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Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov
<span title="2013-06-04">2013</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/72zcmi3smndcrdvxgve7ny6ytq" style="color: black;">Journal of Computational Chemistry</a> </i> &nbsp;
Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960-6.) to include parallelization of the molecular surface and energy  ...  Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules  ...  Barry Honig for the continuous support. The authors thank Shannon Stefl for proofreading the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.23340">doi:10.1002/jcc.23340</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23733490">pmid:23733490</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3707979/">pmcid:PMC3707979</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/soe27vfp5zf7rl4vz6pkbmqnb4">fatcat:soe27vfp5zf7rl4vz6pkbmqnb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922213507/http://tigerprints.clemson.edu/cgi/viewcontent.cgi?article=1403&amp;context=physastro_pubs" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/61/b26155fd801562a9816d74adcd6852585843df34.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.23340"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707979" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Energy and wavelength scaling of shock-ignited inertial fusion targets

S Atzeni, A Marocchino, A Schiavi, G Schurtz
<span title="2013-04-09">2013</span> <i title="IOP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bt7vbjky6zbevclechrlkkahae" style="color: black;">New Journal of Physics</a> </i> &nbsp;
From density functional calculations we find that the low-T magnetic phase is paraelectric and the intermediate magnetic phase ferroelectric, with a size and direction of polarization in good agreement  ...  By mapping the ab-intio result into an effective spin model we show that the system has a manifold of almost degenerate ground states.  ...  We adopt a combination of molecular dynamics and electronic structure calculations to explain the observed properties of polymer/metaloxide interfaces [2,3] in presence of specific molecular interlayers  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/1367-2630/15/4/045004">doi:10.1088/1367-2630/15/4/045004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c4lh6z3uavbktgx4didzjqxoiy">fatcat:c4lh6z3uavbktgx4didzjqxoiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429065330/https://www.fisi.polimi.it/sites/default/files/allegati/FisMat2013%20-%20Book%20of%20Abstracts.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/1367-2630/15/4/045004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> iop.org </button> </a>

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

Jay L. Banks, Hege S. Beard, Yixiang Cao, Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp (+6 others)
<span title="">2005</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/72zcmi3smndcrdvxgve7ny6ytq" style="color: black;">Journal of Computational Chemistry</a> </i> &nbsp;
objectives with respect to sampling and the energy function.  ...  With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields,  ...  The current fixed charge force field model implemented in IMPACT has its origins in the OPLS-AA force field of William Jorgensen and coworkers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.20292">doi:10.1002/jcc.20292</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16211539">pmid:16211539</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2742605/">pmcid:PMC2742605</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rowys6f4grbxzkwttkonhvpqza">fatcat:rowys6f4grbxzkwttkonhvpqza</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110401053830/http://www.columbia.edu/cu/chemistry/groups/berne/papers/jcc_26_1752_2005.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/f4/c8f425923da21fc41bee0b3d0f2657212403c56e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.20292"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742605" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Treatment of geometric singularities in implicit solvent models

Sining Yu, Weihua Geng, G. W. Wei
<span title="2007-06-28">2007</span> <i title="AIP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hnc5ddfunnd3taca63uf5ggldm" style="color: black;">Journal of Chemical Physics</a> </i> &nbsp;
The MIBPB-II solver is extensively validated by the molecular surfaces of few-atom systems and a set of 24 proteins.  ...  Geometric singularities, such as cusps and self-intersecting surfaces, are major obstacles to the accuracy, convergence, and stability of the numerical solution of the Poisson-Boltzmann ͑PB͒ equation.  ...  DMS-0616704 and IIS-0430987. The authors thank Yongcheng Zhou for useful discussions and Nathan Baker for valuable comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.2743020">doi:10.1063/1.2743020</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17614538">pmid:17614538</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qfnur6gdfzdephelun57n7mqqa">fatcat:qfnur6gdfzdephelun57n7mqqa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150824023039/http://users.math.msu.edu:80/users/wei/PAPER/p128.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/55/6a/556ad81ac007c3cd1d40342e287d4478dad949b2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.2743020"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Differential geometry based solvation model. III. Quantum formulation

