Search results for "Dynamics"
showing 10 items of 9782 documents
Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
2019
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …
Analysis of the U L3-edge X-ray absorption spectra in UO2 using molecular dynamics simulations
2017
This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under the project ID s444. The resource allocation within the PSI share at CSCS and on the PSI compute cluster Merlin4 is also acknowledged. D. B. is grateful for a fellowship within the Sciex-NMS programme. A. K. was supported by Latvian Science Council Grant no. 187/2012.
Energy analysis of a non-linear dynamic impact using FEM
2014
In the car industry, the Finite Element Method (FEM) is being more and more used to analyze the crashworthiness performance of vehicles. In order to validate the results, these impact simulations are normally compared with real crash footage and acceleration data. This paper studies the deformation- and energy output of a simple dummy model during a non-linear dynamic impact. The dummy model is crashed into an obstacle at three different velocities to observe the energy dissipated through different damping mechanisms. Furthermore, in impact simulations, material damping plays an important role in energy dissipation. However, it can be difficult to determine realistic damping parameter value…
International workshop on next generation gamma-ray source
2022
Journal of physics / G 49(1), 010502 (2022). doi:10.1088/1361-6471/ac2827
Radiation from multi-GeV electrons and positrons in periodically bent silicon crystal
2014
A periodically bent Si crystal is shown to efficiently serve for producing highly monochromatic radiation in a gamma-ray energy spectral range. A short-period small-amplitude bending yields narrow undulator-type spectral peaks in radiation from multi-GeV electrons and positrons channeling through the crystal. Benchmark theoretical results on the undulator are obtained by simulations of the channeling with a full atomistic approach to the projectile-crystal interactions over the macroscopic propagation distances. The simulations are facilitated by employing the MBN Explorer package for molecular dynamics calculations on the meso-, bio- and nano-scales. The radiation from the ultra-relativist…
X-rays from accretion shocks in classical T Tauri stars: 2D MHD modeling and the role of local absorption
2013
AbstractIn classical T Tauri stars (CTTS) strong shocks are formed where the accretion funnel impacts with the denser stellar chromosphere. Although current models of accretion provide a plausible global picture of this process, some fundamental aspects are still unclear: the observed X-ray luminosity in accretion shocks is order of magnitudes lower than predicted; the observed density and temperature structures of the hot post-shock region are puzzling and still unexplained by models.To address these issues we performed 2D MHD simulations describing an accretion stream impacting onto the chromosphere of a CTTS, exploring different configurations and strengths of the magnetic field. From th…
QPOs expected in rotating accretion flows around a supermassive black hole
2007
It is well known that rotating inviscid accretion flows with adequate injection parameters around black holes could form shock waves close to the black holes, after the flow passes through the outer sonic point and can be virtually stopped by the centrifugal force. We numerically examine such shock waves in 2D accretion flows with 10−5 to 106 Eddington critical accretion rates around a supermassive black hole with 106 M. As the results, the luminosities show QPO phenomena with modulations of a factor 2–3 and with quasi-periods of a few to several hours.
First M87 Event Horizon Telescope Results. VIII. Magnetic Field Structure near The Event Horizon
2021
Full list of authors: Akiyama, Kazunori; Algaba, Juan Carlos; Alberdi, Antxon; Alef, Walter; Anantua, Richard; Asada, Keiichi; Azulay, Rebecca; Baczko, Anne-Kathrin; Ball, David; Baloković, Mislav; Barrett, John; Benson, Bradford A.; Bintley, Dan; Blackburn, Lindy; Blundell, Raymond; Boland, Wilfred; Bouman, Katherine L.; Bower, Geoffrey C.; Boyce, Hope Bremer, Michael; Brinkerink, Christiaan D.; Brissenden, Roger; Britzen, Silke; Broderick, Avery E.; Broguiere, Dominique; Bronzwaer, Thomas; Byun, Do-Young; Carlstrom, John E.; Chael, Andrew; Chan, Chi-kwan; Chatterjee, Shami; Chatterjee, Koushik; Chen, Ming-Tang; Chen, Yongjun; Chesler, Paul M.; Cho, Ilje; Christian, Pierre; Conway, John E.…
A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS
2019
Abstract The effect of the protonation state of the hydroxyl-ethylthiamin diphosphate intermediate, HEThDP, on the enzyme-substrate interactions and their consequences on the biosynthesis of R-phenylacetylcarbinol, R-PAC, by the acetohydroxy acid synthase, AHAS, is addressed by molecular dynamics simulations. It is found that the form of HEThDP, which favors the formation of R-PAC, is that having the 4-aminopyrimidine ring with the N1′ atom protonated and the N4′ atom as aminopyrimidinium ion. Under this form both active sites of AHAS have the ability to perform the catalysis, unlike that observed for the other possible protonation states of N1′ and N4′ atoms.
Some observations on the determination of total heavy metals in sewage sludge by atomic absorption spectrophotometry after a pressurized acid digesti…
1990
Abstract An economical and simple method for the flame atomic absorption spectrometric determination of Cd, Pb, Ni, Cu, Fe, and Zn in sewage sludges is described. Samples are treated with concentrated HNO 3 in a thermal oven using Pyrex glass tubes hermetically sealed with Bakelite screw caps. The effect of the digestion parameters, such as digestion time, acid volume, sample mass, and temperature, were studied. The precision and accuracy of this procedure were evaluated by the analysis of two BCR (Community Bureau of Reference, European Communities) certified sewage sludge samples (CRM 146 and 144).