Institute for Sustainability, Energy, and Environment

Research Output 1987 2018

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Review article
2018

Alley cropping: Global patterns of species composition and function

Wolz, K. J. & DeLucia, E. H. Jan 15 2018 In : Agriculture, Ecosystems and Environment. 252, p. 61-68 8 p.

Research output: Research - peer-reviewReview article

alley cropping
species diversity
crop
crops
Populus
2017

A conundrum for density functional theory: DFT studies may sometimes get the right results for the wrong reasons

Hammes-Schiffer, S. Jan 6 2017 In : Science. 355, 6320, p. 28-29 2 p.

Research output: Research - peer-reviewReview article

Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids

Yu, Y., Cui, C., Wang, J. & Lu, Y. Feb 1 2017 In : Science China Chemistry. 60, 2, p. 188-200 13 p.

Research output: Research - peer-reviewReview article

Metalloproteins
Amino Acids
Azurin
Ribonucleotide Reductases
Catalysts

Catalysts by design: The power of theory

Hammes-Schiffer, S. 2017 In : Accounts of Chemical Research. 50, 3, p. 561-566 6 p.

Research output: Research - peer-reviewReview article

Catalysts
Electrocatalysts
Photocatalysts

DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells

McGhee, C. E., Loh, K. Y. & Lu, Y. Jun 1 2017 In : Current Opinion in Biotechnology. 45, p. 191-201 11 p.

Research output: Research - peer-reviewReview article

Metal ions
Cells
Imaging techniques
Sensors
Catalytic DNA

Functional carbon nanodots for multiscale imaging and therapy

Ostadhossein, F. & Pan, D. May 1 2017 In : Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology. 9, 3, e1436

Research output: Research - peer-reviewReview article

Imaging techniques
Carbon
Therapeutics
Biocompatibility
Nanostructured materials

Potential of global croplands and bioenergy crops for climate change mitigation through deployment for enhanced weathering

Kantola, I. B., Masters, M. D., Beerling, D. J., Long, S. P. & DeLucia, E. H. Apr 1 2017 In : Biology Letters. 13, 4, 0714

Research output: Research - peer-reviewReview article

energy crops
weathering
climate change
cropland
Climate Change

Public finance in a nutshell: A Cobb Douglas teaching tool for general equilibrium tax incidence and excess burden

Fullerton, D. & Ta, C. L. Mar 1 2017 In : National Tax Journal. 70, 1, p. 155-170 16 p.

Research output: Research - peer-reviewReview article

General equilibrium
Cobb-Douglas
Excess burden
Tax incidence
Public finance

Recent advances in DNAzyme-based gene silencing

Fan, H., Zhang, X. & Lu, Y. May 1 2017 In : Science China Chemistry. 60, 5, p. 591-601 11 p.

Research output: Research - peer-reviewReview article

Genes
RNA
DNA
Phosphorylation
Single-Stranded DNA

Rooting for cassava: insights into photosynthesis and associated physiology as a route to improve yield potential

De Souza, A. P., Massenburg, L. N., Jaiswal, D., Cheng, S., Shekar, R. & Long, S. P. Jan 1 2017 In : New Phytologist. 213, 1, p. 50-65 16 p.

Research output: Research - peer-reviewReview article

cassava
rooting
physiology
photosynthesis
Manihot

The "ok, molly" chemistry

Lu, Y. 2017 In : Accounts of Chemical Research. 50, 3, p. 647-651 5 p.

Research output: Research - peer-reviewReview article

2016

Biochemical and biophysical understanding of metal ion selectivity of DNAzymes

Hwang, K., Hosseinzadeh, P. & Lu, Y. 2016 In : Inorganica Chimica Acta. 452, p. 12-24 13 p.

Research output: Research - peer-reviewReview article

Metal ions
Structural properties
Metals
metal ions
selectivity

Contact-facilitated drug delivery with Sn2 lipase labile prodrugs optimize targeted lipid nanoparticle drug delivery

Pan, D., Pham, C. T. N., Weilbaecher, K. N., Tomasson, M. H., Wickline, S. A. & Lanza, G. M. Jan 1 2016 In : Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology. 8, 1, p. 85-106 22 p.

Research output: Research - peer-reviewReview article

Medical nanotechnology
Prodrugs
Lipase
Drug delivery
Phospholipids

Design and engineering of artificial oxygen-activating metalloenzymes

Nastri, F., Chino, M., Maglio, O., Bhagi-Damodaran, A., Lu, Y. & Lombardi, A. Sep 21 2016 In : Chemical Society Reviews. 45, 18, p. 5020-5054 35 p.

