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Atomistic dynamics
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Ebook "Atomistic approaches in modern biology: From quantum chemistry to molecular simulations (Topics in current chemistry, Volume 268)" presents an overview of atomistic theoretical methods applied to molecular biological systems. It thus repesents a bottom-up view of chemistry on biology from a theoretical perspective. This volume is organized in a bottom-up spirit and starts with a review by De Gioia et al. on how chemical reactions at the active site of the hydrogenase metalloenzyme can be analyzed with quantum chemical methods, i.e.
368p
manmanthanhla0201
27-02-2024
1
1
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We study the escape process of nascent proteins at the ribosomal exit tunnel of bacterial Escherichia coli by using molecular dynamics simulations with coarse-grained and atomistic models. It is shown that the effects of hydrophobic and electrostatic interactions on the protein escape at the E. coli’s tunnel are qualitatively similar to those obtained previously at the exit tunnel of archaeal Haloarcula marismortui, despite significant differences in the structures and interactions of the ribosome tunnels from the two organisms.
12p
vispiderman
15-06-2023
7
2
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In this thesis atomistic level modelling is conducted to investigate the design of an environmentally adaptable self-cleaning polymer paint coating that incorporates biomimetics to remain clean in various environmental setting. This work will be used to aid in the development of stay-clean polymer paint coating.
116p
runthenight07
01-03-2023
3
2
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In this work, simulations of xylan oligomers starting from random configurations at different levels of hydration are performed. The simulations show clear evidence of phase separation into water-rich and polymer-rich phases at higher hydration, in spite of standard indicators of equilibrium, such as density and energy, remaining constant.
11p
viginny
30-12-2022
8
2
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A new method is outlined for constructing realistic models of the mesoporous amorphous silica adsorbent, MCM-41. The procedure uses the melt-quench molecular dynamics technique. Previous methods are either computationally expensive or overly simplified, missing key details necessary for agreement with experimental data.
9p
vironald
15-12-2022
5
2
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The system reached equilibrium at around 0.1 µs. The overall 3-dimensional structure was well preserved throughout the simulation. Local residue-based fluctuations were in good agreement with fully atomistic MD simulations. Four distinct snapshots were selected and reverse-mapped to all-atom representations with around 65,000 atoms. Each reverse-mapped system was later subjected to 100 ns of MD simulation for equilibration.
15p
langthannam
29-12-2021
16
0
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The sensing of individual molecules as they pass through nanopores under an external field is a popular research field. The approach is simply based on the detectable temporary blockades in the ionic current as the molecules pass through the nanopores. These signatures of the current have been shown to be a function of nanoparticle and nanopore size and geometry as well as the external electric field. However, models developed in this context fail to predict the experimentally observed behavior in technologically important shorter nanopores.
11p
tudichquannguyet
29-11-2021
5
1
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Gram-negative bacterium Neisseria meningitidis, responsible for human infectious disease meningitis, acquires the iron (Fe3+) ion needed for its survival from human transferrin protein (hTf). For this transport, transferrin binding proteins TbpA and TbpB are facilitated by the bacterium. The transfer cannot occur without TbpA, while the absence of TbpB only slows down the transfer. Thus, understanding the TbpA-hTf binding at the atomic level is crucial for the fight against bacterial meningitis infections.
9p
tudichquannguyet
29-11-2021
8
1
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In this paper a molecular dynamics simulation of nano-metric cutting of copper with a diamond tool is presented. MD simulations require the determination of the interaction of the involved atoms through a function of potential for the materials involved in the analysis and the accurate topography of the studied area, leading to high demand of computational time.
12p
tohitohi
19-05-2020
25
0
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The analytic expressions of the Helmholtz free energy, the Gibbs thermodynamic potential the mean nearest neighbor distance between two atoms, the crystal parameters for bcc, fcc and hcp phases of defective and perfect substitutional alloys AB with interstitial atoms C and structural phase transition temperatures of these alloys at zero pressure and under pressure are derived by the statistical moment method.
11p
viedison2711
03-09-2019
19
0
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The simulated nanocrystalline U0.5Th0.5O2 exhibited a breakdown in the HallePetch relation with mean grain size varying from 3.0 nm to 18.0 nm. Moreover, the elastic modulus of U1-yThyO2 solid solutions with different content of thorium at 300 K was also studied and the results accorded well with the experimental data available in the literature. In addition, the fracture mode of nanocrystalline U0.5Th0.
7p
minhxaminhyeu4
26-06-2019
13
1
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Next, the zonal coupling method between the atomistic and continuum models is described, including an assessment of the energy transfer between both domains for a one-dimensional problem. Finally, a two-dimensional computation is presented of dynamic fracture using the coupled model.
13p
thienthanquydu
21-10-2018
33
0
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