825-838 14 p.

Research output: Contribution to journalReview article

Structural dynamics
Enzymes
Catalytic Domain
Protein Engineering
Post Translational Protein Processing
8 Citations (Scopus)

Gas Cluster Ion Beams for Secondary Ion Mass Spectrometry

Winograd, N., Jun 12 2018, In : Annual Review of Analytical Chemistry. 11, p. 29-48 20 p.

Research output: Contribution to journalReview article

Secondary ion mass spectrometry
Ion beams
Gases
Depth profiling
Kinetic energy
3 Citations (Scopus)

Liquid–liquid phase separation in artificial cells

Crowe, C. D. & Keating, C. D., Oct 6 2018, In : Interface Focus. 8, 5

Research output: Contribution to journalReview article

Artificial Cells
Biological Phenomena
Phase separation
Cytoplasm
Large scale systems
6 Citations (Scopus)

Non-equilibrium coupling of protein structure and function to translation–elongation kinetics

Sharma, A. K. & O'Brien, Jr., E. P., Apr 1 2018, In : Current Opinion in Structural Biology. 49, p. 94-103 10 p.

Research output: Contribution to journalReview article

Proteins
Natural Science Disciplines
Messenger RNA
Protein Folding
Physics
12 Citations (Scopus)

Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry

Poudyal, R. R., Pir Cakmak, F., Keating, C. D. & Bevilacqua, P. C., May 1 2018, In : Biochemistry. 57, 17, p. 2509-2519 11 p.

Research output: Contribution to journalReview article

RNA
Liquids
Phase separation
Prebiotics
Biomolecules
11 Citations (Scopus)

Soft chemistry of ion-exchangeable layered metal oxides

Uppuluri, R., Sen Gupta, A., Rosas, A. S. & Mallouk, T. E., Apr 7 2018, In : Chemical Society Reviews. 47, 7, p. 2401-2430 30 p.

Research output: Contribution to journalReview article

Oxides
Metals
Ions
Chemical reactions
Transition metals
2017
12 Citations (Scopus)

Ammonium Additives to Dissolve Lithium Sulfide through Hydrogen Binding for High-Energy Lithium-Sulfur Batteries

Pan, H., Han, K. S., Vijayakumar, M., Xiao, J., Cao, R., Chen, J., Zhang, J., Mueller, K. T., Shao, Y. & Liu, J., Feb 8 2017, In : ACS Applied Materials and Interfaces. 9, 5, p. 4290-4295 6 p.

Research output: Contribution to journalReview article

Ammonium Compounds
Electrolytes
Hydrogen
Lithium
Sulfur
67 Citations (Scopus)

A New View into the Regulation of Purine Metabolism: The Purinosome

Pedley, A. M. & Benkovic, S., Feb 1 2017, In : Trends in Biochemical Sciences. 42, 2, p. 141-154 14 p.

Research output: Contribution to journalReview article

Metabolism
Multienzyme Complexes
Mitochondria
Enzymes
Metabolites
94 Citations (Scopus)

Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions

Okur, H. I., Hladílková, J., Rembert, K. B., Cho, Y., Heyda, J., Dzubiella, J., Cremer, P. S. & Jungwirth, P., Mar 9 2017, In : Journal of Physical Chemistry B. 121, 9, p. 1997-2014 18 p.

Research output: Contribution to journalReview article

Ions
proteins
Proteins
ions
Salts
9 Citations (Scopus)

Biodegradable Polyphosphazene-Based Blends for Regenerative Engineering

Ogueri, K. S., Ivirico, J. L. E., Nair, L. S., Allcock, H. R. & Laurencin, C. T., Mar 1 2017, In : Regenerative Engineering and Translational Medicine. 3, 1, p. 15-31 17 p.

Research output: Contribution to journalReview article

Biocompatible Materials
Biomaterials
Tissue
Polymers
Regeneration
50 Citations (Scopus)

Chemically Propelled Molecules and Machines

Dey, K. K. & Sen, A., Jun 14 2017, In : Journal of the American Chemical Society. 139, 23, p. 7666-7676 11 p.

Research output: Contribution to journalReview article

Biomimetics
Pumps
Molecules
Fluidics
Propulsion
33 Citations (Scopus)

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry

Cremer, P. S., Flood, A. H., Gibb, B. C. & Mobley, D. L., Dec 19 2017, In : Nature Chemistry. 10, 1, p. 8-16 9 p.

Research output: Contribution to journalReview article

Supramolecular chemistry
Water
Biochemistry
Planets
Earth (planet)
16 Citations (Scopus)

Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle

Hedglin, M. & Benkovic, S., Jun 28 2017, In : Chemical Reviews. 117, 12, p. 7857-7877 21 p.

