Modelling cytoskeletal traffic: an interplay between passive diffusion and active transport

We introduce the totally asymmetric exclusion process with Langmuir kinetics (TASEP-LK) on a network as a microscopic model for active motor protein transport on the cytoskeleton, immersed in the diffusive cytoplasm. We discuss how the interplay between active transport along a network and infinite diffusion in a bulk reservoir leads to a heterogeneous matter distribution on various scales. We find three regimes for steady state transport, corresponding to the scale of the network, of individual segments or local to sites. At low exchange rates strong density heterogeneities develop between different segments in the network. In this regime one has to consider the topological complexity of the whole network to describe transport. In contrast, at moderate exchange rates the transport through the network decouples, and the physics is determined by single segments and the local topology. At last, for very high exchange rates the homogeneous Langmuir process dominates the stationary state. We introduce effective rate diagrams for the network to identify these different regimes. Based on this method we develop an intuitive but generic picture of how the stationary state of excluded volume processes on complex networks can be understood in terms of the single-segment phase diagram.Comment: 5 pages, 7 figure

The role of long-range forces in the phase behavior of colloids and proteins

The phase behavior of colloid-polymer mixtures, and of solutions of globular proteins, is often interpreted in terms of a simple model of hard spheres with short-ranged attraction. While such a model yields a qualitative understanding of the generic phase diagrams of both colloids and proteins, it fails to capture one important difference: the model predicts fluid-fluid phase separation in the metastable regime below the freezing curve. Such demixing has been observed for globular proteins, but for colloids it appears to be pre-empted by the appearance of a gel. In this paper, we study the effect of additional long-range attractions on the phase behavior of spheres with short-ranged attraction. We find that such attractions can shift the (metastable) fluid-fluid critical point out of the gel region. As this metastable critical point may be important for crystal nucleation, our results suggest that long-ranged attractive forces may play an important role in the crystallization of globular proteins. However, in colloids, where refractive index matching is often used to switch off long-ranged dispersion forces, gelation is likely to inhibit phase separation.Comment: EURO-LATEX, 6 pages, 2 figure

Astrophotonic micro-spectrographs in the era of ELTs

The next generation of Extremely Large Telescopes (ELT), with diameters up to 39 meters, will start opera- tion in the next decade and promises new challenges in the development of instruments. The growing field of astrophotonics (the use of photonic technologies in astronomy) can partly solve this problem by allowing mass production of fully integrated and robust instruments combining various optical functions, with the potential to reduce the size, complexity and cost of instruments. In this paper, we focus on developments in integrated micro-spectrographs and their potential for ELTs. We take an inventory of the identified technologies currently in development, and compare the performance of the different concepts. We show that in the current context of single-mode instruments, integrated spectrographs making use of, e.g., a photonic lantern can be a solution to reach the desired performance. However, in the longer term, there is a clear need to develop multimode devices to improve overall the throughput and sensitivity, while decreasing the instrument complexity.Comment: 9 pages. 2 figures. Proceeding of SPIE 9147 "Ground-based and Airborne Instrumentation for Astronomy V

Computing the Least-core and Nucleolus for Threshold Cardinality Matching Games

Cooperative games provide a framework for fair and stable profit allocation in multi-agent systems. \emph{Core}, \emph{least-core} and \emph{nucleolus} are such solution concepts that characterize stability of cooperation. In this paper, we study the algorithmic issues on the least-core and nucleolus of threshold cardinality matching games (TCMG). A TCMG is defined on a graph $G=(V,E)$ and a threshold $T$, in which the player set is $V$ and the profit of a coalition $S\subseteq V$ is 1 if the size of a maximum matching in $G[S]$ meets or exceeds $T$, and 0 otherwise. We first show that for a TCMG, the problems of computing least-core value, finding and verifying least-core payoff are all polynomial time solvable. We also provide a general characterization of the least core for a large class of TCMG. Next, based on Gallai-Edmonds Decomposition in matching theory, we give a concise formulation of the nucleolus for a typical case of TCMG which the threshold $T$ equals $1$. When the threshold $T$ is relevant to the input size, we prove that the nucleolus can be obtained in polynomial time in bipartite graphs and graphs with a perfect matching

