Channel Flow of a Tensorial Shear-Thinning Maxwell Model: Lattice Boltzmann Simulations

We introduce a nonlinear generalized tensorial Maxwell-type constitutive equation to describe shear-thinning glass-forming fluids, motivated by a recent microscopic approach to the nonlinear rheology of colloidal suspensions. The model captures a nonvanishing dynamical yield stress at the glass transition and incorporates normal-stress differences. A modified lattice-Boltzmann (LB) simulation scheme is presented that includes non-Newtonian contributions to the stress tensor and deals with flow-induced pressure differences. We test this scheme in pressure-driven 2D Poiseuille flow of the nonlinear generalized Maxwell fluid. In the steady state, comparison with an analytical solution shows good agreement. The transient dynamics after startup and cessation of the pressure gradient are studied; the simulation reproduces a finite stopping time for the cessation flow of the yield-stress fluid in agreement with previous analytical estimates

Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico

Malaria is one of the world’s most common and serious diseases causing death of about 3 million people each year. Its most severe occurrence is caused by the protozoan Plasmodium falciparum. Biomedical research could enable treating the disease by effectively and specifically targeting essential enzymes of this parasite. However, the parasite has developed resistance to existing drugsmaking it indispensable to discover new drugs. We have established a simple computational tool which analyses the topology of the metabolic network of P. falciparum to identify essential enzymes as possible drug targets.Weinvestigated the essentiality of a reaction in the metabolic network by deleting (knocking-out) such a reaction in silico. The algorithmselected neighbouring compounds of the investigated reaction that had to be produced by alternative biochemical pathways. Using breadth first searches, we tested qualitatively if these products could be generated by reactions that serve as potential deviations of the metabolic flux. With this we identified 70 essential reactions. Our results were compared with a comprehensive list of 38 targets of approved malaria drugs. When combining our approach with an in silico analysis performed recently [Yeh, I., Hanekamp, T., Tsoka, S., Karp, P.D., Altman, R.B., 2004. Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res. 14, 917–924] we could improve the precision of the prediction results. Finally we present a refined list of 22 new potential candidate targets for P. falciparum, half of which have reasonable evidence to be valid targets against micro-organisms and cancer

A systematic study of non-ideal contacts in integer quantum Hall systems

In the present article we investigate the influence of the contact region on the distribution of the chemical potential in integer quantum Hall samples, as well as the longitudinal and Hall resistance as a function of the magnetic field. First we use a standard quantum Hall sample geometry and analyse the influence of the length of the leads where current enters/leaves the sample and the ratio of the contact width to the width of these leads. Furthermore we investigate potential barriers in the current injecting leads and the measurement arms in order to simulate non-ideal contacts. Second we simulate nonlocal quantum Hall samples with applied gating voltage at the metallic contacts. For such samples it has been found experimentally that both the longitudinal and Hall resistance as a function of the magnetic field can change significantly. Using the nonequilibrium network model we are able to reproduce most qualitative features of the experiments.Comment: 29 pages, 16 Figure

Elasticity of smectic liquid crystals with focal conic domains

We study the elastic properties of thermotropic smectic liquid crystals with focal conic domains (FCDs). After the application of the controlled preshear at different temperatures, we independently measured the shear modulus G' and the FCD size L. We find out that these quantities are related by the scaling relation G' ~ \gamma_{eff}/L where \gamma_{eff} is the effective surface tension of the FCDs. The experimentally obtained value of \gamma_{\rm eff} shows the same scaling as the effective surface tension of the layered systems \sqrt{KB} where K and B are the bending modulus and the layer compression modulus, respectively. The similarity of this scaling relation to that of the surfactant onion phase suggests an universal rheological behavior of the layered systems with defects.Comment: 14 pages, 7 figures, accepted for publication in JPC

