Difference between revisions of "Axel Arnold"
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Revision as of 14:28, 7 April 2014
|Phone:||+49 711 685-67609|
|Fax:||+49 711 685-63658|
|Email:||arnolda _at_ icp.uni-stuttgart.de|
|Address:||JP Dr. Axel Arnold|
Institute for Computational Physics
I will teach a course on LB/MD at the Ferienakademie 2014, taking place Sept. 21 - Oct. 3 in Sarntal, South Tyrol. All master or bachelor students in their 3rd year or above from the universities of Stuttgart, Erlangen or Munich can apply for participation.
ESPResSo stands for Extensible Simulation Package for Resarch on Soft matter systems, and is a simulation package mainly for (charged) bead spring models of soft matter. Since the beginning in 2003, I am one of the core developers and am still involved in the current development here at ICP. Also, if you are interested in any of the algorithmic work I do/did - all is implemented in ESPResSo and therefore open source. In particular, my major contributions are:
- a good deal of ESPResSo's core functionality
- GPU accelerated lattice Boltzmann
- MMM2D / MMM1D
- collision detection
Using GPUs for numerical calculations
In the last couple of years, the computational power of graphics cards has grown much faster than that of conventional CPUs, although at the same time the graphics cards have become true general purpose processors. Recent graphics processors reach speeds of up to a Teraflop on a single PCIe-board. With the introduction of easy-to-use programming languages for the GPU hardware, this computational power can be harnessed for many applications. Using NVidia's CUDA, Koos van Meel and I have demonstrated this for classical Molecular Dynamics simulations. However, GPUs are better suited for mesh-based algorithms such as the lattice Boltzmann method, and ESPResSo now contains a GPU-accelerated LB code written by Dominic Röhm. For more information, see here. A number of simple CUDA examples can be found here.
For a quick overview on GPU computing, see this article (1.69 MB) in International Innovation. International Innovation published by Research Media is the leading global dissemination resource for the wider scientific, technology and research communities, dedicated to disseminating the latest science, research and technological innovations on a global level. More information and a complimentary subscription offer to the publication can be found at: www.researchmedia.eu.
Rare Event Sampling
As the name suggests, rare events are events that happen rarely, triggered by spontaneous fluctuations. However, many rare events have dramatic consequences, which is why studying them is important. Examples exist on all length scales, from nucleation, i.e. crystal growth, to earthquakes. While rare events are rare in nature, they simply do not happen on the much more limited system sizes that are accessible to computer simulations. Therefore, special simulation algorithms are required to study rare events. We currently focus on the recent Forward Flux Sampling method of Allen et al, which is a milestoning method that is well-suited to study processes such as nucleation. Our research is in making this technique as easily usable as Molecular Dynamics or other established tools. To this aim, we develop the ("Flexible Rare Event Sampling Harness System" (FRESHS)), an open source meta server that can perform FFS simulations with different back ends such as ESPResSo, GROMACS or LAMMPS. Another important topic is the automatic placement of the milestones, which is not only important to maximize the performance, but also the accuracy of FFS.
Calculation of the electrostatic potential
Due to its long-ranged nature, the electrostatic interaction is very difficult to calculate in periodic systems. However, these systems are often used in computer simulation studies of bulk systems. Therefore, there has been and still is much interest in fast algorithms to calculate the Coulomb sum in periodic boundary conditions. For 3D periodic boundary conditions, many optimized algorithms exist, from the classical Ewald summation to particle-mesh methods, where the best method scale linearly in the number of particles.
My interest is in the calculation of this interaction in 3D systems, where only one or two coordinates are periodically replicated. For these systems, the classical Ewald method is slow to evaluate, and alternative approaches are necessary. I have developed the MMM1D/2D algorithms, and J. de Joannis and I found the electrostatic layer correction (ELC) method. This method consists of a correction term that is fast to calculate and allows to use any method for 3D-periodic boundary conditions for a quasi-2D system.
All these methods are implemented in ESPResSo, if you want to try them out.
