On Solving Pentadiagonal Linear Systems via Transformations

Many authors have studied numerical algorithms for solving the linear systems of pentadiagonal type. The well-known fast pentadiagonal system solver algorithm is an example of such algorithms. The current paper describes new numerical and symbolic algorithms for solving pentadiagonal linear systems via transformations. The proposed algorithms generalize the algorithms presented in El-Mikkawy and Atlan, 2014. Our symbolic algorithms remove the cases where the numerical algorithms fail. The computational cost of our algorithms is better than those algorithms in literature. Some examples are given in order to illustrate the effectiveness of the proposed algorithms. All experiments are carried out on a computer with the aid of programs written in MATLAB

Assessment of atomic charge models for gas-phase computations on polypeptides

The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q0, that is suitable to describe biological systems bearing many locally charged functional groups

Multi-partitioning for ADI-schemes on message passing architectures

A kind of discrete-operator splitting called Alternating Direction Implicit (ADI) has been found to be useful in simulating fluid flow problems. In particular, it is being used to study the effects of hot exhaust jets from high performance aircraft on landing surfaces. Decomposition techniques that minimize load imbalance and message-passing frequency are described. Three strategies that are investigated for implementing the NAS Scalar Penta-diagonal Parallel Benchmark (SP) are transposition, pipelined Gaussian elimination, and multipartitioning. The multipartitioning strategy, which was used on Ethernet, was found to be the most efficient, although it was considered only a moderate success because of Ethernet's limited communication properties. The efficiency derived largely from the coarse granularity of the strategy, which reduced latencies and allowed overlap of communication and computation

Improved recursive Green's function formalism for quasi one-dimensional systems with realistic defects

We derive an improved version of the recursive Green's function formalism (RGF), which is a standard tool in the quantum transport theory. We consider the case of disordered quasi one-dimensional materials where the disorder is applied in form of randomly distributed realistic defects, leading to partly periodic Hamiltonian matrices. The algorithm accelerates the common RGF in the recursive decimation scheme, using the iteration steps of the renormalization decimation algorithm. This leads to a smaller effective system, which is treated using the common forward iteration scheme. The computational complexity scales linearly with the number of defects, instead of linearly with the total system length for the conventional approach. We show that the scaling of the calculation time of the Green's function depends on the defect density of a random test system. Furthermore, we discuss the calculation time and the memory requirement of the whole transport formalism applied to defective carbon nanotubes

A fast algorithm for solving diagonally dominant symmetric quasi-pentadiagonal Toeplitz linear systems

In this paper, we develop a new algorithm for solving diagonally dominant symmetric quasi-pentadiagonal Toeplitz linear systems. Numerical experiments are given in order to illustrate the validity and efficiency of our algorithm.The authors would like to thank the supports of the Portuguese Funds through FCT–Fundação para a Ciência e a Tecnologia, within the Project UID/MAT/00013/2013

Application of the collocation method with b-splines to the gew equation

In this paper, the generalized equal width (GEW) wave equation is solved numerically by using a quintic B-spline collocation algorithm with two different linearization techniques. Also, a linear stability analysis of the numerical scheme based on the von Neumann method is investigated. The numerical algorithm is applied to three test problems consisting of a single solitary wave, the interaction of two solitary waves, and a Maxwellian initial condition. In order to determine the performance of the numerical method, we compute the error in the L2- and L∞ norms and in the invariants I1, I2, and I3 of the GEW equation. These calculations are compared with earlier studies. Afterwards, the motion of solitary waves according to different parameters is designe