Parallel Coupling of Symmetric and Asymmetric Exclusion Processes

A system consisting of two parallel coupled channels where particles in one of them follow the rules of totally asymmetric exclusion processes (TASEP) and in another one move as in symmetric simple exclusion processes (SSEP) is investigated theoretically. Particles interact with each other via hard-core exclusion potential, and in the asymmetric channel they can only hop in one direction, while on the symmetric lattice particles jump in both directions with equal probabilities. Inter-channel transitions are also allowed at every site of both lattices. Stationary state properties of the system are solved exactly in the limit of strong couplings between the channels. It is shown that strong symmetric couplings between totally asymmetric and symmetric channels lead to an effective partially asymmetric simple exclusion process (PASEP) and properties of both channels become almost identical. However, strong asymmetric couplings between symmetric and asymmetric channels yield an effective TASEP with nonzero particle flux in the asymmetric channel and zero flux on the symmetric lattice. For intermediate strength of couplings between the lattices a vertical cluster mean-field method is developed. This approximate approach treats exactly particle dynamics during the vertical transitions between the channels and it neglects the correlations along the channels. Our calculations show that in all cases there are three stationary phases defined by particle dynamics at entrances, at exits or in the bulk of the system, while phase boundaries depend on the strength and symmetry of couplings between the channels. Extensive Monte Carlo computer simulations strongly support our theoretical predictions.Comment: 16 page

A novel method to accurately locate and count large numbers of steps by photobleaching

Photobleaching event counting is a single-molecule fluorescence technique that is increasingly being used to determine the stoichiometry of protein and RNA complexes composed of many subunits in vivo as well as in vitro. By tagging protein or RNA subunits with fluorophores, activating them, and subsequently observing as the fluorophores photobleach, one obtains information on the number of subunits in a complex. The noise properties in a photobleaching time trace depend on the number of active fluorescent subunits. Thus, as fluorophores stochastically photobleach, noise properties of the time trace change stochastically, and these varying noise properties have created a challenge in identifying photobleaching steps in a time trace. Although photobleaching steps are often detected by eye, this method only works for high individual fluorophore emission signal-to-noise ratios and small numbers of fluorophores. With filtering methods or currently available algorithms, it is possible to reliably identify photobleaching steps for up to 20-30 fluorophores and signal-to-noise ratios down to ∼1. Here we present a new Bayesian method of counting steps in photobleaching time traces that takes into account stochastic noise variation in addition to complications such as overlapping photobleaching events that may arise from fluorophore interactions, as well as on-off blinking. Our method is capable of detecting ≥50 photobleaching steps even for signal-to-noise ratios as low as 0.1, can find up to ≥500 steps for more favorable noise profiles, and is computationally inexpensive

Switching on electrocatalytic activity in solid oxide cells

Solid oxide cells (SOCs) can operate with high efficiency in two ways - as fuel cells, oxidizing a fuel to produce electricity, and as electrolysis cells, electrolysing water to produce hydrogen and oxygen gases. Ideally, SOCs should perform well, be durable and be inexpensive, but there are often competitive tensions, meaning that, for example, performance is achieved at the expense of durability. SOCs consist of porous electrodes - the fuel and air electrodes - separated by a dense electrolyte. In terms of the electrodes, the greatest challenge is to deliver high, long-lasting electrocatalytic activity while ensuring cost- and time-efficient manufacture. This has typically been achieved through lengthy and intricate ex situ procedures. These often require dedicated precursors and equipment; moreover, although the degradation of such electrodes associated with their reversible operation can be mitigated, they are susceptible to many other forms of degradation. An alternative is to grow appropriate electrode nanoarchitectures under operationally relevant conditions, for example, via redox exsolution. Here we describe the growth of a finely dispersed array of anchored metal nanoparticles on an oxide electrode through electrochemical poling of a SOC at 2 volts for a few seconds. These electrode structures perform well as both fuel cells and electrolysis cells (for example, at 900 °C they deliver 2 watts per square centimetre of power in humidified hydrogen gas, and a current of 2.75 amps per square centimetre at 1.3 volts in 50% water/nitrogen gas). The nanostructures and corresponding electrochemical activity do not degrade in 150 hours of testing. These results not only prove that in operando methods can yield emergent nanomaterials, which in turn deliver exceptional performance, but also offer proof of concept that electrolysis and fuel cells can be unified in a single, high-performance, versatile and easily manufactured device. This opens up the possibility of simple, almost instantaneous production of highly active nanostructures for reinvigorating SOCs during operation

