Search results for "PERTURBATION"
showing 10 items of 811 documents
Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands
2021
Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm−1 region of the K-BR difference FT-IR spectrum.…
Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA.
2020
Herein we present the results of an in-depth simulation study of LinA and its two variants. In our analysis, we combined the exploration of protein conformational dynamics with and without bound substrates (hexachlorocyclohexane (HCH) isomers) performed using molecular dynamics simulation followed by the extraction of the most frequently visited conformations and their characteristics with a detailed description of the interactions taking place in the active site between the respective HCH molecule and the first shell residues by using symmetry-adapted perturbation theory (SAPT) calculations. A detailed investigation of the conformational space of LinA substates has been accompanied by desc…
Theoretical studies of HIV-1 reverse transcriptase inhibition
2012
Computational methods for accurately calculating the binding affinity of a ligand for a protein play a pivotal role in rational drug design. We herein present a theoretical study of the binding of five different ligands to one of the proteins responsible for the human immunodeficiency virus type 1 (HIV-1) cycle replication; the HIV-1 reverse transcriptase (RT). Two types of approaches are used based on molecular dynamics (MD) simulations within hybrid QM/MM potentials: the alchemical free energy perturbation method, FEP, and the pathway method, in which the ligand is physically pulled away from the binding site, thus rendering a potential of mean force (PMF) for the binding process. Our com…
Precise branching ratios to unbound 12C states from 12N and 12B β-decays
2009
6 pages, 2 tables, 4 figures.--PACS nrs.: 21.45.-v; 23.40.-s; 27.20.+n; 21.60.De.--Printed version published Aug 3, 2009
Un nouveau modèle de transcodage des nombres : aspects développementaux, neuropsychologiques et computationnels
2005
Ce texte est un rapport de fin de recherche issu de l'ACI cognitique.; L'objectif du projet était de produire et valider empiriquement un modèle développemental de transcodage des nombres de leur forme verbale (orale ou écrite) vers leur forme en chiffres. Le modèle, baptisé ADAPT (A Developmental Asemantic Procedural Transcoding model), est un système de production qui transforme un input verbal en chaîne de chiffres par la mise en œuvre de procédures. Celles-ci lisent le contenu de la mémoire de travail et le transforment en récupérant en mémoire à long terme des associations entre formes verbales et formes en chiffres. L'originalité du modèle est sa capacité à apprendre à partir de son f…
Tropical Temperate Toughs over southern Africa: mechanisms and evolution in response to climate change
2015
In the Southern Hemisphere, Southern Africa and the south-west Indian Ocean are one of the three preferred regions where interactions between the tropics and midlatitudes develop. This is the South Indian Convergence Zone (SICZ), where northwest-southeast oriented cloud bands form at the synoptic scale (between 3 and 5 days). These bands are mainly found during the austral summer and are commonly referred to as tropical temperate troughs (TTTs). This research aims at improving our knowledge related to TTTs, with a study on the dynamics associated with these systems, and an analysis of their possible evolution during the 21st century.The first part of this thesis aims at identifying favorab…
Increased Acid Dissociation at the Quartz/Water Interface.
2018
As shown by a quite significant amount of literature, acids at the water surface tend to be “less” acid, meaning that their associated form is favored over the conjugated base. What happens at the solid/liquid interface? In the case of the silica/water interface, we show how the acidity of adsorbed molecules can instead increase. Using a free energy perturbation approach in combination with electronic structure-based molecular dynamics simulations, we show how the acidity of pyruvic acid at the quartz/water interface is increased by almost two units. Such increased acidity is the result of the specific microsolvation at the interface and, in particular, of the stabilization of the deprotona…
Experimental studies of the rheological behavior of a demixing biopolymeric sol
1995
Experimental data are presented concerning a large transient viscosity surge occurring in the course of spinodal demixing of agarose aqueous solutions. The study includes the effects of water perturbation by minor proportions of compatible cosolutes. Three observations are noteworthy. One concerns an upward or downward shift of the spinodal temperature, caused by cosolutes, which agrees with their expected modulation of solvent-induced forces. The second concerns the time of appearance of the viscosity surge. This is observed to follow a critical law, with an exponent independent of polymer concentration and solvent perturbation. The third concerns the inverse-power-law dependence of the vi…
Computational and theoretical studies on lattice thermal conductivity and thermal properties of silicon clathrates
2016
The lattice thermal conductivity is usually an intrinsic property in the study of thermoelectricity. In particular, relatively low lattice thermal conductivity is usually a desired feature when higher thermoelectric efficiency is pursued. The mechanisms which lower the lattice thermal conductivity are not known in sufficient detail and deeper understanding about the phenomena is needed and if such understanding is achieved it can be used to design more efficient thermoelectric materials. In this thesis, the lattice thermal conductivity and other thermal properties of several silicon clathrates, which are known to be promising candidates for the thermoelectric applications, are studied by theoreti…
Using affinity perturbations to detect web traffic anomalies
2013
The initial training phase of machine learning algorithms is usually computationally expensive as it involves the processing of huge matrices. Evolving datasets are challenging from this point of view because changing behavior requires updating the training. We propose a method for updating the training profile efficiently and a sliding window algorithm for online processing of the data in smaller fractions. This assumes the data is modeled by a kernel method that includes spectral decomposition. We demonstrate the algorithm with a web server request log where an actual intrusion attack is known to happen. Updating the kernel dynamically using a sliding window technique, prevents the proble…