Parallel Supercomputer Docking Program of the New Generation: Finding Low Energy Minima Spectrum

2018 ◽  
pp. 314-330 ◽  
Author(s):  
Alexey Sulimov ◽  
Danil Kutov ◽  
Vladimir Sulimov
Keyword(s):  
Low Energy ◽  
Docking Program ◽  
Parallel Supercomputer ◽  
New Generation

scholarly journals Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Igor V. Oferkin ◽  
Ekaterina V. Katkova ◽  
Alexey V. Sulimov ◽  
Danil C. Kutov ◽  
Sergey I. Sobolev ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Quantum Chemical ◽  
Target Function ◽  
Binding Energies ◽  
Low Energy ◽  
Implicit Solvent ◽  
Energy Calculation ◽  
Solvent Models ◽  
Docking Program

The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

scholarly journals Commissioning and early experience with a new-generation low-energy linear accelerator with advanced delivery and imaging functionalities

2011 ◽  
Vol 6 (1) ◽  
pp. 129 ◽  
Author(s):  
Alessandro Clivio ◽  
Giorgia Nicolini ◽  
Eugenio Vanetti ◽  
Antonella Fogliata ◽  
Luca Cozzi
Keyword(s):  
Linear Accelerator ◽  
Early Experience ◽  
Low Energy ◽  
New Generation

scholarly journals New generation low-energy probes for ultralight axion and scalar dark matter

2017 ◽  
Vol 32 (15) ◽  
pp. 1740004 ◽  
Author(s):  
Yevgeny V. Stadnik ◽  
Victor V. Flambaum
Keyword(s):  
Dark Matter ◽  
High Precision ◽  
Topological Defects ◽  
Interaction Constant ◽  
Higher Order ◽  
Classical Field ◽  
Low Energy ◽  
Detection Methods ◽  
Ordinary Matter ◽  
New Generation

We present a brief overview of a new generation of high-precision laboratory and astrophysical measurements to search for ultralight (sub-eV) axion, axion-like pseudoscalar and scalar dark matter (DM), which form either a coherently oscillating classical field or topological defects (solitons). In these new detection methods, the sought effects are linear in the interaction constant between DM and ordinary matter, which is in stark contrast to traditional searches for DM, where the sought effects are quadratic or higher order in the underlying interaction constants (which are extremely small).

Hybrid active suspension system of a helicopter main gearbox

2016 ◽  
Vol 24 (5) ◽  
pp. 956-974 ◽  
Author(s):  
Jonathan Rodriguez ◽  
Paul Cranga ◽  
Simon Chesne ◽  
Luc Gaudiller
Keyword(s):  
System Development ◽  
Active Suspension ◽  
Suspension System ◽  
Low Energy ◽  
Least Mean Square ◽  
Active System ◽  
Active Suspensions ◽  
Suspension Systems ◽  
Development Support ◽  
New Generation

This paper considers experiments on the control of a helicopter gearbox hybrid electromagnetic suspension. As the new generation of helicopters includes variable engine revolutions per minute (RPMs) during flight, it becomes relevant to add active control to their suspension systems. Most active system performance derives directly from the controller construction, its optimization to the system controlled, and the disturbances expected. An investigation on a feedback and feedforward filtered-x least mean square (FXLMS) control applied to an active DAVI suspension has been made to optimize it in terms of narrow-band disturbance rejection. In this paper, we demonstrate the efficiency of a new hybrid active suspension by combining the advantages of two different approaches in vibration control: resonant absorbers and active suspensions. Here, a hybrid active suspension based on the passive vibration filter called DAVI is developed. The objective of this paper is to prove the relevancy of coupling a resonant vibration absorber with a control actuator in order to create an active suspension with larger bandwidth efficiency and low energy consumption. The simulations and experimentation achieved during this suspension system development support this hypothesis and illustrate the efficiency and low energy cost of this smart combination.