Inhomogeneous Coupling in Two-Channel Asymmetric Simple Exclusion Processes

Asymmetric exclusion processes for particles moving on parallel channels with inhomogeneous coupling are investigated theoretically. Particles interact with hard-core exclusion and move in the same direction on both lattices, while transitions between the channels is allowed at one specific location in the bulk of the system. An approximate theoretical approach that describes the dynamics in the vertical link and horizontal lattice segments exactly but neglects the correlation between the horizontal and vertical transport is developed. It allows us to calculate stationary phase diagrams, particle currents and densities for symmetric and asymmetric transitions between the channels. It is shown that in the case of the symmetric coupling there are three stationary phases, similarly to the case of single-channel totally asymmetric exclusion processes with local inhomogeneity. However, the asymmetric coupling between the lattices lead to a very complex phase diagram with ten stationary-state regimes. Extensive Monte Carlo computer simulations generally support theoretical predictions, although simulated stationary-state properties slightly deviate from calculated in the mean-field approximation, suggesting the importance of correlations in the system. Dynamic properties and phase diagrams are discussed by analyzing constraints on the particle currents across the channels

Generalized entropy arising from a distribution of q-indices

It is by now well known that the Boltzmann-Gibbs (BG) entropy $S_{BG}=-k\sum_{i=1}^W p_i \ln p_i$ can be usefully generalized into the entropy $S_q=k (1-\sum_{i=1}^Wp_i^{q}) / (q-1)$ ($q\in \mathcal{R}; S_1=S_{BG}$). Microscopic dynamics determines, given classes of initial conditions, the occupation of the accessible phase space (or of a symmetry-determined nonzero-measure part of it), which in turn appears to determine the entropic form to be used. This occupation might be a uniform one (the usual {\it equal probability hypothesis} of BG statistical mechanics), which corresponds to $q=1$; it might be a free-scale occupancy, which appears to correspond to $q \ne 1$. Since occupancies of phase space more complex than these are surely possible in both natural and artificial systems, the task of further generalizing the entropy appears as a desirable one, and has in fact been already undertaken in the literature. To illustrate the approach, we introduce here a quite general entropy based on a distribution of $q$-indices thus generalizing $S_q$. We establish some general mathematical properties for the new entropic functional and explore some examples. We also exhibit a procedure for finding, given any entropic functional, the $q$-indices distribution that produces it. Finally, on the road to establishing a quite general statistical mechanics, we briefly address possible generalized constraints under which the present entropy could be extremized, in order to produce canonical-ensemble-like stationary-state distributions for Hamiltonian systems.Comment: 14 pages including 3 figure

Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting

Extracellular DNA is engulfed by innate immune cells and digested by endosomal DNase II to generate an immune response. Quantitative information on endosomal stage‐specific cargo processing is a critical parameter to predict and model the innate immune response. Biochemical assays quantify endosomal processing but lack organelle‐specific information, while fluorescence microscopy has provided the latter without the former. Herein, we report a single molecule counting method based on fluorescence imaging that quantitatively maps endosomal processing of cargo DNA in innate immune cells with organelle‐specific resolution. Our studies reveal that endosomal DNA degradation occurs mainly in lysosomes and is negligible in late endosomes. This method can be used to study cargo processing in diverse endocytic pathways and measure stage‐specific activity of processing factors in endosomes.Eine bildgebende Fluoreszenzmethode zur quantitativen Kartierung der endosomalen Prozessierung von Fracht‐DNA in Zellen des angeborenen Immunsystems mit Organellen‐spezifischer Auflösung (organellar single‐molecule, high‐resolution localization and counting; oSHiRLoC) wurde entwickelt. Mithilfe dieser Methode wurde gezeigt, dass die endosomale DNA‐Zersetzung hauptsächlich in Lysosomen erfolgt und in späten Endosomen zu vernachlässigen ist.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148254/1/ange201811746_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148254/2/ange201811746.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148254/3/ange201811746-sup-0001-misc_information.pd

Anomalous sensitivity to initial conditions and entropy production in standard maps: Nonextensive approach

We perform a throughout numerical study of the average sensitivity to initial conditions and entropy production for two symplectically coupled standard maps focusing on the control-parameter region close to regularity. Although the system is ultimately strongly chaotic (positive Lyapunov exponents), it first stays lengthily in weak-chaotic regions (zero Lyapunov exponents). We argue that the nonextensive generalization of the classical formalism is an adequate tool in order to get nontrivial information about this complex phenomenon. Within this context we analyze the relation between the power-law sensitivity to initial conditions and the entropy production.Comment: 9 pages, 12 figure

Phase diagram of two-lane driven diffusive systems

We consider a large class of two-lane driven diffusive systems in contact with reservoirs at their boundaries and develop a stability analysis as a method to derive the phase diagrams of such systems. We illustrate the method by deriving phase diagrams for the asymmetric exclusion process coupled to various second lanes: a diffusive lane; an asymmetric exclusion process with advection in the same direction as the first lane, and an asymmetric exclusion process with advection in the opposite direction. The competing currents on the two lanes naturally lead to a very rich phenomenology and we find a variety of phase diagrams. It is shown that the stability analysis is equivalent to an `extremal current principle' for the total current in the two lanes. We also point to classes of models where both the stability analysis and the extremal current principle fail