Research output: Contribution to journalReview article

DNA
Damage tolerance
Cells
Cell death
DNA-Directed DNA Polymerase
25 Citations (Scopus)
organelles
Biomolecules
Cells
Liquids
compartments
47 Citations (Scopus)

'Fuelled' motion: Phoretic motility and collective behaviour of active colloids

Illien, P., Golestanian, R. & Sen, A., Sep 21 2017, In : Chemical Society Reviews. 46, 18, p. 5508-5518 11 p.

Research output: Contribution to journalReview article

Colloids
Propulsion
Hydrodynamics
Fabrication
2 Citations (Scopus)

In Silicon Approach for Discovery of Chemopreventive Agents

Wang, J., Li, W., Wang, B., Hu, B., Jiang, H., Lai, B., Li, N. & Cheng, M., Aug 1 2017, In : Current Pharmacology Reports. 3, 4, p. 184-195 12 p.

Research output: Contribution to journalReview article

Drug Design
Disclosure
Silicon
Drug Discovery
Molecular Biology

Our First and Next Decades at ACS Nano

Chan, W. C. W., Chhowalla, M., Glotzer, S., Gogotsi, Y., Hafner, J. H., Hammond, P. T., Hersam, M. C., Javey, A., Kagan, C. R., Kataoka, K., Khademhosseini, A., Kotov, N. A., Lee, S. T., Li, Y., Möhwald, H., Mulvaney, P., Nel, A. E., Nordlander, P. J., Parak, W. J., Penner, R. M. & 7 others, Rogach, A. L., Schaak, R. E., Stevens, M. M., Wee, A. T. S., Willson, C. G., Fernandez, L. E. & Weiss, P. S., Aug 22 2017, In : ACS nano. 11, 8, p. 7553-7555 3 p.

Research output: Contribution to journalReview article

19 Citations (Scopus)

Phase separation in organic aerosol

Freedman, M. A., Dec 21 2017, In : Chemical Society Reviews. 46, 24, p. 7694-7705 12 p.

Research output: Contribution to journalReview article

Aerosols
Phase separation
Liquids
Phase transitions
Efflorescence
7 Citations (Scopus)

Semi-empirical refinements of crystal structures using 17O quadrupolar-coupling tensors

Holmes, S. T., Iuliucci, R. J., Mueller, K. T. & Dybowski, C., Feb 14 2017, In : Journal of Chemical Physics. 146, 6, 064201.

Research output: Contribution to journalReview article

Tensors
Crystal structure
tensors
crystal structure
deviation
6 Citations (Scopus)

Stable Open-Shell Phosphorane Based on a Redox-Active Amidodiphenoxide Scaffold

Pistner, A. J., Moon, H. W., Silakov, A., Yennawar, H. P. & Radosevich, A. T., Aug 7 2017, In : Inorganic Chemistry. 56, 15, p. 8661-8668 8 p.

Research output: Contribution to journalReview article

Phosphoranes
Scaffolds
Phosphorus Compounds
phosphorus compounds
Oxidation
11 Citations (Scopus)

The Effect of Pressure on Organic Reactions in Fluids—a New Theoretical Perspective

Chen, B., Hoffmann, R. & Cammi, R., Jan 1 2017, In : Angewandte Chemie - International Edition. 56, 37, p. 11126-11142 17 p.

Research output: Contribution to journalReview article

Open Access
Cycloaddition
Pulse code modulation
Ethylene
Alkadienes
Cyclopentanes
2 Citations (Scopus)

Understanding DNA replication by the bacteriophage T4 replisome

Benkovic, S. & Spiering, M. M., Jan 1 2017, In : Journal of Biological Chemistry. 292, 45, p. 18434-18442 9 p.

Research output: Contribution to journalReview article

Bacteriophage T4
Bacteriophages
DNA Replication
DNA
Proteins
61 Citations (Scopus)

Water splitting dye-sensitized solar cells

Xu, P., McCool, N. S. & Mallouk, T. E., Jun 1 2017, In : Nano Today. 14, p. 42-58 17 p.

Research output: Contribution to journalReview article

Coloring Agents
Photocathodes
Dyes
Water
Solar Energy
2016
35 Citations (Scopus)

Catalytic Motors-Quo Vadimus?

Dey, K. K., Wong, F., Altemose, A. & Sen, A., Feb 1 2016, In : Current Opinion in Colloid and Interface Science. 21, p. 4-13 10 p.

Research output: Contribution to journalReview article

micromotors
Micromotors
Robotic assembly
directional control
fluidics
61 Citations (Scopus)

Genome-Wide Analysis of RNA Secondary Structure

Bevilacqua, P. C., Ritchey, L. E., Su, Z. & Assmann, S. M., Nov 23 2016, In : Annual Review of Genetics. 50, p. 235-266 32 p.

