The Experts below are selected from a list of 37695 Experts worldwide ranked by ideXlab platform
P Faccioli - One of the best experts on this subject based on the ideXlab platform.
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variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent
Physical Review Letters, 2015Co-Authors: S A Beccara, L Fant, P FaccioliAbstract:We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small Computer Cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an α and a β protein performed with the same all-atom force field on the Anton superComputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
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variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent
arXiv: Soft Condensed Matter, 2014Co-Authors: S A Beccara, L Fant, P FaccioliAbstract:We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small Computer Cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against molecular dynamics (MD) simulations of the folding of an alpha- and a beta-protein performed with the same all-atom force field on the Anton superComputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
S A Beccara - One of the best experts on this subject based on the ideXlab platform.
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variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent
Physical Review Letters, 2015Co-Authors: S A Beccara, L Fant, P FaccioliAbstract:We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small Computer Cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an α and a β protein performed with the same all-atom force field on the Anton superComputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
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variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent
arXiv: Soft Condensed Matter, 2014Co-Authors: S A Beccara, L Fant, P FaccioliAbstract:We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small Computer Cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against molecular dynamics (MD) simulations of the folding of an alpha- and a beta-protein performed with the same all-atom force field on the Anton superComputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
L Fant - One of the best experts on this subject based on the ideXlab platform.
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variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent
Physical Review Letters, 2015Co-Authors: S A Beccara, L Fant, P FaccioliAbstract:We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small Computer Cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an α and a β protein performed with the same all-atom force field on the Anton superComputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
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variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent
arXiv: Soft Condensed Matter, 2014Co-Authors: S A Beccara, L Fant, P FaccioliAbstract:We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small Computer Cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against molecular dynamics (MD) simulations of the folding of an alpha- and a beta-protein performed with the same all-atom force field on the Anton superComputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
Raymond A. Shaw - One of the best experts on this subject based on the ideXlab platform.
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Practical methods for automated reconstruction and characterization of particles in digital in-line holograms
Measurement Science and Technology, 2009Co-Authors: Jacob P Fugal, Timothy J. Schulz, Raymond A. ShawAbstract:Hologram reconstruction algorithms often undersample the phase in propagation kernels for typical parameters of holographic optical setups. Given in this paper is an algorithm that addresses this phase undersampling in reconstructing digital in-line holograms of particles for these typical parameters. This algorithm has a lateral sample spacing constant in reconstruction distance, has a diffraction limited resolution, and can be implemented with computational speeds comparable to the fastest of other reconstruction algorithms. This algorithm is shown to be accurate by testing with analytical solutions to the Huygens-Fresnel propagation integral. A low-pass filter can be applied to enforce a uniform minimum particle size detection limit throughout a sample volume, allowing this method to be useful in measuring particle size distributions and number densities. Tens of thousands of holograms of cloud ice particles are digitally reconstructed using the algorithm discussed. Positions of ice particles in the size range of 20 mu m-1.5 mm are obtained using an algorithm that accurately finds the position of large and small particles along the optical axis. The digital reconstruction and particle characterization algorithms are implemented in an automated fashion with no user intervention on a Computer Cluster. Strategies for efficient algorithm implementation on a Computer Cluster are discussed.
Ilhan Bayraktar - One of the best experts on this subject based on the ideXlab platform.
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Computational simulation methods for vehicle thermal management
Applied Thermal Engineering, 2012Co-Authors: Ilhan BayraktarAbstract:Abstract Increasing power requirements along with weight and space constrains requires implementation of more intelligent thermal management systems. The design and development of such systems can only be possible with a thorough understanding of component and system level thermal loads. The present work implements 1-D and 3-D unsteady CFD based simulation tools in a military ground vehicle design process. Both powertrain cooling and HVAC systems are simulated in various operating conditions on a HPC Computer Cluster using multiple fidelity tools. HVAC system variables are optimized with gradient based optimization libraries. The simulation results are compared and validated with experimental tests.