122 research outputs found
Simulation and analysis of in vitro DNA evolution
We study theoretically the in vitro evolution of a DNA sequence by binding to
a transcription factor. Using a simple model of protein-DNA binding and
available binding constants for the Mnt protein, we perform large-scale,
realistic simulations of evolution starting from a single DNA sequence. We
identify different parameter regimes characterized by distinct evolutionary
behaviors. For each regime we find analytical estimates which agree well with
simulation results. For small population sizes, the DNA evolutional path is a
random walk on a smooth landscape. While for large population sizes, the
evolution dynamics can be well described by a mean-field theory. We also study
how the details of the DNA-protein interaction affect the evolution.Comment: 11 pages, 11 figures. Submitted to PNA
Codes and Supersymmetry in One Dimension
Adinkras are diagrams that describe many useful supermultiplets in D=1
dimensions. We show that the topology of the Adinkra is uniquely determined by
a doubly even code. Conversely, every doubly even code produces a possible
topology of an Adinkra. A computation of doubly even codes results in an
enumeration of these Adinkra topologies up to N=28, and for minimal
supermultiplets, up to N=32.Comment: 48 pages, a new version that combines arXiv:0811.3410 and parts of
arXiv:0806.0050, for submission for publicatio
Effective Symmetries of the Minimal Supermultiplet of N = 8 Extended Worldline Supersymmetry
A minimal representation of the N = 8 extended worldline supersymmetry, known
as the `ultra-multiplet', is closely related to a family of supermultiplets
with the same, E(8) chromotopology. We catalogue their effective symmetries and
find a Spin(4) x Z(2) subgroup common to them all, which explains the
particular basis used in the original construction. We specify a constrained
superfield representation of the supermultiplets in the ultra-multiplet family,
and show that such a superfield representation in fact exists for all adinkraic
supermultiplets. We also exhibit the correspondences between these
supermultiplets, their Adinkras and the E(8) root lattice bases. Finally, we
construct quadratic Lagrangians that provide the standard kinetic terms and
afford a mixing of an even number of such supermultiplets controlled by a
coupling to an external 2-form of fluxes.Comment: 13 Figure
A Superfield for Every Dash-Chromotopology
The recent classification scheme of so-called adinkraic off-shell
supermultiplets of N-extended worldline supersymmetry without central charges
finds a combinatorial explosion. Completing our earlier efforts, we now
complete the constructive proof that all of these trillions or more of
supermultiplets have a superfield representation. While different as
superfields and supermultiplets, these are still super-differentially related
to a much more modest number of minimal supermultiplets, which we construct
herein.Comment: 13 pages, integrated illustration
On Graph-Theoretic Identifications of Adinkras, Supersymmetry Representations and Superfields
In this paper we discuss off-shell representations of N-extended
supersymmetry in one dimension, ie, N-extended supersymmetric quantum
mechanics, and following earlier work on the subject codify them in terms of
certain graphs, called Adinkras. This framework provides a method of generating
all Adinkras with the same topology, and so also all the corresponding
irreducible supersymmetric multiplets. We develop some graph theoretic
techniques to understand these diagrams in terms of a relatively small amount
of information, namely, at what heights various vertices of the graph should be
"hung".
We then show how Adinkras that are the graphs of N-dimensional cubes can be
obtained as the Adinkra for superfields satisfying constraints that involve
superderivatives. This dramatically widens the range of supermultiplets that
can be described using the superspace formalism and organizes them. Other
topologies for Adinkras are possible, and we show that it is reasonable that
these are also the result of constraining superfields using superderivatives.
The family of Adinkras with an N-cubical topology, and so also the sequence
of corresponding irreducible supersymmetric multiplets, are arranged in a
cyclical sequence called the main sequence. We produce the N=1 and N=2 main
sequences in detail, and indicate some aspects of the situation for higher N.Comment: LaTeX, 58 pages, 52 illustrations in color; minor typos correcte
Power of Randomization in Automata on Infinite Strings
Probabilistic B\"uchi Automata (PBA) are randomized, finite state automata
that process input strings of infinite length. Based on the threshold chosen
for the acceptance probability, different classes of languages can be defined.
In this paper, we present a number of results that clarify the power of such
machines and properties of the languages they define. The broad themes we focus
on are as follows. We present results on the decidability and precise
complexity of the emptiness, universality and language containment problems for
such machines, thus answering questions central to the use of these models in
formal verification. Next, we characterize the languages recognized by PBAs
topologically, demonstrating that though general PBAs can recognize languages
that are not regular, topologically the languages are as simple as
\omega-regular languages. Finally, we introduce Hierarchical PBAs, which are
syntactically restricted forms of PBAs that are tractable and capture exactly
the class of \omega-regular languages
Modular Invariance and Characteristic Numbers
We show that a general miraculous cancellation formula, the divisibility of
certain characteristic numbers and some other topologiclal results are con-
sequences of the modular invariance of elliptic operators on loop spaces.
Previously we have shown that modular invariance also implies the rigidity of
many elliptic operators on loop spaces.Comment: 14 page
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