Parallel Desolvation Energy Term Calculation for Blind Docking on GPU Architectures

2017 ◽  
Author(s):  
Hocine Saadi ◽  
Nadia Nouali-Taboudjemat ◽  
Abdellatif Rahmoun ◽  
Baldomero Imbernon ◽  
Horacio Perez-Sanchez ◽  
...  
Keyword(s):  
Energy Term ◽  
Desolvation Energy ◽  
Gpu Architectures

An Octree-based, Cartesian CFD Solver for Helios on CPU and GPU Architectures.

2021 ◽  
Author(s):  
Dylan Jude ◽  
Jay Sitaraman ◽  
Andrew M. Wissink
Keyword(s):  
Gpu Architectures

Exploring Applications of STT-RAM in GPU Architectures

2021 ◽  
Vol 68 (1) ◽  
pp. 238-249
Author(s):  
Xiaoxiao Liu ◽  
Mengjie Mao ◽  
Xiuyuan Bi ◽  
Hai Li ◽  
Yiran Chen
Keyword(s):  
Gpu Architectures

scholarly journals Use of scaled-particle theory in the assessment of the Ph4As+/Ph4B− assumption for single ions

1979 ◽  
Vol 57 (1) ◽  
pp. 71-76 ◽  
Author(s):  
Michael H. Abraham ◽  
Asadollah Nasehzadeh
Keyword(s):  
Free Energy ◽  
Recent Work ◽  
Scaled Particle Theory ◽  
Cavity Formation ◽  
Energy Term ◽  
Free Energies ◽  
Particle Theory ◽  
Novel Method ◽  
Energy Of Interaction ◽  
Solvent Molecules

A novel method for the assessment of the Ph4As+/Ph4B− assumption for free energies of transfer of single ions has recently been suggested by Treiner, and used by him to deduce that the assumption is not valid for transfers between water, propylene carbonate, sulpholane, dimethylsulphoxide, N-methyl-2-pyrrolidone, and perhaps also dimethylformamide. The basis of the method is the estimation of the free energy of cavity formation by scaled-particle theory, together with the hypothesis that the free energy of interaction of Ph4As+ (or Ph4B−) with solvent molecules is the same in all solvents, ΔGt0(int) = 0. It is shown in the present paper that (a) whether or not the Ph4As+/Ph4B− assumption applies to transfer to a given solvent depends on which other solvent is taken as the reference solvent in Treiner's method, (b) the calculation of the cavity free energy term by scaled-particle theory and by the theory of Sinanoglu – Reisse – Moura Ramos (SRMR) yields values so different that the method cannot be considered reliable, (c) the calculation of cavity enthalpies and entropies for Ph4As+ or Ph4B− by scaled-particle theory yields results that are chemically not reasonable, (d) the hypothesis that ΔGt0(int) = 0 conflicts with SRMR theory, and (e) the conclusions reached by Treiner are not in accord with recent work that in general supports the Ph4As+/Ph4B− assumption for solvents that are rejected by Treiner.

Local Density Approximations for the Energy of a Periodic Coulomb Model

2003 ◽  
Vol 13 (08) ◽  
pp. 1185-1217 ◽  
Author(s):  
Olivier Bokanowski ◽  
Benoît Grebert ◽  
Norbert J. Mauser
Keyword(s):  
Kinetic Energy ◽  
Local Density ◽  
Exchange Energy ◽  
Asymptotic Approximations ◽  
Exchange Potential ◽  
Energy Term ◽  
Local Exchange ◽  
Coulomb Model ◽  
Local Density Approximations ◽  
Number Of Particles

We deal with local density approximations for the kinetic and exchange energy term, ℰ kin (ρ) and ℰ ex (ρ), of a periodic Coulomb model. We study asymptotic approximations of the energy when the number of particles goes to infinity and for densities close to the constant averaged density. For the kinetic energy, we recover the usual combination of the von-Weizsäcker term and the Thomas–Fermi term. Furthermore, we justify the inclusion of the Dirac term for the exchange energy and the Slater term for the local exchange potential.

GPU-based pseudo-transient finite difference solution for power-law viscous flow in cartesian, polar and spherical coordinates

2021 ◽  
Author(s):  
Emilie Macherel ◽  
Yuri Podladchikov ◽  
Ludovic Räss ◽  
Stefan M. Schmalholz
Keyword(s):  
High Resolution ◽  
Finite Difference ◽  
Viscous Flow ◽  
Power Law ◽  
High Performance ◽  
Viscoelastic Behavior ◽  
Iterative Solution ◽  
Circular Inclusion ◽  
Lithospheric Flexure ◽  
Gpu Architectures

<p>Power-law viscous flow describes well the first-order features of long-term lithosphere deformation. Due to the ellipticity of the Earth, the lithosphere is mechanically analogous to a shell, characterized by a double curvature. The mechanical characteristics of a shell are fundamentally different to the characteristics of plates, having no curvature in their undeformed state. The systematic quantification of the magnitude and the spatiotemporal distribution of strain, strain-rate and stress inside a deforming lithospheric shell is thus of major importance: stress is for example a key physical quantity that controls geodynamic processes such as metamorphic reactions, decompression melting, lithospheric flexure, subduction initiation or earthquakes.</p><p>Stress calculations in a geometrically and mechanically heterogeneous 3-D lithospheric shell require high-resolution and high-performance computing. The pseudo-transient finite difference (PTFD) method recently enabled efficient simulations of high-resolution 3-D deformation processes, implementing an iterative implicit solution strategy of the governing equations for power-law viscous flow. Main challenges for the PTFD method is to guarantee convergence, minimize the required iteration count and speed-up the iterations.</p><p>Here, we present PTFD simulations for simple mechanically heterogeneous (weak circular inclusion) incompressible 2-D power-law viscous flow in cartesian and cylindrical coordinates. The flow laws employ a pseudo-viscoelastic behavior to optimize the iterative solution by exploiting the fundamental characteristics of viscoelastic wave propagation.</p><p>The developed PTFD algorithm executes in parallel on CPUs and GPUs. The development was done in Matlab (mathworks.com), then translated into the Julia language (julialang.org), and finally made compatible for parallel GPU architectures using the ParallelStencil.jl package (https://github.com/omlins/ParallelStencil.jl). We may unveil preliminary results for 3-D spherical configurations including gravity-controlled lithospheric stress distributions around continental plateaus.</p>

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