Search results for " Simulation"
showing 10 items of 4034 documents
Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.
2010
We here present a theoretical study of the alkaline hydrolysis of methyl p-nitrophenyl phosphate (MpNPP(-)) in aqueous solution and in the active site of nucleotide pyrophosphatase/phosphodiesterase (NPP). The analysis of our simulations, carried out by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods, shows that the reaction takes place through different reaction mechanisms depending on the environment. Thus, while in aqueous solution the reaction occurs by means of an A(N)D(N) mechanism, the enzymatic process takes place through a D(N)A(N) mechanism. In the first case, we found associative transition-state (TS) structures, while in the enzyme TS structures have dissoc…
Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods
2015
The promiscuous activity of the enzyme o-succinylbenzoate synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both density functional theory and semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylamino acids, with N-succinyl-R-phenylglycine being the best substrate. We investigated the molecular mechanisms for both reactions exploring the potential energy surface. Then, molecular dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues wi…
A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
2007
Abstract Background Among microbial genomes, genetic information is frequently compressed, exploiting redundancies in the genetic code in order to store information in overlapping genes. We investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution. Results Using a variety of statistical null models we find patterns of compressive coding that can not be explained purely in terms of the selective processes favoring genome minimization or translational coupling. The distribution of overlap lengths follows a fat-tailed distribution, in which a significant proportion of overlaps are in excess of 100 base…
A Self-Contained Cylinder Drive with Indirectly Controlled Hydraulic Lock
2020
This paper presents a self-contained pump-controlled hydraulic linear drive including an innovative load holding sub-circuit. For safety critical applications such as crane manipulators, locking valves or load holding valves are enforced by legislation, but the load holding functionality may also be used actively to decrease the energy consumption for applications where the load is kept stationary for longer periods of time. The system proposed in this paper is based on a simple hydraulic architecture using two variablespeed electric motors each connected to a fixed-displacement pump. This architecture is well-known inacademic literature, but in this paper a novel load holding sub-circuit h…
Fifty Years of PMV Model: Reliability, Implementation and Design of Software for Its Calculation
2019
In most countries, PMV is the reference index for the assessment of thermal comfort conditions in mechanically conditioned environments. It is also the basis to settle input values of the operative temperature for heating and cooling load calculations, sizing of equipment, and energy calculations according to EN 16798-1 and 16798-2 Standards. Over the years, great effort has been spent to study the reliability of PMV, whereas few investigations were addressed to its calculation. To study this issue, the most significant apps devoted to its calculation have been compared with a reference software compliant with EN ISO 7730 and the well-known ASHRAE Thermal Comfort Tool. It has been revealed …
Tuning continua and keyboard layouts
2008
Previous work has demonstrated the existence of keyboard layouts capable of maintaining consistent fingerings across a parametrized family of tunings. This paper describes the general principles underlying layouts that are invariant in both transposition and tuning. Straightforward computational methods for determining appropriate bases for a regular temperament are given in terms of a row-reduced matrix for the temperament-mapping. A concrete description of the range over which consistent fingering can be maintained is described by the valid tuning range. Measures of the resulting keyboard layouts allow direct comparison of the ease with which various chordal and scalic patterns can be fin…
Regularization operators for natural images based on nonlinear perception models.
2006
Image restoration requires some a priori knowledge of the solution. Some of the conventional regularization techniques are based on the estimation of the power spectrum density. Simple statistical models for spectral estimation just take into account second-order relations between the pixels of the image. However, natural images exhibit additional features, such as particular relationships between local Fourier or wavelet transform coefficients. Biological visual systems have evolved to capture these relations. We propose the use of this biological behavior to build regularization operators as an alternative to simple statistical models. The results suggest that if the penalty operator take…
Numerical Simulation of Friction Stir Welding by Natural Element Methods
2008
In this work we address the problem of numerically simulating the Friction Stir Welding process. Due to the special characteristics of this welding method (i.e., high speed of the rotating pin, very large deformations, etc.) finite element methods (FEM) encounter several difficulties. While Lagrangian simulations suffer from mesh distortion, Eulerian or Arbitrary Lagrangian Eulerian (ALE) ones still have difficulties due to the treatment of convective terms, the treatment of the advancing pin, and many others. Meshless methods somewhat alleviate these problems, allowing for an updated Lagrangian framework in the simulation. Accuracy is not affected by mesh distortion (and hence the name mes…
Meshless Simulation of Friction Stir Welding
2007
This paper encompasses our first efforts towards the numerical simulation of friction stir welding by employing a Lagrangian approach. To this end, we have employed a meshless method, namely the Natural Element Method (NEM). Friction Stir welding is a welding process where the union between the work pieces is achieved through the extremely high deformation imposed by a rotating pin, which moves between the two pieces. This extremely high strain is the main responsible of the difficulties associated with the numerical simulation of this forming process. Eulerian and Arbitrary Lagrangian-Eulerian (ALE) frameworks encounter difficulties in some aspects of the simulation. For instance, these ap…
A preliminary comparison between finite element and meshless simulations of extrusion
2009
In this paper the extrusion process of a cross-shaped profile was investigated. In particular, the study was focused on the distortion of extruding profiles when the workpiece and die axis are not aligned. The process was simulated using the finite element method (FEM) and the natural element method (NEM), both implemented in an updated-Lagrangian formulation, in order to avoid the burden associated with the description of free surfaces in ALE or Eulerian formulations. Furthermore, an experimental equipment was developed in order to obtain reliable data in terms of deformed entity, required process load and calculated pressure. At the end, a comparison between the numerical predictions and …