Search results for "Computation"
showing 10 items of 7362 documents
PDE triangular Bézier surfaces: Harmonic, biharmonic and isotropic surfaces
2011
We approach surface design by solving second-order and fourth-order Partial Differential Equations (PDEs). We present many methods for designing triangular Bézier PDE surfaces given different sets of prescribed control points and including the special cases of harmonic and biharmonic surfaces. Moreover, we introduce and study a second-order and a fourth-order symmetric operator to overcome the anisotropy drawback of the harmonic and biharmonic operators over triangular Bézier surfaces. © 2010 Elsevier B.V. All rights reserved.
A third order partial differential equation for isotropic boundary based triangular Bézier surface generation
2011
Abstract We approach surface design by solving a linear third order Partial Differential Equation (PDE). We present an explicit polynomial solution method for triangular Bezier PDE surface generation characterized by a boundary configuration. The third order PDE comes from a symmetric operator defined here to overcome the anisotropy drawback of any operator over triangular Bezier surfaces.
Explicit Bézier control net of a PDE surface
2017
The PDE under study here is a general fourth-order linear elliptic Partial Differential Equation. Having prescribed the boundary control points, we provide the explicit expression of the whole control net of the associated PDE Bézier surface. In other words, we obtain the explicit expressions of the interior control points as linear combinations of free boundary control points. The set of scalar coefficients of these combinations works like a mould for PDE surfaces. Thus, once this mould has been computed for a given degree, real-time manipulation of the resulting surfaces becomes possible by modifying the prescribed information. The work was partially supported by Spanish Ministry of Econo…
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.
2019
Abstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. Results While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are…
A Definitive Pharmacophore Modelling Study on CDK2 ATP Pocket Binders: Tracing the Path of New Virtual High-Throughput Screenings
2020
Cyclin Dependent Kinases-2 (CDK2) are members of 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 indicate 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, onehundred and forty-nine complexes of inhibitors bound in the CDK2-ATP pocket were submitted to short MD simulations (10ns) and free energy calculation. Comparison with experimental data (K<sub>i</sub>, K<sub>d</su…
Comparing molecular dynamics-derived pharmacophore models with docking: A study on CDK-2 inhibitors
2020
Abstract We compared the performance of molecular dynamics (MD)-derived pharmacophore modeling approaches, Common Hit Approach (CHA), and the Molecular dYnamics SHAred PharmacophorE (MYSHAPE) approach, with semi-flexible constrained/unconstrained docking. The aim of this work is to enrich the hit-list of a virtual screening on CDK-2 known inhibitors as a case study. Cyclin-dependent kinases (CDKs) deregulation is associated with cancer growth. CDKs are an attractive target for anticancer agents. MD-derived pharmacophore models have been obtained with LigandScout 4.2.1. Docking analysis has been performed through Glide 7.6. The results highlighted the MYSHAPE approach has a better performanc…
A CNDO/2 study on the additivity and the nature of the non-additivity of the substituent effects on13C NMR shifts in chlorobenzenes and chlorophenols
1980
The general correlation between the electron densities and the 13C NMR chemical shifts is found to be quite poor in the cases discussed. The non-additivities of the substituent effects on the chemical shifts and the CNDO/2 electron densities correlate only weakly. However, when the electron densities are made specific to different types of atomic orbitals, the s electrons have a pronounced effect in all the models tested. This is explained by an indirect effect on the 〈1/r3〉 term of the p electrons. Good correlations are found between the sums of the chemical shifts and the corresponding sums of the substituent charge excesses. The different behaviour of OH and Cl substituents in the additi…
CFD simulation of ZnO nanoparticle precipitation in a supercritical water synthesis reactor
2012
International audience; Continuous hydrothermal flow synthesis process has shown great advantages concerning the control of particle size and morphology through the optimization of supercritical water processing parameters. In particular, micromixing is a key issue of the process for controlling the nucleation mechanism. A Computational Fluid Dynamics (CFD) model is suggested for nanoparticle size determination using a population balance approach. Models for reaction kinetics, thermodynamics, nucleation and growth are presented. The effects of base concentration and hydrodynamics are investigated. Results show that the CFD may be valuable simulation tool for controlling the size and the sha…
Search for CP violation using T-odd correlations in D-0 -> K+K-pi(+)pi(-) decays
2014
A search for $CP$ violation using $T$-odd correlations is performed using the four-body $D^0 \to K^+K^-\pi^+\pi^-$ decay, selected from semileptonic $B$ decays. The data sample corresponds to integrated luminosities of $1.0\,\text{fb}^{-1}$ and $2.0\,\text{fb}^{-1}$ recorded at the centre-of-mass energies of 7 TeV and 8 TeV, respectively. The $CP$-violating asymmetry $a_{CP}^{T\text{-odd}}$ is measured to be $(0.18\pm 0.29\text{(stat)}\pm 0.04\text{(syst)})\%$. Searches for $CP$ violation in different regions of phase space of the four-body decay, and as a function of the $D^0$ decay time, are also presented. No significant deviation from the $CP$ conservation hypothesis is found.
A Fast GPU-Based Motion Estimation Algorithm for H.264/AVC
2012
H.264/AVC is the most recent predictive video compression standard to outperform other existing video coding standards by means of higher computational complexity. In recent years, heterogeneous computing has emerged as a cost-efficient solution for high-performance computing. In the literature, several algorithms have been proposed to accelerate video compression, but so far there have not been many solutions that deal with video codecs using heterogeneous systems. This paper proposes an algorithm to perform H.264/AVC inter prediction. The proposed algorithm performs the motion estimation, both with full-pixel and sub-pixel accuracy, using CUDA to assist the CPU, obtaining remarkable time …