September 2010 - Allocations-admins - mailman3.cels.anl.gov

New LCRC report submitted for qmc_for_nuclei
by support＠lcrc.anl.gov 27 Sep '10

27 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=qmc_for_nu…

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New LCRC report submitted for UNEDF_Optimization
by support＠lcrc.anl.gov 27 Sep '10

27 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=UNEDF_Opti…

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New LCRC report submitted for UNEDF_Optimization
by support＠lcrc.anl.gov 27 Sep '10

27 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=UNEDF_Opti…

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New LCRC report submitted for CCT1
by support＠lcrc.anl.gov 26 Sep '10

26 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=CCT1

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New LCRC report submitted for CCT1
by support＠lcrc.anl.gov 26 Sep '10

26 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=CCT1

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New LCRC report submitted for radix
by support＠lcrc.anl.gov 24 Sep '10

24 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=radix

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[LCRC Accounts] Yearly Allocation Request from Nek5000
by accounts＠lcrc.anl.gov 23 Sep '10

23 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Paul Fischer Project Name: Nek5000 Division: MCS Project title: Scalable CFD Algorithms Associated funding: Applied Math Research Program, Nuclear Energy Advanced Modeling and Simulation Other Systems: ALCF Intrepid (BG/P), 128-core Linux cluster, Cosmea Science: Our mission is to develop and deploy scalable algorithms for simulation-based science applications that rely on numerical solution of partial differential equations. Our primary vehicle for algorithm development is the fluid/thermal simulation code, Nek5000, and its off-shoots, NekCEM (for computational electromagnetics) and NekLBM (for lattice Boltzmann methods). There are approximately 30 research groups worldwide currently using Nek5000. We use Nek5000---and the science applications brought to us through our user community---as vehicles for the development and test of new numerical algorithms that include stabilized high-order methods, scalable linear solvers, advanced timestepping methods, and so forth. We emphasize that these algorithms cannot be developed in isolation from applications, as many of the relevant issues do not arise at small scale or in simple model problems devoid of complex physics and/or geometry. Thus, to address algorithmic issues at the forefront of science-based simulation we require a code that is capable of solving problems _at_scale_ and that is sufficiently flexible to allow adaptation to new physics. Project description: Nek5000 is a petascale fluid/thermal simulation code used for a host of applications including reactor thermal hydraulics, combustion, MHD, oceanography, spatiotemporal chaos, and vascular flow modeling. Nek5000 is a grid-based PDE (partial differential equation) solver in three space dimensions and time. The code has long been at the forefront of high-order methods and scalable algorithms. It was one of the first comprehensive software tools developed for distributed memory parallel platforms. It pioneered the development of high-order discretizations that, because of their ability to accurately capture interacations over a broad range of scales, are now deemed an essential ingredient of petascale simulation science and that are being adapted across virtually all disciplines (e.g., fusion, aeronautics, biofluids and geophysics). We have demonstrated > 80% parallel efficiency on BG/P (strong scaling) out to P=131,072 processors, using only 7300 points/processor at the largest scale. Nek5000 was recognized with a Gordon Bell award in 1999 for scalability and algorithmic quality. Some of the science applications we anticipate addressing in the coming year are: boundary-layer MHD, non-hydrostatic modeling of ocean currents, and film cooling for gas turbine blades. This latter problem is likely to require 50-100K core-hours. Most of the simulations, however, will be performed by the Texas A&M group leading the project with their own compute resources. This is our standard model -- get the problem running, and then turn it over to the research group in charge. In the past, this model has led to very successful collaborations in oceanography ( > 12 publications), spatiotemporal chaos ( > 12 publications), and MHD ( 4 publications and two INCITE awards). We note that we have access to a dedicated 128-core linux cluster (under a nuclear engineering project) and to resource on BG/P through INCITE and discretionay allocations. This request is to address mid-range capabilities -- particularly for those applications that would not fit on the 128-core cluster. Project URL: http://www.mcs.anl.gov/~fischer/sem1b Current FY Hours Used: undetermined amount New FY Requested allocation: 350000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from kv
by accounts＠lcrc.anl.gov 23 Sep '10