Theory and computation of directional nematic phase ordering

A computational study of morphological instabilities of a two-dimensional nematic front under directional growth was performed using a Landau-de Gennes type quadrupolar tensor order parameter model for the first-order isotropic/nematic transition of 5CB (pentyl-cyanobiphenyl). A previously derived energy balance, taking anisotropy into account, was utilized to account for latent heat and an imposed morphological gradient in the time-dependent model. Simulations were performed using an initially homeotropic isotropic/nematic interface. Thermal instabilities in both the linear and non-linear regimes were observed and compared to past experimental and theoretical observations. A sharp-interface model for the study of linear morphological instabilities, taking into account additional complexity resulting from liquid crystalline order, was derived. Results from the sharp-interface model were compared to those from full two-dimensional simulation identifying the specific limitations of simplified sharp-interface models for this liquid crystal system. In the nonlinear regime, secondary instabilities were observed to result in the formation of defects, interfacial heterogeneities, and bulk texture dynamics.Comment: first revisio

Analysis of nickel concentration profiles around the roots of the hyperaccumulator plant Berkheya coddii using MRI and numerical simulations

Investigations of soil-root interactions are hampered by the difficult experimental accessibility of the rhizosphere. Here we show the potential of Magnetic Resonance Imaging (MRI) as a non-destructive measurement technique in combination with numerical modelling to study the dynamics of the spatial distribution of dissolved nickel (Ni2+) around the roots of the nickel hyperaccumulator plant Berkheya coddii. Special rhizoboxes were used in which a root monolayer had been grown, separated from an adjacent inert glass bead packing by a nylon membrane. After applying a Ni2+ solution of 10mgl−1, the rhizobox was imaged repeatedly using MRI. The obtained temporal sequence of 2-dimensional Ni2+ maps in the vicinity of the roots showed that Ni2+ concentrations increased towards the root plane, revealing an accumulation pattern. Numerical modelling supported the Ni2+ distributions to result from advective water flow towards the root plane, driven by transpiration, and diffusion of Ni2+ tending to eliminate the concentration gradient. With the model, we could study how the accumulation pattern of Ni2+ in the root zone transforms into a depletion pattern depending on transpiration rate, solute uptake rate, and Ni2+ concentration in solutio

Non-isothermal model for the direct isotropic/smectic-A liquid crystalline transition

An extension to a high-order model for the direct isotropic/smectic-A liquid crystalline phase transition was derived to take into account thermal effects including anisotropic thermal diffusion and latent heat of phase-ordering. Multi-scale multi-transport simulations of the non-isothermal model were compared to isothermal simulation, showing that the presented model extension corrects the standard Landau-de Gennes prediction from constant growth to diffusion-limited growth, under shallow quench/undercooling conditions. Non-isothermal simulations, where meta-stable nematic pre-ordering precedes smectic-A growth, were also conducted and novel non-monotonic phase-transformation kinetics observed.Comment: First revision: 20 pages, 7 figure

Economic precariousness: A new channel in the housing market cycle

Abstract: Demographic and institutional elements, as important drivers of the housing market, should not be neglected since it is not only financial and monetary elements that matter in the case of the housing market. In this context, one relationship, which still remains unclear, is the relationship between the housing and the labour markets. Some research has been undertaken to support the hypothesis that high rates of homeownership lead to high unemployment via increases in the reservation wage. However, further research is needed to address the possible implications of the institutional settings of the labour market in the dynamics of the housing market. The aim of this paper is to bring some light on the link between both markets. In particular, this contribution explains how the housing cycle could be ‘amplified’ via a new channel, i.e. economic precariousness, which is closely related to job insecurity. Subsequently, we provide evidence in the case of five developed economies, Ireland, the Netherlands, Spain, the United Kingdom and the United States, over the period 1985-2013.Not appicabl

Calculating Milnor Numbers and Versal Component Dimensions from P-Resolution Fans

We use Altmann's toric fan description of P-resolutions to formulate a new description of deformation theory invariants for two-dimensional cyclic quotient singularities. In particular, we show how to calculate the dimensions of the (reduced) versal base space components as well as Milnor numbers of smoothings over them.Comment: 8 pages; 2 figures; v2 added section on Milnor numbers, reworked proof of dimension formula, new example, and new titl