Compact Deterministic Self-Stabilizing Leader Election: The Exponential Advantage of Being Talkative

This paper focuses on compact deterministic self-stabilizing solutions for the leader election problem. When the protocol is required to be \emph{silent} (i.e., when communication content remains fixed from some point in time during any execution), there exists a lower bound of Omega(\log n) bits of memory per node participating to the leader election (where n denotes the number of nodes in the system). This lower bound holds even in rings. We present a new deterministic (non-silent) self-stabilizing protocol for n-node rings that uses only O(\log\log n) memory bits per node, and stabilizes in O(n\log^2 n) rounds. Our protocol has several attractive features that make it suitable for practical purposes. First, the communication model fits with the model used by existing compilers for real networks. Second, the size of the ring (or any upper bound on this size) needs not to be known by any node. Third, the node identifiers can be of various sizes. Finally, no synchrony assumption, besides a weakly fair scheduler, is assumed. Therefore, our result shows that, perhaps surprisingly, trading silence for exponential improvement in term of memory space does not come at a high cost regarding stabilization time or minimal assumptions

Silent MST approximation for tiny memory

In network distributed computing, minimum spanning tree (MST) is one of the key problems, and silent self-stabilization one of the most demanding fault-tolerance properties. For this problem and this model, a polynomial-time algorithm with $O(\log^2\!n)$ memory is known for the state model. This is memory optimal for weights in the classic $[1,\text{poly}(n)]$ range (where $n$ is the size of the network). In this paper, we go below this $O(\log^2\!n)$ memory, using approximation and parametrized complexity. More specifically, our contributions are two-fold. We introduce a second parameter~$s$, which is the space needed to encode a weight, and we design a silent polynomial-time self-stabilizing algorithm, with space $O(\log n \cdot s)$. In turn, this allows us to get an approximation algorithm for the problem, with a trade-off between the approximation ratio of the solution and the space used. For polynomial weights, this trade-off goes smoothly from memory $O(\log n)$ for an $n$-approximation, to memory $O(\log^2\!n)$ for exact solutions, with for example memory $O(\log n\log\log n)$ for a 2-approximation

Memory lower bounds for deterministic self-stabilization

In the context of self-stabilization, a \emph{silent} algorithm guarantees that the register of every node does not change once the algorithm has stabilized. At the end of the 90's, Dolev et al. [Acta Inf. '99] showed that, for finding the centers of a graph, for electing a leader, or for constructing a spanning tree, every silent algorithm must use a memory of $\Omega(\log n)$ bits per register in $n$-node networks. Similarly, Korman et al. [Dist. Comp. '07] proved, using the notion of proof-labeling-scheme, that, for constructing a minimum-weight spanning trees (MST), every silent algorithm must use a memory of $\Omega(\log^2n)$ bits per register. It follows that requiring the algorithm to be silent has a cost in terms of memory space, while, in the context of self-stabilization, where every node constantly checks the states of its neighbors, the silence property can be of limited practical interest. In fact, it is known that relaxing this requirement results in algorithms with smaller space-complexity. In this paper, we are aiming at measuring how much gain in terms of memory can be expected by using arbitrary self-stabilizing algorithms, not necessarily silent. To our knowledge, the only known lower bound on the memory requirement for general algorithms, also established at the end of the 90's, is due to Beauquier et al.~[PODC '99] who proved that registers of constant size are not sufficient for leader election algorithms. We improve this result by establishing a tight lower bound of $\Theta(\log \Delta+\log \log n)$ bits per register for self-stabilizing algorithms solving $(\Delta+1)$-coloring or constructing a spanning tree in networks of maximum degree~$\Delta$. The lower bound $\Omega(\log \log n)$ bits per register also holds for leader election

Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physic

Self-locking mechanical center joint

A device for connecting, rotating and locking together a pair of structural half columns is described. The device is composed of an identical pair of cylindrical hub assemblies connected at their inner faces by a spring loaded hinge; each hub assembly having a structural half column attached to its outer end. Each hub assembly has a spring loading locking ring member movably attached adjacent to its inner face and includes a latch member for holding the locking ring in a rotated position subject to the force of its spring. Each hub assembly also has a hammer member for releasing the latch on the opposing hub assembly when the hub assemblies are rotated together. The spring loaded hinge connecting the hub assemblies rotates the hub assemblies and attached structural half columns together bringing the inner faces of the opposing hub assemblies into contact with one another

Self-assembly of magnetic iron oxide nanoparticles into cuboidal superstructures

This chapter describes the synthesis and some characteristics of magnetic iron oxide nanoparticles, mainly nanocubes, and focus on their self-assembly into crystalline cuboids in dispersion. The influence of external magnetic fields, the concentration of particles, and the temperature on the assembly process is experimentally investigated

An electrostatic interaction between TEA and an introduced pore aromatic drives spring-in-the-door inactivation in Shaker potassium channels

Slow inactivation of Kv1 channels involves conformational changes near the selectivity filter. We examine such changes in Shaker channels lacking fast inactivation by considering the consequences of mutating two residues, T449 just external to the selectivity filter and V438 in the pore helix near the bottom of the selectivity filter. Single mutant T449F channels with the native V438 inactivate very slowly, and the canonical foot-in-the-door effect of extracellular tetraethylammonium (TEA) is not only absent, but the time course of slow inactivation is accelerated by TEA. The V438A mutation dramatically speeds inactivation in T449F channels, and TEA slows inactivation exactly as predicted by the foot-in-the-door model. We propose that TEA has this effect on V438A/T449F channels because the V438A mutation produces allosteric consequences within the selectivity filter and may reorient the aromatic ring at position 449. We investigated the possibility that the blocker promotes the collapse of the outer vestibule (spring-in-the-door) in single mutant T449F channels by an electrostatic attraction between a cationic TEA and the quadrupole moments of the four aromatic rings. To test this idea, we used in vivo nonsense suppression to serially fluorinate the introduced aromatic ring at the 449 position, a manipulation that withdraws electrons from the aromatic face with little effect on the shape, net charge, or hydrophobicity of the aromatic ring. Progressive fluorination causes monotonically enhanced rates of inactivation. In further agreement with our working hypothesis, increasing fluorination of the aromatic gradually transforms the TEA effect from spring-in-the-door to foot-in-the-door. We further substantiate our electrostatic hypothesis by quantum mechanical calculations