23 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Benoit Roux Project Name: kv Division: BIO Project title: Studies of voltage-vgated potassium channel Associated funding: NIH/NIGMS, R01-GM062342 "Computational studies of ion channels" INCITE from Office of Science Other Systems: BG/P, NCSA, PSC, KBT Science: Molecular dynamics of membrane proteins that are affected by the transmembrane voltage Project description: Voltage-gated potassium (Kv) channels are membrane proteins that respond to changes in the transmembrane potential by altering their conformation to allow the passive conduction of K+ ions across the cell membrane. These channels are tetrameric proteins, in which each subunit comprises six transmembrane (TM) helical segments (S1-S6). The ion conduction pore is located at the center of the tetrameric structure and is formed by the S5 and S6 helices from the four subunits. The first four segments (S1-S4) in each subunit form a voltage-sensing domain (VSD) that is located in the lipid membrane at the periphery of the central pore domain (PD). Upon depolarization of the membrane, the VSD in each subunit undergoes a voltage-dependent transition from a resting to an active conformation, which then leads the opening of the intracellular gate of the ion conduction pore. The conformational changes associated with the activation of Kv channels result in the transfer of an electric charge Delta-Q across the membrane, that can be measured experimentally as a small transient capacitive current. In the Shaker K+ channel, the "gating charge" corresponds to the transfer of 12-14 elementary charge (e) along the transmembrane electric field. Correspondingly, a change V in the membrane potential shifts the relative free energy of the closed and open conformations by V*Delta-Q. The gating charge DeltaQ is, thus, a key concept to explain how channel activation is coupled to the membrane potential. Initially postulated by Hodgkin and Huxley in 1952, it was first detected and measured more than 20 years later by Armstrong and Bezanilla. Ultimately, explaining the voltage-gating mechanism of Kv channels in molecular terms requires gaining knowledge of the active and resting conformations, and then showing how those conformations are able to account for the experimentally observed gating charge Delta-Q. Our strategy is to first carefully construct atomic models of the active and resting states of Kv channels that are consistent with all available experimental information using protein structure prediction algorithms. We also have a novel method to compute the gating charge using all-atom MD. Pathak et al. have generated detailed atomic models of Kv1.2 in the open/active and closed/resting states using the Rosetta-Membrane structure prediction program. The model of the open/active state complements the information missing from the X-ray structure of the Kv1.2 channel used as a template, while the S1-S2, S2-S3, and S3-S4 loops in the voltage sensing domain were modeled de novo. These results offer a promising starting point to expand our understanding of voltage gating in Kv channels. Some critical issues must be addressed. Recently, the stability of those structural models in the complex dynamical environment of the lipid bilayer was ascertained using molecular dynamics (Khalili-Araghi et al, 2010) and the gating charge was calculated using a new theory of the membrane potential (Roux, 2008). Our long-term goal is to refine the atomic models of the closed/resting and open/activated states and test their ability to account for the experimentally observed gating charge using all-atom MD and explicit lipid membrane environment. In the coming year, we have 3 specific sub-projects: 1) We want to incorporate additional experimental constraints in the refinement of the resting down-state of the voltage sensor (Macpos et al, 2007). Ernesto Vargas (a graduate student at the University of Chicago) is carrying out this project. 2) We want to predict the effect of side-directed mutations on the channels, namely the effect of substitution along the transmembrane helix S4. David Medovoy (a graduate student at the University of Chicago) is carrying out this project. 3) We want we want to refine the 3d structure of the bacterial voltage-gated channel KvAP using electron paramagnetic resonance (EPR). We will use a new mmethod that has been develop by us (Sompornpisut et al, 2008) and tested on other channels (Vasquez et al, 2008). This work will be carried out by a visiting scholar (Rong Shen). We had originally requested 250K nodehours for the fiscal year, but only half of that, 125K was granted by the Allocation committee. These systems run NAMD on 25 cores at a rate of about 1 day/nanosecond of MD. For a total of 50 ns of simulation total for the 3 projects means that we need about 300,000 nodehours. REFERENCES Pathak, M.M., V. Yarov-Yarovoy, G. Agarwal, B. Roux, P. Barth, S. Kohout, F. Tombola, and E. Y. Isacoff. (2007). "Closing in on the Resting State of the Shaker K+ Channel." Neuron 56, 124-140. Campos, F.V., B. Chanda, B. Roux, and F. Bezanilla. (2007). "Two Atomic Constraints Unambiguously Position the S4 Segment Relative to S1 and S2 Segments in the Closed State of Shaker K Channel." Proceedings of the National Academy of Sciences of the United States of America 104, 7904-7909. Sompornpisut, P., B. Roux, and E. Perozo. 2008. Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. Biophys 95:5349-5361. Vasquez, V., M. Sotomayor, D. M. Cortes, B. Roux, K. Schulten, and E. Perozo. 2008. Three-dimensional architecture of membrane-embedded MscS in the closed conformation. J Mol Biol 378:55-70. Pan, A.C., D. Sezer, and B. Roux. (2008). "Finding Transition Pathways Using the String Method with Swarms of Trajectories." J Phys Chem B 112, 3432-3440. Roux, B. 2008. The membrane potential and its representation by a constant electric field in computer simulations. Biophys J 95:4205-4216. Khalili-Araghi, F., V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, and K. Schulten. 2010. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J 98:2189-2198. Project URL: http://thallium.bsd.uchicago.edu/RouxLab/ Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Justification: We had originally requested 250K nodehours for the fiscal year, but only half of that, 125K was granted by the Allocation committee. These systems run NAMD on 25 cores at a rate of about 1 day/nanosecond of MD. For a total of 50 ns of simulation total for the 3 projects means that we need about 300,000 nodehours. For the resources, we expect to be using NAMD runs of up to 256 CPU. This amounts to: 256 CPU * 24 hours * 50 days = ~300,000 Fusion will be an excellent platform to establish and execute the string method algorithm. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from Bubble
by accounts＠lcrc.anl.gov 23 Sep '10

