Search results for "simulations"
showing 10 items of 288 documents
Anomalous surface diffusion of protons on lipid membranes.
2014
AbstractThe cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive re…
Quantum Simulations of One-Dimensional Nanostructures under Arbitrary Deformations
2016
A powerful technique is introduced for simulating mechanical and electromechanical properties of one-dimensional nanostructures under arbitrary combinations of bending, twisting, and stretching. The technique is based on a novel control of periodic symmetry, which eliminates artifacts due to deformation constraints and quantum finite-size effects, and allows transparent electronic structure analysis. Via density-functional tight-binding implementation, the technique demonstrates its utility by predicting novel electromechanical properties in carbon nanotubes and abrupt behavior in the structural yielding of Au7 and MoS nanowires. The technique drives simulations markedly closer to the reali…
In silico pace-mapping: prediction of left vs. right outflow tract origin in idiopathic ventricular arrhythmias with patient-specific electrophysiolo…
2019
Abstract Aims A pre-operative non-invasive identification of the site of origin (SOO) of outflow tract ventricular arrhythmias (OTVAs) is important to properly plan radiofrequency ablation procedures. Although some algorithms based on electrocardiograms (ECGs) have been developed to predict left vs. right ventricular origins, their accuracy is still limited, especially in complex anatomies. The aim of this work is to use patient-specific electrophysiological simulations of the heart to predict the SOO in OTVA patients. Methods and results An in silico pace-mapping procedure was designed and used on 11 heart geometries, generating for each case simulated ECGs from 12 clinically plausible SOO…
Development of a High Irradiance LED Configuration for Small Field of View Motion Estimation of Fertilizer Particles
2015
International audience; Better characterization of the fertilizer spreading process, especially the fertilizer pattern distribution on the ground, requires an accurate measurement of individual particle properties and dynamics. Both 2D and 3D high speed imaging techniques have been developed for this purpose. To maximize the accuracy of the predictions, a specific illumination level is required. This paper describes the development of a high irradiance LED system for high speed motion estimation of fertilizer particles. A spectral sensitivity factor was used to select the optimal LED in relation to the used camera from a range of commercially available high power LEDs. A multiple objective …
Fast simulation of muons produced at the SHiP experiment using Generative Adversarial Networks
2019
This paper presents a fast approach to simulating muons produced in interactions of the SPS proton beams with the target of the SHiP experiment. The SHiP experiment will be able to search for new long-lived particles produced in a 400~GeV$/c$ SPS proton beam dump and which travel distances between fifty metres and tens of kilometers. The SHiP detector needs to operate under ultra-low background conditions and requires large simulated samples of muon induced background processes. Through the use of Generative Adversarial Networks it is possible to emulate the simulation of the interaction of 400~GeV$/c$ proton beams with the SHiP target, an otherwise computationally intensive process. For th…
Configurations spatio-temporelles des températures et des précipitations au printemps et en été 2003 en Bourgogne : mesures Météo France et simulatio…
2010
International audience; Contexte : En Bourgogne, un collectif pluridisciplinaire piloté par Alterre travaille la question de l'adaptation au changement climatique. Une confrontation entre deux saisons végétatives (1991 et 2003) sélectionnées comme étant représentantes des conditions moyennes actuelles (1988-2007) et futures (seconde moitié du xxie siècle) est développée sur la base d'une méthodologie multi-modèles (climatique, pédologique et hydrologique).Problématique : Au-delà des éléments connus (températures élevées et pluies peu fréquentes de 2003) l'étude vise à caractériser les écarts de conditions climatiques 2003-1991 sur l'ensemble du territoire bourguignon. Les températures de la…
Work Partitioning on Parallel and Distributed Agent-Based Simulation
2017
Work partitioning is a key challenge with ap- plications in many scientific and technological fields. The problem is very well studied with a rich literature on both distributed and parallel computing architectures. In this paper we deal with the work partitioning problem for parallel and distributed agent-based simulations which aims at (i) balancing the overall load distribution, (ii) minimizing, at the same time, the communication overhead due to agents' inter-dependencies. We introduce a classification taxonomy of work partitioning strategies and present a space-based work partitioning ap- proach, based on a Quad-tree data structure, which enables to: identify a good space partitioning …
The Best Hedging Strategy in the Presence of Transaction Costs
2009
Considerable theoretical work has been devoted to the problem of option pricing and hedging with transaction costs. A variety of methods have been suggested and are currently being used for dynamic hedging of options in the presence of transaction costs. However, very little was done on the subject of an empirical comparison of different methods for option hedging with transaction costs. In a few existing studies the different methods are compared by studying their empirical performances in hedging only a plain-vanilla short call option. The reader is tempted to assume that the ranking of the different methods for hedging any kind of option remains the same as that for a vanilla call. The …
Modeling multiple taxis: Tumor invasion with phenotypic heterogeneity, haptotaxis, and unilateral interspecies repellence
2021
We provide a short review of existing models with multiple taxis performed by (at least) one species and consider a new mathematical model for tumor invasion featuring two mutually exclusive cell phenotypes (migrating and proliferating). The migrating cells perform nonlinear diffusion and two types of taxis in response to non-diffusing cues: away from proliferating cells and up the gradient of surrounding tissue. Transitions between the two cell subpopulations are influenced by subcellular (receptor binding) dynamics, thus conferring the setting a multiscale character. We prove global existence of weak solutions to a simplified model version and perform numerical simulations for the full se…
NMR structure of a non-conjugatable, ADP-ribosylation associated, ubiquitin-like domain from Tetrahymena thermophila polyubiquitin locus.
2019
Abstract Background Ubiquitin-like domains (UbLs), in addition to being post-translationally conjugated to the target through the E1-E2-E3 enzymatic cascade, can be translated as a part of the protein they ought to regulate. As integral UbLs coexist with the rest of the protein, their structural properties can differ from canonical ubiquitin, depending on the protein context and how they interact with it. In this work, we investigate T.th-ubl5, a UbL present in a polyubiquitin locus of Tetrahymena thermophila, which is integral to an ADP-ribosyl transferase protein. Only one other co-occurrence of these two domains within the same protein has been reported. Methods NMR, multiple sequence al…