27 research outputs found
Self-assembly of the discrete Sierpinski carpet and related fractals
It is well known that the discrete Sierpinski triangle can be defined as the
nonzero residues modulo 2 of Pascal's triangle, and that from this definition
one can easily construct a tileset with which the discrete Sierpinski triangle
self-assembles in Winfree's tile assembly model. In this paper we introduce an
infinite class of discrete self-similar fractals that are defined by the
residues modulo a prime p of the entries in a two-dimensional matrix obtained
from a simple recursive equation. We prove that every fractal in this class
self-assembles using a uniformly constructed tileset. As a special case we show
that the discrete Sierpinski carpet self-assembles using a set of 30 tiles
Approximate Self-Assembly of the Sierpinski Triangle
The Tile Assembly Model is a Turing universal model that Winfree introduced
in order to study the nanoscale self-assembly of complex (typically aperiodic)
DNA crystals. Winfree exhibited a self-assembly that tiles the first quadrant
of the Cartesian plane with specially labeled tiles appearing at exactly the
positions of points in the Sierpinski triangle. More recently, Lathrop, Lutz,
and Summers proved that the Sierpinski triangle cannot self-assemble in the
"strict" sense in which tiles are not allowed to appear at positions outside
the target structure. Here we investigate the strict self-assembly of sets that
approximate the Sierpinski triangle. We show that every set that does strictly
self-assemble disagrees with the Sierpinski triangle on a set with fractal
dimension at least that of the Sierpinski triangle (roughly 1.585), and that no
subset of the Sierpinski triangle with fractal dimension greater than 1
strictly self-assembles. We show that our bounds are tight, even when
restricted to supersets of the Sierpinski triangle, by presenting a strict
self-assembly that adds communication fibers to the fractal structure without
disturbing it. To verify this strict self-assembly we develop a generalization
of the local determinism method of Soloveichik and Winfree
Scaled tree fractals do not strictly self-assemble
In this paper, we show that any scaled-up version of any discrete
self-similar {\it tree} fractal does not strictly self-assemble, at any
temperature, in Winfree's abstract Tile Assembly Model.Comment: 13 pages, 3 figures, Appeared in the Proceedings of UCNC-2014, pp
27-39; Unconventional Computation and Natural Computation - 13th
International Conference, UCNC 2014, London, ON, Canada, July 14-18, 2014,
Springer Lecture Notes in Computer Science ISBN 978-3-319-08122-
Doubles and Negatives are Positive (in Self-Assembly)
In the abstract Tile Assembly Model (aTAM), the phenomenon of cooperation
occurs when the attachment of a new tile to a growing assembly requires it to
bind to more than one tile already in the assembly. Often referred to as
``temperature-2'' systems, those which employ cooperation are known to be quite
powerful (i.e. they are computationally universal and can build an enormous
variety of shapes and structures). Conversely, aTAM systems which do not
enforce cooperative behavior, a.k.a. ``temperature-1'' systems, are conjectured
to be relatively very weak, likely to be unable to perform complex computations
or algorithmically direct the process of self-assembly. Nonetheless, a variety
of models based on slight modifications to the aTAM have been developed in
which temperature-1 systems are in fact capable of Turing universal computation
through a restricted notion of cooperation. Despite that power, though, several
of those models have previously been proven to be unable to perform or simulate
the stronger form of cooperation exhibited by temperature-2 aTAM systems.
In this paper, we first prove that another model in which temperature-1
systems are computationally universal, namely the restricted glue TAM (rgTAM)
in which tiles are allowed to have edges which exhibit repulsive forces, is
also unable to simulate the strongly cooperative behavior of the temperature-2
aTAM. We then show that by combining the properties of two such models, the
Dupled Tile Assembly Model (DTAM) and the rgTAM into the DrgTAM, we derive a
model which is actually more powerful at temperature-1 than the aTAM at
temperature-2. Specifically, the DrgTAM, at temperature-1, can simulate any
aTAM system of any temperature, and it also contains systems which cannot be
simulated by any system in the aTAM
The Power of Duples (in Self-Assembly): It's Not So Hip To Be Square
In this paper we define the Dupled abstract Tile Assembly Model (DaTAM),
which is a slight extension to the abstract Tile Assembly Model (aTAM) that
allows for not only the standard square tiles, but also "duple" tiles which are
rectangles pre-formed by the joining of two square tiles. We show that the
addition of duples allows for powerful behaviors of self-assembling systems at
temperature 1, meaning systems which exclude the requirement of cooperative
binding by tiles (i.e., the requirement that a tile must be able to bind to at
least 2 tiles in an existing assembly if it is to attach). Cooperative binding
is conjectured to be required in the standard aTAM for Turing universal
computation and the efficient self-assembly of shapes, but we show that in the
DaTAM these behaviors can in fact be exhibited at temperature 1. We then show
that the DaTAM doesn't provide asymptotic improvements over the aTAM in its
ability to efficiently build thin rectangles. Finally, we present a series of
results which prove that the temperature-2 aTAM and temperature-1 DaTAM have
mutually exclusive powers. That is, each is able to self-assemble shapes that
the other can't, and each has systems which cannot be simulated by the other.
Beyond being of purely theoretical interest, these results have practical
motivation as duples have already proven to be useful in laboratory
implementations of DNA-based tiles
Design and construction of the MicroBooNE detector
This paper describes the design and construction of the MicroBooNE liquid
argon time projection chamber and associated systems. MicroBooNE is the first
phase of the Short Baseline Neutrino program, located at Fermilab, and will
utilize the capabilities of liquid argon detectors to examine a rich assortment
of physics topics. In this document details of design specifications, assembly
procedures, and acceptance tests are reported
Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits : A Multi-Ethnic Meta-Analysis of 45,891 Individuals
J. Kaprio, S. Ripatti ja M.-L. Lokki työryhmien jäseniä.Peer reviewe
Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.
Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways
Whole-genome sequencing reveals host factors underlying critical COVID-19
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease