A Stochastic Approach to Shortcut Bridging in Programmable Matter

In a self-organizing particle system, an abstraction of programmable matter, simple computational elements called particles with limited memory and communication self-organize to solve system-wide problems of movement, coordination, and configuration. In this paper, we consider a stochastic, distributed, local, asynchronous algorithm for "shortcut bridging", in which particles self-assemble bridges over gaps that simultaneously balance minimizing the length and cost of the bridge. Army ants of the genus Eciton have been observed exhibiting a similar behavior in their foraging trails, dynamically adjusting their bridges to satisfy an efficiency trade-off using local interactions. Using techniques from Markov chain analysis, we rigorously analyze our algorithm, show it achieves a near-optimal balance between the competing factors of path length and bridge cost, and prove that it exhibits a dependence on the angle of the gap being "shortcut" similar to that of the ant bridges. We also present simulation results that qualitatively compare our algorithm with the army ant bridging behavior. Our work gives a plausible explanation of how convergence to globally optimal configurations can be achieved via local interactions by simple organisms (e.g., ants) with some limited computational power and access to random bits. The proposed algorithm also demonstrates the robustness of the stochastic approach to algorithms for programmable matter, as it is a surprisingly simple extension of our previous stochastic algorithm for compression.Comment: Published in Proc. of DNA23: DNA Computing and Molecular Programming - 23rd International Conference, 2017. An updated journal version will appear in the DNA23 Special Issue of Natural Computin

Granular discharge and clogging for tilted hoppers

We measure the flux of spherical glass beads through a hole as a systematic function of both tilt angle and hole diameter, for two different size beads. The discharge increases with hole diameter in accord with the Beverloo relation for both horizontal and vertical holes, but in the latter case with a larger small-hole cutoff. For large holes the flux decreases linearly in cosine of the tilt angle, vanishing smoothly somewhat below the angle of repose. For small holes it vanishes abruptly at a smaller angle. The conditions for zero flux are discussed in the context of a {\it clogging phase diagram} of flow state vs tilt angle and ratio of hole to grain size

Symmetries of Large N Matrix Models for Closed Strings

We obtain the symmetry algebra of multi-matrix models in the planar large N limit. We use this algebra to associate these matrix models with quantum spin chains. In particular, certain multi-matrix models are exactly solved by using known results of solvable spin chain systems.Comment: 12 pages, 1 eps figure, RevTex, some minor typos in the publised version are correcte

DBM-DB: the diamondback moth genome database

The diamondback moth Genome Database (DBM-DB) is a central online repository for storing and integrating genomic data of diamondback moth (DBM), Plutella xylostella (L.). It provides comprehensive search tools and downloadable datasets for scientists to study comparative genomics, biological interpretation and gene annotation of this insect pest. DBM-DB contains assembled transcriptome datasets from multiple DBM strains and developmental stages, and the annotated genome of P. xylostella (version 2). We have also integrated publically available ESTs from NCBI and a putative gene set from a second DBM genome (KONAGbase) to enable users to compare different gene models. DBM-DB was developed with the capacity to incorporate future data resources, and will serve as a long-term and open-access database that can be conveniently used for research on the biology, distribution and evolution of DBM. This resource aims to help reduce the impact DBM has on agriculture using genomic and molecular tools.Weiqi Tang, Liying Yu, Weiyi He, Guang Yang, Fushi Ke, Simon W. Baxter, Shijun You, Carl J. Douglas and Minsheng Yo

Self-dual noncommutative \phi^4-theory in four dimensions is a non-perturbatively solvable and non-trivial quantum field theory

