tag:joss.theoj.org,2005:/papers/tagged/Structural%20dynamicsJournal of Open Source Software2024-01-29T16:38:15ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/42112024-01-29T16:38:15Z2024-01-30T08:20:19ZChitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulationsaccepted1.02023-02-15 16:12:05 UTC932024-01-29 16:38:15 UTC920245771DavidMalaspinaInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-5420-9534JordiFaraudoInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-6315-499310.21105/joss.05771https://doi.org/10.5281/zenodo.3274725Tcl, Rich Text Formathttps://joss.theoj.org/papers/10.21105/joss.05771.pdfVMD, chitin polymer structure, molecular dynamics, tcltag:joss.theoj.org,2005:Paper/42062023-04-17T08:01:50Z2023-04-18T00:02:31ZSolvationAnalysis: A Python toolkit for understanding liquid solvation structure in classical molecular dynamics simulationsacceptedv0.2.02023-02-14 19:07:27 UTC842023-04-17 08:01:50 UTC820235183OrionArcherCohenMaterials Science Division, Lawrence Berkeley National Laboratory, United States of America0000-0003-3940-2456HugoMacdermott-OpeskinAustralian National University, Australia0000-0002-7393-7457LaurenLeeMaterials Science Division, Lawrence Berkeley National Laboratory, United States of AmericaTingzhengHouInstitute of Materials Research, Shenzhen International Graduate School, Tsinghua University, China0000-0002-7163-2561KaraD.FongMaterials Science Division, Lawrence Berkeley National Laboratory, United States of America0000-0002-0711-097XRyanKingsburyEnergy Storage & Distributed Resources Division, Lawrence Berkeley National Laboratory, United States of America0000-0002-7168-3967JingyangWangMaterials Science Division, Lawrence Berkeley National Laboratory, United States of America0000-0003-3307-5132KristinA.PerssonDepartment of Materials Science, University of California, United States of America, Molecular Foundry, Lawrence Berkeley National Laboratory, United States of America0000-0003-2495-550910.21105/joss.05183https://doi.org/10.5281/zenodo.7806199Pythonhttps://joss.theoj.org/papers/10.21105/joss.05183.pdfpython, chemistry, electrolytes, molecular dynamics, solvation structuretag:joss.theoj.org,2005:Paper/36772022-09-23T14:44:23Z2022-09-26T12:03:03Zsolid_dmft: gray-boxing DFT+DMFT materials simulations with TRIQSaccepted3.1.12022-06-24 14:30:46 UTC772022-09-23 14:44:23 UTC720224623MaximilianE.MerkelMaterials Theory, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland0000-0003-2589-9625AlbertoCartaMaterials Theory, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland0000-0003-0705-0281SophieBeckCenter for Computational Quantum Physics, Flatiron Institute, 162 5th Avenue, New York, NY 10010, USA0000-0002-9336-6065AlexanderHampelCenter for Computational Quantum Physics, Flatiron Institute, 162 5th Avenue, New York, NY 10010, USA0000-0003-1041-861410.21105/joss.04623https://doi.org/10.5281/zenodo.7105085PHPhttps://joss.theoj.org/papers/10.21105/joss.04623.pdfPython, electronic structure theory, solid-state, computational materials science, correlated electrons, dynamical mean-field theorytag:joss.theoj.org,2005:Paper/27432022-07-04T16:31:16Z2022-07-05T00:00:39ZTsgFEM: Tensegrity Finite Element Methodacceptedv1.12021-06-09 07:07:34 UTC752022-07-04 16:31:16 UTC720223390ShuoMaCollege of Civil Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China0000-0003-3789-2893MuhaoChenDepartment of Aerospace Engineering, Texas A&M University, College Station, Texas, USA0000-0003-1812-6835RobertE.SkeltonDepartment of Aerospace Engineering, Texas A&M University, College Station, Texas, USA0000-0001-6503-911510.21105/joss.03390https://doi.org/10.5281/zenodo.6729686MATLABhttps://joss.theoj.org/papers/10.21105/joss.03390.pdfTensegrity systems, Multibody dynamics, Flexible structures, Prestressable structures, Finite element method, Linearized tensegrity dynamics, Elastic and plastic deformationtag:joss.theoj.org,2005:Paper/31722022-05-25T14:32:40Z2022-05-26T00:01:21ZGXBeam: A Pure Julia Implementation of Geometrically Exact Beam Theoryacceptedv0.3.12021-11-16 20:23:22 UTC732022-05-25 14:32:40 UTC720223997TaylorMcDonnellDepartment of Mechanical Engineering, Brigham Young University, Provo, UT, 84602, USA0000-0001-7993-5703AndrewNingDepartment of Mechanical Engineering, Brigham Young University, Provo, UT, 