Zhan Chen, Guo-Wei Wei
<span title="2011-11-21">2011</span> <i title="AIP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hnc5ddfunnd3taca63uf5ggldm" style="color: black;">Journal of Chemical Physics</a> </i> &nbsp;
As most force field models are parameterized for a certain class of molecules or materials, the use of partial charges limits the accuracy and applicability of our earlier models.  ...  To this end, we construct a new multiscale total energy functional which consists of not only polar and nonpolar solvation contributions, but also the electronic kinetic and potential energies.  ...  ACKNOWLEDGMENTS The authors thank Dr. Wei Li for useful discussions of quantum calculations. This work was supported in part by NSF Grant Nos. DMS-0616704 and CCF-0936830, and NIH Grant No.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.3660212">doi:10.1063/1.3660212</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22112067">pmid:22112067</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3248025/">pmcid:PMC3248025</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4vk55qkugbg27gij53evtrjzzy">fatcat:4vk55qkugbg27gij53evtrjzzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808115235/http://users.math.msu.edu/users/wei/paper/p150.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/74/58/74582773bcd62f44e31043852008acea5e708691.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.3660212"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248025" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L.A. Barba, Tsuyoshi Hamada
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wfenstutwram7ghf2w6rgf5gyu" style="color: black;">Computer Physics Communications</a> </i> &nbsp;
The applications demonstrated include the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of lysozyme molecules.  ...  We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution.  ...  In our application, we use two types of fast summation: in the first, we replace the source points with a discretization of the induced charge on the molecular surface σ, evaluate the field at the same  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpc.2011.02.013">doi:10.1016/j.cpc.2011.02.013</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/62eidsyjknf5fhfmq266gybk6u">fatcat:62eidsyjknf5fhfmq266gybk6u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429090240/http://t2r2.star.titech.ac.jp/rrws/file/CTT100686130/ATD100000413/" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/89/c8898269b26235dad3e6aee50be0b87650ae944f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpc.2011.02.013"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Review of Simulation Techniques for Aquifer Thermal Energy Storage (ATES) [chapter]

J.W. MERCER, C.R. FAUST, W.J. MILLER, F.J. PEARSON
<span title="">1982</span> <i title="Elsevier"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qigk2meicrbw3aoyt3p2oyrbpi" style="color: black;">Advances in Hydroscience</a> </i> &nbsp;
They are valuable for performing calculations in systems in which rapid reactions are likely to occur.  ...  Assuming that models are applied appropriately, the primary limitation on model calculations is the data base used to construct the model.  ...  A-7 Using Equations (A-7), and choosing smaller and smaller values of 6X, 6y, 6Z and 6t, and using the definition of a derivative, Equation ( ENERGY BALANCE The energy balance may be determined by  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-021813-4.50007-x">doi:10.1016/b978-0-12-021813-4.50007-x</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rc4shooienaxrlrdmc3xocqqwm">fatcat:rc4shooienaxrlrdmc3xocqqwm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726032718/https://digital.library.unt.edu/ark:/67531/metadc1110590/m2/1/high_res_d/6069851.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1e/60/1e60cb1331693f5e57a7b856958c3f7165dcf0e5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-0-12-021813-4.50007-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Classical Electrostatics for Biomolecular Simulations

G. Andrés Cisneros, Mikko Karttunen, Pengyu Ren, Celeste Sagui
<span title="2013-08-27">2013</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3jiv5gamdrch7lswaebpzyrjmi" style="color: black;">Chemical Reviews</a> </i> &nbsp;
Acknowledgments We would like to thank Robert E. Duke for sharing with us his experience with truncation methods. We would like to thank the support we have received for this work.  ...  Welch Foundation (F-1691), and the National Institutes of Health (R01GM106137), and C.S thanks NSF grants 1021883 and 1148144.  ...  Charge-groups can be used with cutoff, reaction field and Ewald-based methods.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/cr300461d">doi:10.1021/cr300461d</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23981057">pmid:23981057</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3947274/">pmcid:PMC3947274</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/436zql6ojzgnbhd2q3hs7x5fhq">fatcat:436zql6ojzgnbhd2q3hs7x5fhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191130031518/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3947274&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f7/00/f70024c5761c64d4bae51be59eb637522328b563.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/cr300461d"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947274" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Multiscale geometric modeling of macromolecules I: Cartesian representation

