Search results for " computation"
showing 10 items of 1478 documents
A fast dual boundary element method for 3D anisotropic crack problems
2009
In the present paper a fast solver for dual boundary element analysis of 3D anisotropic crack problems is formulated, implemented and tested. The fast solver is based on the use of hierarchical matrices for the representation of the collocation matrix. The admissible low rank blocks are computed by adaptive cross approximation (ACA). The performance of ACA against the accuracy of the adopted computational scheme for the evaluation of the anisotropic kernels is investigated, focusing on the balance between the kernel representation accuracy and the accuracy required for ACA. The system solution is computed by a preconditioned GMRES and the preconditioner is built exploiting the hierarchical …
Influence of bed roughness on flow and turbulence structure around a partially-buried, isolated freshwater mussel
2023
The present study uses eddy-resolving numerical simulations to investigate how bed roughness affects flow and turbulence structure around an isolated, partially-buried mussel (Unio elongatulus) aligned with the incoming flow. The rough-bed simulations resolve the flow past the exposed part of a gravel bed, whose surface is obtained from a laboratory experiment that also provides some additional data for validation of the numerical model. Results are also discussed for the limiting case of a horizontal smooth bed. Additionally, the effects of varying the level of burial of the mussel inside the substrate and the discharge through the two mussel siphons are investigated via a set of simulatio…
Varieties Generated by Certain Models of Reversible Finite Automata
2006
Reversible finite automata with halting states (RFA) were first considered by Ambainis and Freivalds to facilitate the research of Kondacs-Watrous quantum finite automata. In this paper we consider some of the algebraic properties of RFA, namely the varieties these automata generate. Consequently, we obtain a characterization of the boolean closure of the classes of languages recognized by these models.
A fast Fourier transform based direct solver for the Helmholtz problem
2018
This article is devoted to the efficient numerical solution of the Helmholtz equation in a two‐ or three‐dimensional (2D or 3D) rectangular domain with an absorbing boundary condition (ABC). The Helmholtz problem is discretized by standard bilinear and trilinear finite elements on an orthogonal mesh yielding a separable system of linear equations. The main key to high performance is to employ the fast Fourier transform (FFT) within a fast direct solver to solve the large separable systems. The computational complexity of the proposed FFT‐based direct solver is O(N log N) operations. Numerical results for both 2D and 3D problems are presented confirming the efficiency of the method discussed…
Adding Transitivity and Counting to the Fluted Fragment
2023
We study the impact of adding both counting quantifiers and a single transitive relation to the fluted fragment - a fragment of first-order logic originating in the work of W.V.O. Quine. The resulting formalism can be viewed as a multi-variable, non-guarded extension of certain systems of description logic featuring number restrictions and transitive roles, but lacking role-inverses. We establish the finite model property for our logic, and show that the satisfiability problem for its k-variable sub-fragment is in (k+1)-NExpTime. We also derive ExpSpace-hardness of the satisfiability problem for the two-variable, fluted fragment with one transitive relation (but without counting quantifiers…
CUDA-BLASTP: Accelerating BLASTP on CUDA-enabled graphics hardware
2011
Scanning protein sequence database is an often repeated task in computational biology and bioinformatics. However, scanning large protein databases, such as GenBank, with popular tools such as BLASTP requires long runtimes on sequential architectures. Due to the continuing rapid growth of sequence databases, there is a high demand to accelerate this task. In this paper, we demonstrate how GPUs, powered by the Compute Unified Device Architecture (CUDA), can be used as an efficient computational platform to accelerate the BLASTP algorithm. In order to exploit the GPU's capabilities for accelerating BLASTP, we have used a compressed deterministic finite state automaton for hit detection as wel…
Numerical simulation of river-bed variations: Sensitivity analyses with respect of the initial hydraulic roughness
2020
Two elements affect the efficacy of the numerical models of mobile-bed evolution: the prediction of the hydraulic roughness, related with both sediment distribution on the bed and flow depth, and the prediction of the hydraulic sorting, when the distribution of sediments on the bed is not uniform. In this work the bed profile variation is simulated, by using a numerical model proposed in previous works, in function of the variation of the friction factor, that reflects the coarsening of median sediment diameter, due to armouring process, and the variation of flow conditions. The variation of grains-size distribution of the bed material is predicted by using a probabilistic approach and the …
Molecular mechanics models for the image charge, a comment on “including image charge effects in the molecular dynamics simulations of molecules on m…
2017
We re-investigate the image charge model of Iori and Corni (Iori and Corni, J. Comput. Chem. 2008, 29, 1656). We find that a simple symmetrization of their model allows to obtain quantitatively correct results for the electrostatic interaction of a water molecule with a metallic surface. This symmetrization reduces the magnitude of the electrostatic interaction to less than 10% of the total interaction energy. © 2017 Wiley Periodicals, Inc.
Optimal Heating of an Indoor Swimming Pool
2020
This work presents the derivation of a model for the heating process of the air of a glass dome, where an indoor swimming pool is located in the bottom of the dome. The problem can be reduced from a three dimensional to a two dimensional one. The main goal is the formulation of a proper optimization problem for computing the optimal heating of the air after a given time. For that, the model of the heating process as a partial differential equation is formulated as well as the optimization problem subject to the time-dependent partial differential equation. This yields the optimal heating of the air under the glass dome such that the desired temperature distribution is attained after a given…
Organocatalysts Fold to Generate an Active Site Pocket for the Mannich Reaction
2017
Catalysts containing urea, thiourea and tertiary amine groups fold into a three-dimensional organized structure in solution both in the absence as well as in the presence of substrates or substrate analogues, as indicated by solution NMR and computational studies. These foldamer catalysts promote Mannich reactions with both aliphatic and aromatic imines and malonate esters. Hammett plot and secondary kinetic isotope effects provide evidence for the C-C bond forming event as the turnoverlimiting step of the Mannich reaction. Computational studies suggest two viable pathways for the C-C bond formation step, differing in the activation modes of the malonate and imine substrates. The results sh…