84602, USA0000-0003-2190-823X10.21105/joss.03997https://doi.org/10.5281/zenodo.6558458Juliahttps://joss.theoj.org/papers/10.21105/joss.03997.pdfstructural dynamics, finite element analysis, beam elementstag:joss.theoj.org,2005:Paper/31632022-02-05T08:41:42Z2022-02-06T00:00:29ZCacatoo: building, exploring, and sharing spatially structured models of biological systemsacceptedv1.0.02021-11-09 14:35:39 UTC702022-02-05 08:41:42 UTC720223948Bramvan DijkMax Planck Institute for Evolutionary Biology0000-0002-6330-693410.21105/joss.03948https://doi.org/10.5281/zenodo.5918404JavaScripthttps://joss.theoj.org/papers/10.21105/joss.03948.pdfjavascript, spatial structure, dynamics, individual-based models, microbial ecology and evolutiontag:joss.theoj.org,2005:Paper/19482022-01-19T22:05:32Z2022-01-20T00:01:36ZpyFBS: A Python package for Frequency Based Substructuringaccepted0.1.12020-08-19 14:15:54 UTC692022-01-19 22:05:32 UTC720223399TomažBregarGorenje d.o.o., Partizanska 12, 3503 Velenje, SloveniaAhmedElMahmoudiTechnical University of Munich, Institute of Applied Mechanics, Boltzmannstr. 15, 85748 Garching, GermanyMihaKodričFaculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, SloveniaDomenOcepekFaculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, SloveniaFrancescoTrainottiTechnical University of Munich, Institute of Applied Mechanics, Boltzmannstr. 15, 85748 Garching, GermanyMihaPogačarFaculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, SloveniaMertGöldeliTechnical University of Munich, Institute of Applied Mechanics, Boltzmannstr. 15, 85748 Garching, GermanyGregorČeponFaculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, SloveniaMihaBoltežarFaculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, SloveniaDanielJ.RixenTechnical University of Munich, Institute of Applied Mechanics, Boltzmannstr. 15, 85748 Garching, Germany10.21105/joss.03399https://doi.org/10.5281/zenodo.5876734Pythonhttps://joss.theoj.org/papers/10.21105/joss.03399.pdfStructural dynamics, Frequency Based Substructuring, System Equivalent Model Mixing, Transfer Path Analysistag:joss.theoj.org,2005:Paper/14732021-01-16T14:52:59Z2021-02-15T11:31:01ZfastSF: A parallel code for computing the structure functions of turbulenceacceptedv1.0.02020-02-06 12:49:58 UTC572021-01-16 14:52:59 UTC620212185ShubhadeepSadhukhanDepartment of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India0000-0002-7278-5041ShashwatBhattacharyaDepartment of Mechanical Engineering, Indian Institute of Technology Kanpur 208016, India0000-0001-7462-7680MahendraK.VermaDepartment of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India0000-0002-3380-456110.21105/joss.02185https://doi.org/10.5281/zenodo.4420031Python, C++https://joss.theoj.org/papers/10.21105/joss.02185.pdfstructure functions, turbulence, fluid dynamicstag:joss.theoj.org,2005:Paper/15952020-10-02T09:48:56Z2021-02-15T11:30:51ZSysIdentPy: A Python package for System Identification using NARMAX modelsaccepted0.1.12020-05-20 12:26:39 UTC542020-10-02 09:48:56 UTC520202384WilsonRochaLacerdaGCoM - Modeling and Control Group at Federal University of São João del-Rei, Brazil0000-0002-3263-1152LuanPascoal Costada AndradeGCoM - Modeling and Control Group at Federal University of São João del-Rei, BrazilSamuelCarlos PessoaOliveiraGCoM - Modeling and Control Group at Federal University of São João del-Rei, BrazilSamirAngelo MilaniMartinsGCoM - Modeling and Control Group at Federal University of São João del-Rei, Brazil, Department of Electrical Engineering at Federal University of São João del-Rei, Brazil10.21105/joss.02384https://doi.org/10.5281/zenodo.4026516Pythonhttps://joss.theoj.org/papers/10.21105/joss.02384.pdfSystem Identification, NARMAX, Dynamical Systems, Model Structure Selectiontag:joss.theoj.org,2005:Paper/15402020-06-03T10:40:49Z2021-02-15T11:30:54Ztaurenmd: A command-line interface for analysis of Molecular Dynamics simulations.acceptedv0.8.92020-03-03 20:18:24 UTC502020-06-03 10:40:49 UTC520202175JoãoM.C.TeixeiraPrevious, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain, Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada0000-0002-9113-062210.21105/joss.02175https://doi.org/10.5281/zenodo.3843326Pythonhttps://joss.theoj.org/papers/10.21105/joss.02175.pdfMolecular Dynamics, Structural Biology, Proteins, DNA, RNA, Biochemistry