Research output: Research - peer-reviewReview article

Oxygen
Metals
Proteins

Experimental and Computational Mechanistic Studies Guiding the Rational Design of Molecular Electrocatalysts for Production and Oxidation of Hydrogen

Raugei, S., Helm, M. L., Hammes-Schiffer, S., Appel, A. M., O'Hagan, M., Wiedner, E. S. & Bullock, R. M. Jan 19 2016 In : Inorganic Chemistry. 55, 2, p. 445-460 16 p.

Research output: Research - peer-reviewReview article

electrocatalysts
oxidation
protons
hydrogen
Electrocatalysts

Fluorescent nanoprobes for sensing and imaging of metal ions: Recent advances and future perspectives

Zhang, J. J., Cheng, F. F., Li, J. J., Zhu, J. J. & Lu, Y. Jun 1 2016 In : Nano Today. 11, 3, p. 309-329 21 p.

Research output: Research - peer-reviewReview article

Nanoprobes
Nanostructured materials
Metal ions
Imaging techniques
Nanostructures

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

Schilter, D., Camara, J. M., Huynh, M. T., Hammes-Schiffer, S. & Rauchfuss, T. B. Aug 10 2016 In : Chemical Reviews. 116, 15, p. 8693-8749 57 p.

Research output: Research - peer-reviewReview article

Hydrides
Metals
Hydrogen
Bearings (structural)
Protonation
molecular spectroscopy
cavities
expansion
Molecular spectroscopy
molecular ions

Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active Site

Chambers, G. M., Huynh, M. T., Li, Y., Hammes-Schiffer, S., Rauchfuss, T. B., Reijerse, E. & Lubitz, W. Jan 19 2016 In : Inorganic Chemistry. 55, 2, p. 419-431 13 p.

Research output: Research - peer-reviewReview article

International System of Units
methylidyne
Carbon Monoxide
nickel-iron hydrogenase
enzymes

Plants in silico: Why, why now and what?-an integrative platform for plant systems biology research

Zhu, X. G., Lynch, J. P., Lebauer, D. S., Millar, A. J., Stitt, M. & Long, S. P. May 1 2016 In : Plant Cell and Environment. 39, 5, p. 1049-1057 9 p.

Research output: Research - peer-reviewReview article

Systems Biology
Computer Simulation
Research
Biological Sciences
Ecosystem

Recent developments of liposomes as nanocarriers for theranostic applications

Xing, H., Hwang, K. & Lu, Y. 2016 In : Theranostics. 6, 9, p. 1336-1352 17 p.

Research output: Research - peer-reviewReview article

Liposomes
Theranostic Nanomedicine
Therapeutics
Lipid Bilayers
Genetic Therapy

Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities

Bhagi-Damodaran, A., Petrik, I. & Lu, Y. Oct 1 2016 In : Israel Journal of Chemistry. 56, 9-10, p. 773-790 18 p.

Research output: Research - peer-reviewReview article

Myoglobin
copper oxidase
nitric-oxide reductase
Nitrous Oxide
Hydrogen bonds
2015

Nanomaterial-based biosensors using dual transducing elements for solution phase detection

Li, N., Su, X. & Lu, Y. May 7 2015 In : Analyst. 140, 9, p. 2916-2943 28 p.

Research output: Research - peer-reviewReview article

Nanostructured materials
Biosensors
Nanostructures
Biosensing Techniques
transducer

Perspectives on electrostatics and conformational motions in enzyme catalysis

Hanoian, P., Liu, C. T., Hammes-Schiffer, S. & Benkovic, S. Feb 17 2015 In : Accounts of Chemical Research. 48, 2, p. 482-489 8 p.

Research output: Research - peer-reviewReview article

Static Electricity
Catalysis
Enzymes
Tetrahydrofolate Dehydrogenase
Hydrides

Redesigning photosynthesis to sustainably meet global food and bioenergy demand

Ort, D. R. , Merchant, S. S. , Alric, J. , Barkan, A. , Blankenship, R. E. , Bock, R. , Croce, R. , Hanson, M. R. , Hibberd, J. M. , Long, S. P. , Moore, T. A. , Moroney, J. , Niyogi, K. K. , Parry, M. A. J. , Peralta-Yahya, P. P. , Prince, R. C. , Redding, K. E. , Spalding, M. H. , Van Wijk, K. J. , Vermaas, W. F. J. & 5 others Von Caemmerer, S., Weber, A. P. M., Yeates, T. O., Yuan, J. S. & Zhu, X. G. Jul 14 2015 In : Proceedings of the National Academy of Sciences of the United States of America. 112, 28, p. 8529-8536 8 p.

