Directed Percolation and the Abstract Tile Assembly Model

Self-assembly is a process by which simple components build complex structures through local interactions. Directed percolation is a statistical physical model for describing competitive spreading processes on lattices. The author describes an algorithm which can transform a tile assembly system in the abstract Tile Assembly Model into a directed percolation problem, and then shows simulations of the aTAM which support this algorithm. The author also investigates two new constructs designed for Erik Winfree\u27s abstract Tile Assembly Model called the NULL tile and temperature 1.5. These constructs aid the translation between self-assembly and directed percolation and may assist self-assembly researchers in designing tilesets in the aTAM with non-deterministic local properties, but guaranteed global properties. Temperature 1.5 results indicate the brittleness of the standard temperature 2 tile assembly system, and the NULL tile is shown to assist simulations of large assembly processes while also reinforcing the need for variable temperature models to more closely simulate laboratory self-assembly

Shuttle Ground Operations Efficiencies/Technologies (SGOE/T) study. Volume 2: Ground Operations evaluation

The Ground Operations Evaluation describes the breath and depth of the various study elements selected as a result of an operational analysis conducted during the early part of the study. Analysis techniques used for the evaluation are described in detail. Elements selected for further evaluation are identified; the results of the analysis documented; and a follow-on course of action recommended. The background and rationale for developing recommendations for the current Shuttle or for future programs is presented

Nonterrestrial utilization of materials: Automated space manufacturing facility

Four areas related to the nonterrestrial use of materials are included: (1) material resources needed for feedstock in an orbital manufacturing facility, (2) required initial components of a nonterrestrial manufacturing facility, (3) growth and productive capability of such a facility, and (4) automation and robotics requirements of the facility

A permeabilized cell model for studying cell division: a comparison of anaphase chromosome movement and cleavage furrow constriction in lysed PtK1 cells.

After lysis in a Brij 58-polyethylene glycol medium, PtK1 cells are permeable to small molecules, such as erythrosin B, and to proteins, such as rhodamine-labeled FAB, myosin subfragment-1, and tubulin. Holes are present in the plasma membrane, and the mitochondria are swollen and distorted, but other membrane-bounded organelles of the lysed cell model are not noticeably altered. After lysis, the mitotic apparatus is functional; chromosomes move poleward and the spindle elongates. Cells lysed while in cytokinesis will continue to divide for several minutes. Addition of crude tubulin extracts, MAP-free tubulin, or taxol to the lysis medium retards anaphase chromosome movements but does not affect cleavage. On the other hand, N-ethylmaleimide-modified myosin subfragment-1, phalloidin, and cytochalasin B inhibit cleavage but have no effect on anaphase chromosome movements under identical lysis conditions. These results suggest that actomyosin plays no functional role in anaphase chromosome movement in mammalian tissue culture cells and that microtubule depolymerization is a rate-limiting step for chromosome-to-pole movements

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

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

Computations for Symbolic Substitutions

We provide a survey of results from symbolic dynamics and algebraic topology relating to Grout, a new user-friendly program developed to calculate combinatorial properties and topological invariants of a large class of symbolic substitutions. We study their subshifts (and related spaces) with an emphasis on examples of computations. We implement a check to verify that no counterexample exists to the so-called strong coincidence conjecture for a large number of substitutions on three and four letters

Designing the self-assembly of arbitrary shapes using minimal complexity building blocks

The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a novel pipeline, we explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyse their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks and the angular and spatial tolerances on their interactions on the kinetics and yield of the target assembly. We show that the resource-saving solution with minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realisation of multicomponent shapes using DNA nanostructures as building blocks.Comment: 12 page

Random sampling of lattice configurations using local Markov chains

Algorithms based on Markov chains are ubiquitous across scientific disciplines, as they provide a method for extracting statistical information about large, complicated systems. Although these algorithms may be applied to arbitrary graphs, many physical applications are more naturally studied under the restriction to regular lattices. We study several local Markov chains on lattices, exploring how small changes to some parameters can greatly influence efficiency of the algorithms. We begin by examining a natural Markov Chain that arises in the context of "monotonic surfaces", where some point on a surface is sightly raised or lowered each step, but with a greater rate of raising than lowering. We show that this chain is rapidly mixing (converges quickly to the equilibrium) using a coupling argument; the novelty of our proof is that it requires defining an exponentially increasing distance function on pairs of surfaces, allowing us to derive near optimal results in many settings. Next, we present new methods for lower bounding the time local chains may take to converge to equilibrium. For many models that we study, there seems to be a phase transition as a parameter is changed, so that the chain is rapidly mixing above a critical point and slow mixing below it. Unfortunately, it is not always possible to make this intuition rigorous. We present the first proofs of slow mixing for three sampling problems motivated by statistical physics and nanotechnology: independent sets on the triangular lattice (the hard-core lattice gas model), weighted even orientations of the two-dimensional Cartesian lattice (the 8-vertex model), and non-saturated Ising (tile-based self-assembly). Previous proofs of slow mixing for other models have been based on contour arguments that allow us prove that a bottleneck in the state space constricts the mixing. The standard contour arguments do not seem to apply to these problems, so we modify this approach by introducing the notion of "fat contours" that can have nontrivial area. We use these to prove that the local chains defined for these models are slow mixing. Finally, we study another important issue that arises in the context of phase transitions in physical systems, namely how the boundary of a lattice can affect the efficiency of the Markov chain. We examine a local chain on the perfect and near-perfect matchings of the square-octagon lattice, and show for one boundary condition the chain will mix in polynomial time, while for another it will mix exponentially slowly. Strikingly, the two boundary conditions only differ at four vertices. These are the first rigorous proofs of such a phenomenon on lattice graphs.Ph.D.Committee Chair: Randall, Dana; Committee Member: Heitsch, Christine; Committee Member: Mihail, Milena; Committee Member: Trotter, Tom; Committee Member: Vigoda, Eri