Self-Assembly of Tiles: Theoretical Models, the Power of Signals, and Local Computing

DNA-based self-assembly is an autonomous process whereby a disordered system of DNA sequences forms an organized structure or pattern as a consequence of Watson-Crick complementarity of DNA sequences, without external direction. Here, we propose self-assembly (SA) hypergraph automata as an automata-theoretic model for patterned self-assembly. We investigate the computational power of SA-hypergraph automata and show that for every recognizable picture language, there exists an SA-hypergraph automaton that accepts this language. Conversely, we prove that for any restricted SA-hypergraph automaton, there exists a Wang Tile System, a model for recognizable picture languages, that accepts the same language. Moreover, we investigate the computational power of some variants of the Signal-passing Tile Assembly Model (STAM), as well as propose the concept of {\it Smart Tiles}, i.e., tiles with glues that can be activated or deactivated by signals, and which possess a limited amount of local computing capability. We demonstrate the potential of smart tiles to perform some robotic tasks such as replicating complex shapes

ATLAS Upgrade Instrumentation in the US

Planned upgrades of the LHC over the next decade should allow the machine to operate at a center of mass energy of 14 TeV with instantaneous luminosities in the range 5--7e34 cm^-2 s^-1. With these parameters, ATLAS could collect 3,000 fb^-1 of data in approximately 10 years. However, the conditions under which this data would be acquired are much harsher than those currently encountered at the LHC. For example, the number of proton-proton interactions per bunch crossing will rise from the level of 20--30 per 50 ns crossing observed in 2012 to 140--200 every 25 ns. In order to deepen our understanding of the newly discovered Higgs boson and to extend our searches for physics beyond that new particle, the ATLAS detector, trigger, and readout will have to undergo significant upgrades. In this whitepaper we describe R&D necessary for ATLAS to continue to run effectively at the highest luminosities foreseen from the LHC. Emphasis is placed on those R&D efforts in which US institutions are playing a leading role.Comment: Snowmass contributed paper, 24 pages, 12 figure

Self-Replication via Tile Self-Assembly (Extended Abstract)

In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues. These modifications consist of an extension to 3D, the ability of tiles to form "flexible" bonds that allow bound tiles to rotate relative to each other, and allowing tiles of multiple shapes within the same system. We call this new model the STAM*, and we present a series of constructions within it that are capable of self-replicating behavior. Namely, the input seed assemblies to our STAM* systems can encode either "genomes" specifying the instructions for building a target shape, or can be copies of the target shape with instructions built in. A universal tile set exists for any target shape (at scale factor 2), and from a genome assembly creates infinite copies of the genome as well as the target shape. An input target structure, on the other hand, can be "deconstructed" by the universal tile set to form a genome encoding it, which will then replicate and also initiate the growth of copies of assemblies of the target shape. Since the lengths of the genomes for these constructions are proportional to the number of points in the target shape, we also present a replicator which utilizes hierarchical self-assembly to greatly reduce the size of the genomes required. The main goals of this work are to examine minimal requirements of self-assembling systems capable of self-replicating behavior, with the aim of better understanding self-replication in nature as well as understanding the complexity of mimicking it

TAO Conceptual Design Report: A Precision Measurement of the Reactor Antineutrino Spectrum with Sub-percent Energy Resolution

The Taishan Antineutrino Observatory (TAO, also known as JUNO-TAO) is a satellite experiment of the Jiangmen Underground Neutrino Observatory (JUNO). A ton-level liquid scintillator detector will be placed at about 30 m from a core of the Taishan Nuclear Power Plant. The reactor antineutrino spectrum will be measured with sub-percent energy resolution, to provide a reference spectrum for future reactor neutrino experiments, and to provide a benchmark measurement to test nuclear databases. A spherical acrylic vessel containing 2.8 ton gadolinium-doped liquid scintillator will be viewed by 10 m^2 Silicon Photomultipliers (SiPMs) of >50% photon detection efficiency with almost full coverage. The photoelectron yield is about 4500 per MeV, an order higher than any existing large-scale liquid scintillator detectors. The detector operates at -50 degree C to lower the dark noise of SiPMs to an acceptable level. The detector will measure about 2000 reactor antineutrinos per day, and is designed to be well shielded from cosmogenic backgrounds and ambient radioactivities to have about 10% background-to-signal ratio. The experiment is expected to start operation in 2022

Research and Technology

Langley Research Center is engaged in the basic an applied research necessary for the advancement of aeronautics and space flight, generating advanced concepts for the accomplishment of related national goals, and provding research advice, technological support, and assistance to other NASA installations, other government agencies, and industry. Highlights of major accomplishments and applications are presented

Detailed investigation of a vaporising fuel spray. Part 1: Experimental investigation of time averaged spray

