Search results for "SIMULATION"
showing 10 items of 5095 documents
Nanoparticles Size Distribution Assessment During Early Synthesis Stages
2021
Nanotechnology, an innovative field of material science, designs and produces nanostructures materials with unique properties that make them suited for various bioengineering applications. The shape and the dimension are the main variables depending on the method of synthesis or chemical precursors. Silver nanoparticles obtained through chemical synthesis exhibit as strong antibacterial effect if their size lays in a well-defined range. However, a small size of such particles, in the range of nanometers to several tens of nanometers, requires specific techniques as Dynamic Light Scattering or Transmission Electron Microscopy, both being affected by certain assumptions or by the high cost an…
A new method to evaluate the influence of the glenosphere positioning on stability and range of motion of a reverse shoulder prosthesis
2019
Abstract Purpose Shoulder instability and reduced range of motion are two common complications of a total reverse shoulder arthroplasty. In this work, a new approach is proposed to estimate how the glenoid component positioning can influence the stability and the range of motion of a reverse shoulder prosthesis. Materials and methods A standard reverse shoulder prosthesis has been analysed. To perform virtual simulation of the shoulder-prosthesis assembly, all the components of the prosthesis have been acquired via a 3D laser scanner and the solid models of the shoulder bones have been reconstructed through CT images. Loads on the shoulder joint have been estimated using anatomical models d…
Time and work generalised precedence relationships in project scheduling with pre-emption: An application to the management of Service Centres
2012
Abstract In this paper we present an application of project scheduling concepts and solution procedures for the solution of a complex problem that comes up in the daily management of many company Service Centres. The real problem has been modelled as a multi-mode resource-constrained project scheduling problem with pre-emption, time and work generalised precedence relationships with minimal and maximal time lags between the tasks and due dates. We present a complete study of work GPRs which includes proper definitions, a new notation and all possible conversions amongst them. Computational results that show the efficiency of the proposed hybrid genetic algorithm and the advantages of allowi…
Mechanism change in a simulation of peer review: from junk support to elitism
2014
Abstract Peer review works as the hinge of the scientific process, mediating between research and the awareness/acceptance of its results. While it might seem obvious that science would regulate itself scientifically, the consensus on peer review is eroding; a deeper understanding of its workings and potential alternatives is sorely needed. Employing a theoretical approach supported by agent-based simulation, we examined computational models of peer review, performing what we propose to call redesign, that is, the replication of simulations using different mechanisms. Here, we show that we are able to obtain the high sensitivity to rational cheating that is present in literature. In additio…
A Rayleigh-Ritz approach for postbuckling analysis of variable angle tow composite stiffened panels
2018
Abstract A Rayleigh-Ritz solution approach for generally restrained multilayered variable angle tow stiffened plates in postbuckling regime is presented. The plate model is based on the first order shear deformation theory and accounts for geometrical nonlinearity through the von Karman’s assumptions. Stiffened plates are modelled as assembly of plate-like elements and penalty techniques are used to join the elements in the assembled structure and to apply the kinematical boundary conditions. General symmetric and unsymmetric stacking sequences are considered and Legendre orthogonal polynomials are employed to build the trial functions. A computer code was developed to implement the propose…
Unveiling the reaction mechanism of novel copper N-alkylated tetra-azacyclophanes with outstanding superoxide dismutase activity.
2020
Quantum chemical and multiscale calculations reveal the mechanistic pathway of two superoxide dismutase mimetic N-alkylated tetra-azacyclophane copper complexes with remarkable activity. The arrangement of the binding site afforded by the bulky alkyl substituents and the coordinated water molecule as a proton source play key roles in the reaction mechanism.
Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease.
2021
We present a detailed computational analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against the SARS-CoV-2 3CL protease. Alchemical free energy calculations suggest that positions P3 and P4 could be susceptible to improvement in order to get a larger binding strength. QM/MM simulations unveil the reaction mechanism for covalent inhibition, showing that the nitrile warhead facilitates the recruitment of a water molecule for the proton transfer step.
Dynamics and reactivity in Thermus aquaticus N6-adenine methyltransferase.
2014
M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine to the N6 position of an adenine, a process described only in prokaryotes. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex where the target adenine is flipped out into the active site. Key protein–DNA interactions established by the target adenine in the active site are described in detail. The relaxed structure was used for a combined quantum mechanics/molecular mechanics exploration of the reaction mechanism using the string method. According to our free energy calculations the reaction takes…
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…