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Cite Many-body dynamics of chemically propelled nanomotors

Peter Colberg 1 year ago
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 <h1>About nano-dimer</h1>
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-<p><a href="http://colberg.org/nano-dimer/">Nano-dimer</a> is a molecular modelling software to study the dynamics of chemically powered self-propelled nanomotors <span class="citation">(Kapral 2013)</span>. The software combines molecular dynamics and multi-particle collision dynamics <span class="citation">(Malevanets and Kapral 1999; Malevanets and Kapral 2000; Ihle and Kroll 2001)</span> to simulate the molecular motion of a single to hundreds of sphere-dimer motors <span class="citation">(Rückner and Kapral 2007)</span> and their long-range hydrodynamic interaction in a solvent comprising several million particles.</p>
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+<p><a href="http://colberg.org/nano-dimer/">Nano-dimer</a> is a molecular modelling software to study the dynamics of chemically powered self-propelled nanomotors <span class="citation">(Kapral 2013; Colberg and Kapral 2017)</span>. The software combines molecular dynamics and multi-particle collision dynamics <span class="citation">(Malevanets and Kapral 1999; Malevanets and Kapral 2000; Ihle and Kroll 2001)</span> to simulate the molecular motion of a single to hundreds of sphere-dimer motors <span class="citation">(Rückner and Kapral 2007)</span> and their long-range hydrodynamic interaction in a solvent comprising several million particles.</p>
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 <p>Nano-dimer relies on novel computational techniques to scale from a multi-core processor to a parallel accelerator with thousands of scalar cores. The simulation algorithms are composed in the <a href="https://www.khronos.org/registry/cl/sdk/1.2/docs/man/xhtml/">OpenCL C</a> language using <a href="http://colberg.org/lua-templet/">run-time code generation</a>, which allows running simulations with optimal efficiency across a variety of devices, such as AMD GPUs, NVIDIA GPUs, and Intel CPUs.</p>
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 <p>A simulation is orchestrated using <a href="http://www.lua.org/about.html">Lua</a> scripts run with <a href="http://luajit.org/luajit.html">LuaJIT</a>, an interpreter and <a href="https://en.wikipedia.org/wiki/Tracing_just-in-time_compilation">tracing just-in-time compiler</a> for the Lua language that provides native C data structures through its foreign function interface (<a href="http://luajit.org/ext_ffi.html">FFI</a>). Particle trajectories of nanomotors and solvent, and a versatile set of structural and dynamical observables are stored in an <a href="http://nongnu.org/h5md/">H5MD</a> file, a file format for molecular data <span class="citation">(Buyl, Colberg, and Höfling 2014)</span> based on the hierarchical data format (<a href="http://www.hdfgroup.org/HDF5/">HDF5</a>).</p>
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-<h2 id="references" class="references unnumbered">References</h2>
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+<h2 id="references" class="unnumbered">References</h2>
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 <div id="ref-Buyl2014">
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-<p>Buyl, Pierre de, Peter H. Colberg, and Felix Höfling. 2014. “H5MD: A Structured, Efficient, and Portable File Format for Molecular Data.” <em>Computer Physics Communications</em> 185 (6): 1546–53. <a href="http://doi.org/10.1016/j.cpc.2014.01.018">doi:10.1016/j.cpc.2014.01.018</a>.</p>
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+<p>Buyl, Pierre de, Peter H. Colberg, and Felix Höfling. 2014. “H5MD: A Structured, Efficient, and Portable File Format for Molecular Data.” <em>Computer Physics Communications</em> 185 (6): 1546–53. doi:<a href="https://doi.org/10.1016/j.cpc.2014.01.018">10.1016/j.cpc.2014.01.018</a>.</p>
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+</div>
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+<div id="ref-Colberg2017">
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+<p>Colberg, Peter H., and Raymond Kapral. 2017. “Many-Body Dynamics of Chemically Propelled Nanomotors.” <em>J. Chem. Phys.</em> 147: 064910. doi:<a href="https://doi.org/10.1063/1.4997572">10.1063/1.4997572</a>.</p>
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 <div id="ref-Ihle2001">
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-<p>Ihle, T., and D. M. Kroll. 2001. “Stochastic Rotation Dynamics: A Galilean-Invariant Mesoscopic Model for Fluid Flow.” <em>Phys. Rev. E</em> 63: 020201. <a href="http://doi.org/10.1103/PhysRevE.63.020201">doi:10.1103/PhysRevE.63.020201</a>.</p>
