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

Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment

Within the crowded and complex environment of the cell, a protein experiences stabilizing excluded-volume effects and destabilizing quinary interactions with other proteins. Which of these prevail, needs to be determined on a case-by-case basis. PAPS synthases are dimeric and bifunctional enzymes, providing activated sulfate in the form of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for sulfation reactions. The human PAPS synthases PAPSS1 and PAPSS2 differ significantly in their protein stability as PAPSS2 is a naturally fragile protein. PAPS synthases bind a series of nucleotide ligands and some of them markedly stabilize these proteins. PAPS synthases are of biomedical relevance as destabilizing point mutations give rise to several pathologies. Genetic defects in PAPSS2 have been linked to bone and cartilage malformations as well as a steroid sulfation defect. All this makes PAPS synthases ideal to study protein unfolding, ligand binding, and the stabilizing and destabilizing factors in their cellular environment. This review provides an overview on current concepts of protein folding and stability and links this with our current understanding of the different disease mechanisms of PAPSS2-related pathologies with perspectives for future research and application

Transport, magnetic, thermodynamic and optical properties in Ti-doped Sr_2RuO_4

We report on electrical resistivity, magnetic susceptibility and magnetization, on heat capacity and optical experiments in single crystals of Sr_2Ru_(1-x)Ti_xO_4. Samples with x=0.1 and 0.2 reveal purely semiconducting resistivity behavior along c and the charge transport is close to localization within the ab-plane. A strong anisotropy in the magnetic susceptibility appears at temperatures below 100 K. Moreover magnetic ordering in c-direction with a moment of order 0.01 mu_B/f.u. occurs at low temperatures. On doping the low-temperature linear term of the heat capacity becomes reduced significantly and probably is dominated by spin fluctuations. Finally, the optical conductivity reveals the anisotropic character of the dc resistance, with the in-plane conductance roughly following a Drude-type behavior and an insulating response along c

Trees over Infinite Structures and Path Logics with Synchronization

We provide decidability and undecidability results on the model-checking problem for infinite tree structures. These tree structures are built from sequences of elements of infinite relational structures. More precisely, we deal with the tree iteration of a relational structure M in the sense of Shelah-Stupp. In contrast to classical results where model-checking is shown decidable for MSO-logic, we show decidability of the tree model-checking problem for logics that allow only path quantifiers and chain quantifiers (where chains are subsets of paths), as they appear in branching time logics; however, at the same time the tree is enriched by the equal-level relation (which holds between vertices u, v if they are on the same tree level). We separate cleanly the tree logic from the logic used for expressing properties of the underlying structure M. We illustrate the scope of the decidability results by showing that two slight extensions of the framework lead to undecidability. In particular, this applies to the (stronger) tree iteration in the sense of Muchnik-Walukiewicz.Comment: In Proceedings INFINITY 2011, arXiv:1111.267

A novel heavy-fermion state in CaCu_3Ru_4O12

We have measured susceptibility, specific heat, resistivity, and thermopower of CaCu$_3$Ti$_{4-x}$Ru$_x$O$_{12}$ and CaCu$_{3-y}$Mn$_y$Ru$_4$O$_{12}$, and have found that CaCu$_3$Ru$_4$O$_{12}$ can be regarded as a heavy-fermion oxide in d-electron systems. The Kondo temperature is near 200 K, and the susceptibility (1.4$\times10^{-3}$ emu/Cu mol) and the electron specific heat coefficient (28 mJ/Cu molK$^2$) are moderately enhanced. The resistivity is proportional to $T^2$ at low temperatures, and satisfies the Kadowaki-Woods relation. The heavy-fermion state comes from the interaction between the localized moment of Cu 3d and the conduction electron of Ru 4d. An insulator-metal transition occurs between $x=1.5$ and 4 in CaCu$_3$Ti$_{4-x}$Ru$_x$O$_{12}$, which can be regarded as a transition from magnetic insulator to heavy-fermion metal.Comment: 4 pages, 5 figures, submitted to J. Phys. Soc. Jp

Wakeful rest alleviates interference-based forgetting

Retroactive interference (RI)—the disruptive influence of events occurring after the formation of a new memory—is one of the primary causes of forgetting. Placing individuals within an environment that postpones interference should, therefore, greatly reduce the likelihood of information being lost from memory. For example, a short period of wakeful rest should diminish interference-based forgetting. To test this hypothesis, participants took part in a foreign language learning activity and were shown English translations of 20 Icelandic words for immediate recall. Half of the participants were then given an 8-min rest before completing a similar or dissimilar interfering distractor task. The other half did not receive a rest until after the distractor task, at which point interference had already taken place. All participants were then asked to translate the Icelandic words for a second time. Results revealed that retention was significantly worse at the second recall test, but being allowed a brief rest before completing the distractor task helped reduce the amount of forgetting. Taking a short, passive break can shield new memories from RI and alleviate forgetting.ERAS Scheme, University of Wolverhampto

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

Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment

Within the crowded and complex environment of the cell, a protein experiences stabilizing excluded-volume effects and destabilizing quinary interactions with other proteins. Which of these prevail, needs to be determined on a case-by-case basis. PAPS synthases are dimeric and bifunctional enzymes, providing activated sulfate in the form of 3′-phosphoadenosine-5′-phosphosulfate (PAPS) for sulfation reactions. The human PAPS synthases PAPSS1 and PAPSS2 differ significantly in their protein stability as PAPSS2 is a naturally fragile protein. PAPS synthases bind a series of nucleotide ligands and some of them markedly stabilize these proteins. PAPS synthases are of biomedical relevance as destabilizing point mutations give rise to several pathologies. Genetic defects in PAPSS2 have been linked to bone and cartilage malformations as well as a steroid sulfation defect. All this makes PAPS synthases ideal to study protein unfolding, ligand binding, and the stabilizing and destabilizing factors in their cellular environment. This review provides an overview on current concepts of protein folding and stability and links this with our current understanding of the different disease mechanisms of PAPSS2-related pathologies with perspectives for future research and application

Traditionally taught students learn; actively engaged students remember

A common narrative in physics education research is that students taught in lecture-based classes learn less than those taught with activity-based reformed methods. We show this narrative is simplistic and misses important dynamics of student learning. In particular, we find students of both methods show equal short-term learning gains on a conceptual question dealing with electric potential. For traditionally taught students, this learning rapidly decays on a time scale of weeks, vanishing by the time of the typical end-of-term post-test. For students in reform-based classes, however, the knowledge is retained and may even be enhanced by subsequent instruction. This difference explains the many previous pre- and post-test studies that have found minimal learning gains in lecture-based courses. Our findings suggest a more nuanced model of student learning, one that is sensitive to time-dependent effects such as forgetting and interference. In addition, the findings suggest that lecture-based courses, by incorporating aspects designed to reinforce student understanding of previously covered topics, might approach the long-term learning found in research-based pedagogies