Physiological function and catalytic versatility of bacterial multihaem cytochromescinvolved in nitrogen and sulfur cycling

Bacterial MCCs (multihaem cytochromes c) represent widespread respiratory electron-transfer proteins. In addition, some of them convert substrates such as nitrite, hydroxylamine, nitric oxide, hydrazine, sulfite, thiosulfate or hydrogen peroxide. In many cases, only a single function is assigned to a specific MCC in database entries despite the fact that an MCC may accept various substrates, thus making it a multifunctional catalyst that can play diverse physiological roles in bacterial respiration, detoxification and stress defence mechanisms. The present article briefly reviews the structure, function and biogenesis of selected MCCs that catalyse key reactions in the biogeochemical nitrogen and sulfur cycles

Imaging through turbulence with a quadrature-phase optical interferometer

We present an improved technique for imaging through turbulence at visible wavelengths using a rotation shearing pupil-plane interferometer, intended for astronomical and terrestrial imaging applications. While previous astronomical rotation shearing interferometers have made only visibility modulus measurements, this interferometer makes four simultaneous measurements on each interferometric baseline, with phase differences of π/2 between each measurement, allowing complex visibility measurements (modulus and phase) across the entire input pupil in a single exposure. This technique offers excellent wavefront resolution, allowing operation at visible wavelengths on large apertures, is potentially immune to amplitude fluctuations (scintillation), and may offer superior calibration capabilities to other imaging techniques. The interferometer has been tested in the laboratory under weakly aberrating conditions and at Palomar Observatory under ordinary astronomical observing conditions. This research is based partly on observations obtained at the Hale Telescope

Ag-coverage-dependent symmetry of the electronic states of the Pt(111)-Ag-Bi interface: The ARPES view of a structural transition

We studied by angle-resolved photoelectron spectroscopy the strain-related structural transition from a pseudomorphic monolayer (ML) to a striped incommensurate phase in an Ag thin film grown on Pt(111). We exploited the surfactant properties of Bi to grow ordered Pt(111)-xMLAg-Bi trilayers with 0 < x < 5 ML, and monitored the dispersion of the Bi-derived interface states to probe the structure of the underlying Ag film. We find that their symmetry changes from threefold to sixfold and back to threefold in the Ag coverage range studied. Together with previous scanning tunneling microscopy and photoelectron diffraction data, these results provide a consistent microscopic description of the coverage-dependent structural transition.Comment: 10 pages, 9 figure

Exclusion processes on networks as models for cytoskeletal transport

We present a study of exclusion processes on networks as models for complex transport phenomena and in particular for active transport of motor proteins along the cytoskeleton. We argue that active transport processes on networks spontaneously develop density heterogeneities at various scales. These heterogeneities can be regulated through a variety of multi-scale factors, such as the interplay of exclusion interactions, the non-equilibrium nature of the transport process and the network topology. We show how an effective rate approach allows to develop an understanding of the stationary state of transport processes through complex networks from the phase diagram of one single segment. For exclusion processes we rationalize that the stationary state can be classified in three qualitatively different regimes: a homogeneous phase as well as inhomogeneous network and segment phases. In particular, we present here a study of the stationary state on networks of three paradigmatic models from non-equilibrium statistical physics: the totally asymmetric simple exclusion process, the partially asymmetric simple exclusion process and the totally asymmetric simple exclusion process with Langmuir kinetics. With these models we can interpolate between equilibrium (due to bi-directional motion along a network or infinite diffusion) and out-of-equilibrium active directed motion along a network. The study of these models sheds further light on the emergence of density heterogeneities in active phenomena.Comment: 55 pages, 26 figure