Narrow-band red-emitting Mn4+-doped hexafluoride phosphors: synthesis, optoelectronic properties, and applications in white light-emitting diodes

2016 ◽  
Vol 4 (46) ◽  
pp. 10759-10775 ◽  
Author(s):  
Hoang-Duy Nguyen ◽  
Ru-Shi Liu
Keyword(s):  
White Light ◽  
Light Emitting Diodes ◽  
Narrow Band ◽  
Low Energy ◽  
Light Emitting ◽  
Low Energy Consumption ◽  
Long Lifetime ◽  
White Light Emitting Diodes ◽  
New Generation ◽  
Blue Chip

White light-emitting diodes (LEDs), including a blue-chip and yellow-emitting phosphor, are regarded as the new-generation of lighting sources because of their low energy consumption, long lifetime, and environmentally friendliness.

A survey of the LEAR experimental programme

1989 ◽  
Vol 67 (12) ◽  
pp. 1186-1192
Author(s):  
Jean Duclos
Keyword(s):  
Low Energy ◽  
Fundamental Symmetries ◽  
Text Production ◽  
Experimental Programme ◽  
New Generation

During the first period of operation of the low energy antiproton ring (LEAR) from 1983 to 1986, antiproton beams were supplied for several experiments at an intensity between 105 and [Formula: see text]. A first exploration was made of several subjects in physics, including [Formula: see text] and [Formula: see text]–nucleus interactions, [Formula: see text]–atoms, and various annihilation channels. After an improvement by a factor of 5 for the [Formula: see text] production at CERN in 1987, a new generation of experiments is expected to complete the previous studies and to cover new subjects concerning fundamental symmetries.

Finding the Right Problems: Some HREM Applications to Interfaces

1984 ◽  
Vol 42 ◽  
pp. 376-379
Author(s):  
D. Cherns
Keyword(s):  
Grain Boundaries ◽  
High Resolution Electron Microscopy ◽  
Boundary Structure ◽  
Atomic Structures ◽  
Grain Boundary Structure ◽  
Resolution Electron ◽  
Point To Point ◽  
The Right ◽  
New Generation ◽  
Better Than

The use of high resolution electron microscopy (HREM) to determine the atomic structure of grain boundaries and interfaces is a topic of great current interest. Grain boundary structure has been considered for many years as central to an understanding of the mechanical and transport properties of materials. Some more recent attention has focussed on the atomic structures of metalsemiconductor interfaces which are believed to control electrical properties of contacts. The atomic structures of interfaces in semiconductor or metal multilayers is an area of growing interest for understanding the unusual electrical or mechanical properties which these new materials possess. However, although the point-to-point resolutions of currently available HREMs, ∼2-3Å, appear sufficient to solve many of these problems, few atomic models of grain boundaries and interfaces have been derived. Moreover, with a new generation of 300-400kV instruments promising resolutions in the 1.6-2.0 Å range, and resolutions better than 1.5Å expected from specialist instruments, it is an appropriate time to consider the usefulness of HREM for interface studies.

Dissociated Σ=27 boundaries in silicon

1988 ◽  
Vol 46 ◽  
pp. 624-625
Author(s):  
A. Garg ◽  
W.A.T. Clark ◽  
J.P. Hirth
Keyword(s):  
Electron Diffraction ◽  
Local Minimum ◽  
Boundary Energy ◽  
Coincidence Site Lattice ◽  
Boundary Plane ◽  
Low Energy ◽  
Theoretical Understanding ◽  
Site Lattice ◽  
Kikuchi Pattern ◽  
Analysis Techniques

In the last twenty years, a significant amount of work has been done in the theoretical understanding of grain boundaries. The various proposed grain boundary models suggest the existence of coincidence site lattice (CSL) boundaries at specific misorientations where a periodic structure representing a local minimum of energy exists between the two crystals. In general, the boundary energy depends not only upon the density of CSL sites but also upon the boundary plane, so that different facets of the same boundary have different energy. Here we describe TEM observations of the dissociation of a Σ=27 boundary in silicon in order to reduce its surface energy and attain a low energy configuration.The boundary was identified as near CSL Σ=27 {255} having a misorientation of (38.7±0.2)°/[011] by standard Kikuchi pattern, electron diffraction and trace analysis techniques. Although the boundary appeared planar, in the TEM it was found to be dissociated in some regions into a Σ=3 {111} and a Σ=9 {122} boundary, as shown in Fig. 1.

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