Search results for "Simulation."
showing 10 items of 4779 documents
Observation of Kuznetsov-Ma soliton dynamics in optical fibre
2012
International audience; The nonlinear Schro¨dinger equation (NLSE) is a central model of nonlinear science, applying to hydrodynamics, plasma physics, molecular biology and optics. The NLSE admits only few elementary analytic solutions, but one in particular describing a localized soliton on a finite background is of intense current interest in the context of understanding the physics of extreme waves. However, although the first solution of this type was the Kuznetzov-Ma (KM) soliton derived in 1977, there have in fact been no quantitative experiments confirming its validity. We report here novel experiments in optical fibre that confirm the KM soliton theory, completing an important serie…
Phase Behavior of Active Swimmers in Depletants: Molecular Dynamics and Integral Equation Theory
2013
We study the structure and phase behavior of a binary mixture where one of the components is self-propelling in nature. The inter-particle interactions in the system were taken from the Asakura-Oosawa model, for colloid-polymer mixtures, for which the phase diagram is known. In the current model version the colloid particles were made active using the Vicsek model for self-propelling particles. The resultant active system was studied by molecular dynamics methods and integral equation theory. Both methods produce results consistent with each other and demonstrate that the Vicsek model based activity facilitates phase separation, thus broadening the coexistence region.
Co-simulation of bio-inspired multi-agent algorithms
2020
This paper reports on the co-simulation of a team of robots deployed in an exploration task, coordinated by a bio-inspired exploration algorithm. The co-simulation integrates the high-level exploration algorithm with detailed implementations of the robot controllers and kinematic models. Co-simulation results are used to find and correct mismatches between submodels.
Semantic interoperability between BIM and GIS – review of existing standards and depiction of a novel approach
2019
International audience; When it comes to Big Data ecosystems, main technical challenges pertain to defining links between data, information and knowledge, thus reaching interoperability. Interoperability issues are addressed in the context of data curation related tasks. Interoperability is a major prerequisite for achieving data automation, validation, thus fighting counter-productiveness (notably through data incentivisation). The demand for interoperable, reusable and open data is more and more present, thus pushing forward the research for innovation data curation approaches. This article gives a high level description of our approach for bridging the interoperability gap among GIS (Geo…
Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors.
2011
Reliable and effective virtual high-throughput screening (vHTS) methods are desperately needed to minimize the expenses involved in drug discovery projects. Here, we present an improvement to the negative image-based (NIB) screening: the shape, the electrostatics, and the solvation state of the target protein’s ligand-binding site are included into the vHTS. Additionally, the initial vHTS results are postprocessed with molecular mechanics/generalized Born surface area (MMGBSA) calculations to estimate the favorability of ligand-protein interactions. The results show that docking produces very good early enrichment for phosphodiesterase-5 (PDE-5); however, in general, the NIB and the ligand-…
Variational methods for the steady state response of elastic–plastic solids subjected to cyclic loads
2003
Abstract Solids (or structures) of elastic–plastic internal variable material models and subjected to cyclic loads are considered. A minimum net resistant power theorem, direct consequence of the classical maximum intrinsic dissipation theorem of plasticity theory, is envisioned which describes the material behavior by determining the plastic flow mechanism (if any) corresponding to a given stress/hardening state. A maximum principle is provided which characterizes the optimal initial stress/hardening state of a cyclically loaded structure as the one such that the plastic strain and kinematic internal variable increments produced over a cycle are kinematically admissible. A steady cycle min…
A Portable Dynamic Laser Speckle System for Sensing Long-Term Changes Caused by Treatments in Painting Conservation
2018
[EN] Dynamic laser speckle (DLS) is used as a reliable sensor of activity for all types of materials. Traditional applications are based on high-rate captures (usually greater than 10 frames-per-second, fps). Even for drying processes in conservation treatments, where there is a high level of activity in the first moments after the application and slower activity after some minutes or hours, the process is based on the acquisition of images at a time rate that is the same in moments of high and low activity. In this work, we present an alternative approach to track the drying process of protective layers and other painting conservation processes that take a long time to reduce their levels …
Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives.
2015
Abstract Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importanc…
Post-Translational Regulation of CYP450s Metabolism As Revealed by All-Atoms Simulations of the Aromatase Enzyme.
2019
Phosphorylation by kinases enzymes is a widespread regulatory mechanism able of rapidly altering the function of target proteins. Among these are cytochrome P450s (CYP450), a superfamily of enzymes performing the oxidation of endogenous and exogenous substrates thanks to the electron supply of a redox partner. In spite of its pivotal role, the molecular mechanism by which phosphorylation modulates CYP450s metabolism remains elusive. Here by performing microsecond-long all-atom molecular dynamics simulations, we disclose how phosphorylation regulates estrogen biosynthesis, catalyzed by the Human Aromatase (HA) enzyme. Namely, we unprecedentedly propose that HA phosphorylation at Y361 markedl…
All-Atom simulations disclose how cytochrome reductase reshapes the substrate access/egress routes of its partner cyp450s
2020
Cytochromes P450 enzymes (CYP450s) promote the oxidative metabolism of a variety of substrates via the electrons supplied by the cytochrome P450 reductase (CPR) and upon formation of a CPR/CYP450 adduct. In spite of the pivotal regulatory importance of this process, the impact of CPR binding on the functional properties of its partner CYP450 remains elusive. By performing multiple microsecond-long all-Atom molecular dynamics simulations of a 520â »000-Atom model of a CPR/CYP450 adduct embedded in a membrane mimic, we disclose the molecular terms for their interactions, considering the aromatase (HA) enzyme as a proxy of the CYP450 family. Our study strikingly unveils that CPR binding alters…