Search results for "computational"
showing 10 items of 5884 documents
Chromatic sums for colorings avoiding monochromatic subgraphs
2015
Abstract Given graphs G and H, a vertex coloring c : V ( G ) → N is an H-free coloring of G if no color class contains a subgraph isomorphic to H. The H-free chromatic number of G, χ ( H , G ) , is the minimum number of colors in an H-free coloring of G. The H-free chromatic sum of G , Σ ( H , G ) , is the minimum value achieved by summing the vertex colors of each H-free coloring of G. We provide a general bound for Σ ( H , G ) , discuss the computational complexity of finding this parameter for different choices of H, and prove an exact formulas for some graphs G. For every integer k and for every graph H, we construct families of graphs, G k with the property that k more colors than χ ( …
Prediction of Molecular Volume and Surface of Alkanes by Molecular Topology.
2003
Molecular volume and molecular surface are expressed as a function of topological degree in alkane graphs. This allows not only a straightforward approach to calculate such physicochemical magnitudes but also an interpretation of the role of the local vertex invariant (LOVI) or valence degree, delta, as well as the connectivity indices in the prediction of physicochemical properties. The interpretation is based on the concept of molecular accessibility (as introduced by Estrada, J. Phys. Chem. A 2002, 106, 9085) for which precise mathematical definitions are provided.
QSPR Modeling of Hydrocarbon Dipole Moments by Means of Correlation Weighting of Local Graph Invariants
2003
Hydrocarbon dipole moments are calculated by means of correlation weighting of local graph invariants within the context of QSPR theory. This sort of flexible topological descriptor is used for several parameters: local invariants of k th vertex in the labeled hydrogen filled graph extended connectivity of zero-, first- and second-orders, number of paths of length 2 at k th vertex and valence shell of the k th vertex. The models predict hydrocarbon dipole moments in a quite sensible way. The best model is that one based upon numbers of path length 2 correlation weighting.
Implementation and application of the actuator line model by OpenFOAM for a vertical axis wind turbine
2017
University of Stavanger has started The Smart Sustainable Campus & Energy Lab project, to gain knowledge and facilitate project based education in the field of renewable and sustainable energy and increase the research effort in the same area. This project includes the future installation of a vertical axis wind turbine on the campus roof. A newly developed Computational Fluid Dynamics (CFD) model by OpenFOAM have been implemented to study the wind behavior over the building and the turbine performance. The online available wind turbine model case from Bachant, Goude and Wosnik from 2016 is used as the starting point. This is a Reynolds-Averaged Navier-Stokes equations (RANS) case set up th…
Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in the entire postnatal and adult mouse brain
2021
The formation of new blood vessels and the establishment of vascular networks are crucial during brain development, in the adult healthy brain, as well as in various diseases of the central nervous system. Here, we describe a step-by-step protocol for our recently developed method that enables hierarchical imaging and computational analysis of vascular networks in postnatal and adult mouse brains. The different stages of the procedure include resin-based vascular corrosion casting, scanning electron microscopy, synchrotron radiation and desktop microcomputed tomography imaging, and computational network analysis. Combining these methods enables detailed visualization and quantification of t…
Analytical chemistry on many-center chiral compounds based on vibrational circular dichroism: Absolute configuration assignments and determination of…
2019
The absolute configuration of a chiral molecule is key to its biological activity. Being able to find out what this configuration is, is thus crucial for a wide range of applications. The difficulties associated with such a determination steeply rise as the number of chiral centers in a given compound becomes larger. Concurrently, it becomes increasingly more challenging to determine the levels and identity of potential stereochemical contaminants in a given sample with one and the same technique, leading in practice to extensive and laborious efforts employing multiple analytical techniques. Here, experimental and theoretical studies based on Vibrational Circular Dichroism (VCD) are presen…
The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.
2014
The vibronic spectra of the green fluorescent protein chromophore analogues p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) and 3,5-tert-butyl-HBDI (35Bu) are similar in the vacuum, but very different in water or ethanol. To understand this difference, we have computed the vibrationally resolved solution spectra of these chromophores, using the polarizable continuum model (PCM) to account for solvent effects on the (harmonic) potential energy surfaces (PES). In agreement with experiment, we found that the vibrational progression increases with the polarity of the solvent, but we could neither reproduce the broadening, nor the large difference between the absorption spectra of HBDI and…
Comparative theoretical study of transition structures, barrier heights, and reaction energies for the intramolecular tautomerization in acetaldehyde…
1998
The transition structures associated with the possible intramolecular tautomerization for acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems as models of keto/enol and imine/enamine interconversion processes, respectively, were characterized. The relative stabilities of the tautomers and the associated barrier heights were calculated. Ab initio analytical gradients and second derivatives at the HF level of theory and 3-21G, 6-31G, 6-31G**, 6-31++G**, and 6-311++G** basis-set, DFT (BP86/6-311++G** and BLYP/6-311++G**), and semiempirical (AM1 and PM3) procedures were used to identify the stationary points. Correlation effects were estimated using the perturbational approach at MP2…
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
2015
Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the de…
A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Rec…
2016
Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the use of multiple crystal structures of the same protein containing different co-crystallized ligands can help elucidate the role of the ligand on a protein's active conformation, and then explore the most common interactions between small molecules and the receptor. In this work, we evaluated the contribution of the combined use of MD on crystal structures containing the same protein but different ligands to examine the crucial ligand-protein interactions within the complexes. The study was carried out on peroxisome proliferator-activat…