Nucleation and long range interactions
Nucleation, the onset of crystal growth, is classically viewed as a quasi-static process that is governed by chemical potential differences and surface tension. However, when charges come into play, for example when crystallizing proteins or charged colloidal particles, the latter assumption might be wrong, as even small nuclei tend to form facets. When studying colloidal particles, also hydrodynamic interactions have a strong influence on the crystal growth speed and nucleation rate. This is in particular important, since colloidal particles are commonly assumed to be a model system for nucleation in more complex systems, such as metal melts. However, in a true melt, hydrodynamic interactions are very different, so that results from colloids might not be transferred immediately onto metallic systems. On the other hand, the strong influence of long-range hydrodynamic interactions allows for new ways of facilitating nucleation, e.g. by choosing appropriate confining geometries.
(Charged) soft matter
Mostly using ESPResSo and the above-mentioned electrostatics methods, I investigated several systems of interest in soft matter physics. For example:
- attraction of like-charged rods in the presence of multivalent counterions (here, MMM1D was used).
- segregation and relaxation of polymers in confinement.
As it seems, one of my favorite activities is reviewing papers for the Journal of Chemical Physics. At least, I became one of their top 20 reviewers 2011.
- projector.sh (5 KB) is a script that you can use to switch between internal and external displays on laptops. In the simplest form, it just toggles between internal display only and both internal and external display, which is basically the functionality that you would expect from the display switch fn-key. I tested it both with xrandr and the Nvidia driver, so it should work with most hardware.
- mount.sh (1 KB) and umount.sh (1 KB) are two scripts that perform the respective operations semiautomatically using the udisks command of Ubuntu and other current Linux distributions. If you a tiling window manager such as awesome or ratpoison, you probably also want to be able to mount USB devices from the terminal. These scripts simplify this process.
mount does the following:
- without arguments, shows the mounted partitions, just as plain mount would do
- with parameter "-a" looks for the first unmounted, mountable partition and mounts it. The devices it looks for are /dev/sd*1 and /dev/mmcblk*p1, which is what you will typically find with USB sticks.
- otherwise, the parameter should be a partition to mount, e.g. /dev/sdb1
The partitions are mounted using udisks, so are mounted to a new mount point in /media as reported.
umount just takes this mount point to unmount the partition, just as a plain umount would do, but in a second step tries to detach the device. USB HDDs will typically retract their heads in this case and stop spinning, rather than performing the fast head retract that they do if they are just powered off.
Here are some useful enhanced widgets for Awesome.
- Battery monitor (2 KB). Based on acpitool like the version suggested on the Awesome wiki, but also supports broken laptops that do not report remaining time.
- Network monitor (3 KB). Displays throughput of network devices, e.g. to check that UMTS is still sending/receiving.
- Keyboard switching widget (1 KB). Based on the example in the Awesome wiki, but allows to also specify variants, such as "nodeadkeys" for the German keyboard layout.
- K. Kratzer, J. T. Berryman, A. Taudt, J. Zeman, A. Arnold.
- The Flexible Rare Event Sampling Harness System (FRESHS). Comp. Phys. Comm. (2014).
- M. U. Bohner, J. Zeman, J. Smiatek, A. Arnold, and J. Kästner.
- Nudged-elastic band used to find reaction coordinates based on the free energy. J. Chem. Phys. 140:074109 (2014).
- T. Koeddermann, D. Reith, and A. Arnold.
- Accurate Calculations of Partition Coefficients (log POW and log PMW) with Atomistic Simulation Methods. Chemie Ingenieur Technik 85.9:1439-1440 (2013).
- A. Arnold, F. Fahrenberger, C. Holm, O. Lenz, M. Bolten, H. Dachsel, R. Halver, I. Kabadshow, F. Gähler, F. Heber, J. Iseringhausen, M. Hofmann, M. Pippig, D. Potts, and G. Sutmann.
- Comparison of scalable fast methods for long-range interactions. Phys. Rev. E 88:063308 (2013).
- A. Arnold, K. Breitsprecher, F. Fahrenberger, S. Kesselheim, O. Lenz, C. Holm.
- Efficient Algorithms for Electrostatic Interactions Including Dielectric Contrasts. Entropy 15:4569-4588 (2013).
- T. Köddermann, D. Reith and A. Arnold.
- Why the Partition Coefficient of Ionic Liquids is concentration-dependent. J. Phys. Chem. B 117:10711 (2013).
- S. Gekle and A. Arnold.
- Comment on “Anomalous Dielectric Behavior of Nanoconfined Electrolytic Solutions”. Phys. Rev. Lett. 111:089801 (2013).
