Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

On Selfadjoint Homogeneous Operators

We study unbounded selfadjoint operators that are unitarily equivalent to their affine transformation. We investigate transformation properties of an operator-valued M-function associated with given affine-invariant operator as well as spectral properties of operators that occur in that investigation.     

Chiral Oligo- and Polyphosphites (Phosphonites,Phosphinites) on the Base of Specifically Orientated in Space Hydroxylcontaining Compounds. Synthesis,Structure, and Investigation of Complexation

Abstract

The effective methods of phosphorylation of complex systems with specifically orientated in space hydroxyl groups, namely dianhydro-D-mannitol(A), -D-sor-bitol(B), cyclodextrines(C), and cellulose(D) (A-D, where R=H), have been elaborated.     

Furanose Bicyclophosphites as Synthons of Modified Nucleoside Diphosphates

Abstract

Previously we synthesized and examined in detail 1,2- alkylideneglucofuanose 3,5,6-bicyclophosphites; mono- and bicyclophosphates with peculiar chemical and physiological activity were obtained on their base [1]. During the study of their structural dependence, we modified the hydrocarbonic moiety, synthesiz-ed 1,2,3- and 3,5,6-bicyclophosphites and cyclophosphates of gulofuanose, and correlated their features with those of glucose analogues. Furthermore, an additional phosphonate moiety (obtained by a stereoselective reaction of an appropriate ketonic sugar with silylphosphites) was introduced into the glucofuranose 3,5,6-bicyclophosphite molecule to the third carbon atom. As a result, the monosaccharide matrix gained two functional groups containing tri- and fourcoordinated phosphorus.     

Queues with waiting time dependent service

Motivated by service levels in terms of the waiting-time distribution seen, for instance, in call centers, we consider two models for systems with a service discipline that depends on the waiting time. The first model deals with a single server that continuously adapts its service rate based on the waiting time of the first customer in line. In the second model, one queue is served by a primary server which is supplemented by a secondary server when the waiting of the first customer in line exceeds a threshold. Using level crossings for the waiting-time process of the first customer in line, we derive steady-state waiting-time distributions for both models. The results are illustrated with numerical examples.     

Planning Formula One race strategies using discrete-event simulation

A discrete-event simulation model that imitates most on-track events, including car failures, passing manoeuvres and pit stops during a Formula One race, is presented. The model is intended for use by a specific team. It will enable decision-makers to plan and evaluate their race strategy, consequently providing them with a possible competitive advantage. The simulation modelling approach presented in this paper captures the mechanical complexities and physical interactions of a race car with its environment through a time-based approach. Model verification and validation are demonstrated using three races from the 2005 season. The application of the model is illustrated by evaluating the race strategies employed by a specific team during these three races.