Institution
Pacific Northwest National Laboratory
Facility•Richland, Washington, United States•
About: Pacific Northwest National Laboratory is a facility organization based out in Richland, Washington, United States. It is known for research contribution in the topics: Catalysis & Aerosol. The organization has 11581 authors who have published 27934 publications receiving 1120489 citations. The organization is also known as: PNL & PNNL.
Topics: Catalysis, Aerosol, Mass spectrometry, Ion, Adsorption
Papers published on a yearly basis
Papers
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Sandia National Laboratories1, Chevron Corporation2, National Institute of Standards and Technology3, Oak Ridge National Laboratory4, Natural Resources Canada5, Pacific Northwest National Laboratory6, Marathon Oil7, Lawrence Livermore National Laboratory8, National Renewable Energy Laboratory9, Philips10
TL;DR: In this article, a novel approach was developed to formulate surrogate fuels having characteristics that are representative of diesel fuels produced from real-world refinery streams, which can provide a better understanding of fundamental fuel-composition and property effects on combustion and emissions-formation processes in internal-combustion engines.
Abstract: In this study, a novel approach was developed to formulate surrogate fuels having characteristics that are representative of diesel fuels produced from real-world refinery streams. Because diesel fuels typically consist of hundreds of compounds, it is difficult to conclusively determine the effects of fuel composition on combustion properties. Surrogate fuels, being simpler representations of these practical fuels, are of interest because they can provide a better understanding of fundamental fuel-composition and property effects on combustion and emissions-formation processes in internal-combustion engines. In addition, the application of surrogate fuels in numerical simulations with accurate vaporization, mixing, and combustion models could revolutionize future engine designs by enabling computational optimization for evolving real fuels. Dependable computational design would not only improve engine function, it would do so at significant cost savings relative to current optimization strategies that rel...
241 citations
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TL;DR: The Dynameomics database is used, a repository of high‐quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles and concludes that for DSS/BS3, a distance constraint of 26–30 Å between Cα atoms is appropriate.
Abstract: Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 A long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 A apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 A is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS3, a distance constraint of 26–30 A between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods.
241 citations
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Clemson University1, Cornell University2, Pacific Northwest National Laboratory3, Universidade Nova de Lisboa4, Washington University in St. Louis5, University College Dublin6, University of Copenhagen7, University of Oklahoma8, University of Manchester9, University of California, San Diego10, OpenEye Scientific Software11
TL;DR: This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics.
Abstract: The pK(a) -cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pK(a) values and protein electrostatics in general. The first round of the pK(a) -cooperative, which challenged computational labs to carry out blind predictions against pK(a) s experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6-10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics. Here, we briefly outline existing approaches for pK(a) calculations, emphasizing methods that were used by the participants in calculating the blind pK(a) values in the first round of the cooperative. We then point out some of the difficulties encountered by the participating groups in making their blind predictions, and finally try to provide some insights for future developments aimed at improving the accuracy of pK(a) calculations.
241 citations
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TL;DR: In this paper, a HRTEM study of several diesel soot samples collected on Diesel Particulate Filters (DPF) under conditions relevant to practical applications of DPF technology, revealed nano-structure, to the best of our knowledge, not reported previously for diesel soots.
240 citations
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TL;DR: In this article, first-principle density functional theory (DFT) calculations were used to construct an intrinsic kinetic database that was used in a variable time step kinetic Monte Carlo simulation to follow the kinetics and the molecular transformations in the selective hydrogenation of acetylene-ethylene feeds over Pd and Pd-Ag surfaces.
240 citations
Authors
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Name | H-index | Papers | Citations |
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Yi Cui | 220 | 1015 | 199725 |
Derek R. Lovley | 168 | 582 | 95315 |
Xiaoyuan Chen | 149 | 994 | 89870 |
Richard D. Smith | 140 | 1180 | 79758 |
Taeghwan Hyeon | 139 | 563 | 75814 |
Jun Liu | 138 | 616 | 77099 |
Federico Capasso | 134 | 1189 | 76957 |
Jillian F. Banfield | 127 | 562 | 60687 |
Mary M. Horowitz | 127 | 557 | 56539 |
Frederick R. Appelbaum | 127 | 677 | 66632 |
Matthew Jones | 125 | 1161 | 96909 |
Rainer Storb | 123 | 905 | 58780 |
Zhifeng Ren | 122 | 695 | 71212 |
Wei Chen | 122 | 1946 | 89460 |
Thomas E. Mallouk | 122 | 549 | 52593 |