- K. Kratzer, A. Arnold and R. J. Allen.
- Automatic, optimized interface placement in forward flux sampling simulations. J. Chem. Phys. 138:164112 (2013).
- A. Arnold, O. Lenz, S. Kesselheim, R. Weeber, F. Fahrenberger, D. Roehm, P. Kosovan and C. Holm.
- ESPResSo 3.1 - Molecular Dynamics Software for Coarse-Grained Models. In M. Griebel, M. A. Schweitzer, Meshfree Methods for Partial Differential Equations VI, Lecture Notes in Computational Science and Engineering, Vol. 89, Springer (2013). ISBN 978-3-642-32979-1.
- M. Sega, S. S. Kantorovich, A. Arnold, and C. Holm.
- On the Calculation of the Dielectric Properties of Liquid Ionic Systems. In Y. P. Kalmykov, Recent Advances in Broadband Dielectric Spectroscopy, NATO Science for Peace and Security Series B: Physics and Biophysics, Springer (2013).
- Y. Dorozhko, K. Kratzer, Y. Yudin, A. Arnold, C. W. Glass and M. Resch.
- Rare Event Sampling using the Science Experimental Grid Laboratory. In B.H.V. Topping, P. Iványi, Proceedings of the Fourteenth International Conference on Civil, Structural and Environmental Engineering Computing, Civil-Comp Press, Paper 207 (2013).
- J. D. Halverson, T. Brandes, O. Lenz, A. Arnold, S. Bevc, V. Starchenko, K. Kremer, T. Stuehn, and D. Reith.
- ESPResSo++: A modern multiscale simulation package for soft matter systems. Comp. Phys. Comm. 184:1129-1149 (2012).
- M. Weigel, A. Arnold, P. Virnau (Editors).
- Computer Simulations on Graphics Processing Units. Eur. Phys. J. ST 210 (2012).
- T. Brandes, A. Arnold, T. Soddemann and D. Reith.
- CPU vs. GPU - Performance comparison for the Gram-Schmidt algorithm. Eur. Phys. J. ST 210:73-88 (2012).
- D. Roehm and A. Arnold.
- Lattice Boltzmann simulations on GPUs with ESPResSo. Eur. Phys. J. ST 210:89-100 (2012).
- N. Gribova, A. Arnold, T. Schilling, C. Holm.
- How Close to Two Dimensions Does a Lennard-Jones System Need to Be to Produce a Hexatic Phase?. J. Chem. Phys. 135:054514 (2011).
- A. Arnold.
- Fourier Transformed-Based Methods for Long-Range Interactions: Ewald, P3M and More. In G. Sutmann, P. Gibbon, and T. Lippert, Fast Methods for Long-Range Interactions in Complex Systems. IAS Series Vol. 6, FZ Jülich (2011).
- A. Arnold, O. Lenz und C. Holm.
- Simulating Charged Systems with ESPResSo. In G. Sutmann, P. Gibbon, and T. Lippert, Fast Methods for Long-Range Interactions in Complex Systems. IAS Series Vol. 6, FZ Jülich (2011).
- V. Ballenegger, A. Arnold and J. J. Cerdà.
- Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions. J. Chem. Phys. 131:094107 (2009).
- T. Kalkbrenner, A. Arnold and S. Tans.
- Internal Dynamics of Supercoiled DNA Molecules. Biophysical Journal 96:4951-4955 (2009).
- S. Tyagi, A. Arnold and C. Holm.
- Electrostatic layer correction with image charges: A linear scaling method to treat slab 2D+h systems with dielectric interfaces. J. Chem. Phys. 129:204102 (2008).
- A. Arnold and C. Holm.
- Interactions of like-charged rods at low temperatures: Analytical theory vs. simulations. Euro. Phys. J. E, DOI:10.1140/epje/i2007-10347-4, 2008.
- J. A. van Meel, A. Arnold, D. Frenkel, S. F. Portegies Zwart and R. G. Belleman.
- Harvesting graphics power for MD simulations. Molecular Simulation 34(3):259-266, 2008.
- A. Arnold, B. Bozorgui, D. Frenkel, B.-Y. Ha and S. Jun.
- Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement. J. Chem. Phys. 127:164903, 2007.
