Search results for "Computer Science Application"
showing 10 items of 3998 documents
GLASS TRANSITION IN THIN POLYMER FILMS: A MOLECULAR DYNAMICS STUDY
2002
A melt of nonentangled polymer chains confined between two smooth and purely repulsive walls is studied for various film thicknesses D and temperatures. The dynamics of the supercooled films is qualitatively identical to that of the bulk, but the walls lead to faster relaxation. To quantify this observation we analyze the data by the mode-coupling theory (MCT) of the glass transition. We find that the critical temperature of MCT, Tc(D), decreases with D and that T - Tc(D) is a relevant temperature scale. The static structure factor and dynamic correlation functions at intermediate times coincide with bulk behavior when compared to the same T - Tc(D).
Simulation of Dense Polymer Systems in Two and Three Dimensions
1991
Dense polymer systems are modeled by self- and mutually avoiding walks on lattices. Both simple models where the step length is one lattice spacing and more complicated models where the step length is distinctly longer and may fluctuate (“bond fluctuation model”) are discussed, and it is shown that the computer simulation of such models gives useful insight to understand the thermodynamic phase behavior and the relaxational dynamics of dense polymer solutions and polymer melts. The huge demands in computing power needed for a successful simulation of such systems can be covered by parallel computers such as the multitransputer facility of the University of Mainz.
KINETICS OF POLYMER EJECTION FROM CAPSID CONFINEMENT: SCALING CONSIDERATIONS AND COMPUTER EXPERIMENT
2012
We investigate the ejection dynamics of a flexible polymer chain out of confined environment by means of scaling considerations and Monte Carlo simulations. Situations of this kind arise in different physical contexts, including a flexible synthetic polymer partially confined in a nanopore and a viral genome partially ejected from its capsid. In the case of cylindric confinement the entropic driving force which pulls the chain out of the pore is argued to be constant once a few persistent lengths are out of the pore. We demonstrate that in this case the ejection dynamics follows a [Formula: see text]-law with elapsed time t. The mean ejection time τ depends nonmonotonically on chain length…
Relationships between kinetic constants and the amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway
2012
The kinetic models of metabolic pathways represent a system of biochemical reactions in terms of metabolic fluxes and enzyme kinetics. Therefore, the apparent differences of metabolic fluxes might reflect distinctive kinetic characteristics, as well as sequence-dependent properties of the employed enzymes. This study aims to examine possible linkages between kinetic constants and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolytic pathway. The values of Michaelis-Menten constant (K M), turnover number (k cat), and specificity constant (k sp = k cat/K M) were taken from BRENDA (15, 17, and 16 values, respectively) and protein sequences of nine…
Nonlocal van der Waals Approach Merged with Double-Hybrid Density Functionals: Toward the Accurate Treatment of Noncovalent Interactions
2015
Noncovalent interactions drive the self-assembly of weakly interacting molecular systems to form supramolecular aggregates, which play a major role in nanotechnology and biochemistry. In this work, we present a thorough assessment of the performance of different double-hybrid density functionals (PBE0-DH-NL, revPBE0-DH-NL, B2PLYP-NL, and TPSS0-DH-NL), as well as their parent hybrid and (meta)GGA functionals, in combination with the most modern version of the nonlocal (NL) van der Waals correction. It is shown that this nonlocal correction can be successfully coupled with double-hybrid density functionals thanks to the short-range attenuation parameter b, which has been optimized against ref…
Toward Understanding the Photochemistry of Photoactive Yellow Protein: A CASPT2/CASSCF and Quantum Theory of Atoms in Molecules Combined Study of a M…
2009
Photochemical processes that take place in biological molecules have become an increasingly important research topic for both experimentalists and theoreticians. In this work, we report the reaction mechanism of a model of the photoactive yellow protein (PYP) chromophore in vacuo. The results obtained here, using a strategy based on the simultaneous use of the minimum energy path concept and the quantum theory of atoms in molecules applied to this excited state process, suggest a possible way in which the protein could increase the efficiency of the reaction. The role played by other electronic states of the same and different spin multiplicities in the reaction process is also analyzed, wi…
Effect of structural parameters on the polarizabilities of methanol clusters: a hirshfeld study
2008
The polarizabilities of fifty methanol clusters (CH3OH)n, n = 1 to 12, were calculated at the B3LYP/6-311++G** level of theory and partitioned into molecular contributions using the Hirshfeld-I method. The resulting molecular polarizabilities were found to be determined by the polarizabilities of the two parts of the molecule, the hydrophilic hydroxyl group and the hydrophobic methyl group, each exhibiting a different dependency upon the local environment. The polarizability of the hydroxyl group was found to be dependent on the number, type, and strength of the hydrogen bonds a methanol molecule makes, whereas the polarizability of the methyl groups is mostly influenced by sterical hindran…
(+)-(E)-Chrysanthenyl Acetate: A Molecule with Interesting Biological Properties Contained in the Anthemis secundiramea (Asteraceae) Flowers
2020
Anthemis secundiramea is a perennial herb native widespread throughout the Mediterranean basin. The oil obtained from the flowers of this plant has antimicrobial properties against gram-positive and -negative bacteria, and inhibits the biofilm formation. The extract of A. secundiramea also has antioxidant activity&mdash
A Mixture of Dietary Plant Sterols at Nutritional Relevant Serum Concentration Inhibits Extrinsic Pathway of Eryptosis Induced by Cigarette Smoke Ext…
2023
Cell death program of red blood cells (RBCs), called eryptosis, is characterized by activation of caspases and scrambling of membrane phospholipids with externalization of phosphatidylserine (PS). Excessive eryptosis confers a procoagulant phenotype and is implicated in impairment of microcirculation and increased prothrombotic risk. It has recently been reported that cigarette smokers have high levels of circulating eryptotic erythrocytes, and a possible contribution of eryptosis to the vaso-occlusive complications associated to cigarette smoke has been postulated. In this study, we demonstrate how a mixture of plant sterols (MPtS) consisting of β-sitosterol, campesterol and stigmasterol, …
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistic…
2008
Abstract Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster…