Investigation of an Unusual Phase Transition Freezing on heating of liquid solution
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1 Investigation of an Unusual Phase Transition Freezing on heating of liquid solution Calin Gabriel Floare National Institute for R&D of Isotopic and Molecular Technologies, Cluj-Napoca, Romania Max von Laue Paul Langevin Joseph Fourier
2 Cluj-Napoca - Romania Cluj in Bird s eye view by Georg Houfnagel after a painting by Egidius van der Rye. The city center - air view from south-west (1930)
3 Our cluster Hewlett Packard Blade C7000 with 16 Proliant BL280c G6 (2 Intel Quad-core Xeon 2.93 GHz, 16 Gb RAM, 500 Gb HDD) running, TORQUE, MAUI, GANGLIA ( NAGIOS, configured from scratch - Scientific Linux 5.3 (Boron) We installed different Intel compilers, mathematical and MPI libraries We are using different Quantum chemistry codes like: AMBER, GROMACS, NAMD, LAMMPS, CPMD, CP2K, Gaussian, GAMESS, MOLPRO, DFTB+, Siesta, VASP, Accelrys Materials Studio We are hosting also the RO-14-ITIM Grid site (
4 The story of a serendipitous discovery 1 α-cyclodextrine, αcd: the association of 6 glucose units: (C 6 O 5 H 10 ) 6 4-methylpyridine, 4MP: C 6 NH 7..and a bit of water 1 M. Plazanet, C. Floare, M. R. Johnson, R. Schweins, H. P. Tommsdorff, Freezing on heating of liquid solutions, J. Chem. Phys., 121(11), 5031 (2004), ILL Annual Report 2004, and the papers which followed.
5 Temperature C Solid phase Liquid phase Concentration, αcd[g]/4mp[l] 200g/l ~ 1 αcd for 50 4MP
6 A movie by A. Filhol, Laue-Langevin Institute Azobenzene : melts at 66 o C CD-4MP : freezes at 66 o C
7 Concentration mg/ml Solubility αcd in 4MP Temperature C
8 How we can rationalize these surprising observations? As temperature increases, entropy must increase, how is this compatible with the observation that crystalline order is established and that molecular motions are slowed down? Characterize the changes of the structure and of the molecular dynamics by: elastic and inelastic neutron scattering neutron and X-ray diffraction, low-field NMR and molecular dynamics simulations
9 NEUTRON SCATTERING AT THE INSTITUTE LAUE-LANGEVIN (ILL) X-ray SCATTERING AT ESRF
10
11 a) Hysteresis-like fixed window (elastic) scan, IN10, ILL; b) Quasi-elastic neutron spectra, IN5, ILL
12 F. Ding and N. Dokholyan, Trends in Biotechnology 23(9) 450 (2005)
13 Model studied system: NPT molecular dynamics simulations using Accelrys CERIUS 2 v4.6 with COMPASS forcefield running on different SGI workstation A periodic box with the dimensions 24Å 24Å 24Å, containing: one -CD molecule 50 molecules of 4MP 826 atoms
14 20 -CD molecules 1120 molecules of 4MP 240 water molecules NPT ensemble MD using AMBER9 (60 Å) 3 box atoms speed of 0.22ns day (1 core), 0.39ns day (2 cores) and 0.69 (4 cores) Infiniband is needed for a further scale up An AMBER benchmark on IBM SP5 cluster (IBM p575 Power 5, bassi.nersc.gov, cpu nodes, 1.9 GHz Power 5+ cpu, 2 MB L2 cache, 36 MB L3 cache, 32 GB memory per node) produced 22ns/day when using 256 cores, on a system containing around atoms. Initially we have to optimize the force fields using the force-matching method 100 ns long trajectories at different temperatures must be calculated for good statistics Hydrogen-bond dynamics formation analysis and cluster Correlation coefficients This system will be studied at CINECA, Italy, on a project founded by HPC-Europa2 program on 256 CPUs
15 1 Million atoms Simulation Dream Amber 11 GPU performance compared with that on
16 GPU Codes
17 Milu (Miramare Interoperable Lite User Interface), a tool to set up easily an UI on (almost) any machine ( BEMuSE: Bias-Exchange Metadynamics Submission Environment ( EPICO elab Procedure for Installation and Configuration ( Training Tools: GRID Seed ( Moodle Platform (
18 Running AMBER on GRID Giulio Rastelli and col. from University of Modena already deployed AMBER on GRID. Contacts were established with the institution distributing Amber regarding the license policy on the grid. The outcome of the negotiation was that we were allowed to deploy Amber on the grid under the following conditions*: Each cluster deploying Amber had to have at least one license. Grid users allowed to use Amber had to come from one of the laboratories owning an Amber license. Grid users allowed to use Amber under the conditions described above could deploy their computations on all the grid clusters. * Vincent Breton, Doman Kim, and Giulio Rastelli, WISDOM: A Grid-Enabled Drug Discovery Initiative against Malaria, in Grid Computing: Infrastructure, Service and Applications, Di Lizhe Wang,Wei Jie,Jinjun Chen, pp. 373
19 To know more about it : Freezing on heating of liquid solutions, M. Plazanet, C. Floare, M.R. Johnson, R. Schweins, H.P. Trommsdorff, J. Chem. Phys. 121 (2004) 5031 J. Chem. Phys. 125 (2005) Chem. Phys. 317 (2006) 153 Chem. Phys. 331 (2006) 35 J. Phys. Cond. Mat. 19 (2007) Phys. Chem. Chem. Phys. 12 (2010) 7026
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22 PhysicsWeb, 24/09/2004 Science News, 16/10/2004 Physics World, 11/2004 ILL bulletin, 11/2004 Science et avenir, 12/2004 Science et vie, 01/2005 Geo magasine, german edition, 01/2005
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24 Thank you for your attention
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