Pictures worth a thousand tiles, a geometrical programming language for self-assembly

International audienceWe present a novel way to design self-assembling systems using a notion of signal (or ray) akin to what is used in analyzing the behavior of cellular automata. This allows purely geometrical constructions, with a smaller specification and easier analysis. We show how to design a system of signals for a given set of shapes, and how to transform these signals into a set of tiles which self-assemble into the desired shapes. We show how to use this technique on three examples : squares (with optimal assembly time and a small number of tiles), general polygons, and a quasi periodic pattern : Robinson tiling

Interconnection network with a shared whiteboard: Impact of (a)synchronicity on computing power

In this work we study the computational power of graph-based models of distributed computing in which each node additionally has access to a global whiteboard. A node can read the contents of the whiteboard and, when activated, can write one message of O(log n) bits on it. When the protocol terminates, each node computes the output based on the final contents of the whiteboard. We consider several scheduling schemes for nodes, providing a strict ordering of their power in terms of the problems which can be solved with exactly one activation per node. The problems used to separate the models are related to Maximal Independent Set, detection of cycles of length 4, and BFS spanning tree constructions

DNA Tile Self-Assembly for 3D-Surfaces: Towards Genus Identification

We introduce a new DNA tile self-assembly model: the Surface Flexible Tile Assembly Model (SFTAM), where 2D tiles are placed on host 3D surfaces made of axis-parallel unit cubes glued together by their faces, called polycubes. The bonds are flexible, so that the assembly can bind on the edges of the polycube. We are interested in the study of SFTAM self-assemblies on 3D surfaces which are not always embeddable in the Euclidean plane, in order to compare their different behaviors and to compute the topological properties of the host surfaces. We focus on a family of polycubes called order-1 cuboids. Order-0 cuboids are polycubes that have six rectangular faces, and order-1 cuboids are made from two order-0 cuboids by substracting one from the other. Thus, order-1 cuboids can be of genus 0 or of genus 1 (then they contain a tunnel). We are interested in the genus of these structures, and we present a SFTAM tile assembly system that determines the genus of a given order-1 cuboid. The SFTAM tile assembly system which we design, contains a specific set Y of tile types with the following properties. If the assembly is made on a host order-1 cuboid C of genus 0, no tile of Y appears in any producible assembly, but if C has genus 1, every terminal assembly contains at least one tile of Y. Thus, for order-1 cuboids our system is able to distinguish the host surfaces according to their genus, by the tiles used in the assembly. This system is specific to order-1 cuboids but we can expect the techniques we use to be generalizable to other families of shapes

Allowing each node to communicate only once in a distributed system: shared whiteboard models

International audienceIn this paper we study distributed algorithms on massive graphs where links represent a particular relationship between nodes (for instance, nodes may represent phone numbers and links may indicate telephone calls). Since such graphs are massive they need to be processed in a distributed way. When computing graph-theoretic properties, nodes become natural units for distributed computation. Links do not necessarily represent communication channels between the computing units and therefore do not restrict the communication flow. Our goal is to model and analyze the computational power of such distributed systems where one computing unit is assigned to each node. Communication takes place on a whiteboard where each node is allowed to write at most one message. Every node can read the contents of the whiteboard and, when activated, can write one small message based on its local knowledge. When the protocol terminates its output is computed from the final contents of the whiteboard. We describe four synchronization models for accessing the whiteboard. We show that message size and synchronization power constitute two orthogonal hierarchies for these systems.We exhibit problems that separate these models, i.e., that can be solved in one model but not in a weaker one, even with increased message size. These problems are related to maximal independent set and connectivity. We also exhibit problems that require a given message size independently of the synchronization model