Research output: Contribution to journalReview article

Genome
RNA
Base Pairing
RNA Splicing
RNA Probes
38 Citations (Scopus)

Synthetic Micro/Nanomotors and Pumps: Fabrication and Applications

Wong, F., Dey, K. K. & Sen, A., Jul 1 2016, In : Annual Review of Materials Research. 46, p. 407-432 26 p.

Research output: Contribution to journalReview article

Pumps
Fabrication
Propulsion
Flow of fluids
Mechanics
2015
15 Citations (Scopus)

A generalized-Yvon-Born-Green method for coarse-grained modeling: Advances, Challenges, and Insight

Rudzinski, J. F. & Noid, W. G., Sep 26 2015, In : European Physical Journal: Special Topics. 224, 12, p. 2193-2216 24 p.

Research output: Contribution to journalReview article

Statistical mechanics
Inverse problems
Peptides
Integral equations
Large scale systems
34 Citations (Scopus)

Auxiliary iron-sulfur cofactors in radical SAM enzymes

Lanz, N. D. & Booker, S. J., Jun 1 2015, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1853, 6, p. 1316-1334 19 p.

Research output: Contribution to journalReview article

Sulfur
Methionine
Iron
Enzymes
Protein S
148 Citations (Scopus)

Chemical conversion pathways for carbohydrates

Chatterjee, C., Pong, F. & Sen, A., Jan 1 2015, In : Green Chemistry. 17, 1, p. 40-71 32 p.

Research output: Contribution to journalReview article

Carbohydrates
carbohydrate
Biomass
Polysaccharides
polysaccharide
8 Citations (Scopus)

Coordinated DNA replication by the bacteriophage T4 replisome

Noble, E., Spiering, M. M. & Benkovic, S., Jun 19 2015, In : Viruses. 7, 6, p. 3186-3200 15 p.

Research output: Contribution to journalReview article

Bacteriophage T4
DNA Replication
Proteins
Holoenzymes
DNA
21 Citations (Scopus)

Imaging mass spectrometry on the nanoscale with cluster ion beams

Winograd, N., Jan 6 2015, In : Analytical Chemistry. 87, 1, p. 328-333 6 p.

Research output: Contribution to journalReview article

Projectiles
Ion beams
Mass spectrometry
Imaging techniques
Secondary ion mass spectrometry
120 Citations (Scopus)

Infrared fibers

Tao, G., Ebendorff-Heidepriem, H., Stolyarov, A. M., Danto, S., Badding, J. V., Fink, Y., Ballato, J. & Abouraddy, A. F., Jun 30 2015, In : Advances in Optics and Photonics. 7, 2, p. 379-458 80 p.

Research output: Contribution to journalReview article

fibers
electrical engineering
fabrication
materials science
infrared spectra
71 Citations (Scopus)

Mechanistic diversity of radical S-adenosylmethionine (SAM)-dependent methylation

Bauerle, M. R., Schwalm, E. L. & Booker, S. J., Feb 13 2015, In : Journal of Biological Chemistry. 290, 7, p. 3995-4002 8 p.

Research output: Contribution to journalReview article

S-Adenosylmethionine
Methylation
Carbon
Atoms
Enzymes
36 Citations (Scopus)

Mössbauer spectroscopy of Fe/S proteins

Pandelia, M. E., Lanz, N. D., Booker, S. J. & Krebs, C., Jun 1 2015, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1853, 6, p. 1395-1405 11 p.

Research output: Contribution to journalReview article

Protein S
Spectrum Analysis
Hydrogenase
Electron Spin Resonance Spectroscopy
Sulfur
65 Citations (Scopus)

Perspectives on electrostatics and conformational motions in enzyme catalysis

Hanoian, P., Liu, C. T., Hammes-Schiffer, S. & Benkovic, S., Jan 1 2015, In : Accounts of Chemical Research. 48, 2, p. 482-489 8 p.

Research output: Contribution to journalReview article

Catalysis
Electrostatics
Tetrahydrofolate Dehydrogenase
Hydrides
Enzymes
19 Citations (Scopus)

Potential Sites for Ice Nucleation on Aluminosilicate Clay Minerals and Related Materials

Freedman, M. A., Oct 1 2015, In : Journal of Physical Chemistry Letters. 6, 19, p. 3850-3858 9 p.

