Search results for "Computation"
showing 10 items of 7362 documents
A negotiation protocol to improve long distance truck parking
2017
High-accuracy approximation of piecewise smooth functions using the Truncation and Encode approach
2017
Abstract In the present work, we analyze a technique designed by Geraci et al. in [1,11] named the Truncate and Encode (TE) strategy. It was presented as a non-intrusive method for steady and non-steady Partial Differential Equations (PDEs) in Uncertainty Quantification (UQ), and as a weakly intrusive method in the unsteady case. We analyze the TE algorithm applied to the approximation of functions, and in particular its performance for piecewise smooth functions. We carry out some numerical experiments, comparing the performance of the algorithm when using different linear and non-linear interpolation techniques and provide some recommendations that we find useful in order to achieve a hig…
Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex
2020
Abstract The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable 19F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the 19F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleepi…
Theoretical study of the interaction between sodium ion and a cyclopeptidic tubular structure.
2007
DFT calculations have been carried out to describe the pathway of a sodium ion along the stacking direction of a tubular structure set up by five cyclopeptidic units, which can be considered a suitable model of a hollow tubular structure of indefinite length. A lattice of points inside the tubular structure is defined and the DFT interaction energy values with a sodium ion are obtained. The data allow predicting a zigzag path of the ion inside the hosting structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Recent advances on aptamer-based biosensors to detection of platelet-derived growth factor.
2018
Platelet-derived growth factor (PDGF-BB), a significant serum cytokine, is an important protein biomarker in diagnosis and recognition of cancer, which straightly rolled in proceeding of various cell transformations, including tumor growth and its development. Fibrosis, atherosclerosis are certain appalling diseases, which PDGF-BB is near to them. Generally, the expression amount of PDGF-BB increases in human life-threatening tumors serving as an indicator for tumor angiogenesis. Thus, identification and quantification of PDGF-BB in biomedical fields are particularly important. Affinity chromatography, immunohistochemical methods and enzyme-linked immunosorbent assay (ELISA), conventional m…
Dissecting signaling and functions of adhesion G protein-coupled receptors
2012
G protein-coupled receptors (GPCRs) comprise an expanded superfamily of receptors in the human genome. Adhesion class G protein-coupled receptors (adhesion-GPCRs) form the second largest class of GPCRs. Despite the abundance, size, molecular structure, and functions in facilitating cell and matrix contacts in a variety of organ systems, adhesion-GPCRs are by far the most poorly understood GPCR class. Adhesion-GPCRs possess a unique molecular structure, with extended N-termini containing various adhesion domains. In addition, many adhesion-GPCRs are autoproteolytically cleaved into an N-terminal fragment (NTF, NT, α-subunit) and C-terminal fragment (CTF, CT, β-subunit) at a conserved GPCR au…
Modeling multiple taxis: Tumor invasion with phenotypic heterogeneity, haptotaxis, and unilateral interspecies repellence
2021
We provide a short review of existing models with multiple taxis performed by (at least) one species and consider a new mathematical model for tumor invasion featuring two mutually exclusive cell phenotypes (migrating and proliferating). The migrating cells perform nonlinear diffusion and two types of taxis in response to non-diffusing cues: away from proliferating cells and up the gradient of surrounding tissue. Transitions between the two cell subpopulations are influenced by subcellular (receptor binding) dynamics, thus conferring the setting a multiscale character. We prove global existence of weak solutions to a simplified model version and perform numerical simulations for the full se…
Zebrafish xenografts as a tool for in vivo studies on human cancer
2012
The zebrafish has become a powerful vertebrate model for genetic studies of embryonic development and organogenesis and increasingly for studies in cancer biology. Zebrafish facilitate the performance of reverse and forward genetic approaches, including mutagenesis and small molecule screens. Moreover, several studies report the feasibility of xenotransplanting human cells into zebrafish embryos and adult fish. This model provides a unique opportunity to monitor tumor-induced angiogenesis, invasiveness, and response to a range of treatments in vivo and in real time. Despite the high conservation of gene function between fish and humans, concern remains that potential differences in zebrafis…