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+<p>Ihle, T., and D. M. Kroll. 2001. “Stochastic Rotation Dynamics: A Galilean-Invariant Mesoscopic Model for Fluid Flow.” <em>Phys. Rev. E</em> 63: 020201. doi:<a href="https://doi.org/10.1103/PhysRevE.63.020201">10.1103/PhysRevE.63.020201</a>.</p>
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 <div id="ref-Kapral2013">
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-<p>Kapral, Raymond. 2013. “Perspective: Nanomotors Without Moving Parts That Propel Themselves in Solution.” <em>Journal of Chemical Physics</em> 138 (2): 020901. <a href="http://doi.org/10.1063/1.4773981">doi:10.1063/1.4773981</a>.</p>
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+<p>Kapral, Raymond. 2013. “Perspective: Nanomotors Without Moving Parts That Propel Themselves in Solution.” <em>Journal of Chemical Physics</em> 138 (2): 020901. doi:<a href="https://doi.org/10.1063/1.4773981">10.1063/1.4773981</a>.</p>
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 <div id="ref-Malevanets1999">
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-<p>Malevanets, Anatoly, and Raymond Kapral. 1999. “Mesoscopic Model for Solvent Dynamics.” <em>Journal of Chemical Physics</em> 110 (17): 8605–13. <a href="http://doi.org/10.1063/1.478857">doi:10.1063/1.478857</a>.</p>
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+<p>Malevanets, Anatoly, and Raymond Kapral. 1999. “Mesoscopic Model for Solvent Dynamics.” <em>Journal of Chemical Physics</em> 110 (17): 8605–13. doi:<a href="https://doi.org/10.1063/1.478857">10.1063/1.478857</a>.</p>
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 <div id="ref-Malevanets2000">
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-<p>———. 2000. “Solute Molecular Dynamics in a Mesoscale Solvent.” <em>Journal of Chemical Physics</em> 112 (16): 7260–69. <a href="http://doi.org/10.1063/1.481289">doi:10.1063/1.481289</a>.</p>
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+<p>———. 2000. “Solute Molecular Dynamics in a Mesoscale Solvent.” <em>Journal of Chemical Physics</em> 112 (16): 7260–9. doi:<a href="https://doi.org/10.1063/1.481289">10.1063/1.481289</a>.</p>
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 <div id="ref-Rueckner2007">
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-<p>Rückner, Gunnar, and Raymond Kapral. 2007. “Chemically Powered Nanodimers.” <em>Phys. Rev. Lett.</em> 98 (15): 150603. <a href="http://doi.org/10.1103/PhysRevLett.98.150603">doi:10.1103/PhysRevLett.98.150603</a>.</p>
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+<p>Rückner, Gunnar, and Raymond Kapral. 2007. “Chemically Powered Nanodimers.” <em>Phys. Rev. Lett.</em> 98 (15): 150603. doi:<a href="https://doi.org/10.1103/PhysRevLett.98.150603">10.1103/PhysRevLett.98.150603</a>.</p>
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@@ -3,7 +3,7 @@ title: About nano-dimer
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 [Nano-dimer] is a molecular modelling software to study the dynamics of
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-chemically powered self-propelled nanomotors [@Kapral2013].
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+chemically powered self-propelled nanomotors [@Kapral2013; @Colberg2017].
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 The software combines molecular dynamics and multi-particle collision
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 dynamics [@Malevanets1999; @Malevanets2000; @Ihle2001] to simulate the
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 molecular motion of a single to hundreds of sphere-dimer motors

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   doi = {10.1016/j.cpc.2011.01.009}
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 }
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+@article{Colberg2017,
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+  author = {Peter H. Colberg and Raymond Kapral},
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+  title = {Many-body dynamics of chemically propelled nanomotors},
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+  journal = {J. Chem. Phys.},
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+  year = {2017},
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+  volume = {147},
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+  pages = {064910},
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+  doi = {10.1063/1.4997572}
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+}
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 @article{Cook1957,
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   author = {J. M. Cook},
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   title = {Rational Formulae for the Production of a Spherically Symmetric

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