Scientific computing

This study develops unconditionally monotone finite-difference scheme of second-order of local approximation on uniform grids for the initial boundary problem value for the Gamma equation through the establishment of two-side estimates for the scheme’s solution.

8p tamynhan6 14-09-2020 18 2   Download

The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.

234p runthenight04 02-02-2023 13 3   Download

The thesis mainly aims to solve the following tasks: Firstly, the thesis extensively analyzes a wide range of existing approaches for the ME detection in scientific document images. Then, the thesis investigates and proposes novel methods to improve the detection accuracy of MEs. After enhancing the detection accuracy of MEs, the thesis investigates and pro poses a framework to improve the accuracy of the recognition of MEs in scientific document images.

27p closefriend09 16-11-2021 23 4   Download

The thesis mainly aims to solve the following tasks: Firstly, the thesis extensively analyzes a wide range of existing approaches for the ME detection in scientific document images. Then, the thesis investigates and proposes novel methods to improve the detection accuracy of MEs. After enhancing the detection accuracy of MEs, the thesis investigates and pro poses a framework to improve the accuracy of the recognition of MEs in scientific document images.

154p mintmintt 05-10-2021 17 4   Download

Research objectives: To study rainfall-runoff changes, to downscale rainfall and surface over time and space, and to establish scientific base for calculation of design flood for transportation structures.

28p dolphintaletale 23-04-2021 31 6   Download

N-Acetylglucosamine is a major component of com-plex carbohydrates. The mammalian salvage pathway of N-acetylglucosamine recruitment from glycoconjugate deg-radation or nutritional sources starts with phosphorylation byN-acetylglucosamine kinase. In this studywe describe the identification of two active site cysteines of the sugar kinase by site-directed mutagenesis and computer-based structure prediction.

7p research12 23-04-2013 35 2   Download

A computer program has been evaluated for subsite map calculations of depolymerases. The program runs inWIN-DOWSanduses the experimentallydeterminedbond cleavage frequencies (BCFs) for determination of the number of subsites, the position of the catalytic site and for calculation of subsite binding energies. The apparent free energy values were optimized by minimization of the differences of the measured and calculated BCF data.

6p tumor12 22-04-2013 42 5   Download

Protein molecular modelling and ligand docking were employed for the design of anthraquinone galactosyl-bio-mimetic dye ligands (galactosyl-mimodyes) for the target enzyme galactose dehydrogenase (GaDH). Using appro-priate modelling methodology, a GaDH model was build based on a glucose-fructose oxidoreductase (GFO) protein template.

15p tumor12 22-04-2013 50 2   Download

Two dimensional electrophoresis has revealed a micro-heterogeneity in the recombinant human phenylalanine hydroxylase (hPAH) protomer,that is the result of sponta-neous nonenzymatic deamidations of labile asparagine (Asn) residues [Solstad,T. and Flatmark,T. (2000)Eur. J. Biochem.267,6302–6310].

10p tumor12 20-04-2013 29 2   Download

The wealth of available genomic data has spawned a corresponding interest in computational methods that can impart biological meaning and context to these experiments. Traditional computational methods have drawn rela-tionships between pairs of proteins or genes based on notions of equality or similarity between their patterns of occurrence or behavior. For exam-ple, two genes displaying similar variation in expression, over a number of experiments, may be predicted to be functionally related.

9p fptmusic 12-04-2013 46 4   Download

Due to the unavoidable nonbiological variations accompanying many experiments, it is imperative to consider a way of unravelling the functional interaction structure of a cellular network (e.g. signalling cascades or gene networks) by using the qualitative information of time-series experimental data instead of computation through the measured absolute values.

10p fptmusic 11-04-2013 52 3   Download

To achieve a structural context for the analysis of G-protein coupled recep-tor (GPCR) oligomers, molecular modeling must be used to predict the corresponding interaction interfaces. The task is complicated by the paucity of detailed structural data at atomic resolution, and the large number of possible modes in which the bundles of seven transmembrane (TM) seg-ments of the interacting GPCR monomers can be packed together into dimers and⁄or higher-order oligomers.

13p fptmusic 11-04-2013 51 3   Download

The transmembrane topology of presenilins is still the subject of debate despite many experimental topology studies using antibodies or gene fusions. The results from these studies are partly contradictory and conse-quently several topology models have been proposed. Studies of preseni-lin-interacting proteins have produced further contradiction, primarily regarding the location of the C-terminus.

0p awards 06-04-2013 36 3   Download

The glyoxalase pathway ofLeishmania infantumwas kinetically character-ized as a trypanothione-dependent system. Using time course analysis based on parameter fitting with a genetic algorithm, kinetic parameters were estimated for both enzymes, with trypanothione derived substrates. A Kmof 0.253 mmand aVof 0.21lmolÆmin )1 Æmg )1 for glyoxalase I, and a Kmof 0.098 mmand aVof 0.18lmolÆmin )1 Æmg )1 for glyoxalase II, were obtained.

11p awards 06-04-2013 48 2   Download

This work presents a computational analysis of the molecular characteris-tics shared by the adenylation domains from traditional nonribosomal pep-tide synthetases (NRPSs) and the group of the freestanding homologous enzymes: a-aminoadipate semialdehyde dehydrogenase, a-aminoadipate reductase and the protein Ebony. The results of systematic sequence com-parisons allow us to conclude that a specificity-conferring code, similar to that described for the NRPSs, can be recognized in such enzymes.

13p awards 05-04-2013 35 3   Download

Toovercome the difficultyof characterizing the structures of the extracellular loops (eLPs) ofGprotein-coupledreceptors (GPCRs) other than rhodopsin, we have explored a strategy to generate a three-dimensional structural model for a GPCR, the thromboxane A2 receptor. This three-dimen-sional structurewas completedby the assembly of theNMR structures of the computation-guided constrained peptides that mimicked the extracellular loops and connected to the conserved seven transmembrane domains.

11p awards 05-04-2013 40 4   Download

We used a combined computer and biochemical approach to characterize human pyridoxine 5¢-phosphate oxidase (PNPO).The human PNPOgene is composed of seven exons and six introns, and spans approximately 8 kb.All exon/intron junctions contain the gt/ag consensus splicing site.The absence of TATA-like sequences, the presence of Sp1-binding sites and more importantly, the presence of CpG islands in the regulatory region of thePNPOgene are characteristic features of housekeeping genes.

10p dell39 03-04-2013 48 3   Download

Recent and increasing use of computational tools in the field of nicotinic receptors has led to the publication of several models of ligand–receptor interactions. Thesemodels are all basedon the crystal structure at 2.7 A˚ resolutionof aprotein related to the extracellular N-terminus of nicotinic acetyl-choline receptors (nAChRs), the acetylcholine binding pro-tein. In the absence of any X-ray or NMR information on nAChRs, this new structure has provided a reliable alter-native to study the nAChR structure....

8p dell39 03-04-2013 43 4   Download

To address questions of protein stability, researchers have increasingly turned to combinatorial approaches that permit the rapid analysis of libraries of protein variants. Phage-displayhasprovedtobeapowerful tool foranalyzingprotein stabilitydue to the large library sizeand the robustnessof the phageparticle toavarietyofdenaturingconditions.

7p dell39 03-04-2013 36 5   Download

We have investigated the molecular mechanisms that produce different structural and functional behavior in the monomeric and trimeric forms of seminal vesicle protein no. 4, a protein with immunomodulatory, anti-inflamma-tory, and procoagulant activity secreted from the rat seminal vesicle epithelium. The monomeric and trimeric forms were characterized in solution by CD.

9p dell39 03-04-2013 35 5   Download