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Introduction This tutorial is designed to guide users of VMD and NAMD through all the steps required to set up a membrane protein system for molecular dynamics simulations. The tutorial assumes that you already have a working knowledge of VMD and NAMD. For the accompanying VMD and NAMD tutorials go to: This tutorial has been designed specifically for VMD(More)
Membrane transporters rely on highly coordinated structural transitions between major conformational states for their function, to prevent simultaneous access of the substrate binding site to both sides of the membrane--a mode of operation known as the alternating access model. Although this mechanism successfully accounts for the efficient exchange of the(More)
Zusammenfassung Numerical Experience with Newton-like Methods for Nonlinear Algebraic Systems. In this paper we present an extensive computational experience with several Newton-like methods, namely Newton's method, the ABS Huang method, the ABS row update method and six Quasi-Newton methods. The methods are first tested on 31 families of problems with(More)
Glutamate transporters (GluTs) are the primary regulators of extracellular concentration of the neurotransmitter glutamate in the central nervous system. In this study, we have investigated the dynamics and coupling of the substrate and Na(+) binding sites, and the mechanism of cotransport of Na(+) ions, using molecular dynamics simulations of a(More)
High mortality following aneurysmal subarachnoid hemorrhage (aSAH) occurs in the early phase, but the underlying mechanism of early brain injury (EBI) in aSAH was less elucidated. In this study, we aimed to investigate the association of apolipoprotein E (APOE) genotypes and early cerebral perfusion after aSAH. We collected venous blood of aSAH patients on(More)
When using Genetic Algorithm (GA) to optimize the feature space of pattern classification problems, the performance improved is not only determined by the data set used, but also depend on the classifier. This work compares the improvements acquired by GA optimized feature transformations on several simple classifiers. Some traditional feature(More)
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of(More)
Ischemic stroke, characterized by the disturbance of the blood supply to the brain, is a severe worldwide health threat with high mortality and morbidity. However, there is no effective pharmacotherapy for ischemic injury. Currently, combined treatment is highly recommended for this devastating injury. In the present study, we investigated neuroprotective(More)