Super Massive Computations in Theoretical Physics

Contribution List

12. Atomistic Simulation of Single Molecule Experiments: Molecular Machines and a Dynasome.

Helmut Grubmüller

11/02/2015, 15:00

Proteins are biological nanomachines which operate at many length and time scales. We combined single molecule, x-ray crystallographic, and cryo-EM data with atomistic simulations to elucidate how these functions are performed at the molecular level. Examples include the mechanics of energy conversion in F-ATP synthase and tRNA translocation within the ribosome. We will show that tRNA...

16. Variational Molecular Dynamics

Silvio Beccara

11/02/2015, 16:30

The Variational Molecular Dynamics (VMD) approach is a framework aimed at the efficient computation of the most probable folding pathways connecting denatured protein configurations with the native state. Its high computational efficiency enables the simulation of very slow (up to hours) transitions on large systems (hundreds of residues), with realistic atomistic force fields. The VMD...

13. Zn induced structural aggregation patterns of β-amyloid peptides by first-principle simulations and XAS measurements

Velia Minicozzi

11/02/2015, 16:50

We show in this work that in the presence of Zn ions a peculiar structural aggregation pattern of β-amyloid peptides in which metal ions are sequentially coordinated to either three or four histidines of nearby peptides is favored. To stabilize this configuration a deprotonated imidazole ring from one of the histidines forms a bridge connecting two adjacent Zn ions. Though present in zeolite...

15. Ab initio simulations of X-ray Absorption Spectroscopy spectra. The case of Cu(II) ions in water.

Francesco Stellato (R)

11/02/2015, 17:10

The possibilities offered by high performance parallel computing forfirst principle simulations of systems composed by a large number of atoms are opening up the way to new approaches not only for ab initio molecular dynamics simulations, but also for providing improved models for the interpretation of experimental data. In this context, we are developing a strategy to compute the electron...

14. First-principles simulations at the nanoscale (and towards the exascale) with Quantum ESPRESSO.

Paolo Giannozzi

11/02/2015, 17:30

17. Computing the visible universe via large-scale simulations of QCD.

Constantia Alexandrou.

12/02/2015, 09:30

Quantum Chromodynamics (QCD) is the fundamental theory of the strong interactions that describe, among other phenomena, the binding of nucleons to form nuclei, nuclear fission, supernovae and stellar evolution. Most of the visible matter in the universe is generated via the strong interactions. Understanding the complex phenomena that are due to the strong force is particularly demanding not...

18. Chiral symmetry breaking in QCD Lite

Leonardo Giusti (M)

12/02/2015, 11:00

We compute the spectral density of the (Hermitean) Dirac operator in Quantum Chromodynamics with two light degenerate quarks near the origin. We use CLS lattices generated with two flavours of O(a)-improved Wilson fermions corresponding to pseudoscalar meson masses down to 190 MeV, and with spacings in the range 0.05--0.08 fm. Thanks to the coverage of parameter space, we can extrapolate our...

19. Confinement and extreme conditions in lattice QCD

Leonardo Cosmai (BA)

12/02/2015, 11:20

We discuss some results obtained in studying the QCD vacuum structure at zero temperature and the QCD phase diagram at finite temperature and baryon density.

20. Properties of strongly interacting matter in extreme conditions.

Francesco Negro (PI)

12/02/2015, 11:40

We discuss recent results obtained by lattice QCD simulations and regarding the properties of strongly interacting matter at finite temperature and density, or in the presence of external background fields.

21. Non-perturbative renormalization of the energy-momentum tensor in SU(3) Yang-Mills theory.

Michele Pepe (MIB)

12/02/2015, 12:00

We present a strategy for a non-perturbative determination of the finite renormalization constants of the energy-momentum tensorin the SU(3) Yang-Mills theory. The computation is performed by imposing on the lattice suitable Ward Identites in a finite box in presence of shifted boundary conditions. We show accurate numerical data for values of the bare coupling g0^2 ranging for 0 to 1.

22. Adopting modern hardware for lattice QCD calculations.

Mario Schröck, Silvano Simula (ROMA3)

12/02/2015, 12:20

The calculation of observables in lattice quantum chromodynamics (QCD) requires to solve many linear equation systems with matrices ofrank up to several millions. We discuss the adoption of modern highly parallel computer hardware, in particular GPUs and Intel MICs, to accelerate this task.

