Search results for "Computational Mathematic"
showing 10 items of 987 documents
Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors
2009
Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular docking experiments on the 187 Hsp90 inhibitors included in the BindingDB, a pu…
Implicit-explicit methods for a class of nonlinear nonlocal gradient flow equations modelling collective behaviour
2019
Abstract The numerical solution of nonlinear convection-diffusion equations with nonlocal flux by explicit finite difference methods is costly due to the local spatial convolution within the convective numerical flux and the disadvantageous Courant-Friedrichs-Lewy (CFL) condition caused by the diffusion term. More efficient numerical methods are obtained by applying second-order implicit-explicit (IMEX) Runge-Kutta time discretizations to an available explicit scheme for such models in Carrillo et al. (2015) [13] . The resulting IMEX-RK methods require solving nonlinear algebraic systems in every time step. It is proven, for a general number of space dimensions, that this method is well def…
Star-polynomial identities: computing the exponential growth of the codimensions
2017
Abstract Can one compute the exponential rate of growth of the ⁎-codimensions of a PI-algebra with involution ⁎ over a field of characteristic zero? It was shown in [2] that any such algebra A has the same ⁎-identities as the Grassmann envelope of a finite dimensional superalgebra with superinvolution B. Here, by exploiting this result we are able to provide an exact estimate of the exponential rate of growth e x p ⁎ ( A ) of any PI-algebra A with involution. It turns out that e x p ⁎ ( A ) is an integer and, in case the base field is algebraically closed, it coincides with the dimension of an admissible subalgebra of maximal dimension of B.
Highlighting numerical insights of an efficient SPH method
2018
Abstract In this paper we focus on two sources of enhancement in accuracy and computational demanding in approximating a function and its derivatives by means of the Smoothed Particle Hydrodynamics method. The approximating power of the standard method is perceived to be poor and improvements can be gained making use of the Taylor series expansion of the kernel approximation of the function and its derivatives. The modified formulation is appealing providing more accurate results of the function and its derivatives simultaneously without changing the kernel function adopted in the computation. The request for greater accuracy needs kernel function derivatives with order up to the desidered …
A generalized Newton iteration for computing the solution of the inverse Henderson problem
2020
We develop a generalized Newton scheme IHNC for the construction of effective pair potentials for systems of interacting point-like particles.The construction is made in such a way that the distribution of the particles matches a given radial distribution function. The IHNC iteration uses the hypernetted-chain integral equation for an approximate evaluation of the inverse of the Jacobian of the forward operator. In contrast to the full Newton method realized in the Inverse Monte Carlo (IMC) scheme, the IHNC algorithm requires only a single molecular dynamics computation of the radial distribution function per iteration step, and no further expensive cross-correlations. Numerical experiments…
Improving the stability bound for the PPH nonlinear subdivision scheme for data coming from strictly convex functions
2021
Abstract Subdivision schemes are widely used in the generation of curves and surfaces, and therefore they are applied in a variety of interesting applications from geological reconstructions of unaccessible regions to cartoon film productions or car and ship manufacturing. In most cases dealing with a convexity preserving subdivision scheme is needed to accurately reproduce the required surfaces. Stability respect to the initial input data is also crucial in applications. The so called PPH nonlinear subdivision scheme is proven to be both convexity preserving and stable. The tighter the stability bound the better controlled is the final output error. In this article a more accurate stabilit…
Global convergence and rate of convergence of a method of centers
1994
We consider a method of centers for solving constrained optimization problems. We establish its global convergence and that it converges with a linear rate when the starting point of the algorithm is feasible as well as when the starting point is infeasible. We demonstrate the effect of the scaling on the rate of convergence. We extend afterwards, the stability result of [5] to the infeasible case anf finally, we give an application to semi-infinite optimization problems.
A velocity–diffusion method for a Lotka–Volterra system with nonlinear cross and self-diffusion
2009
The aim of this paper is to introduce a deterministic particle method for the solution of two strongly coupled reaction-diffusion equations. In these equations the diffusion is nonlinear because we consider the cross and self-diffusion effects. The reaction terms on which we focus are of the Lotka-Volterra type. Our treatment of the diffusion terms is a generalization of the idea, introduced in [P. Degond, F.-J. Mustieles, A deterministic approximation of diffusion equations using particles, SIAM J. Sci. Stat. Comput. 11 (1990) 293-310] for the linear diffusion, of interpreting Fick's law in a deterministic way as a prescription on the particle velocity. Time discretization is based on the …
A parallel and sensitive software tool for methylation analysis on multicore platforms.
2015
Abstract Motivation: DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. Results: We present a new software tool, called HPG-Methyl, which efficiently maps bis…
New QM/MM implementation of the DFTB3 method in the gromacs package.
2015
The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…