31,588 research outputs found
Extending the Modern Synthesis: The evolution of ecosystems
The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis
Extending DIRAC File Management with Erasure-Coding for efficient storage
The state of the art in Grid style data management is to achieve increased
resilience of data via multiple complete replicas of data files across multiple
storage endpoints. While this is effective, it is not the most space-efficient
approach to resilience, especially when the reliability of individual storage
endpoints is sufficiently high that only a few will be inactive at any point in
time. We report on work performed as part of GridPP\cite{GridPP}, extending the
Dirac File Catalogue and file management interface to allow the placement of
erasure-coded files: each file distributed as N identically-sized chunks of
data striped across a vector of storage endpoints, encoded such that any M
chunks can be lost and the original file can be reconstructed. The tools
developed are transparent to the user, and, as well as allowing up and
downloading of data to Grid storage, also provide the possibility of
parallelising access across all of the distributed chunks at once, improving
data transfer and IO performance. We expect this approach to be of most
interest to smaller VOs, who have tighter bounds on the storage available to
them, but larger (WLCG) VOs may be interested as their total data increases
during Run 2. We provide an analysis of the costs and benefits of the approach,
along with future development and implementation plans in this area. In
general, overheads for multiple file transfers provide the largest issue for
competitiveness of this approach at present.Comment: 21st International Conference on Computing for High Energy and
Nuclear Physics (CHEP2015
Without magic bullets: the biological basis for public health interventions against protein folding disorders
Protein folding disorders of aging like Alzheimer's and Parkinson's diseases currently present intractable medical challenges. 'Small molecule' interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary 'physics' or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty's (2010a) elegant exploration of the genetic code. The formalism produces large-scale, quasi-equilibrium 'resilience' states representing normal and pathological protein folding regulation under a cellular-level cognitive paradigm similar to that proposed by Atlan and Cohen (1998) for the immune system. Generalization to long times produces diffusion models of protein folding disorders in which epigenetic or life history factors determine the rate of onset of regulatory failure, in essence, a premature aging driven by familiar synergisms between disjunctions of resource allocation and need in the context of socially or physiologically toxic exposures and chronic powerlessness at individual and group scales. Application of an HPA axis model is made to recent observed differences in Alzheimer's onset rates in White and African American subpopulations as a function of an index of distress-proneness
Extending Tlusty's method to the glycome: Tuning the repertoire of glycan determinants
We apply Tlusty's information-theoretic analysis of the genetic code to the glycome, using a cognitive paradigm in which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The resulting dynamic model suggests the possibility of observing spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity. These effects may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition
Non-Malleable Codes for Small-Depth Circuits
We construct efficient, unconditional non-malleable codes that are secure
against tampering functions computed by small-depth circuits. For
constant-depth circuits of polynomial size (i.e. tampering
functions), our codes have codeword length for a -bit
message. This is an exponential improvement of the previous best construction
due to Chattopadhyay and Li (STOC 2017), which had codeword length
. Our construction remains efficient for circuit depths as
large as (indeed, our codeword length remains
, and extending our result beyond this would require
separating from .
We obtain our codes via a new efficient non-malleable reduction from
small-depth tampering to split-state tampering. A novel aspect of our work is
the incorporation of techniques from unconditional derandomization into the
framework of non-malleable reductions. In particular, a key ingredient in our
analysis is a recent pseudorandom switching lemma of Trevisan and Xue (CCC
2013), a derandomization of the influential switching lemma from circuit
complexity; the randomness-efficiency of this switching lemma translates into
the rate-efficiency of our codes via our non-malleable reduction.Comment: 26 pages, 4 figure
Optimized Surface Code Communication in Superconducting Quantum Computers
Quantum computing (QC) is at the cusp of a revolution. Machines with 100
quantum bits (qubits) are anticipated to be operational by 2020
[googlemachine,gambetta2015building], and several-hundred-qubit machines are
around the corner. Machines of this scale have the capacity to demonstrate
quantum supremacy, the tipping point where QC is faster than the fastest
classical alternative for a particular problem. Because error correction
techniques will be central to QC and will be the most expensive component of
quantum computation, choosing the lowest-overhead error correction scheme is
critical to overall QC success. This paper evaluates two established quantum
error correction codes---planar and double-defect surface codes---using a set
of compilation, scheduling and network simulation tools. In considering
scalable methods for optimizing both codes, we do so in the context of a full
microarchitectural and compiler analysis. Contrary to previous predictions, we
find that the simpler planar codes are sometimes more favorable for
implementation on superconducting quantum computers, especially under
conditions of high communication congestion.Comment: 14 pages, 9 figures, The 50th Annual IEEE/ACM International Symposium
on Microarchitectur
`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation
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