Search results for "Simulation."

Inhibitor-Induced Dimerization of an Essential Oxidoreductase from African Trypanosomes

2018

Trypanosomal and leishmanial infections claim tens of thousands of lives each year. The metabolism of these unicellular eukaryotic parasites differs from the human host and their enzymes thus constitute promising drug targets. Tryparedoxin (Tpx) from Trypanosoma brucei is the essential oxidoreductase in the parasite's hydroperoxide-clearance cascade. In vitro and in vivo functional assays show that a small, selective inhibitor efficiently inhibits Tpx. With X-ray crystallography, SAXS, analytical SEC, SEC-MALS, MD simulations, ITC, and NMR spectroscopy, we show how covalent binding of this monofunctional inhibitor leads to Tpx dimerization. Intra- and intermolecular inhibitor-inhibitor, pro…

Theoretical study of the interaction between sodium ion and a cyclopeptidic tubular structure.

2007

DFT calculations have been carried out to describe the pathway of a sodium ion along the stacking direction of a tubular structure set up by five cyclopeptidic units, which can be considered a suitable model of a hollow tubular structure of indefinite length. A lattice of points inside the tubular structure is defined and the DFT interaction energy values with a sodium ion are obtained. The data allow predicting a zigzag path of the ion inside the hosting structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007

Modeling multiple taxis: Tumor invasion with phenotypic heterogeneity, haptotaxis, and unilateral interspecies repellence

2021

We provide a short review of existing models with multiple taxis performed by (at least) one species and consider a new mathematical model for tumor invasion featuring two mutually exclusive cell phenotypes (migrating and proliferating). The migrating cells perform nonlinear diffusion and two types of taxis in response to non-diffusing cues: away from proliferating cells and up the gradient of surrounding tissue. Transitions between the two cell subpopulations are influenced by subcellular (receptor binding) dynamics, thus conferring the setting a multiscale character. We prove global existence of weak solutions to a simplified model version and perform numerical simulations for the full se…

Passenger Car Equivalent for Heavy Vehicles Crossing Turbo-roundabouts

2016

Abstract Turbo-roundabouts represent an innovative scheme of modern roundabouts which provides a spiraling traffic flow and requires drivers to choose their direction before entering the intersection, since raised lane separators mark the lanes on the ring. The configuration of the turbo-roundabout makes that patterns of conflict at entries with one and two conflicting traffic streams can coexist. This paper presents research efforts aimed at measuring quantitatively the effect of heavy vehicles on operational conditions of a turbo-roundabout. The study starts from the initial belief that the greatest constraints to the vehicular trajectories imposed by the turbo-roundabout necessarily impl…

A dynamic subgrid-scale tensorial eddy viscosity model

1999

In the Navier-Stokes equations the removal of the turbulent fluctuating velocities with a frequency above a certain fixed threshold, employed in the Large Eddy Simulation (LES), causes the appearance of a turbulent stress tensor that requires a number of closure assumptions. In this paper insufficiencies are demonstrated for those closure models which are based on a scalar eddy viscosity coefficient. A new model, based on a tensorial eddy viscosity, is therefore proposed; it employs the Germano identity [1] and allows dynamical evaluation of the single required input coefficient. The tensorial expression for the eddy viscosity is deduced by removing the widely used scalar assumption of the …

Direct Numerical Simulation of Pulsatile Turbulent Channel Flow

2008

A mathematical model of the self-averaging Pitot tube

2005

Abstract Flowmeters with self-averaging Pitot tubes are more and more often applied in practice. Their advantages are practically no additional flow losses, usability in the case of high temperature of fluids and simplicity of fitting. A mathematical model of a self-averaging Pitot tube including the influence of the probe shape, selected constructional features and flow conditions on the quantity of differential pressure gained has been given in this paper. The values and ranges of variations of the coefficients established for the model have been assessed on the basis of the numerically computed velocity and pressure fields around and inside the probe. Velocity and pressure fields were ca…

Large-Eddy Simulation: A Critical Survey of Models and Applications

1994

NMR structure of a non-conjugatable, ADP-ribosylation associated, ubiquitin-like domain from Tetrahymena thermophila polyubiquitin locus.

2019

Abstract Background Ubiquitin-like domains (UbLs), in addition to being post-translationally conjugated to the target through the E1-E2-E3 enzymatic cascade, can be translated as a part of the protein they ought to regulate. As integral UbLs coexist with the rest of the protein, their structural properties can differ from canonical ubiquitin, depending on the protein context and how they interact with it. In this work, we investigate T.th-ubl5, a UbL present in a polyubiquitin locus of Tetrahymena thermophila, which is integral to an ADP-ribosyl transferase protein. Only one other co-occurrence of these two domains within the same protein has been reported. Methods NMR, multiple sequence al…

Strain gradient plasticity, strengthening effects and plastic limit analysis

2010

Abstract Within the framework of isotropic strain gradient plasticity, a rate-independent constitutive model exhibiting size dependent hardening is formulated and discussed with particular concern to its strengthening behavior. The latter is modelled as a (fictitious) isotropic hardening featured by a potential which is a positively degree-one homogeneous function of the effective plastic strain and its gradient. This potential leads to a strengthening law in which the strengthening stress, i.e. the increase of the plastically undeformed material initial yield stress, is related to the effective plastic strain through a second order PDE and related higher order boundary conditions. The plas…