Particle interactions and lattice dynamics: Scenarios for efficient bidirectional stochastic transport?

Intracellular transport processes driven by molecular motors can be described by stochastic lattice models of self-driven particles. Here we focus on bidirectional transport models excluding the exchange of particles on the same track. We explore the possibility to have efficient transport in these systems. One possibility would be to have appropriate interactions between the various motors' species, so as to form lanes. However, we show that the lane formation mechanism based on modified attachment/detachment rates as it was proposed previously is not necessarily connected to an efficient transport state and is suppressed when the diffusivity of unbound particles is finite. We propose another interaction mechanism based on obstacle avoidance that allows to have lane formation for limited diffusion. Besides, we had shown in a separate paper that the dynamics of the lattice itself could be a key ingredient for the efficiency of bidirectional transport. Here we show that lattice dynamics and interactions can both contribute in a cooperative way to the efficiency of transport. In particular, lattice dynamics can decrease the interaction threshold beyond which lanes form. Lattice dynamics may also enhance the transport capacity of the system even when lane formation is suppressed.Comment: 25 pages, 17 figures, 2 table

ATPγS stalls splicing after B complex formation but prior to spliceosome activation.

The ATP analog ATPγS inhibits pre-mRNA splicing in vitro, but there have been conflicting reports as to which step of splicing is inhibited by this small molecule and its inhibitory mechanism remains unclear. Here we have dissected the effect of ATPγS on pre-mRNA splicing in vitro. Addition of ATPγS to splicing extracts depleted of ATP inhibited both catalytic steps of splicing. At ATPγS concentrations ≥0.5 mM, precatalytic B complexes accumulate, demonstrating a block prior to or during the spliceosome activation stage. Affinity purification of the ATPγS-stalled B complexes (B(ATPγS)) and subsequent characterization of their abundant protein components by 2D gel electrophoresis revealed that B(ATPγS) complexes are compositionally more homogeneous than B complexes previously isolated in the presence of ATP. In particular, they contain little or no Prp19/CDC5L complex proteins, indicating that these proteins are recruited after assembly of the precatalytic spliceosome. Under the electron microscope, B(ATPγS) complexes exhibit a morphology highly similar to B complexes, indicating that the ATPγS-induced block in the transformation of the B to B(act) complex is not due to a major structural defect. Likely mechanisms whereby ATPγS blocks spliceosome assembly at the activation stage, including inhibition of the RNA helicase Brr2, are discussed. Given their more homogeneous composition, B complexes stalled by ATPγS may prove highly useful for both functional and structural analyses of the precatalytic spliceosome and its conversion into an activated B(act) spliceosomal complex

Spontaneous symmetry breaking in a two-lane model for bidirectional overtaking traffic

First we consider a unidirectional flux \omega_bar of vehicles each of which is characterized by its `natural' velocity v drawn from a distribution P(v). The traffic flow is modeled as a collection of straight `world lines' in the time-space plane, with overtaking events represented by a fixed queuing time tau imposed on the overtaking vehicle. This geometrical model exhibits platoon formation and allows, among many other things, for the calculation of the effective average velocity w=\phi(v) of a vehicle of natural velocity v. Secondly, we extend the model to two opposite lanes, A and B. We argue that the queuing time \tau in one lane is determined by the traffic density in the opposite lane. On the basis of reasonable additional assumptions we establish a set of equations that couple the two lanes and can be solved numerically. It appears that above a critical value \omega_bar_c of the control parameter \omega_bar the symmetry between the lanes is spontaneously broken: there is a slow lane where long platoons form behind the slowest vehicles, and a fast lane where overtaking is easy due to the wide spacing between the platoons in the opposite direction. A variant of the model is studied in which the spatial vehicle density \rho_bar rather than the flux \omega_bar is the control parameter. Unequal fluxes \omega_bar_A and \omega_bar_B in the two lanes are also considered. The symmetry breaking phenomenon exhibited by this model, even though no doubt hard to observe in pure form in real-life traffic, nevertheless indicates a tendency of such traffic.Comment: 50 pages, 16 figures; extra references adde

The critical exponents of the two-dimensional Ising spin glass revisited: Exact Ground State Calculations and Monte Carlo Simulations