23. A perturbative study of the Schrödinger Functional in Lattice QCD.

Pol Vilaseca Mainar

12/02/2015, 12:40

Strong interactions are (so far) correctly described by Quantum Chromodinamics (QCD). This theory explains accurately phenomena from the scale of hadronic physics at low energies to the production of jets in high energy collisions and quark-gluon plasmas. Due to the property of asymptotic freedom, the theory can be studied at high energies by means of perturbation theory. At low energies, a...

24. Numerical simulations of fluids at high and at low Reynolds numbers.

Federico Toschi (INFN)

12/02/2015, 15:00

In this talk we will review few recent results relative to the direct numerical simulation of turbulent and laminar fluids. We will discuss some of the open challenges in particular in relation to the transport of particulate matter.

25. Magnetic field amplification and the search for Magneto-Rotational-Instability in bar-mode unstable Neutron stars.

Roberto De Pietri (PR)

12/02/2015, 16:30

Thanks to the recent advances in high performance computing, it is opening the possibility to tackle new problems on the dynamics of magnetic fields inside neutron stars where very-high-resolution three-dimensional simulations in full General Relativity are needed. We present results on the possible roles that magnetic instabilities may have the evolution of neutron star during matter unstable...

26. The Einstein toolkit on SUMA systems.

Michele Brambilla (INFN)

12/02/2015, 16:50

Recent progress on Numerical Relativity and General Relativistic Magneto Hydrodynamics (GRMHD) are opening new windows on our understanding of possible sources of Gravitational Waves (GWs) that would be detected in the coming years by the INFN gravitational wave observatory VIRGO. Unfortunately the power and memory required for cutting edge simulations with the desired accuracy require...

33. Distributed Polychronous Spiking Neural Net (DPSNN) application code for evaluation of off-the-shelf and custom systems dedicated to neural network simulations

Elena Pastorelli

12/02/2015, 17:10

In the framework of the EURETILE European project, a natively distributed application has been developed, as a representative of plastic spiking neural network simulators. The DPSNN-STDP (Distributed Simulation of Polychronous Spiking Neural Network with synaptic Spike-Timing Dependent Plasticity) will be used in the context of the CORTICONIC European FET project to produce simulations of...

27. NaNet: a network interface card family for GPU-based real-time systems.

Andrea Biagioni (ROMA1)

12/02/2015, 17:30

The NaNet project aims to deliver a low-latency, high-throughput data transport mechanism for GPU-based real-time systems. The goal is a FPGA-based PCIe Network Interface Card (NIC) design with GPUDirect P2P/RDMA capability featuring a configurable and extensible set of data transmission channels. An ad-hoc network stack protocol offload engine and a data stream processing stage combined with...

28. Multi-dimensional Torus networks for current and next generation HPC systems: APEnet+ status and perspectives.

Roberto Ammendola (ROMA2)

12/02/2015, 17:50

The Apenet family interconnect cards have been out for more than a decade, pursuing the legacy of the APE custom massively parallel computing machines and bringing few concepts (3D-torus network, high bandwidth, low latency) to commodity clusters. Over the years we have been added key features to our custom network, like Remote-DMA programming paradigm or, lately, NVidia peer-to-peer...

29. The European Supercomputer Projects DEEP and DEEP-ER.

Norbert Eicker (Julich Supercomputer Centre), Thomas Lippert

13/02/2015, 09:30

30. Theocluster ZEFIRO.

Giuseppe Caruso (P)

13/02/2015, 11:00

Attualmente il theocluster denominato 'Zefiro' (cluster per il calcolo di fisica teorica) di nuova installazione finanziato da GR IV e dal progetto SUMA è costituito da 32 macchine ciascuna con 512 Gb di ram e 4 processori (ciascuno da 16 core); conta in totale 2048 core di calcolo AMD Opteron 6380 (2,5GHz) e collegamento Infiniband QDR gestiti da uno switch Mellanox IS5100 a 108 porte....

31. Portability, efficiency and maintainability: the case of OpenACC

Dr Enrico Calore (INFN, Sezione di Ferrara)

13/02/2015, 11:20

An increasing number of HPC systems rely on heterogeneous node architectures combining traditional multicore CPUs with power efficient accelerators. Writing efficient applications for these systems could be cumbersome today, since porting may require code rewriting using new programming languages, such CUDA or OpenCL, threatening maintainability, stability and correctness. Several...

32. Round Table and Conclusions

13/02/2015, 11:40

11. Registration