Research output: Research - peer-reviewReview article

Photosynthesis
Food
Synthetic Biology
Biofuels
Population Growth
Crassulacean acid metabolism
agriculture
cells
Acids
economic sustainability

Waterborne Viruses: A Barrier to Safe Drinking Water

Gall, A. M., Mariñas, B. J., Lu, Y. & Shisler, J. L. Jun 1 2015 In : PLoS Pathogens. 11, 6, e1004867

Research output: Research - peer-reviewReview article

2014

A meta-analysis of soil organic matter response to soil management practices: An approach to evaluate conservation indicators

Ugarte, C. M., Kwon, H., Andrews, S. S. & Wander, M. M. Sep 1 2014 In : Journal of Soil and Water Conservation. 69, 5, p. 422-430 9 p.

Research output: Research - peer-reviewReview article

meta-analysis
soil management
soil organic matter
management practice
indicator

DNA as sensors and imaging agents for metal ions

Xiang, Y. & Lu, Y. Feb 17 2014 In : Inorganic Chemistry. 53, 4, p. 1925-1942 18 p.

Research output: Research - peer-reviewReview article

metal ions
deoxyribonucleic acid
sensors
Metal ions
DNA

Energy positive domestic wastewater treatment: The roles of anaerobic and phototrophic technologies

Shoener, B. D., Bradley, I. M., Cusick, R. D. & Guest, J. S. 2014 In : Environmental Sciences: Processes and Impacts. 16, 6, p. 1204-1222 19 p.

Research output: Research - peer-reviewReview article

energy
wastewater treatment
Wastewater treatment
Waste Water
Technology

Functional DNA nanomaterials for sensing and imaging in living cells

Torabi, S. F. & Lu, Y. Aug 2014 In : Current Opinion in Biotechnology. 28, p. 88-95 8 p.

Research output: Research - peer-reviewReview article

Nanostructured materials
Cells
Imaging techniques
DNA
Nanostructures

Functional tuning and expanding of myoglobin by rational protein design

Lin, Y., Wang, J. & Lu, Y. 2014 In : Science China Chemistry. 57, 3, p. 346-355 10 p.

Research output: Research - peer-reviewReview article

Myoglobin
Tuning
Proteins
Metalloproteins
Nitrite Reductases

Hydrogen tunneling in enzymes and biomimetic models

Layfield, J. P. & Hammes-Schiffer, S. Apr 9 2014 In : Chemical Reviews. 114, 7, p. 3466-3494 29 p.

Research output: Research - peer-reviewReview article

Biomimetics
Hydrogen
Enzymes
Physical Phenomena
Protons

Metalloenzyme design and engineering through strategic modifications of native protein scaffolds

Petrik, I. D., Liu, J. & Lu, Y. Apr 2014 In : Current Opinion in Chemical Biology. 19, 1, p. 67-75 9 p.

Research output: Research - peer-reviewReview article

Proteins
Scaffolds
Protein Engineering
Catalysis
Catalytic Domain

Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers

Liu, J., Chakraborty, S., Hosseinzadeh, P., Yu, Y., Tian, S., Petrik, I., Bhagi, A. & Lu, Y. Apr 23 2014 In : Chemical Reviews. 114, 8, p. 4366-4369 4 p.

Research output: Research - peer-reviewReview article

Metalloproteins
Cytochromes
Sulfur
Copper
Iron

Permaculture for agroecology: Design, movement, practice, and worldview. A review

Ferguson, R. S. & Lovell, S. T. 2014 In : Agronomy for Sustainable Development. 34, 2, p. 251-274 24 p.

Research output: Research - peer-reviewReview article

permaculture
agroecology
systems engineering
Sustainable development
integrated agricultural systems

Urban home food gardens in the Global North: Research traditions and future directions

Taylor, J. R. & Lovell, S. T. 2014 In : Agriculture and Human Values. 31, 2, p. 285-305 21 p.