The critical exponents for $T\to0$ of the two-dimensional Ising spin glass model with Gaussian couplings are determined with the help of exact ground states for system sizes up to $L=50$ and by a Monte Carlo study of a pseudo-ferromagnetic order parameter. We obtain: for the stiffness exponent $y(=\theta)=-0.281\pm0.002$, for the magnetic exponent $\delta=1.48 \pm 0.01$ and for the chaos exponent $\zeta=1.05\pm0.05$. From Monte Carlo simulations we get the thermal exponent $\nu=3.6\pm0.2$. The scaling prediction $y=-1/\nu$ is fulfilled within the error bars, whereas there is a disagreement with the relation $y=1-\delta$.Comment: 8 pages RevTeX, 7 eps-figures include

Towards a realistic microscopic description of highway traffic

Simple cellular automata models are able to reproduce the basic properties of highway traffic. The comparison with empirical data for microscopic quantities requires a more detailed description of the elementary dynamics. Based on existing cellular automata models we propose an improved discrete model incorporating anticipation effects, reduced acceleration capabilities and an enhanced interaction horizon for braking. The modified model is able to reproduce the three phases (free-flow, synchronized, and stop-and-go) observed in real traffic. Furthermore we find a good agreement with detailed empirical single-vehicle data in all phases.Comment: 7 pages, 7 figure

An empirical test for cellular automaton models of traffic flow

Based on a detailed microscopic test scenario motivated by recent empirical studies of single-vehicle data, several cellular automaton models for traffic flow are compared. We find three levels of agreement with the empirical data: 1) models that do not reproduce even qualitatively the most important empirical observations, 2) models that are on a macroscopic level in reasonable agreement with the empirics, and 3) models that reproduce the empirical data on a microscopic level as well. Our results are not only relevant for applications, but also shed new light on the relevant interactions in traffic flow.Comment: 28 pages, 36 figures, accepted for publication in PR

Phase diagrams of La1−xCaxMnO3\rm La_{1-x}Ca_xMnO_3 in Double Exchange Model with added antiferromagnetic and Jahn-Teller interaction

The phase diagram of the multivalent manganites $\rm La_{1-x}Ca_xMnO_3$, in space of temperature and doping $x$, is a challenge for the theoretical physics. It is an important test for the model used to study these compounds and the method of calculation. To obtain theoretically this diagram for $x<0.5$, we consider the two-band Double Exchange Model for manganites with added Jahn-Teller coupling and antiferromagnetic Heisenberg term. In order to calculate Curie and N\'{e}el temperatures we derive an effective Heisenberg model for a vector which describes the local orientation of the total magnetization of the system. The exchange constants of this model are different for different space directions and depend on the density of $e_g$ electrons, antiferromagnetic constants and the Jahn-Teller energy. To reproduce the well known phase transitions from A-type antiferromagnetism to ferromagnetism at low $x$ and C-type antiferromagnetism to G-type antiferromagnetism at large $x$, we argue that the antiferromagnetic exchange constants should depend on the lattice direction. We show that ferromagnetic to A-type antiferromagnetic transition results from the Jahn-Teller distortion. Accounting adequately for the magnon-magnon interaction, Curie and N\'{e}el temperatures are calculated. The results are in very good agreement with the experiment and provide values for the model parameters, which best describe the behavior of the critical temperature for $x<0.5$.Comment: 13 pages, 5 figure

Manipulation of drugs to achieve the required dose is intrinsic to paediatric practice but is not supported by guidelines or evidence

Background: A lack of age-appropriate formulations can make it difficult to administer medicines to children. A manipulation of the dosage form may be required to achieve the required dose. This study aimed to describe medicines that are manipulated to achieve the required dose in paediatric practice.Method: A structured, undisguised observational study and postal survey. The observational study investigated drug manipulations occurring in clinical practice across three sites. The questionnaire, administered to a sample of paediatric nurses throughout the UK, surveyed manipulations conducted and nurses' experiences and views.Results: The observational study identified 310 manipulations, of which 62% involved tablets, 21% were intravenous drugs and 10% were sachets. Of the 54 observed manipulations 40 involved tablets with 65% of the tablets being cut and 30% dispersed to obtain a smaller dose. 188 manipulations were reported by questionnaire respondents, of these 46% involved tablets, 12% were intravenous drugs, and 12% were nebuliser solutions. Manipulations were predominantly, but not exclusively, identified in specialist clinical areas with more highly dependent patients. Questionnaire respondents were concerned about the accuracy of the dose achieved following manipulations and the lack of practice guidance.Conclusion: Manipulations to achieve the required dose occur throughout paediatric in-patient settings. The impact of manipulations on the efficacy of the drugs, the accuracy of the dose and any adverse effects on patients is not known. There is a need to develop evidence-based guidance for manipulations of medicines in children