Search results for " Simulation"
showing 10 items of 4034 documents
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…
Aerodynamics of an isolated ski jumping ski
2019
A single isolated ski was suspended from a six-component wind tunnel balance and three angles, the angle of attack, the yaw angle and the edge angle were adjustable during the test. Increasing yaw angle from 0 to 15° increased the lift coefficient CL from 0.42 to 0.90 at edge angle 0° and from 0.70 to 0.87 at edge angle 10°, respectively. Increasing yaw angle also increased the sensitivity of the ski to changes in edge angle, i.e., increasing the edge angle (20°–45°) decreased the CL and the ratio $$C_{L}^{2}/{C_D}$$ with large yaw angles. However, to maximize the lift-to-drag ratio with a typical angle of attack of 30° in ski jumping, it may be reasonable to have an edge angle of 5°–10° on…
The minimal model of Hahn for the Calvin cycle.
2018
There are many models of the Calvin cycle of photosynthesis in the literature. When investigating the dynamics of these models one strategy is to look at the simplest possible models in order to get the most detailed insights. We investigate a minimal model of the Calvin cycle introduced by Hahn while he was pursuing this strategy. In a variant of the model not including photorespiration it is shown that there exists exactly one positive steady state and that this steady state is unstable. For generic initial data either all concentrations tend to infinity at lates times or all concentrations tend to zero at late times. In a variant including photorespiration it is shown that for suitable v…
Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization
2016
International audience; We report a computational investigation of the hydrogen abstraction (H-abstraction) induced by triplet benzophenone (3BP) on thymine nucleobase and backbone sugar. The chemical process is studied using both high level multiconfigurational perturbation and density functional theory. Both methods show good agreement in predicting small kinetic barriers. Furthermore the behavior of benzophenone in DNA is simulated using molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. The accessibility of benzophenone to the labile hydrogens within B-DNA is demonstrated, as well as the driving force for this reaction. We evidence a strong dependence of the H-…
Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila
2018
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics …