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detection by mass spectrometry, by combining molecular dynamics simulations and experiments (Figure 1).1-5 The present PhD thesis will investigate the effects of additional specific ions in fluid samples
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from E. coli using molecular simulations to understand electron transfer between the second heme b and heme d [4]. To this end, we performed molecular dynamics simulations of the protein within a
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systems (LIED, Université Paris Cité), experts in classical atomistic simulations (molecular dynamics and coarse-graining, LMCE, CEA/DAM/DIF), as well as specialists in continuum simulations (finite element
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Inria, the French national research institute for the digital sciences | Villers les Nancy, Lorraine | France | 10 days ago
(graph neural networks and transformers) The objective is to learn conformational heterogeneity directly from molecular dynamics simulations and to identify and predict allosteric communication pathways
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-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation. J Mol Biol, 2023. 435(9): p. 167951.https://hal.science/hal-03929029 [3] Valimehr, S., et al
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at the molecular scale. Grand Canonical Monte Carlo (GCMC) simulations will be performed to predict adsorption isotherms and selectivities. Molecular dynamics simulations will be used to investigate diffusion
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Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation. J Mol Biol. 2023;435:167951. https://hal.science/hal-03929029 [3] Valimehr S, Vuillemot R, Kazemi
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polarization (M1–M2 continuum and activation states). Bacterial phenotypic heterogeneity (replication, dormancy, intracellular survival). Integrate single-cell transcriptomic data to build molecular dynamical
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simulations. Two complementary strategies will be employed: structure-based virtual screening (docking simulations + molecular dynamics) and ligand-based virtual screening (machine learning models). We have
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physical parameters, namely the anisotropies and the diffusion coefficients, will be obtained from molecular dynamics calculations in collaboration with Science et Ingénierie, Matériaux, Procédés (SIMAP