Search results for "computational simulation"
showing 10 items of 10 documents
The transition state and cognate concepts
2019
Abstract This review aims firstly to clarify the meanings of key terms and concepts associated with the idea of the transition state, as developed by theoreticians and applied by experimentalist, and secondly to provide an update to the meaning and significance of the transition state in an era when computational simulation, in which complexity is being increasingly incorporated, is commonly employed as a means by which to bridge the realms of theory and experiment. The relationship between the transition state and the potential-energy surface for an elementary reaction is explored, with discussion of the following terms: saddle point, minimum-energy reaction path, reaction coordinate, acti…
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
2019
This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs. Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixe…
Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water
2011
2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of 1030 classical solvent water molecules at 300 K. This provides a simple model for glycosyl transfer in water. The AM1/TIP3P surfaces with 2D-spline corrections at either MPWB1K/6-31+G(d,p) or MP2/6-31+G(d,p) contain a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a DN*AN mechanism. MD analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections for vibrational zero-…
A robust and efficient method for obtaining the complex modes in inhomogeneously filled waveguides
2003
In this paper, we present a computational simulation of the complex wave propagation in inhomogeneously filled waveguides with lossless and lossy dielectrics. We use a biorthonormal-basis method as a numerical technique. The behavior of complex modes in different waveguides whose characterization with other methods involves some difficulties is analyzed. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 37: 218–222, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10875
The effect of a liquid CTBN rubber modifier on the thermo-kinetic parameters of an epoxy resin during a pultrusion process
2003
Abstract Rheo-kinetic behaviour of an epoxy resin, coupled with an anhydride hardener, with different CTBN liquid rubber concentration (0–15 phr), used in fibre reinforced plastics, was analysed comparing experimental data with theoretical models. The modelling of technological pultrusion process for thermoset matrix composites, developed through a numerical code realised with MATLAB, is reported, too. The model includes conduction and cure heat, degree of cure and viscosity evolution during the curing within the die. Considerable differences in process condition, using different rubber amount, are obtained. The numerical modelling of process conditions shows that the CTBN rubber presence i…
Computational simulation of the lifetime of the methoxymethyl cation in water. A simple model for a glycosyl cation: when is an intermediate an inter…
2010
A two-dimensional free-energy surface is constructed for transfer of the methoxymethyl cation between two water molecules. These atoms are treated quantum mechanically within a box of >1000 classical solvent water molecules, and the molecular dynamics of the whole system is considered at 300 K. This provides a simple model for glycosyl transfer in water. The best surface obtained (MPWB1K/6-31+G(d,p) corrected AMI/TIP3P) contains a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a stepwise mechanism. Molecular dynamics analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections fo…
Desarrollo de habilidades de modelación desde las ecuaciones más simples de la Hidrodinámica
2017
[EN] The development of modeling skills is a very important issue in Science teaching nowadays. The present workillustrates how, from the simplest equations of hydrodynamics, it is possible to contribute to this end. Bernoulliand continuity equations are included in Physics syllabi of secondary and university levels, and can be seen as alinking between general and professional education. By means of the proposed project, students are taken throughgeneral stages which are usually present in any engineering project or research work based on modeling and simu-lation. such as the formulation of the problem, the statement of the Physics model, a computational simulationand the comparison between…
Viruses are ancient parasites that have influenced the evolution of contemporary and archaic forms of life
2010
Personalized Cardiac Computational Models: From Clinical Data to Simulation of Infarct-Related Ventricular Tachycardia.
2019
In the chronic stage of myocardial infarction, a significant number of patients develop life-threatening ventricular tachycardias (VT) due to the arrhythmogenic nature of the remodeled myocardium. Radiofrequency ablation (RFA) is a common procedure to isolate reentry pathways across the infarct scar that are responsible for VT. Unfortunately, this strategy show relatively low success rates; up to 50% of patients experience recurrent VT after the procedure. In the last decade, intensive research in the field of computational cardiac electrophysiology (EP) has demonstrated the ability of three-dimensional (3D) cardiac computational models to perform in-silico EP studies. However, the personal…
On the Finite Element Modeling of the Lumbar Spine: A Schematic Review
2023
Finite element modelling of the lumbar spine is a challenging problem. Lower back pain is among the most common pathologies in the global populations, owing to which the patient may need to undergo surgery. The latter may differ in nature and complexity because of spinal disease and patient contraindications (i.e., aging). Today, the understanding of spinal column biomechanics may lead to better comprehension of the disease progression as well as to the development of innovative therapeutic strategies. Better insight into the spine’s biomechanics would certainly guarantee an evolution of current device-based treatments. In this setting, the computational approach appears to be a remarkable …