Kelin Xia, Xin Feng, Zhan Chen, Yiying Tong, Guo-Wei Wei
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/f7kkigxhzjakref5b42jt4uoya" style="color: black;">Journal of Computational Physics</a> </i> &nbsp;
The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system.  ...  After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions.  ...  G.W.W. acknowledges the Mathematical Biosciences Institute for hosting valuable workshops.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jcp.2013.09.034">doi:10.1016/j.jcp.2013.09.034</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24327772">pmid:24327772</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3855405/">pmcid:PMC3855405</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rpprqea3mzfibdx7la3kdhcmkm">fatcat:rpprqea3mzfibdx7la3kdhcmkm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150901165620/http://users.math.msu.edu/users/xiakelin/paper/p8.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e0/ef/e0ef97e54ce5a752d9e07122f624b9437628a692.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jcp.2013.09.034"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855405" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Modelling and Simulation of Sol-Gel Nanocomposites [chapter]

Paola Posocco, Sabrina Pricl, Maurizio Fermeglia
<span title="">2014</span> <i title="Springer New York"> Sol-Gel Nanocomposites </i> &nbsp;
Finally, it is shown how macroscopic properties of the sol-gel nanocomposite of interest are estimated using the multiscale molecular simulation protocol described.  ...  Calculated values at different scales, but particularly at macroscale are compared with experimental data to show the reliability of the proposed approach.  ...  It is based on 5 consecutive steps. In the first step (1), COMPASS force field [46] is used to generate the molecular models of GPTMS monomers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-1209-4_2">doi:10.1007/978-1-4939-1209-4_2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/byjwtfniq5ga7abhmttigbch5y">fatcat:byjwtfniq5ga7abhmttigbch5y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710005403/https://www.springer.com/cda/content/document/cda_downloaddocument/9781493912087-c2.pdf?SGWID=0-0-45-1466509-p176774834" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d2/67/d2678c46d13d1fac346ab823b1eed5e267121dc0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-1209-4_2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Recent developments in Geant4

Makoto Asai, Andrea Dotti, Marc Verderi, Dennis H. Wright
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fbubbos3yzdy7kw53whrhfm23a" style="color: black;">Annals of Nuclear Energy</a> </i> &nbsp;
It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection.  ...  Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available  ...  Acknowledged as well is the generous support of experiment collaborations and universities who have allowed their members to contribute significant time and effort to the development, testing and validation  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.anucene.2014.08.021">doi:10.1016/j.anucene.2014.08.021</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pwzqs55ocvc5phczmftd64ycti">fatcat:pwzqs55ocvc5phczmftd64ycti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170426061410/http://www.ccs.neu.edu/home/gene/papers/geant4-16.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d2/2a/d22a8ff42ff0e1c6ccf48218379466846723e373.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.anucene.2014.08.021"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations [chapter]

Alex Tek, Matthieu Chavent, Marc Baaden, Olivier Delalande, Patrick Bourdot, Nicolas Ferey
<span title="2012-03-30">2012</span> <i title="InTech"> Protein-Protein Interactions - Computational and Experimental Tools </i> &nbsp;
using an haptic device, and a study about the opening and closure of the Guanylate Kinase enzyme.  ...  Such applications are now in the reach of state-of-art desktop computing.  ...  Flexible parts are immersed into a grid and guided by a potential field induced by the rigid component, computed before the simulation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/36568">doi:10.5772/36568</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/piy3kpfmmjf2xfmupn3umwg3am">fatcat:piy3kpfmmjf2xfmupn3umwg3am</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727040638/https://api.intechopen.com/chapter/pdf-download/34342" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/2d/a02db85c7f62ff0d929d158eea15db2982fa1a08.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/36568"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Roadmap on optical energy conversion