Connectivity Lower Bounds in Broadcast Congested Clique

We prove three new lower bounds for graph connectivity in the 1-bit broadcast congested clique model, BCC(1). First, in the KT-0 version of BCC(1), in which nodes are aware of neighbors only through port numbers, we show an ?(log n) round lower bound for Connectivity even for constant-error randomized Monte Carlo algorithms. The deterministic version of this result can be obtained via the well-known "edge-crossing" argument, but, the randomized version of this result requires establishing new combinatorial results regarding the indistinguishability graph induced by inputs. In our second result, we show that the ?(log n) lower bound result extends to the KT-1 version of the BCC(1) model, in which nodes are aware of IDs of all neighbors, though our proof works only for deterministic algorithms. This result substantially improves upon the existing ?(log^* n) deterministic lower bound (Jurdzi?ski et el., SIROCCO 2018) for this problem. Since nodes know IDs of their neighbors in the KT-1 model, it is no longer possible to play "edge-crossing" tricks; instead we present a reduction from the 2-party communication complexity problem Partition in which Alice and Bob are given two set partitions on [n] and are required to determine if the join of these two set partitions equals the trivial one-part set partition. While our KT-1 Connectivity lower bound holds only for deterministic algorithms, in our third result we extend this ?(log n) KT-1 lower bound to constant-error Monte Carlo algorithms for the closely related ConnectedComponents problem. We use information-theoretic techniques to obtain this result. All our results hold for the seemingly easy special case of Connectivity in which an algorithm has to distinguish an instance with one cycle from an instance with multiple cycles. Our results showcase three rather different lower bound techniques and lay the groundwork for further improvements in lower bounds for Connectivity in the BCC(1) model

Study by modeling and simulation of open-switch fault diagnosis for five-level converters

In this paper, an open-switch fault diagnosis method for five-level H-Bridge Neutral Point Piloted (HB-NPP) or T-type converters is proposed. While fault tolerant operation is based on three steps (fault detection, fault localization and system reconfiguration), a fast fault diagnosis, including both fault detection and localization, is mandatory to make a suitable response to an open-circuit fault in one of the switches of the converter. Furthermore, fault diagnosis is necessary in embedded and safety critical applications, to prevent further damage and perform continuity of service.In this paper, we present an open-switch fault diagnosis method, based on the switches control orders and the observation of the converter output voltage level. In five-level converters such as HB-NPP and T-type topologies, some switches are mostly 'on' at the same time. Therefore, the fault localization is quite complicated. The fault diagnosis method we proposed is capable to detect and localize an open-switch fault in all cases. Computer simulations are carried out by using Matlab Simulink and SimPowerSystem toolbox to validate the proposed approach

Reconstruire un graphe en une ronde

International audienceNous étudions quelles propriétés d'un réseau peuvent être calculées à partir d'une petite quantité d'informations locales fournie par ses noeuds. Notre modèle est une restriction de CONGEST, un modèle distribué classique. Il est proche du modèle de complexité de communication avec messages simultanés de Babai et al. Chacun des n noeuds --qui ne connaissent que leur identifiant, ceux de leurs voisins et la taille du graphe-- envoie un message de taille O(log(n)) bits à une entité centrale, le superviseur. Celui-ci doit alors déterminer une certaine propriété du réseau. Nous montrons que des questions telles que: ''Est-ce que le graphe contient un triangle? un carré ? Quel est son diamètre?" ne peuvent pas être résolues dans ce modèle. En revanche, pour de nombreuses classes de graphes : celles de dégénérescence bornée (incluant les graphes planaires, ceux de largeur arborescente bornée... ), les sommets peuvent succinctement donner une description complète du graphe au superviseur. Nous laissons ouverte la question de décider la connexité

Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology

Applications of isothermal titration calorimetry - the research and technical developments from 2011 to 2015

Isothermal titration calorimetry is a widely used biophysical technique for studying the formation or dissociation of molecular complexes. Over the last 5years, much work has been published on the interpretation of isothermal titration calorimetry (ITC) data for single binding and multiple binding sites. As over 80% of ITC papers are on macromolecules of biological origin, this interpretation is challenging. Some researchers have attempted to link the thermodynamics constants to events at the molecular level. This review highlights work carried out using binding sites characterized using x-ray crystallography techniques that allow speculation about individual bond formation and the displacement of individual water molecules during ligand binding and link these events to the thermodynamic constants for binding. The review also considers research conducted with synthetic binding partners where specific binding events like anion-π and π-π interactions were studied. The revival of assays that enable both thermodynamic and kinetic information to be collected from ITC data is highlighted. Lastly, published criticism of ITC research from a physical chemistry perspective is appraised and practical advice provided for researchers unfamiliar with thermodynamics and its interpretation