A laser tomographic light scattering technique provides rapid and accurate high resolution measurements of droplet sizes, concentrations, and vaporization. Measurements using a computer interfaced thermocouple are presented and it is found that the potential exists for separating gas and liquid temperature measurements and diagnosing local spray density by in situ analysis of the response characteristics of the thermocouple. The thermocouple technique provides a convenient means for measuring mean gas velocity in both hot and cold two phase flows. The experimental spray is axisymmetric and has carefully controlled initial and boundary conditions. The flow is designed to give relatively insignificant transfer of momentum and mass from spray to air flow. The effects of (1) size-dependent droplet dispersion by the turbulence, (2) the initial spatial segregation of droplet sizes during atomization, and (3) the interaction between droplets and coherent large eddies are diagnosed

Coupling of cytoplasm and adhesion dynamics determines cell polarization and locomotion

Observations of single epidermal cells on flat adhesive substrates have revealed two distinct morphological and functional states, namely a non-migrating symmetric unpolarized state and a migrating asymmetric polarized state. These states are characterized by different spatial distributions and dynamics of important biochemical cell components: F-actin and myosin-II form the contractile part of the cytoskeleton, and integrin receptors in the plasma membrane connect F-actin filaments to the substratum. In this way, focal adhesion complexes are assembled, which determine cytoskeletal force transduction and subsequent cell locomotion. So far, physical models have reduced this phenomenon either to gradients in regulatory control molecules or to different mechanics of the actin filament system in different regions of the cell. Here we offer an alternative and self-organizational model incorporating polymerization, pushing and sliding of filaments, as well as formation of adhesion sites and their force dependent kinetics. All these phenomena can be combined into a non-linearly coupled system of hyperbolic, parabolic and elliptic differential equations. Aim of this article is to show how relatively simple relations for the small-scale mechanics and kinetics of participating molecules may reproduce the emergent behavior of polarization and migration on the large-scale cell level.Comment: v2 (updates from proof): add TOC, clarify Fig. 4, fix several typo

Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly

Inspired by biology’s most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Analogous high-dimensional, highly interconnected computational architectures also arise within information-processing molecular systems inside living cells, such as signal transduction cascades and genetic regulatory networks. Might collective modes analogous to neural computation be found more broadly in other physical and chemical processes, even those that ostensibly play non-information-processing roles? Here we examine nucleation during self-assembly of multicomponent structures, showing that high-dimensional patterns of concentrations can be discriminated and classified in a manner similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends sensitively on the extent of colocalization of high-concentration tiles within the three structures. The system was trained in silico to classify a set of 18 grayscale 30 × 30 pixel images into three categories. Experimentally, fluorescence and atomic force microscopy measurements during and after a 150 hour anneal established that all trained images were correctly classified, whereas a test set of image variations probed the robustness of the results. Although slow compared to previous biochemical neural networks, our approach is compact, robust and scalable. Our findings suggest that ubiquitous physical phenomena, such as nucleation, may hold powerful information-processing capabilities when they occur within high-dimensional multicomponent systems

Mechanical Design of the HGCal Wedges with Thermal Gradient

After the discovery of the Higgs Boson, the purpose of the world's largest and most powerful particle accelerator, the Large Hadron Collider (LHC), seemed to have been achieved. Despite the fact that the Standard Model apparently complies with most experimental data up to this day, the majority of particle physicists feel that it is not a complete framework [1]. Therefore, there are still many unresolved problems in the physics of elementary particles. That is the reason why, in 2013, the European Strategy for Particle Physics announced its update. The High-Luminosity Large Hadron Collider (HL-LHC) project aims to increase luminosity by a factor of 10 beyond the LHC’s design. The higher the luminosity, the more data the experiments can gather to allow scientists to observe rare processes. Its development depends on several technological innovations, like the High-Granularity Calorimeter (HGCal), a major upgrade of the Compact Muon Solenoid (CMS) detector. [2] This project analyses the design and optimisation processes of the supports (wedges) which join the calorimeter (HGCal) to the related parts of the CMS detector. Specifically, the study focuses on the intermediate wedges. The main challenge is to create an optimal configuration for both the operational (vertical) and the assembly (horizontal) position. For this reason, a series of mechanical, magnetic and thermal considerations must be taken into account. This includes withstanding a mass of 200 tons and 50 °� of thermal difference. In order to achieve this goal, it is first necessary to analyse the functionality of the detector. This in-depth research allows a precise problem definition. Later, the preliminary design of the intermediate wedges is studied. By analysing the finite element results, the optimisation steps are established. At the end, the final version, the results of its analyses and some suggestions for the building process are presented. In the final result analyses, a hybrid configuration of fixed and hinged intermediate wedges was presented. In the operational position, stresses and vertical load values were lowered. In addition, a thermal analysis concluded that the heat transfer was sufficient for meeting the given requirements. In the assembly analysis, it was verified that the supports are not buckling or permanently deforming