Svetlana V Boriskina, Martin A Green, Kylie Catchpole, Eli Yablonovitch, Matthew C Beard, Yoshitaka Okada, Stephan Lany, Talia Gershon, Andriy Zakutayev, Mohammad H Tahersima, Volker J Sorger, Michael J Naughton (+24 others)
<span title="2016-06-24">2016</span> <i title="IOP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ohjzwmpi25bm5hfuwnimdgk6fe" style="color: black;">Journal of Optics</a> </i> &nbsp;
Kirchoff's law dictates that some photons, their associated energy, and entropy are sent back to the heat source, (b) comparison of three different efficiencies, the Carnot, the Landsberg, and efficiency  ...  Acknowledgments I would like to thank my colleagues at ANU and, in particular, T White, N Lal, and C Barugkin for their contributions to the work described in this paper.  ...  By using constructive interference, it is possible to coherently combine the electric fields from the different antennas of an array. This would allow the control of the antenna array far field.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/2040-8978/18/7/073004">doi:10.1088/2040-8978/18/7/073004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wy25dfymhzdvtjmbqtqec2ilsq">fatcat:wy25dfymhzdvtjmbqtqec2ilsq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724050326/https://cloudfront.escholarship.org/dist/prd/content/qt6vd5t8q9/qt6vd5t8q9.pdf?t=p9x64t" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fc/be/fcbeb3b8c34d08597951d1626ba30522c22cbbeb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/2040-8978/18/7/073004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> iop.org </button> </a>

Recent advances in defect electrocatalysts: Preparation and characterization

Zhaohui Xiao, Chao Xie, Yanyong Wang, Ru Chen, Shuangyin Wang
<span title="">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fhd4qlry6najrbkkah3qflwquu" style="color: black;">Journal of Energy Chemistry</a> </i> &nbsp;
Although challenges in the characterization of defect structures in the electrocatalytic reaction process remain, the dynamic evolution of defect sites is predicted to be helpful for designing and preparing  ...  Furthermore, due to an insufficient understanding of the defect-structureproperty relationships, future possibilities for the reasonable design of defect electrocatalysts to obtain desirable performance  ...  Acknowledgments This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 21573066, 21825201, 2187350, 51402100 and 21905088).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jechem.2020.04.063">doi:10.1016/j.jechem.2020.04.063</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4e5qqslz4nctxhgltv3i7b57e4">fatcat:4e5qqslz4nctxhgltv3i7b57e4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210731195155/https://www.sciengine.com/doi/pdf/260FD29D08734789A093B277200F490E" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/6b/3f6b75c85ec0dacce66c10b5da4d8231f4c463d9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jechem.2020.04.063"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation

Alexander H. Boschitsch, Marcia O. Fenley
<span title="">2004</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/72zcmi3smndcrdvxgve7ny6ytq" style="color: black;">Journal of Computational Chemistry</a> </i> &nbsp;
The motivation for and formulation of such a decomposition are presented together with the numerical method for calculating the linear and correction potentials.  ...  Results are presented for a spherical cavity containing a central charge, where the objective is to compare computed 1D nonlinear PBE solutions against ones obtained with alternate numerical solution methods  ...  Xiang-Jun Lu and Wilma Olson for making available their 3DNA program. The authors are grateful to Drs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.20000">doi:10.1002/jcc.20000</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15027106">pmid:15027106</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wkt2mzbmdzaazc43resw3t6awm">fatcat:wkt2mzbmdzaazc43resw3t6awm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070115234827/http://cvcweb.ices.utexas.edu:80/collections/papers/references/hybrid.bem.fdm.for.nlpbe.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/71/6c/716cbdaf7a6bee9b23b2e6c70356c6c36e44bbe3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jcc.20000"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>
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