43,689 research outputs found
On Conflict Free DNA Codes
DNA storage has emerged as an important area of research. The reliability of
DNA storage system depends on designing the DNA strings (called DNA codes) that
are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy
a special constraint. Each codeword of the DNA code has a specific property
that any two consecutive sub-strings of the DNA codeword will not be the same
(a generalization of homo-polymers constraint). This is in addition to the
usual constraints such as Hamming, reverse, reverse-complement and
-content. We believe that the new constraint will help further in reducing
the errors during reading and writing data into the synthetic DNA strings. We
also present a construction (based on a variant of stochastic local search
algorithm) to calculate the size of the DNA codes with all the above
constraints, which improves the lower bounds from the existing literature, for
some specific cases. Moreover, a recursive isometric map between binary vectors
and DNA strings is proposed. Using the map and the well known binary codes we
obtain few classes of DNA codes with all the constraints including the property
that the constructed DNA codewords are free from the hairpin-like secondary
structures.Comment: 12 pages, Draft (Table VI and Table VII are updated
What is Life?
In searching for life in extraterrestrial space, it is essential to act based on an unequivocal definition of life. In the twentieth century, life was defined as cells that self-replicate, metabolize, and are open for mutations, without which genetic information would remain unchangeable, and evolution would be impossible. Current definitions of life derive from statistical mechanics, physics, and chemistry of the twentieth century in which life is
considered to function machine like, ignoring a central role of communication. Recent observations show that context-dependent meaningful communication and network formation (and control) are central to all life forms. Evolutionary relevant new nucleotide sequences now appear to have originated from social agents such as viruses, their parasitic relatives, and related RNA networks, not from errors. By applying the known
features of natural languages and communication, a new twenty-first century definition of life can be reached in which communicative interactions are central to all processes of life.
A new definition of life must integrate the current empirical knowledge about interactions between cells, viruses, and RNA networks to provide a better explanatory power than the twentieth century narrative
Law of Genome Evolution Direction : Coding Information Quantity Grows
The problem of the directionality of genome evolution is studied. Based on
the analysis of C-value paradox and the evolution of genome size we propose
that the function-coding information quantity of a genome always grows in the
course of evolution through sequence duplication, expansion of code, and gene
transfer from outside. The function-coding information quantity of a genome
consists of two parts, p-coding information quantity which encodes functional
protein and n-coding information quantity which encodes other functional
elements except amino acid sequence. The evidences on the evolutionary law
about the function-coding information quantity are listed. The needs of
function is the motive force for the expansion of coding information quantity
and the information quantity expansion is the way to make functional innovation
and extension for a species. So, the increase of coding information quantity of
a genome is a measure of the acquired new function and it determines the
directionality of genome evolution.Comment: 16 page
Molecular access to multi-dimensionally encoded information
Polymer scientist have only recently realized that information storage on the molecular level is not only restricted to DNA-based systems. Similar encoding and decoding of data have been demonstrated on synthetic polymers that could overcome some of the drawbacks associated with DNA, such as the ability to make use of a larger monomer alphabet. This feature article describes some of the recent data storage strategies that were investigated, ranging from writing information on linear sequence-defined macromolecules up to layer-by-layer casted surfaces and QR codes. In addition, some strategies to increase storage density are elaborated and some trends regarding future perspectives on molecular data storage from the literature are critically evaluated. This work ends with highlighting the demand for new strategies setting up reliable solutions for future data management technologies
Frustration in Biomolecules
Biomolecules are the prime information processing elements of living matter.
Most of these inanimate systems are polymers that compute their structures and
dynamics using as input seemingly random character strings of their sequence,
following which they coalesce and perform integrated cellular functions. In
large computational systems with a finite interaction-codes, the appearance of
conflicting goals is inevitable. Simple conflicting forces can lead to quite
complex structures and behaviors, leading to the concept of "frustration" in
condensed matter. We present here some basic ideas about frustration in
biomolecules and how the frustration concept leads to a better appreciation of
many aspects of the architecture of biomolecules, and how structure connects to
function. These ideas are simultaneously both seductively simple and perilously
subtle to grasp completely. The energy landscape theory of protein folding
provides a framework for quantifying frustration in large systems and has been
implemented at many levels of description. We first review the notion of
frustration from the areas of abstract logic and its uses in simple condensed
matter systems. We discuss then how the frustration concept applies
specifically to heteropolymers, testing folding landscape theory in computer
simulations of protein models and in experimentally accessible systems.
Studying the aspects of frustration averaged over many proteins provides ways
to infer energy functions useful for reliable structure prediction. We discuss
how frustration affects folding, how a large part of the biological functions
of proteins are related to subtle local frustration effects and how frustration
influences the appearance of metastable states, the nature of binding
processes, catalysis and allosteric transitions. We hope to illustrate how
Frustration is a fundamental concept in relating function to structural
biology.Comment: 97 pages, 30 figure
Arrival of the Fittest
Prometheus, the fifth film of the Alien franchise, maintains narrative connections to the original four films but the inclusion of new aliens—the Engineers—radically shifts the feminist politic of the series. There is a move away from centralising the monster and the repressed feminine, through images of horror and bodily abjection, toward a politic of carnival, seen in representations of multiple grotesque bodies and subversion of the affect of primal scenes. Carnival is a space where the authority and stability of current social powers and orders are challenged and subverted. This article contends that in Prometheus such a process occurs in the deliberate mixing of scientific knowledge and religious cosmologies, the ambivalent relationship of horror and SF genres to science and scientific knowledge, the gendered complexities of the specific bodies of astronauts and of scientists, and disruptions of the notion of gaze and viewer positioning in the opening scenes
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