Search results for "computational"
showing 4 items of 5884 documents
Mechanisms of irreversible aquaporin-10 inhibition by organogold compounds studied by combined biophysical methods and atomistic simulations
2021
Abstract The inhibition of glycerol permeation via human aquaporin-10 (hAQP10) by organometallic gold complexes has been studied by stopped-flow fluorescence spectroscopy, and its mechanism has been described using molecular modelling and atomistic simulations. The most effective hAQP10 inhibitors are cyclometalated Au(III) C^N compounds known to efficiently react with cysteine residues leading to the formation of irreversible C–S bonds. Functional assays also demonstrate the irreversibility of the binding to hAQP10 by the organometallic complexes. The obtained computational results by metadynamics show that the local arylation of Cys209 in hAQP10 by one of the gold inhibitors is mapped int…
Compression and load balancing for efficient sparse matrix-vector product on multicore processors and graphics processing units
2021
We contribute to the optimization of the sparse matrix-vector product by introducing a variant of the coordinate sparse matrix format that balances the workload distribution and compresses both the indexing arrays and the numerical information. Our approach is multi-platform, in the sense that the realizations for (general-purpose) multicore processors as well as graphics accelerators (GPUs) are built upon common principles, but differ in the implementation details, which are adapted to avoid thread divergence in the GPU case or maximize compression element-wise (i.e., for each matrix entry) for multicore architectures. Our evaluation on the two last generations of NVIDIA GPUs as well as In…
Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments
2020
Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations have reinvigorated the hypothesis that changes in genome-segment frequencies can lead to changes in virus-gene expression that might be adaptive. Here we explore this hypothesis by developing models of bipartite virus infection, leading to a threefold contribution. First, we show that th…
On the ‘expanded local mode’ approach applied to the methane molecule: isotopic substitutions CH3D ←CH4 and CHD3 ←CH4
2014
Operator perturbation theory and the symmetry properties of the axially symmetric XYZ3 (C3v) type molecules are used for the determination of the spectroscopic parameters in the form of functions of structural parameters and parameters of the intramolecular potential function. Several relations between sets of spectroscopic parameters of these molecules are obtained. The ‘expanded local mode’ model and the general isotopic substitution theory are used to estimate the relations between spectroscopic parameters of CH3D and CHD3, on one hand, and with the Td symmetric isotopic species, CH4, on the other hand. Test calculations with the isotopic relations show that even without including prior …