The static friction preventing the free sliding of nanosized rare gas solid islands physisorbed on incommensurate crystalline surfaces is not completely understood. Simulations modeled on Kr/Pb(111) ...highlight the importance and the scaling behavior of the island's edge contribution to static friction.
One of the most promising techniques used for studying the electronic properties of materials is based on Density Functional Theory (DFT) approach and its extensions. DFT has been widely applied in ...traditional solid state physics problems where periodicity and symmetry play a crucial role in reducing the computational workload. With growing compute power capability and the development of improved DFT methods, the range of potential applications is now including other scientific areas such as Chemistry and Biology. However, cross disciplinary combinations of traditional Solid-State Physics, Chemistry and Biology drastically improve the system complexity while reducing the degree of periodicity and symmetry. Large simulation cells containing of hundreds or even thousands of atoms are needed to model these kind of physical systems. The treatment of those systems still remains a computational challenge even with modern supercomputers. In this paper we describe our work to improve the scalability of Quantum ESPRESSO (Giannozzi et al., 2009 3) for treating very large cells and huge numbers of electrons. To this end we have introduced an extra level of parallelism, over electronic bands, in three kernels for solving computationally expensive problems: the Sternheimer equation solver (Nuclear Magnetic Resonance, package QE-GIPAW), the Fock operator builder (electronic ground-state, package PWscf) and most of the Car–Parrinello routines (Car–Parrinello dynamics, package CP). Final benchmarks show our success in computing the Nuclear Magnetic Response (NMR) chemical shift of a large biological assembly, the electronic structure of defected amorphous silica with hybrid exchange–correlation functionals and the equilibrium atomic structure of height Porphyrins anchored to a Carbon Nanotube, on many thousands of CPU cores.
Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water models applied to ...simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based accelerator MD-GRAPE 3 was used to accelerate substantially the computation of non-bonded forces, while GPU-based platforms were also used in conjunction with CUDA-enabled versions of the LAMMPS MD software packages to reduce computational time dramatically. The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance relative to power consumption, it is seen that GPU-based computing is quite attractive.
The static friction preventing the free sliding of nanosized rare gas solid islands physisorbed on incommensurate crystalline surfaces is not completely understood. Simulations modeled on Kr/Pb(111) ...highlight the importance and the scaling behavior of the island's edge contribution to static friction.
The free "superlubric" sliding of a physisorbed rare gas island is paradoxically hindered even on a perfect incommensurate crystalline surface by portions of the island's own edges. As a consequence, the island's static friction scales for growing area with a lower power than 1/2.
beta sub(2)-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of beta sub(2)-microglobulin structure, dynamics, and thermodynamics in ...solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of beta sub(2)-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of beta sub(2)-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of beta sub(2)-microglobulin provides details of the binding modes of the drug and a rationale for its effect. Proteins 2011. copyright 2010 Wiley-Liss, Inc.
The static friction preventing the free sliding of nanosized rare gas solid islands physisorbed on incommensurate crystalline surfaces is not completely understood. Simulations modeled on Kr/Pb(111) ...highlights the importance and the scaling behavior of the island's edge contribution to static friction.
One of the most promising techniques used for studying the electronic properties of materials is based on Density Functional Theory (DFT) approach and its extensions. DFT has been widely applied in ...traditional solid state physics problems where periodicity and symmetry play a crucial role in reducing the computational workload. With growing compute power capability and the development of improved DFT methods, the range of potential applications is now including other scientific areas such as Chemistry and Biology. However, cross disciplinary combinations of traditional Solid-State Physics, Chemistry and Biology drastically improve the system complexity while reducing the degree of periodicity and symmetry. Large simulation cells containing of hundreds or even thousands of atoms are needed to model these kind of physical systems. The treatment of those systems still remains a computational challenge even with modern supercomputers. In this paper we describe our work to improve the scalability of Quantum ESPRESSO \cite{Quantum-Espresso} for treating very large cells and huge numbers of electrons. To this end we have introduced an extra level of parallelism, over \emph{\emph{electronic bands}}, in three kernels for solving computationally expensive problems: the Sternheimer equation solver (Nuclear Magnetic Resonance, package QE-GIPAW), the Fock operator builder (electronic ground-state, package PWscf) and most of the Car-Parrinello routines (Car-Parrinello dynamics, package CP). Final benchmarks show our success in computing the Nuclear Magnetic Response (NMR) chemical shift of a large biological assembly, the electronic structure of defected amorphous silica with hybrid exchange-correlation functionals and the equilibrium atomic structure of height Porphyrins anchored to a Carbon Nanotube, on many thousands of CPU cores.
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