Search results for "molecular dynamics"
showing 10 items of 1075 documents
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…
TOWARD ENRICHED VHTS FOR CDK2 INHIBITORS: MOLECULAR DYNAMICS, PHARMACOPHORE MODELLING, AND DOCKING
2019
Cyclin-Dependent Kinases-2 (CDK2) are members of the serine/threonine protein kinases family. They play an important role in the regulation events of the eukaryotic cell division cycle, especially during the G1 to S phase transition. Experimental evidence indicates that excessive expression of CDK2s should cause abnormal cell cycle regulation. Therefore, since a long time, CDK2s have been considered potential therapeutic targets for cancer therapy. In this work, we collected one-hundred and forty-nine complexes of inhibitors bound in the CDK2-ATP pocket submitting to short MD simulations (10ns) and free energy calculation by means of MM-GBSA. The calculate ∆G values have been compared with …
Adsorbents and columns in analytical high-performance liquid chromatography: A perspective with regard to development and understanding
2012
A brief historical survey is presented on the evaluation of silica adsorbents in analytical HPLC. The theory of analytical HPLC is mostly still being based on the height equivalent to a theoretical plate concept and the van Deemter equation that was derived from gas phase adsorption involving a linear adsorption isotherm and fast mass transfer kinetics. One can obviously wonder whether the use of the van Deemter equation is relevant and valid for the evaluation of the performance of HPLC systems, where most often the liquid solutes involve charged molecules in electrolytes and in very many cases the adsorbates are macromolecules having diffusion coefficients of small magnitude. Instead of t…