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Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical properties of oscillat ...
In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene–gene, ...
The effects of internal dynamics in diffusion-driven encounters between macro-molecules represent a problem of broad relevance in molecular biology. In this view, we investigate a typical antigen-antibody reaction chain, based on a coarse-grained mechanica ...
In the Shannon-theoretic analysis of joint source-channel coding problems, achievability is usually established via a two-stage approach: The sources are compressed into bits, and these bits are reliably communicated across the noisy channels. Random codin ...
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With the increasing availability of experimental data on gene-gene and protein-protein interactions, modeling of gene regulatory networks has gained a special attention lately. To have a better understanding of these networks it is necessary to capture the ...
Recent developments in identifying Lagrangian coherent structures from finite-time velocity data have provided a theoretical basis for understanding chaotic transport in general flows with aperiodic dependence on time. As these theoretical developments are ...
A series of ca. 20-ns molecular dynamics simulation runs of the N-terminal H4 histone tail in its un- and tetraacetylated forms were performed using three different long-range electrostatic treatments namely, spherical-cutoff, reaction field, and particle ...
Recently, several approaches for communications using chaos have been presented, often showing less than acceptable performance. In this paper, a short introduction to the topic is given, and it is shown that such methods can be efficient—if the informatio ...
The structural and dynamical properties of the four a-helix bundle Due Ferri 1, which is a generic mimic of diiron proteins, have been explored using d. functional theory (DFT) based and hybrid quantum/classical mol. dynamics (QM/MM) simulations. Four quan ...
The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 and 400 K. Density-functional theory, p ...