4,369 research outputs found
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement
We propose a novel theoretical biomolecular design to implement any Boolean
circuit using the mechanism of DNA strand displacement. The design is scalable:
all species of DNA strands can in principle be mixed and prepared in a single
test tube, rather than requiring separate purification of each species, which
is a barrier to large-scale synthesis. The design is time-responsive: the
concentration of output species changes in response to the concentration of
input species, so that time-varying inputs may be continuously processed. The
design is digital: Boolean values of wires in the circuit are represented as
high or low concentrations of certain species, and we show how to construct a
single-input, single-output signal restoration gate that amplifies the
difference between high and low, which can be distributed to each wire in the
circuit to overcome signal degradation. This means we can achieve a digital
abstraction of the analog values of concentrations. Finally, the design is
energy-efficient: if input species are specified ideally (meaning absolutely 0
concentration of unwanted species), then output species converge to their ideal
concentrations at steady-state, and the system at steady-state is in (dynamic)
equilibrium, meaning that no energy is consumed by irreversible reactions until
the input again changes.
Drawbacks of our design include the following. If input is provided
non-ideally (small positive concentration of unwanted species), then energy
must be continually expended to maintain correct output concentrations even at
steady-state. In addition, our fuel species - those species that are
permanently consumed in irreversible reactions - are not "generic"; each gate
in the circuit is powered by its own specific type of fuel species. Hence
different circuits must be powered by different types of fuel. Finally, we
require input to be given according to the dual-rail convention, so that an
input of 0 is specified not only by the absence of a certain species, but by
the presence of another. That is, we do not construct a "true NOT gate" that
sets its output to high concentration if and only if its input's concentration
is low. It remains an open problem to design scalable, time-responsive,
digital, energy-efficient molecular circuits that additionally solve one of
these problems, or to prove that some subset of their resolutions are mutually
incompatible.Comment: version 2: the paper itself is unchanged from version 1, but the
arXiv software stripped some asterisk characters out of the abstract whose
purpose was to highlight words. These characters have been replaced with
underscores in version 2. The arXiv software also removed the second
paragraph of the abstract, which has been (attempted to be) re-inserted.
Also, although the secondary subject is "Soft Condensed Matter", this
classification was chosen by the arXiv moderators after submission, not
chosen by the authors. The authors consider this submission to be a
theoretical computer science paper
Gunrock: A High-Performance Graph Processing Library on the GPU
For large-scale graph analytics on the GPU, the irregularity of data access
and control flow, and the complexity of programming GPUs have been two
significant challenges for developing a programmable high-performance graph
library. "Gunrock", our graph-processing system designed specifically for the
GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on
operations on a vertex or edge frontier. Gunrock achieves a balance between
performance and expressiveness by coupling high performance GPU computing
primitives and optimization strategies with a high-level programming model that
allows programmers to quickly develop new graph primitives with small code size
and minimal GPU programming knowledge. We evaluate Gunrock on five key graph
primitives and show that Gunrock has on average at least an order of magnitude
speedup over Boost and PowerGraph, comparable performance to the fastest GPU
hardwired primitives, and better performance than any other GPU high-level
graph library.Comment: 14 pages, accepted by PPoPP'16 (removed the text repetition in the
previous version v5
Satellite Navigation for the Age of Autonomy
Global Navigation Satellite Systems (GNSS) brought navigation to the masses.
Coupled with smartphones, the blue dot in the palm of our hands has forever
changed the way we interact with the world. Looking forward, cyber-physical
systems such as self-driving cars and aerial mobility are pushing the limits of
what localization technologies including GNSS can provide. This autonomous
revolution requires a solution that supports safety-critical operation,
centimeter positioning, and cyber-security for millions of users. To meet these
demands, we propose a navigation service from Low Earth Orbiting (LEO)
satellites which deliver precision in-part through faster motion, higher power
signals for added robustness to interference, constellation autonomous
integrity monitoring for integrity, and encryption / authentication for
resistance to spoofing attacks. This paradigm is enabled by the 'New Space'
movement, where highly capable satellites and components are now built on
assembly lines and launch costs have decreased by more than tenfold. Such a
ubiquitous positioning service enables a consistent and secure standard where
trustworthy information can be validated and shared, extending the electronic
horizon from sensor line of sight to an entire city. This enables the
situational awareness needed for true safe operation to support autonomy at
scale.Comment: 11 pages, 8 figures, 2020 IEEE/ION Position, Location and Navigation
Symposium (PLANS
Fractional diffusion modeling of ion channel gating
An anomalous diffusion model for ion channel gating is put forward. This
scheme is able to describe non-exponential, power-law like distributions of
residence time intervals in several types of ion channels. Our method presents
a generalization of the discrete diffusion model by Millhauser, Salpeter and
Oswald [Proc. Natl. Acad. Sci. USA 85, 1503 (1988)] to the case of a
continuous, anomalous slow conformational diffusion. The corresponding
generalization is derived from a continuous time random walk composed of
nearest neighbor jumps which in the scaling limit results in a fractional
diffusion equation. The studied model contains three parameters only: the mean
residence time, a characteristic time of conformational diffusion, and the
index of subdiffusion. A tractable analytical expression for the characteristic
function of the residence time distribution is obtained. In the limiting case
of normal diffusion, our prior findings [Proc. Natl. Acad. Sci. USA 99, 3552
(2002)] are reproduced. Depending on the chosen parameters, the fractional
diffusion model exhibits a very rich behavior of the residence time
distribution with different characteristic time-regimes. Moreover, the
corresponding autocorrelation function of conductance fluctuations displays
nontrivial features. Our theoretical model is in good agreement with
experimental data for large conductance potassium ion channels
Fully-dynamic Approximation of Betweenness Centrality
Betweenness is a well-known centrality measure that ranks the nodes of a
network according to their participation in shortest paths. Since an exact
computation is prohibitive in large networks, several approximation algorithms
have been proposed. Besides that, recent years have seen the publication of
dynamic algorithms for efficient recomputation of betweenness in evolving
networks. In previous work we proposed the first semi-dynamic algorithms that
recompute an approximation of betweenness in connected graphs after batches of
edge insertions.