Research output: Contribution to journalReview article

Aluminosilicates
Ice
Clay minerals
clays
ice
810 Citations (Scopus)

Recent Advances in Two-Dimensional Materials beyond Graphene

Bhimanapati, G. R., Lin, Z., Meunier, V., Jung, Y., Cha, J., Das, S., Xiao, D., Son, Y., Strano, M. S., Cooper, V. R., Liang, L., Louie, S. G., Ringe, E., Zhou, W., Kim, S. S., Naik, R. R., Sumpter, B. G., Terrones, H., Xia, F., Wang, Y. & 7 others, Zhu, J., Akinwande, D., Alem, N., Schuller, J. A., Schaak, R. E., Terrones Maldonado, M. & Robinson, J. A., Nov 6 2015, In : ACS Nano. 9, 12, p. 11509-11539 31 p.

Research output: Contribution to journalReview article

Graphite
Graphene
graphene
transition metals
Transition metals
59 Citations (Scopus)

Synthetic Nano- and Micromachines in Analytical Chemistry: Sensing, Migration, Capture, Delivery, and Separation

Duan, W., Wang, W., Das, S., Yadav, V., Mallouk, T. E. & Sen, A., Jul 22 2015, In : Annual Review of Analytical Chemistry. 8, p. 311-333 23 p.

Research output: Contribution to journalReview article

Micromotors
Chemical analysis
Flow of fluids
Pumps
63 Citations (Scopus)

The RNA structurome: Transcriptome-wide structure probing with next-generation sequencing

Kwok, C. K., Tang, Y., Assmann, S. M. & Bevilacqua, P. C., Jan 1 2015, In : Trends in Biochemical Sciences. 40, 4, p. 221-232 12 p.

Research output: Contribution to journalReview article

Transcriptome
RNA
Cells
Polyadenylation
Physiology
2014
26 Citations (Scopus)

Amplified responses in materials using linear polymers that depolymerize from end-to-end when exposed to specific stimuli

Phillips, S. T., Robbins, J. S., Dilauro, A. M. & Olah, M. G., Oct 5 2014, In : Journal of Applied Polymer Science. 131, 19, 40992.

Research output: Contribution to journalReview article

Polymers
Depolymerization
Molecules
Intelligent materials
Surface properties
60 Citations (Scopus)

Continuous head-to-tail depolymerization: An emerging concept for imparting amplified responses to stimuli-responsive materials

Phillips, S. T. & Dilauro, A. M., Apr 15 2014, In : ACS Macro Letters. 3, 4, p. 298-304 7 p.

Research output: Contribution to journalReview article

Depolymerization
Polymers
Innovation
5 Citations (Scopus)

Targeting structural dynamics of the RNA-dependent RNA polymerase for anti-viral strategies

Boehr, D. D., Liu, X. & Yang, X., Jan 1 2014, In : Current Opinion in Virology. 9, p. 194-200 7 p.

Research output: Contribution to journalReview article

RNA Replicase
Viruses
Attenuated Vaccines
Drug Design
RNA Viruses
20 Citations (Scopus)

The expanding role of paper in point-of-care diagnostics

Phillips, S. T. & Lewis, G. G., Mar 1 2014, In : Expert Review of Molecular Diagnostics. 14, 2, p. 123-125 3 p.

Research output: Contribution to journalReview article

Point-of-Care Systems
Costs and Cost Analysis
51 Citations (Scopus)

The unique chemistry of benzoxaboroles: Current and emerging applications in biotechnology and therapeutic treatments

Liu, C. T., Tomsho, J. W. & Benkovic, S., Aug 15 2014, In : Bioorganic and Medicinal Chemistry. 22, 16, p. 4462-4473 12 p.

Research output: Contribution to journalReview article

Biotechnology
Acyclic Acids
Boronic Acids
Chemical reactivity
Materials science
2013
157 Citations (Scopus)

An international initiative on long-term behavior of high-level nuclear waste glass

Gin, S., Abdelouas, A., Criscenti, L. J., Ebert, W. L., Ferrand, K., Geisler, T., Harrison, M. T., Inagaki, Y., Mitsui, S., Mueller, K. T., Marra, J. C., Pantano, C. G., Pierce, E. M., Ryan, J. V., Schofield, J. M., Steefel, C. I. & Vienna, J. D., Jan 1 2013, In : Materials Today. 16, 6, p. 243-248 6 p.

Research output: Contribution to journalReview article

Radioactive Waste
radioactive wastes
Radioactive wastes
Radioactive waste vitrification
vitrification
345 Citations (Scopus)

Design and development of photoanodes for water-splitting dye-sensitized photoelectrochemical cells

Swierk, J. R. & Mallouk, T. E., Mar 21 2013, In : Chemical Society Reviews. 42, 6, p. 2357-2387 31 p.

Research output: Contribution to journalReview article

Photoelectrochemical cells
Coloring Agents
Water
Oxidation
Catalysts