412 research outputs found
Studying Parallel Evolutionary Algorithms: The cellular Programming Case
Parallel evolutionary algorithms, studied to some extent over the past few years, have proven empirically worthwhile—though there seems to be lacking a better understanding of their workings. In this paper we concentrate on cellular (fine-grained) models, presenting a number of statistical measures, both at the genotypic and phenotypic levels. We demonstrate the application and utility of these measures on a specific example, that of the cellular programming evolutionary algorithm, when used to evolve solutions to a hard problem in the cellular-automata domain, known as synchronization
On RAF Sets and Autocatalytic Cycles in Random Reaction Networks
The emergence of autocatalytic sets of molecules seems to have played an
important role in the origin of life context. Although the possibility to
reproduce this emergence in laboratory has received considerable attention,
this is still far from being achieved. In order to unravel some key properties
enabling the emergence of structures potentially able to sustain their own
existence and growth, in this work we investigate the probability to observe
them in ensembles of random catalytic reaction networks characterized by
different structural properties. From the point of view of network topology, an
autocatalytic set have been defined either in term of strongly connected
components (SCCs) or as reflexively autocatalytic and food-generated sets
(RAFs). We observe that the average level of catalysis differently affects the
probability to observe a SCC or a RAF, highlighting the existence of a region
where the former can be observed, whereas the latter cannot. This parameter
also affects the composition of the RAF, which can be further characterized
into linear structures, autocatalysis or SCCs. Interestingly, we show that the
different network topology (uniform as opposed to power-law catalysis systems)
does not have a significantly divergent impact on SCCs and RAFs appearance,
whereas the proportion between cleavages and condensations seems instead to
play a role. A major factor that limits the probability of RAF appearance and
that may explain some of the difficulties encountered in laboratory seems to be
the presence of molecules which can accumulate without being substrate or
catalyst of any reaction.Comment: pp 113-12
Phase transition and landscape statistics of the number partitioning problem
The phase transition in the number partitioning problem (NPP), i.e., the
transition from a region in the space of control parameters in which almost all
instances have many solutions to a region in which almost all instances have no
solution, is investigated by examining the energy landscape of this classic
optimization problem. This is achieved by coding the information about the
minimum energy paths connecting pairs of minima into a tree structure, termed a
barrier tree, the leaves and internal nodes of which represent, respectively,
the minima and the lowest energy saddles connecting those minima. Here we apply
several measures of shape (balance and symmetry) as well as of branch lengths
(barrier heights) to the barrier trees that result from the landscape of the
NPP, aiming at identifying traces of the easy/hard transition. We find that it
is not possible to tell the easy regime from the hard one by visual inspection
of the trees or by measuring the barrier heights. Only the {\it difficulty}
measure, given by the maximum value of the ratio between the barrier height and
the energy surplus of local minima, succeeded in detecting traces of the phase
transition in the tree. In adddition, we show that the barrier trees associated
with the NPP are very similar to random trees, contrasting dramatically with
trees associated with the spin-glass and random energy models. We also
examine critically a recent conjecture on the equivalence between the NPP and a
truncated random energy model
Blackwell-Optimal Strategies in Priority Mean-Payoff Games
We examine perfect information stochastic mean-payoff games - a class of
games containing as special sub-classes the usual mean-payoff games and parity
games. We show that deterministic memoryless strategies that are optimal for
discounted games with state-dependent discount factors close to 1 are optimal
for priority mean-payoff games establishing a strong link between these two
classes
An approximation approach for the deviation matrix of continuous-time Markov processes with application to Markov decision theory
We present an update formula that allows the expression of the deviation matrix of a continuous-time Markov process with denumerable state space having generator matrix Q* through a continuous-time Markov process with generator matrix Q. We show that under suitable stability conditions the algorithm converges at a geometric rate. By applying the concept to three different examples, namely, the M/M/1 queue with vacations, the M/G/1 queue, and a tandem network, we illustrate the broad applicability of our approach. For a problem in admission control, we apply our approximation algorithm toMarkov decision theory for computing the optimal control policy. Numerical examples are presented to highlight the efficiency of the proposed algorithm. © 2010 INFORMS
The origin of large molecules in primordial autocatalytic reaction networks
Large molecules such as proteins and nucleic acids are crucial for life, yet
their primordial origin remains a major puzzle. The production of large
molecules, as we know it today, requires good catalysts, and the only good
catalysts we know that can accomplish this task consist of large molecules.
Thus the origin of large molecules is a chicken and egg problem in chemistry.
Here we present a mechanism, based on autocatalytic sets (ACSs), that is a
possible solution to this problem. We discuss a mathematical model describing
the population dynamics of molecules in a stylized but prebiotically plausible
chemistry. Large molecules can be produced in this chemistry by the coalescing
of smaller ones, with the smallest molecules, the `food set', being buffered.
Some of the reactions can be catalyzed by molecules within the chemistry with
varying catalytic strengths. Normally the concentrations of large molecules in
such a scenario are very small, diminishing exponentially with their size.
ACSs, if present in the catalytic network, can focus the resources of the
system into a sparse set of molecules. ACSs can produce a bistability in the
population dynamics and, in particular, steady states wherein the ACS molecules
dominate the population. However to reach these steady states from initial
conditions that contain only the food set typically requires very large
catalytic strengths, growing exponentially with the size of the catalyst
molecule. We present a solution to this problem by studying `nested ACSs', a
structure in which a small ACS is connected to a larger one and reinforces it.
We show that when the network contains a cascade of nested ACSs with the
catalytic strengths of molecules increasing gradually with their size (e.g., as
a power law), a sparse subset of molecules including some very large molecules
can come to dominate the system.Comment: 49 pages, 17 figures including supporting informatio
The F-BAR protein pacsin2 inhibits asymmetric VE-cadherin internalization from tensile adherens junctions
Vascular homoeostasis, development and disease critically depend on the regulation of endothelial cell-cell junctions. Here we uncover a new role for the F-BAR protein pacsin2 in the control of VE-cadherin-based endothelial adhesion. Pacsin2 concentrates at focal adherens junctions (FAJs) that are experiencing unbalanced actomyosin-based pulling. FAJs move in response to differences in local cytoskeletal geometry and pacsin2 is recruited consistently to the trailing end of fast-moving FAJs via a mechanism that requires an intact F-BAR domain. Photoconversion, photobleaching, immunofluorescence and super-resolution microscopy reveal polarized dynamics, and organization of junctional proteins between the front of FAJs and their trailing ends. Interestingly, pacsin2 recruitment inhibits internalization of the VE-cadherin complex from FAJ trailing ends and is important for endothelial monolayer integrity. Together, these findings reveal a novel junction protective mechanism during polarized trafficking of VE-cadherin, which supports barrier maintenance within dynamic endothelial tissue
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