In this paper we propose the first fully-dynamic approximation algorithms
(for weighted and unweighted undirected graphs that need not to be connected)
with a provable guarantee on the maximum approximation error. The transfer to
fully-dynamic and disconnected graphs implies additional algorithmic problems
that could be of independent interest. In particular, we propose a new upper
bound on the vertex diameter for weighted undirected graphs. For both weighted
and unweighted graphs, we also propose the first fully-dynamic algorithms that
keep track of such upper bound. In addition, we extend our former algorithm for
semi-dynamic BFS to batches of both edge insertions and deletions.
Using approximation, our algorithms are the first to make in-memory
computation of betweenness in fully-dynamic networks with millions of edges
feasible. Our experiments show that they can achieve substantial speedups
compared to recomputation, up to several orders of magnitude
Data Portraits and Intermediary Topics: Encouraging Exploration of Politically Diverse Profiles
In micro-blogging platforms, people connect and interact with others.
However, due to cognitive biases, they tend to interact with like-minded people
and read agreeable information only. Many efforts to make people connect with
those who think differently have not worked well. In this paper, we
hypothesize, first, that previous approaches have not worked because they have
been direct -- they have tried to explicitly connect people with those having
opposing views on sensitive issues. Second, that neither recommendation or
presentation of information by themselves are enough to encourage behavioral
change. We propose a platform that mixes a recommender algorithm and a
visualization-based user interface to explore recommendations. It recommends
politically diverse profiles in terms of distance of latent topics, and
displays those recommendations in a visual representation of each user's
personal content. We performed an "in the wild" evaluation of this platform,
and found that people explored more recommendations when using a biased
algorithm instead of ours. In line with our hypothesis, we also found that the
mixture of our recommender algorithm and our user interface, allowed
politically interested users to exhibit an unbiased exploration of the
recommended profiles. Finally, our results contribute insights in two aspects:
first, which individual differences are important when designing platforms
aimed at behavioral change; and second, which algorithms and user interfaces
should be mixed to help users avoid cognitive mechanisms that lead to biased
behavior.Comment: 12 pages, 7 figures. To be presented at ACM Intelligent User
Interfaces 201
A rare case of long-term graft complication in a patient of middle aortic syndrome
Middle aortic syndrome (MAS) is rare entity described as a progressive narrowing of the aorta between the aortic arch and terminal bifurcation of the aorta. Surgical treatment is with the use of grafts for bypassing the narrow aortic segment. Rarely, graft complications may occur over long periods of time due to the axial growth of the patient and loss of tensile strength of the graft material. This is a case of MAS, presenting 34 years after initial surgery due to aneurysmal dilation of the graft, treated with redo surgery and complete recovery of the patient
An exact analytical solution for generalized growth models driven by a Markovian dichotomic noise
Logistic growth models are recurrent in biology, epidemiology, market models,
and neural and social networks. They find important applications in many other
fields including laser modelling. In numerous realistic cases the growth rate
undergoes stochastic fluctuations and we consider a growth model with a
stochastic growth rate modelled via an asymmetric Markovian dichotomic noise.
We find an exact analytical solution for the probability distribution providing
a powerful tool with applications ranging from biology to astrophysics and
laser physics
Ballistic Applications of Glass and Kevlar Fibre Vinylester Composites
Void-free E-glass and Kevlar-49 fibre reinforced vinylester laminates prepared under compression moulding were found to have Charpy impact strength of 576 KJlm2 and 304 KJlm2, respectively. Ballistic immunisation tests carried out on the glass reinforced vinylester laminates with thickness ranging from 12 mm to 54 mm against 7.62 mm rifle bullets produced an exponential relationship between the per cent attenuation in bullet velocity and the areal density of the laminates; whereas the relationship was linear for 9 mm carbine fire with laminate thicknessvarying from 5.5 mm to 12 mm
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