scispace - formally typeset
Search or ask a question
Institution

United States Department of Energy

GovernmentWashington D.C., District of Columbia, United States
About: United States Department of Energy is a government organization based out in Washington D.C., District of Columbia, United States. It is known for research contribution in the topics: Coal & Catalysis. The organization has 13656 authors who have published 14177 publications receiving 556962 citations. The organization is also known as: DOE & Department of Energy.
Topics: Coal, Catalysis, Combustion, Oxide, Hydrogen


Papers
More filters
Journal ArticleDOI
TL;DR: A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid-solid transformations involving both atomic and unit-cell degrees of freedom and it is demonstrated that the method is robust for mechanisms dominated either by atomic motion or by unit- cell deformation.
Abstract: A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid–solid transformations involving both atomic and unit-cell degrees of freedom. We combine atomic and cell degrees of freedom into a unified description of the crystal structure so that calculated reaction paths are insensitive to the choice of periodic cell. For the rock-salt to wurtzite transition in CdSe, we demonstrate that the method is robust for mechanisms dominated either by atomic motion or by unit-cell deformation; notably, the lowest-energy transition mechanism found by our G-SSNEB changes with cell size from a concerted transformation of the cell coordinates in small cells to a nucleation event in large cells. The method is efficient and can be applied to systems in which the force and stress tensor are calculated using density functional theory.

687 citations

Journal ArticleDOI
Alexander Andrew Myburg1, Dario Grattapaglia2, Dario Grattapaglia3, Gerald A. Tuskan4, Gerald A. Tuskan5, Uffe Hellsten5, Richard D. Hayes5, Jane Grimwood6, Jerry Jenkins6, Erika Lindquist5, Hope Tice5, Diane Bauer5, David Goodstein5, Inna Dubchak5, Alexandre Poliakov5, Eshchar Mizrachi1, Anand Raj Kumar Kullan1, Steven G. Hussey1, Desre Pinard1, Karen Van der Merwe1, Pooja Singh1, Ida Van Jaarsveld1, Orzenil B. Silva-Junior3, Roberto C. Togawa3, Marília de Castro Rodrigues Pappas3, Danielle A. Faria3, Carolina Sansaloni3, Cesar Petroli3, Xiaohan Yang4, Priya Ranjan4, Timothy J. Tschaplinski4, Chu-Yu Ye4, Ting Li4, Lieven Sterck7, Kevin Vanneste7, Florent Murat8, Marçal Soler9, Hélène San Clemente9, Naijib Saidi9, Hua Cassan-Wang9, Christophe Dunand9, Charles A. Hefer10, Charles A. Hefer1, Erich Bornberg-Bauer11, Anna R. Kersting11, Anna R. Kersting12, Kelly J. Vining13, Vindhya Amarasinghe13, Martin Ranik13, Sushma Naithani13, Justin Elser13, Alexander Boyd13, Aaron Liston13, Joseph W. Spatafora13, Palitha Dharmwardhana13, Rajani Raja13, Christopher M. Sullivan13, Elisson Romanel14, Elisson Romanel15, Marcio Alves-Ferreira14, Carsten Külheim16, William J. Foley16, Victor Carocha, Jorge A. P. Paiva17, David Kudrna18, Sérgio Hermínio Brommonschenkel19, Giancarlo Pasquali20, Margaret Byrne, Philippe Rigault, Josquin Tibbits21, Antanas V. Spokevicius22, Rebecca C. Jones23, Dorothy A. Steane23, Dorothy A. Steane24, René E. Vaillancourt23, Brad M. Potts23, Fourie Joubert1, Kerrie Barry5, Georgios J. Pappas25, Steven H. Strauss13, Pankaj Jaiswal13, Jacqueline Grima-Pettenati9, Jérôme Salse8, Yves Van de Peer7, Yves Van de Peer1, Daniel S. Rokhsar5, Jeremy Schmutz5, Jeremy Schmutz6 
19 Jun 2014-Nature
TL;DR: Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes, which shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils.
Abstract: Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

679 citations

Journal ArticleDOI
17 Oct 2003-Science
TL;DR: One category of functional sequences postulated to lie in gene deserts is gene regulatory sequences, which are related to transcriptional regulation and regulation of transcriptional reprograming.
Abstract: Approximately 25% of the genome consists of gene-poor regions greater than 500 kb, termed gene deserts ([ 1 ][1]). These segments have been minimally explored, and their functional significance remains elusive. One category of functional sequences postulated to lie in gene deserts is gene regulatory

644 citations

Journal ArticleDOI
TL;DR: This work compares the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and relates the genomic features to trophic strategy for these organisms and defines their molecular mechanisms of adaptation.
Abstract: Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.

642 citations

Journal ArticleDOI
05 Jun 2003-Nature
TL;DR: This experimental verification of negative refraction of electromagnetic waves in a two-dimensional dielectric photonic crystal that has a periodically modulated positive permittivity and a permeability of unity is demonstrated.
Abstract: Materials that can bend light in the opposite direction to normal ('left-handed' materials) reverse the way in which refraction usually works — this negative refractive index is due to simultaneously negative permeability and permittivity1,2,3. Here we demonstrate negative refraction of electromagnetic waves in a two-dimensional dielectric photonic crystal that has a periodically modulated positive permittivity and a permeability of unity4,5,6. This experimental verification of negative refraction is a step towards the realization of a 'superlens' that will be able to focus features smaller than the wavelength of light.

635 citations


Authors

Showing all 13660 results

NameH-indexPapersCitations
Martin White1962038232387
Paul G. Richardson1831533155912
Jie Zhang1784857221720
Krzysztof Matyjaszewski1691431128585
Yang Gao1682047146301
David Eisenberg156697112460
Marvin Johnson1491827119520
Carlos Escobar148118495346
Joshua A. Frieman144609109562
Paul Jackson141137293464
Greg Landsberg1411709109814
J. Conway1401692105213
Pushpalatha C Bhat1391587105044
Julian Borrill139387102906
Cecilia Elena Gerber1381727106984
Network Information
Related Institutions (5)
Lawrence Berkeley National Laboratory
66.5K papers, 4.1M citations

92% related

École Polytechnique Fédérale de Lausanne
98.2K papers, 4.3M citations

90% related

Centre national de la recherche scientifique
382.4K papers, 13.6M citations

89% related

ETH Zurich
122.4K papers, 5.1M citations

88% related

Texas A&M University
164.3K papers, 5.7M citations

88% related

Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20233
202223
2021633
2020601
2019654
2018598