Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Study of High-Temperature Behaviour of ZnO by Ab Initio Molecular Dynamics Simulations and X-ray Absorption Spectroscopy
2021
Wurtzite-type zinc oxide (w-ZnO) is a widely used material with a pronounced structural anisotropy along the c axis, which affects its lattice dynamics and represents a difficulty for its accurate description using classical models of interatomic interactions. In this study, ab initio molecular dynamics (AIMD) was employed to simulate a bulk w-ZnO phase in the NpT ensemble in the high-temperature range from 300 K to 1200 K. The results of the simulations were validated by comparison with the experimental Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra and known diffraction data. AIMD NpT simulations reproduced well the thermal expansion of the lattice, and the pronounced …
New QM/MM implementation of the DFTB3 method in the gromacs package.
2015
The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…
Computer Simulation Studies of Chain Dynamics in Polymer Brushes
2012
Center-of-mass and single monomer motion in grafted chains comprising a strongly stretched polymer brush in thermal equilibrium are studied by large scale molecular dynamics and Monte Carlo simulations of a coarse-grained model. Good solvent conditions are assumed. Our findings seriously question earlier theoretical predictions about the relaxation described by Rouse dynamics of brush coatings. Thus, the correlation functions of parallel and perpendicular components of the mean distance of the center-of-mass from the grafting site, the squared gyration radius and end-to-end distance, are found to deviate strongly from a simple exponential decay. While the relaxation times extracted from the…
Finite-size effects of Kirkwood–Buff integrals from molecular simulations
2017
The modelling of thermodynamic properties of liquids from local density fluctuations is relevant to many chemical and biological processes. The Kirkwood–Buff (KB) theory connects the microscopic structure of isotropic liquids with macroscopic properties such as partial derivatives of activity coefficients, partial molar volumes and compressibilities. Originally, KB integrals were formulated for open and infinite systems which are difficult to access with standard Molecular Dynamics (MD) simulations. Recently, KB integrals for finite and open systems were formulated (J Phys Chem Lett. 2013;4:235). From the scaling of KB integrals for finite subvolumes, embedded in larger reservoirs, with the…
Gravimetric and FTIR study of the interaction of tetramethylethylene on a MFI zeolite
2005
The adsorption of tetramethylethylene on a high siliceous ZSM-5 zeolite was performed by thermogravimetry, in situ FTIR spectroscopy and molecular dynamics simulation. Sorption and spectroscopic data were analysed as a function of loading and compared with molecular dynamics simulated results to characterize the adsorption process. The isotherm at 298 K does not show any deviation from the type I behaviour. The presence of admolecules in micropores does not or weakly affect zeolite framework vibration bands but induces an additional band at around 1715 cm−1 mainly due to a contribution of the microporous surface of the adsorbent. A confinement effect of the adsorbate is characterized during…
First-principles simulations of hydrogen peroxide formation catalyzed by small neutral gold clusters.
2009
Energetics and dynamical pathways for hydrogen peroxide formation from H(2) and O(2) bound to neutral gold dimers and tetramers have been investigated by applying several strategies: T = 0 K geometry optimizations, constrained Car-Parrinello molecular dynamics simulations at T = 300 K and metadynamics at T = 300 K. The competing reaction channels for water and hydrogen peroxide formation have been found and characterized. In each case, the reaction barriers for Au cluster catalyzed proton transfer are less than 1 eV. Water formation is a competitive reaction channel, and the relative weight of H(2)O and H(2)O(2) products may depend on the chosen Au cluster size. Dynamic simulations demonstr…
Atypical titration curves for GaAl12Keggin-ions explained by a joint experimental and simulation approach
2018
Although they have been widely used as models for oxide surfaces, the deprotonation behaviors of the Keggin-ions (MeAl127+) and typical oxide surfaces are very different. On Keggin-ions, the deprotonation occurs over a very narrow pH range at odds with the broad charging curve of larger oxide surfaces. Depending on the Me concentration, the deprotonation curve levels off sooner (high Me concentration) or later (for low Me concentration). The leveling off shows the onset of aggregation before which the Keggin-ions are present as individual units. We show that the atypical titration data previously observed for some GaAl12 solutions in comparison to the originally reported data can be explain…
Cross-section-constrained top-quark mass measurement from dilepton events at the tevatron
2008
We report the first top quark mass measurement that uses a cross section constraint to improve the mass determination. This measurement is made with a dilepton $t\bar{t}$ event sample collected with the CDF II detector. From a data sample corresponding to an integrated luminosity of 1.2 fb$^{-1}$, we measure a top quark mass of $\rm{170.7^{+4.2}_{-3.9}(stat)\pm2.6(syst)}$ $\rm{\pm2.4(theory) GeV/{\it{c}}^{2}}$. The measurement without the cross section constraint results in a top quark mass of $\rm{169.7^{+5.2}_{-4.9}(stat)\pm3.1(syst) GeV/{\it{c}}^{2}}$.
Inhibitor-Induced Dimerization of an Essential Oxidoreductase from African Trypanosomes
2018
Trypanosomal and leishmanial infections claim tens of thousands of lives each year. The metabolism of these unicellular eukaryotic parasites differs from the human host and their enzymes thus constitute promising drug targets. Tryparedoxin (Tpx) from Trypanosoma brucei is the essential oxidoreductase in the parasite's hydroperoxide-clearance cascade. In vitro and in vivo functional assays show that a small, selective inhibitor efficiently inhibits Tpx. With X-ray crystallography, SAXS, analytical SEC, SEC-MALS, MD simulations, ITC, and NMR spectroscopy, we show how covalent binding of this monofunctional inhibitor leads to Tpx dimerization. Intra- and intermolecular inhibitor-inhibitor, pro…
NMR structure of a non-conjugatable, ADP-ribosylation associated, ubiquitin-like domain from Tetrahymena thermophila polyubiquitin locus.
2019
Abstract Background Ubiquitin-like domains (UbLs), in addition to being post-translationally conjugated to the target through the E1-E2-E3 enzymatic cascade, can be translated as a part of the protein they ought to regulate. As integral UbLs coexist with the rest of the protein, their structural properties can differ from canonical ubiquitin, depending on the protein context and how they interact with it. In this work, we investigate T.th-ubl5, a UbL present in a polyubiquitin locus of Tetrahymena thermophila, which is integral to an ADP-ribosyl transferase protein. Only one other co-occurrence of these two domains within the same protein has been reported. Methods NMR, multiple sequence al…