We study quartic matrix models with partition function Z[E,J]=\int dM \exp(trace(JM-EM^2-(\lambda/4)M^4)). The integral is over the space of Hermitean NxN-matrices, the external matrix E encodes the dynamics, \lambda>0 is a scalar coupling constant and the matrix J is used to generate correlation functions. For E not a multiple of the identity matrix, we prove a universal algebraic recursion formula which gives all higher correlation functions in terms of the 2-point function and the distinct eigenvalues of E. The 2-point function itself satisfies a closed non-linear equation which must be solved case by case for given E. These results imply that if the 2-point function of a quartic matrix model is renormalisable by mass and wavefunction renormalisation, then the entire model is renormalisable and has vanishing \beta-function. As main application we prove that Euclidean \phi^4-quantum field theory on four-dimensional Moyal space with harmonic propagation, taken at its self-duality point and in the infinite volume limit, is exactly solvable and non-trivial. This model is a quartic matrix model, where E has for N->\infty the same spectrum as the Laplace operator in 4 dimensions. Using the theory of singular integral equations of Carleman type we compute (for N->\infty and after renormalisation of E,\lambda) the free energy density (1/volume)\log(Z[E,J]/Z[E,0]) exactly in terms of the solution of a non-linear integral equation. Existence of a solution is proved via the Schauder fixed point theorem. The derivation of the non-linear integral equation relies on an assumption which we verified numerically for coupling constants 0<\lambda\leq (1/\pi).Comment: LaTeX, 64 pages, xypic figures. v4: We prove that recursion formulae and vanishing of \beta-function hold for general quartic matrix models. v3: We add the existence proof for a solution of the non-linear integral equation. A rescaling of matrix indices was necessary. v2: We provide Schwinger-Dyson equations for all correlation functions and prove an algebraic recursion formula for their solutio

Roughening Induced Deconstruction in (100) Facets of CsCl Type Crystals

The staggered 6-vertex model describes the competition between surface roughening and reconstruction in (100) facets of CsCl type crystals. Its phase diagram does not have the expected generic structure, due to the presence of a fully-packed loop-gas line. We prove that the reconstruction and roughening transitions cannot cross nor merge with this loop-gas line if these degrees of freedom interact weakly. However, our numerical finite size scaling analysis shows that the two critical lines merge along the loop-gas line, with strong coupling scaling properties. The central charge is much larger than 1.5 and roughening takes place at a surface roughness much larger than the conventional universal value. It seems that additional fluctuations become critical simultaneously.Comment: 31 pages, 9 figure

Stringing Spins and Spinning Strings

We apply recently developed integrable spin chain and dilatation operator techniques in order to compute the planar one-loop anomalous dimensions for certain operators containing a large number of scalar fields in N =4 Super Yang-Mills. The first set of operators, belonging to the SO(6) representations [J,L-2J,J], interpolate smoothly between the BMN case of two impurities (J=2) and the extreme case where the number of impurities equals half the total number of fields (J=L/2). The result for this particular [J,0,J] operator is smaller than the anomalous dimension derived by Frolov and Tseytlin [hep-th/0304255] for a semiclassical string configuration which is the dual of a gauge invariant operator in the same representation. We then identify a second set of operators which also belong to [J,L-2J,J] representations, but which do not have a BMN limit. In this case the anomalous dimension of the [J,0,J] operator does match the Frolov-Tseytlin prediction. We also show that the fluctuation spectra for this [J,0,J] operator is consistent with the string prediction.Comment: 27 pages, 4 figures, LaTex; v2 reference added, typos fixe

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes

The ribosome is an evolutionarily conserved organelle essential for cellular function. Ribosome construction requires assembly of approximately 80 different ribosomal proteins (RPs) and four different species of rRNA. As RPs co-assemble into one multi-subunit complex, mutation of the genes that encode RPs might be expected to give rise to phenocopies, in which the same phenotype is associated with loss-of-function of each individual gene. However, a more complex picture is emerging in which, in addition to a group of shared phenotypes, diverse RP gene-specific phenotypes are observed. Here we report the first two mouse mutations (Rps7(Mtu) and Rps7(Zma)) of ribosomal protein S7 (Rps7), a gene that has been implicated in Diamond-Blackfan anemia. Rps7 disruption results in decreased body size, abnormal skeletal morphology, mid-ventral white spotting, and eye malformations. These phenotypes are reported in other murine RP mutants and, as demonstrated for some other RP mutations, are ameliorated by Trp53 deficiency. Interestingly, Rps7 mutants have additional overt malformations of the developing central nervous system and deficits in working memory, phenotypes that are not reported in murine or human RP gene mutants. Conversely, Rps7 mouse mutants show no anemia or hyperpigmentation, phenotypes associated with mutation of human RPS7 and other murine RPs, respectively. We provide two novel RP mouse models and expand the repertoire of potential phenotypes that should be examined in RP mutants to further explore the concept of RP gene-specific phenotypes.This research was supported in part by the Intramural Research Program of NHGRI, NIH, and the Wellcome Trust and by NHMRC Australia grant 366746. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript