Entropic transport - A test bed for the Fick-Jacobs approximation

Biased diffusive transport of Brownian particles through irregularly shaped, narrow confining quasi-one-dimensional structures is investigated. The complexity of the higher dimensional diffusive dynamics is reduced by means of the so-called Fick-Jacobs approximation, yielding an effective one-dimensional stochastic dynamics. Accordingly, the elimination of transverse, equilibrated degrees of freedom stemming from geometrical confinements and/or bottlenecks cause entropic potential barriers which the particles have to overcome when moving forward noisily. The applicability and the validity of the reduced kinetic description is tested by comparing the approximation with Brownian dynamics simulations in full configuration space. This non-equilibrium transport in such quasi-one-dimensional irregular structures implies for moderate-to-strong bias a characteristic violation of the Sutherland-Einstein fluctuation-dissipation relation.Comment: 15 pages, 6 figures ; Phil. Trans. R. Soc. A (2009), in pres

Entropic Stochastic Resonance

We present a novel scheme for the appearance of Stochastic Resonance when the dynamics of a Brownian particle takes place in a confined medium. The presence of uneven boundaries, giving rise to an entropic contribution to the potential, may upon application of a periodic driving force result in an increase of the spectral amplification at an optimum value of the ambient noise level. This Entropic Stochastic Resonance (ESR), characteristic of small-scale systems, may constitute a useful mechanism for the manipulation and control of single-molecules and nano-devices.Comment: 4 pages, 3 figure

Embedded-Cluster Calculations in a Numeric Atomic Orbital Density-Functional Theory Framework

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level DFT calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).Comment: 12 pages, 4 figure

Entropically-induced asymmetric passage times of charged tracers across corrugated channels

We analyze the diffusion of charged and neutral tracers suspended in an electrolyte embedded in a channel of varying cross section. Making use of systematic approximations, the diffusion equation governing the motion of tracers is mapped into an effective 1D equation describing the dynamics along the longitudinal axis of the channel where its varying-section is encoded as an effective entropic potential. This simplified approach allows us to characterize tracer diffusion under generic confinement by measuring their mean first passage time (MFPT). In particular, we show that the interplay between geometrical confinement and electrostatic interactions strongly affect the MFTP of tracers across corrugated channels hence leading to alternative means to control tracers translocation across charged pores. Finally, our results show that the MFPTs of a charged tracer in opposite directions along an asymmetric channel may differ We expect our results to be relevant for biological as well synthetic devices whose dynamics is controlled by the detection of diluted tracer

Density of mechanisms within the flexibility window of zeolites

By treating idealized zeolite frameworks as periodic mechanical trusses, we show that the number of flexible folding mechanisms in zeolite frameworks is strongly peaked at the minimum density end of their flexibility window. 25 of the 197 known zeolite frameworks exhibit an extensive flexibility, where the number of unique mechanisms increases linearly with the volume when long wavelength mechanisms are included. Extensively flexible frameworks therefore have a maximum in configurational entropy, as large crystals, at their lowest density. Most real zeolites do not exhibit extensive flexibility, suggesting that surface and edge mechanisms are important, likely during the nucleation and growth stage. The prevalence of flexibility in real zeolites suggests that, in addition to low framework energy, it is an important criterion when searching large databases of hypothetical zeolites for potentially useful realizable structures.Comment: 11 pages, 3 figure

On the elastic constants of the zeolite chlorosodalite

The use of force-field based molecular modeling to predict the elastic constants of the zeolite chlorosodalite is described. Theoretical predictions of the on-axis and off-axis elastic constants strongly suggest that an error exists in the published elastic constants of the material. When the previous experimental data are corrected by transposing the published directional ultrasound velocities, excellent agreement is observed between the off-axis plots of sodalite produced by experiment and modeling. Further confirmation of the prediction is supplied by considering the Zener ratios of other inorganic materials that possess cubic symmetry. ©2006 American Institute of Physics

Do Leaf Cutting Ants Cut Undetected? Testing the Effect of Ant-Induced Plant Defences on Foraging Decisions in Atta colombica

Leaf-cutting ants (LCAs) are polyphagous, yet highly selective herbivores. The factors that govern their selection of food plants, however, remain poorly understood. We hypothesized that the induction of anti-herbivore defences by attacked food plants, which are toxic to either ants or their mutualistic fungus, should significantly affect the ants' foraging behaviour. To test this “induced defence hypothesis,” we used lima bean (Phaseolus lunatus), a plant that emits many volatile organic compounds (VOCs) upon herbivore attack with known anti-fungal or ant-repellent effects. Our results provide three important insights into the foraging ecology of LCAs. First, leaf-cutting by Atta ants can induce plant defences: Lima bean plants that were repeatedly exposed to foraging workers of Atta colombica over a period of three days emitted significantly more VOCs than undamaged control plants. Second, the level to which a plant has induced its anti-herbivore defences can affect the LCAs' foraging behaviour: In dual choice bioassays, foragers discriminated control plants from plants that have been damaged mechanically or by LCAs 24 h ago. In contrast, strong induction levels of plants after treatment with the plant hormone jasmonic acid or three days of LCA feeding strongly repelled LCA foragers relative to undamaged control plants. Third, the LCA-specific mode of damaging leaves allows them to remove larger quantities of leaf material before being recognized by the plant: While leaf loss of approximately 15% due to a chewing herbivore (coccinelid beetle) was sufficient to significantly increase VOC emission levels after 24 h, the removal of even 20% of a plant's leaf area within 20 min by LCAs did not affect its VOC emission rate after 24 h. Taken together, our results support the “induced defence hypothesis” and provide first empirical evidence that the foraging behaviour of LCAs is affected by the induction of plant defence responses

In vitro assessment of adsorbents aiming to prevent deoxynivalenol and zearalenone mycotoxicoses

The high prevalence of the Fusarium mycotoxins, deoxynivalenol (DON) and zearalenone (ZON) in animal feeds in mild climatic zones of Europe and North America results in considerable economic losses, as these toxins affect health and productivity particularly of pigs from all age groups. The use of mycotoxin adsorbents as feed additives is one of the most prominent approaches to reduce the risk for mycotoxicoses in farm animals, and to minimise carry-over of mycotoxins from contaminated feeds into foods of animal origin. Successful aflatoxin adsorption by means of different substances (phyllosilicate minerals, zeolites, activated charcoal, synthetic resins or yeast cell-wall-derived products) has been demonstrated in vivo and in vitro. However, attempts to adsorb DON and ZON have been less encouraging. Here we describe the adsorption capacity of a variety of potential binders, including compounds that have not been evaluated before, such as humic acids. All compounds were tested at realistic inclusion levels for their capacity to bind ZON and DON, using an in vitro method that resembles the different pH conditions in the gastro-intestinal tract of pigs. Mycotoxin adsorption was assessed by chemical methods and distinct bioassays, using specific markers of toxicity as endpoints of toxicity in cytological assays. Whereas none of the tested substances was able to bind DON in an appreciable percentage, some of the selected smectite clays, humic substances and yeast-wall derived products efficiently adsorbed ZON (>70%). Binding efficiency was indirectly confirmed by the reduction of toxicity in the in vitro bioassays. In conclusion, the presented test protocol allows the rapid screening of potential mycotoxin binders. Like other in vitro assays, the presented protocol combining chemical and biological assays cannot completely simulate the conditions of the gastro-intestinal tract, and hence in vivo experiments remain mandatory to assess the efficacy of mycotoxin binders under practical conditions