Research output: Research - peer-reviewReview article

gardens
foods
home gardens
community gardens
urban agriculture
2013

Altered dynamics of forest recovery under a changing climate

Anderson-Teixeira, K. J., Miller, A. D., Mohan, J. E., Hudiburg, T. W., Duval, B. D. & DeLucia, E. H. Jul 2013 In : Global Change Biology. 19, 7, p. 2001-2021 21 p.

Research output: Research - peer-reviewReview article

Recovery
climate
Carbon Monoxide
Climate change
Ecosystems

An emerging understanding of mechanisms governing insect herbivory under elevated CO2

Zavala, J. A., Nabity, P. D. & DeLucia, E. H. Jan 7 2013 In : Annual Review of Entomology. 58, p. 79-97 19 p.

Research output: Research - peer-reviewReview article

herbivores
insects
herbivory
insect
chemistry

Cosmic-ray astrochemistry

Indriolo, N. & McCall, B. J. Oct 17 2013 In : Chemical Society Reviews. 42, 19, p. 7763-7773 11 p.

Research output: Research - peer-reviewReview article

Cosmic rays
Ionization
Gases
Gamma rays
Ions

CyberGIS software: A synthetic review and integration roadmap

Wang, S., Anselin, L., Bhaduri, B., Crosby, C., Goodchild, M. F., Liu, Y. & Nyerges, T. L. Nov 2013 In : International Journal of Geographical Information Science. 27, 11, p. 2122-2145 24 p.

Research output: Research - peer-reviewReview article

software
geographic information system
science
Geographic information systems
spatial analysis

Life cycle assessment applied to wastewater treatment: State of the art

Corominas, L., Foley, J., Guest, J. S., Hospido, A., Larsen, H. F., Morera, S. & Shaw, A. Oct 1 2013 In : Water Research. 47, 15, p. 5480-5492 13 p.

Research output: Research - peer-reviewReview article

life cycle
state of the art
wastewater treatment
methodology
decision

Toward cool C4 crops

Long, S. P. & Spence, A. K. Apr 2013 In : Annual Review of Plant Biology. 64, p. 701-722 22 p.

Research output: Research - peer-reviewReview article

Zea mays
crops
Photosynthesis
Climate
Nitrogen
Azurin
Copper
Amino Acids
Proteins
Microbiology
2012

Accelerating yield potential in soybean: Potential targets for biotechnological improvement

Ainsworth, E. A., Yendrek, C. R., Skoneczka, J. A. & Long, S. P. Jan 2012 In : Plant, Cell and Environment. 35, 1, p. 38-52 15 p.

Research output: Research - peer-reviewReview article

soybeans
Soybeans
carbon
Carbon
abortion (plants)

DNA aptamer functionalized nanomaterials for intracellular analysis, cancer cell imaging and drug delivery

Xing, H., Wong, N. Y., Xiang, Y. & Lu, Y. Aug 2012 In : Current Opinion in Chemical Biology. 16, 3-4, p. 429-435 7 p.

Research output: Research - peer-reviewReview article

Harvesting Carbon from Eastern US Forests: Opportunities and: Impacts of an Expanding Bioenergy Industry

Davis, S. C., Dietze, M., DeLucia, E., Field, C., Loarie, S., Hamburg, S. P., Parton, W., Potts, M., Ramage, B., Wang, D., Youngs, H. & Long, S. P. 2012 In : Forests. 3, 2, p. 370-397 28 p.

Research output: Research - peer-reviewReview article

bioenergy
industry
carbon
biomass
bioenergy industry

Measuring indirect land use change with biofuels: Implications for policy

Khanna, M. & Crago, C. L. Aug 2012 In : Annual Review of Resource Economics. 4, p. 161-184 24 p.

Research output: Research - peer-reviewReview article

Biofuels
Land use change
Influence factors
Price transmission
Land use

Mitigating land loss in coastal Louisiana by controlled diversion of Mississippi River sand

Nittrouer, J. A., Best, J. L., Brantley, C., Cash, R. W., Czapiga, M., Kumar, P. & Parker, G. Aug 2012 In : Nature Geoscience. 5, 8, p. 534-537 4 p.

Research output: Research - peer-reviewReview article

sand
river
land
loss
spillway

Storage ring measurements of the dissociative recombination of H 3 +

Kreckel, H., Petrignani, A., Novotny, O., Crabtree, K., Buhr, H., McCall, B. J. & Wolf, A. Nov 13 2012 In : Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 370, 1978, p. 5088-5100 13 p.

Research output: Research - peer-reviewReview article

Recombination
Ring
Storage rings
coefficients
Coefficient