Computational complexity of weighted splitting schemes on parallel computers

In models of complicated physical-chemical processes operator splitting is very often applied in order to achieve sufficient accuracy as well as efficiency of the numerical solution. The recently rediscovered weighted splitting schemes have the great advantage of being parallelizable on operator level, which allows us to reduce the computational time if parallel computers are used. In this paper, the computational times needed for the weighted splitting methods are studied in comparison with the sequential (S) splitting and the Marchuk-Strang (MSt) splitting and are illustrated by numerical experiments performed by use of simplified versions of the Danish Eulerian model (DEM).

Comparison of the computational cost of a Monte Carlo and deterministic algorithm for computing bilinear forms of matrix powers

In this paper we consider bilinear forms of matrix polynomials and show that these polynomials can be used to construct solutions for the problems of solving systems of linear algebraic equations, matrix inversion and finding extremal eigenvalues. An almost Optimal Monte Carlo (MAO) algorithm for computing bilinear forms of matrix polynomials is presented. Results for the computational costs of a balanced algorithm for computing the bilinear form of a matrix power is presented, i.e., an algorithm for which probability and systematic errors are of the same order, and this is compared with the computational cost for a corresponding deterministic method.

Computer simulations of structures, energetics and dynamics of myoglobin center dot center dot center dot ligand complexes

Myoglobin has been studied in considerable detail using different experimental and computational techniques over the past decades. Recent developments in time-resolved spectroscopy have provided experimental data amenable to detailed atomistic simulations. The main theme of the present review are results on the structures, energetics and dynamics of ligands ( CO, NO) interacting with myoglobin from computer simulations. Modern computational methods including free energy simulations, mixed quantum mechanics/molecular mechanics simulations, and reactive molecular dynamics simulations provide insight into the dynamics of ligand dynamics in confined spaces complementary to experiment. Application of these methods to calculate and understand experimental observations for myoglobin interacting with CO and NO are presented and discussed.

Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

Electronic properties of 4,4 ',5,5 '-tetramethyl-2,2 '-biphosphinine (tmbp) in the redox series fac-[Mn(Br)(CO)(3)(tmbp)], [Mn(CO)(3)(tmbp)](2), and [Mn(CO)(3)(tmbp)](-): crystallographic, spectroelectrochemical, and DFT computational study

Stepwise electrochemical reduction of the complex fac-[Mn(Br)(CO)(3)(tmbp)] (tmbp = 4,4',5,5'-tetramethyl-2,2'-biphosphinine) produces the dimer [Mn(CO)(3)(tmbp)](2) and the five-coordinate anion [Mn(CO)(3)(tmbp)](-). All three members of the redox series have been characterized by single-crystal X-ray diffraction. The crystallographic data provide valuable insight into the localization of the added electrons on the (carbonyl)manganese and tmbp centers. In particular, the formulation of the two-electron-reduced anion as [Mn-0(CO)(3)(tmbp(-))](-) also agrees with the analysis of its IR nu(CO) wavenumbers and with the results of density functional theoretical (DFT) MO calculations on this compound. The strongly delocalized pi-bonding in the anion stabilizes its five-coordinate geometry and results in the appearance of several mixed Mn-to-tmbp charge-transfer/IL(tmbp) transitions in the near-UV-vis spectral region. A thorough voltammetric and UV-vis/IR spectroelectrochemical study of the reduction path provided evidence for a direct formation of [Mn(CO)(3)(tmbp)](-) via a two-electron ECE mechanism involving the [Mn(CO)(3)(tmbp)](.) radical transient. At ambient temperature [Mn(CO)(3)(tmbp)](-) reacts rapidly with nonreduced fac-[Mn(Br)(CO)(3)(tmbp)] to produce [Mn(CO)(3)(tmbp)](2). Comparison with the analogous 2,2'-bipyridine complexes has revealed striking similarity in the bonding properties and reactivity, despite the stronger pi-acceptor character of the tmbp ligand.

Titanocene anticancer complexes and their binding mode of action to human serum albumin: a computational study

Due to the pivotal role played by human serum albumin (HSA) in the transport and cytotoxicity of titanocene complexes, a docking study has been performed on a selected set of titanocene complexes to aid in the current understanding of the potential mode of action of these titanocenes upon binding HSA. Analysis of the docking results has revealed potential binding at the known drug binding sites in HSA and has provided some explanation for the specificity and subsequent cytotoxicity of these titanocenes. Additionally, a new alternative binding site for these titanocenes has been postulated.