From owner-chemistry@ccl.net Fri Nov 12 10:34:01 2021 From: "Achim Zielesny achim.zielesny%w-hs.de" To: CCL Subject: CCL: New open Dissipative Particle Dynamics (DPD) related projects Message-Id: <-54494-211112082559-25051-EcPAruBmMLVdpObB+93CAA#%#server.ccl.net> X-Original-From: "Achim Zielesny" Date: Fri, 12 Nov 2021 08:25:56 -0500 Sent to CCL by: "Achim Zielesny" [achim.zielesny^^w-hs.de] Dear CCL Community, For all those interested in mesoscopic simulation and Dissipative Particle Dynamics (DPD), we would like to point out our recent open projects on GitHub. MFsim (https://github.com/zielesny/MFsim) is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd (see below) as its default DPD simulation kernel. The environment integrates and supports the complete preparation-simulation-evaluation triad of a mesoscopic simulation task. Productive highlights are a SPICES (see below) molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim enables customized extensions for different fields of research. For the MS Windows operating system a comfortable "Single Click" installer is available. MFsim has already been used for a biomolecular DPD study of cyclic peptide/membrane interactions (https://doi.org/10.1186/s13321-020-00432-9). Jdpd (https://github.com/zielesny/Jdpd) is an open Java DPD simulation kernel with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated all-in-one simulation systems like MFsim. SPICES (https://github.com/zielesny/SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like DPD by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and mesoscopic simulation support in combination with an open Java Graphical User Interface viewer application for visual topological inspection of SPICES definitions are provided. Comments, hints, suggestions and (not really) bugs are very welcome! Best regards, Achim Zielesny Westphalian University of Applied Sciences Department of Engineering and Natural Sciences Institute for Bioinformatics and Chemoinformatics August-Schmidt-Ring 10 D-45665 Recklinghausen, Germany E-Mail: achim.zielesny~~w-hs.de Further references and links: - K. van den Broek, M. Epple, L. S. Kersten, H. Kuhn and A. Zielesny, Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation, Journal of Chemical Information an Modeling (2021), 61, 3027-3040 (https://doi.org/10.1021/acs.jcim.1c00332) ChemRxiv preprint: https://doi.org/10.26434/chemrxiv.14135783.v1 - K. van den Broek, M. Daniel, M. Epple, J.-M. Hein, H. Kuhn, S. Neumann, A. Truszkowski and A. Zielesny, MFsim - an open Java all-in-one rich-client simulation environment for mesoscopic simulation, Journal of Cheminformatics (2020), 12:29 (https://doi.org/10.1186/s13321-020-00432-9) - K. van den Broek, H. Kuhn and A. Zielesny, Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics, Journal of Cheminformatics (2018), 10:25 (https://doi.org/10.1186/s13321-018-0278-7) - K. van den Broek, M. Daniel, M. Epple, H. Kuhn, J. Schaub and A. Zielesny, SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation, Journal of Cheminformatics (2018), 10:35 (https://doi.org/10.1186/s13321-018-0294-7) - A. Truszkowski, M. Daniel, H. Kuhn, S. Neumann, C. Steinbeck, A. Zielesny and M. Epple, A molecular fragment cheminformatics roadmap for mesoscopic simulation, Journal of Cheminformatics (2014), 6:45 (https://doi.org/10.1186/s13321-014-0045-3) - Animations: - MFsim - Installation and initial test (Windows OS): https://w-hs.sciebo.de/s/MkijPlqo2STDw2W - MFsim - Simulation of a DMPC bilayer membrane model: https://w-hs.sciebo.de/s/wgaUbo9CdiSB3dn - MFsim - Cyclotide-membrane sandwich interaction model: https://w-hs.sciebo.de/s/QTIhqhQyBR9tSRW - Plasma membrane cholesterol mobility: https://w-hs.sciebo.de/s/BphC3r3fhcXc3EK - kB1 and cO2 backbone flexibility: https://w-hs.sciebo.de/s/OXJdy4we5qgufr7 - kB1 membrane interaction: https://w-hs.sciebo.de/s/mPl2E2PEtkqtWv6 - kB1 hydrophobic patch mutants membrane interaction: https://w-hs.sciebo.de/s/JyQNKNdtVqbYKyi - Quantitative cyclotide-membrane interaction analysis: https://w-hs.sciebo.de/s/VGwXDawV4a05JUC