Search results for "SIMULATION"
showing 10 items of 5095 documents
Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates.
1994
Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted…
Modeling Atmospheric Turbulence via Rapid Distortion Theory: Spectral Tensor of Velocity and Buoyancy
2017
Abstract A spectral tensor model is presented for turbulent fluctuations of wind velocity components and temperature, assuming uniform vertical gradients in mean temperature and mean wind speed. The model is built upon rapid distortion theory (RDT) following studies by Mann and by Hanazaki and Hunt, using the eddy lifetime parameterization of Mann to make the model stationary. The buoyant spectral tensor model is driven via five parameters: the viscous dissipation rate ε, length scale of energy-containing eddies L, a turbulence anisotropy parameter , gradient Richardson number (Ri) representing the local atmospheric stability, and the rate of destruction of temperature variance . Model outp…
How to define variation of physical properties normal to an undulating one-dimensional object.
2009
One-dimensional flexible objects are abundant in physics, from polymers to vortex lines to defect lines and many more. These objects structure their environment and it is natural to assume that the influence these objects exert on their environment depends on the distance from the line-object. But how should this be defined? We argue here that there is an intrinsic length scale along the undulating line that is a measure of its "stiffness" (i.e., orientational persistence), which yields a natural way of defining the variation of physical properties normal to the undulating line. We exemplify how this normal variation can be determined from a computer simulation for the case of a so-called b…
Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target.
2014
Body weight control is a mechanism finely regulated by several hormonal, metabolic, and nervous pathways. The leptin receptor (Ob-R) is crucial for energy homeostasis and regulation of food uptake. Leptin is a 16 kDa hormone that is mainly secreted by fat cells into the bloodstream, and under normal circumstances, circulating levels are proportionate to the fat body mass. Sensing of elevated leptin levels by the hypothalamic neurocircutry activates a negative feedback loop resulting in reduced food intake and increased energy expenditure. Decreased concentrations lead to opposite effects. Therefore rational design of leptin agonists constitute an appealing challenge in the battle against ob…
Tracking Polariton Relaxation with Multiscale Molecular Dynamics Simulations
2019
When photoactive molecules interact strongly with confined light modes in optical cavities, new hybrid light–matter states form. They are known as polaritons and correspond to coherent superpositions of excitations of the molecules and of the cavity photon. The polariton energies and thus potential energy surfaces are changed with respect to the bare molecules, such that polariton formation is considered a promising paradigm for controlling photochemical reactions. To effectively manipulate photochemistry with confined light, the molecules need to remain in the polaritonic state long enough for the reaction on the modified potential energy surface to take place. To understand what determine…
Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-…
2020
Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS…
Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atom Simulations
2020
The severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic is setting the global health crisis of our time, causing a devastating societal and economic burden. An idiosyncratic trait of coronaviruses is the presence of spike glycoproteins on the viral envelope, which mediate the virus binding to specific host receptor, enabling its entry into the human cells. In spite of the high sequence identity of SARS-CoV-2 with its closely related SARS-CoV emerged in 2002, the atomic-level determinants underlining the molecular recognition of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor and, thus, the rapid virus spread into human body, remain unresolved. Here, multi-m…
The ATLAS Simulation Infrastructure
2010
52 páginas, 10 figuras, 18 tablas.-- This article is distributed under the terms of the Creative Commons Attribution Noncommercial License.-- et al. (The ATLAS Collaboration).
Uncertainty analysis of life cycle assessment of asphalt surfacings
2023
The Life Cycle Assessment (LCA) of asphalt pavements are associated with significant uncertainty resulting from variability in the quantity and impact of individual components, the quality of data for each component, and variability of asphalt durability. This study presents a framework to quantify and incorporate the uncertainty of LCA and asphalt durability data into LCA of asphalt surfacings. The suggested framework includes: estimating the uncertainty of asphalt production processes by the pedigree matrix method, conducting a deterministic LCA, applying Monte Carlo Simulation (MCS) to estimate the probability density functions (PDFs) of the considered impacts using the uncertainty data,…
Numerical prediction of ventilated planing flat plates for the design of Air Cavity Ships
2017
In recent years, a great world issue is the respect for the environment. Each researcher, in his competence field, proposes new technologies and new approaches in order to reduce the environmental impact of a product or of an industrial process. In the naval field, the main way in order to reduce the environmental impact of the ship during the navigation is the reduction of the drag resistance and so the reduction of requested power. There are many ways in order to obtain a reduction of drag. This paper investigates, with a preliminary numerical study by means of Computational Fluid Dynamics (CFD), the Air Cavity Ships technology (ACS). A first part of the paper concerns the study of the ri…