Computational Complexity in Tile Self-Assembly

One of the most fundamental and well-studied problems in Tile Self-Assembly is the Unique Assembly Verification (UAV) problem. This algorithmic problem asks whether a given tile system uniquely assembles a specific assembly. The complexity of this problem in the 2-Handed Assembly Model (2HAM) at a constant temperature is a long-standing open problem since the model was introduced. Previously, only membership in the class coNP was known and that the problem is in P if the temperature is one (τ = 1). The problem is known to be hard for many generalizations of the model, such as allowing one step into the third dimension or allowing the temperature of the system to be a variable, but the most fundamental version has remained open. In this Thesis I will cover verification problems in different models of self-assembly leading to the proof that the UAV problem in the 2HAM is hard even with a small constant temperature (τ = 2), and finally answer the complexity of this problem (open since 2013). Further, this result proves that UAV in the staged self-assembly model is coNP-complete with a single bin and stage (open since 2007), and that UAV in the q-tile model is also coNP-complete (open since 2004). We reduce from Monotone Planar 3-SAT with Neighboring Variable Pairs, a special case of 3SAT recently proven to be NP-hard

Pomeron Physics at the LHC

We present current and ongoing research aimed at identifying Pomeron effects at the LHC in both the weak and strongly coupled regimes of QCD.Comment: 11 pages, 9 figures, 1 table. ISMD-2017 proceedings, will be published on-line on the EPJ Web of Conferences; References adde

Plasmonic edge states: an electrostatic eigenmode description

We consider periodic arrangements of metal nanostructures and study the effect of periodicity on the localised surface plasmon resonance of the structures within an electrostatic eigenmode approximation. We show that within this limit, the collective surface plasmon resonances of the periodic structures can be expressed in terms of superpositions of the eigenmodes of uncoupled nanostructures that exhibit a standing--wave character delocalised across the entire periodic structure. The formalism derived successfully enables the design and accounts for the observation of plasmonic edge-states in periodic structures

The Great Escape: Phosphorylation of Ena/VASP by PKA Promotes Filopodial Formation

The Ena/VASP family of proteins consists of adaptor molecules that localize to subcellular sites of actin polymerization. The role of Ena/VASP proteins in the regulation of cell motility and axon outgrowth has been controversial. Recently, these proteins have been proposed to function as anticapping factors, which may have differential effects on filopodial versus lammelipodial actin-based protrusions. A study by Lebrand et al. in this issue of Neuron supports this model and identifies PKA as a key regulator of Ena/VASP function downstream of the chemoattractant Netrin

Adjacent pioneer commissural interneuron growth cones switch from contact avoidance to axon fasciculation after midline crossing

AbstractCommissural interneurons (CI) of the vertebrate spinal cord are guided ventrally toward the floor plate, but subsequently cross the midline and select a longitudinal fascicle at specific dorsal–ventral (D–V) positions. We examined at high resolution the detailed behaviors of individual pathfinding CI growth cones on the ipsilateral and contralateral sides of the spinal cord of living Xenopus embryos. We find that pre-crossing CI growth cones exhibit distinct pathfinding behaviors compared to post-crossing axons and that the behavioral switch occurs immediately upon crossing to the contralateral side. Groups of pioneer commissural axons typically extend simultaneously toward the ventral midline following discrete paths with separation between adjacent commissurals apparently maintained through contact inhibition. In contrast, shortly after crossing the midline, commissural axons turn longitudinally and begin to fasciculate with other crossed CIs. However, growth cones of crossed commissurals often select their final D–V longitudinal track through a series of rapid step-like dorsal adjustments that may be due to differential fasciculation with longitudinal axons. Together, our results suggest that guidance of commissural axons is controlled in part through interactions among CIs that switch rapidly from avoidance to fasciculation after midline crossing

Concurrent Chains Schedules as a Method to Study Choice Between Alcohol Associated Conditioned Reinforcers

An extensive body of research using concurrent-chains schedules of reinforcement has shown that choice for one of two differentially valued food-associated stimuli is dependent upon the overall temporal context in which those stimuli are embedded. The present experiments examined whether the concurrent chains procedure was useful for the study of behavior maintained by alcohol and alcohol-associated stimuli. In Experiment 1, rats responded on concurrent-chains schedules with equal variable-interval (VI) 10-s schedules in the initial links. Across conditions, fixed-interval schedules in the terminal links were varied to yield 1:1, 9:1, and 1:9 ratios of alcohol delivery. Initial-link response rates reflected changes in terminal-link schedules, with greater relative responding in the rich terminal link. In Experiment 2, terminal-link schedules remained constant with a 9:1 ratio of alcohol delivery rates while the length of two equal duration initial-link schedules was varied. Preference for the rich terminal link was less extreme when initial links were longer (i.e., the initial-link effect), as has been previously reported with food reinforcers. This result suggests that the conditioned reinforcing value of an alcohol associated stimulus depends on the temporal context in which it is embedded. The concurrent-chains procedure and quantitative models of concurrent chains performance may provide a useful framework within which to study how contextual variables modulate preference for drug-associated conditioned reinforcers

Filopodial Calcium Transients Regulate Growth Cone Motility and Guidance through Local Activation of Calpain

AbstractSpontaneous intracellular calcium ([Ca2+]i) transients in growth cone filopodia reduce filopodial motility, slow neurite outgrowth, and promote turning when generated asymmetrically; however, the downstream effectors of these Ca2+-dependent behaviors are unknown. We report that Ca2+ transients in filopodia activate the intracellular protease calpain, which slows neurite outgrowth and promotes repulsive growth cone turning upon local activation. Active calpain alters the balance between tyrosine kinase and phosphatase activities in filopodia, resulting in a net decrease in tyrosine phosphorylation, which mediates both filopodial stabilization and reduced lamellipodial protrusion. Our findings indicate that locally generated Ca2+ signals repel axon outgrowth through calpain-dependent regulation of phosphotyrosine signaling at integrin-mediated adhesion sites

Src-Dependent Tyrosine Phosphorylation at the Tips of Growth Cone Filopodia Promotes Extension

Extracellular cues guide axon outgrowth by activating intracellular signaling cascades that control the growth cone cytoskeleton. However, the spatial and temporal coordination of signaling intermediates remains essentially unknown. Live imaging of tyrosine phosphorylation in growth cones revealed dynamic phospho-tyrosine (PY) signals in filopodia that directly correlate with filopodial behavior. Local PY signals are generated at distal tips of filopodia during extension and are lost during retraction. Active Src family kinases localize to the tips of filopodia, and Src activity regulates both filopodial dynamics and local PY signaling. Positive guidance cues stimulate filopodial motility by locally increasing tyrosine phosphorylation in a cell division cycle 42 (Cdc42)-dependent manner. Locally reduced Src activity on one side of the growth cone generates an asymmetry in filopodial motility and PY signaling that promotes repulsive turning, suggesting that local changes in filopodial PY levels may underlie growth cone pathfinding decisions. p21-activated kinase (PAK), a Cdc42 effector whose activity is regulated by Src phosphorylation, also localizes to the tips of extending filopodia and controls filopodial motility. Coordinated activation of cytoskeletal effector proteins by GTPase binding and Src-mediated tyrosine phosphorylation may function to produce specific growth cone behaviors in response to guidance cues