23 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Zeke Insepov Project Name: Bubble Division: MCS Project title: Ab-initio simulation of bubbles in dense media Associated funding: RERTR Other Systems: Blue Gene Science: Summary of the project: Fission gases form small bubbles in nuclear fuels that leads to lattice swelling and cracking. Our simulation will be useful for understanding this phenomenon. To date assessments of chemistry and physics of imploding vapor-gas filled bubbles has been conducted with continuum mechanics formulations in conjunction with empirically-derived equations of state. The multitude of condensation-evaporation phenomena at liquid-gas interface, dissociation and ionization phenomena which can occur during super compression and super heating for complex molecules has not been possible to assess on a molecular dynamics scale. In collaboration with the University of Palermo, Italy, researchers at Purdue University aim to conduct scoping assessments of above-mentioned phenomena - in cooperation with Dr. Zeke Insepov of Argonne National Laboratory. Scoping assessment tool targeted for use is the Siesta code package which uses a linear-scaling density functional approach for capturing the physics and chemistry on the molecular dynamics scale. DFT molecular dynamics simulations can be performed for a number of points of the phase diagram region corresponding to the transient conditions the liquid-bubble interface experiences during the supercompression cycles. This should give information about chemical reactions that can change the behavior of the interface itself, an issue which is not explicitly taken into consideration in the empirical equation of states. Project description: computational methods: Density Functional Molecular Dynamics simulations using the siesta method programming model: parallel experiments planned: molecular dynamics simulations software requirements: fortran compiler (e.g. openmpi) sizes of calculations run on and/or planned for LCRC or other systems: hundreds of picoseconds time scale MD simulations on 100-500 atoms systems expected number of project members: 5 We expect a total of 5 project members (two including a student from Purdue University, and three staff from the University of Palermo). Results of assessments are expected to lead to joint proposals to NSF, DoE (Office of Science, and NE), and DARPA. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 3000000 Justification: We recently purchased a new software - vasp - that will be widely applied to nuclear fuel simulation. One of the applications of the vasp software is the new interatomic potential for the Molybdenum-Xenon system that has been recognized as a breakthrough achievement for the future metal fuel simulations. Thank You, The LCRC Accounts System

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New LCRC report submitted for Comp_Nanocatalysis
by support＠lcrc.anl.gov 23 Sep '10

23 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=Comp_Nanoc…

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