- S. Tyagi, A. Arnold and C. Holm.
- ICMMM2D: An accurate method to include planar dielectric interfaces via image charge summation. J. Chem. Phys. 127:154723, 2007.
- A. Arnold and S. Jun.
- Time scale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria. Phys. Rev. E 76:031901, 2007.
- S. Jun, A. Arnold and B.-Y. Ha.
- Confined space and effective interactions of multiple self-avoiding chains. Phys. Rev. Lett. 98:128303, 2007.
- H. Limbach, A. Arnold, B. A. Mann and C. Holm.
- ESPResSo - An Extensible Simulation Package for Research on Soft Matter Systems. Comp. Phys. Comm. 174:704-727, 2006.
- A. Arnold, B. A. F. Mann and C. Holm.
- Simulating Charged Systems with ESPResSo. In Lecture Notes in Physics, 703, Springer, 2006.
- A. Arnold and C. Holm.
- Efficient methods to compute long range interactions for soft matter systems. In C. Holm and K. Kremer, Advanced Computer Simulation Approaches for Soft Matter Sciences II, 59-109, Springer, 2005.
- A. Arnold and C. Holm.
- MMM1D: A method for calculating electrostatic interactions in one-dimensional periodic geometries. J. Chem. Phys. 123(14):144103, 2005.
- A. Arnold.
- Computer simulations of charged systems in partially periodic geometries. Disseration, J. Gutenberg-Universität, Mainz, Germany, 2004.
- A. Naji, A. Arnold, C. Holm and R. R. Netz.
- Attraction and unbinding of like--charged rods. Europhys. Lett. 67:130-136, 2004.
- M. Deserno, A. Arnold and C. Holm.
- Attraction and ionic correlations between charged stiff polyelectrolytes. Macromolecules 36(1):249-259, 2003.
- A. Arnold and C. Holm.
- MMM2D: A fast and accurate summation method for electrostatic interactions in 2D slab geometries. Comp. Phys. Comm. 148(3):327-348, 2002.
- J. de Joannis, A. Arnold and C. Holm.
- Electrostatics in Periodic Slab Geometries II. J. Chem. Phys. 117:2503-2512, 2002.
- A. Arnold, J. de Joannis and C. Holm.
- Electrostatics in Periodic Slab Geometries I. J. Chem. Phys. 117:2496-2502, 2002.
- A. Arnold and C. Holm.
- A novel method for calculating electrostatic interactions in 2D periodic slab geometries. Chem. Phys. Lett. 354(3):324-330, 2002.
- A. Arnold.
- Berechnung der elektrostatischen Wechselwirkung in 2d+h periodischen Systemen. Diploma thesis, J. Gutenberg-Universität, Mainz, Germany, 2001.
|since Jan. 2010||Post-doctoral researcher at the ICP, University of Stuttgart, Germany|
|Jan. 2008 - Dec. 2009||Post-doctoral researcher at the Fraunhofer institute SCAI, St. Augustin, Germany|
|Nov. 2005 - Dec. 2007||Post-doctoral researcher at the FOM-institute AMOLF, Amsterdam, The Netherlands|
|Dec. 2004 - Oct. 2005||Post-doctoral researcher at the Max-Planck-Institute for Polymer Research and the Frankfurt Institute for Advanced Studies (FIAS)|
|Dec. 2004||Doctor rer. nat. awarded at the Johannes Gutenberg-University of Mainz. Thesis:|
|since 2003||One of the core developers of ESPResSo|
|Oct. 2001- Dec. 2004||Doctorate studies at the Max-Planck-Institute for Polymer Research in Mainz, Germany|
|Oct. 2001||Diploma in Mathematics at the Johannes Gutenberg- University of Mainz. Thesis:|
|Oct. 1996 - Oct.2001||Studies of Mathematics at the Johannes Gutenberg-University of Mainz|
|1998 - 2002||Participating in the RoboCup, a worldwide competition on multi-agent systems, as member of the Mainz Rolling Brains|
- Languages: German and English (fluent), Russian, Dutch (beginner)
- Computing languages: C, C++, Tcl/Tk, Python, MPI, CUDA, shell scripting
- System administration: Unix (Linux, Tru64, AIX, Irix, Solaris), MacOS/Darwin, Windows