5,486 research outputs found
Part 1: a process view of nature. Multifunctional integration and the role of the construction agent
This is the first of two linked articles which draw s on emerging understanding in the field of biology and seeks to communicate it to those of construction, engineering and design. Its insight is that nature 'works' at the process level, where neither function nor form are distinctions, and materialisation is both the act of negotiating limited resource and encoding matter as 'memory', to sustain and integrate processes through time. It explores how biological agents derive work by creating 'interfaces' between adjacent locations as membranes, through feedback. Through the tension between simultaneous aggregation and disaggregation of matter by agents with opposing objectives, many functions are integrated into an interface as it unfolds. Significantly, biological agents induce flow and counterflow conditions within biological interfaces, by inducing phase transition responses in the matte r or energy passing through them, driving steep gradients from weak potentials (i.e. shorter distances and larger surfaces). As with biological agents, computing, programming and, increasingly digital sensor and effector technologies share the same 'agency' and are thus convergent
The Trade-off Between Bioenergy and Emissions When Land Is Scarce
Agricultural biofuels require the use of scarce land, and this land has opportunity cost. We explore the objective function of a social planner who includes a land constraint in the optimization decision to minimize environmental cost. The results show that emissions should be measured on a per acre basis. Conventional agricultural life cycle assessments for biofuels report carbon emissions on a per gallon basis, thereby ignoring the implications of land scarcity and implicitly assuming an infinite supply of the inputs needed for production. Switchgrass and corn are then modeled as competing alternatives to show how the inclusion of a land constraint can influence life cycle rankings and alter policy conclusions.biofuels, biomass, energy policy, land use, life cycle analysis, Agricultural and Food Policy, Environmental Economics and Policy, Q16, Q48, Q58,
The phase transition in random catalytic sets
The notion of (auto) catalytic networks has become a cornerstone in
understanding the possibility of a sudden dramatic increase of diversity in
biological evolution as well as in the evolution of social and economical
systems. Here we study catalytic random networks with respect to the final
outcome diversity of products. We show that an analytical treatment of this
longstanding problem is possible by mapping the problem onto a set of
non-linear recurrence equations. The solution of these equations show a crucial
dependence of the final number of products on the initial number of products
and the density of catalytic production rules. For a fixed density of rules we
can demonstrate the existence of a phase transition from a practically
unpopulated regime to a fully populated and diverse one. The order parameter is
the number of final products. We are able to further understand the origin of
this phase transition as a crossover from one set of solutions from a quadratic
equation to the other.Comment: 7 pages, ugly eps files due to arxiv restriction
The Number of Different Binary Functions Generated by NK-Kauffman Networks and the Emergence of Genetic Robustness
We determine the average number , of \textit{NK}-Kauffman
networks that give rise to the same binary function. We show that, for , there exists a connectivity critical value such that () for and
for . We find that is not a
constant, but scales very slowly with , as . The problem of genetic robustness emerges as a statistical property
of the ensemble of \textit{NK}-Kauffman networks and impose tight constraints
in the average number of epistatic interactions that the genotype-phenotype map
can have.Comment: 4 figures 18 page
Particle Topology, Braids, and Braided Belts
Recent work suggests that topological features of certain quantum gravity
theories can be interpreted as particles, matching the known fermions and
bosons of the first generation in the Standard Model. This is achieved by
identifying topological structures with elements of the framed Artin braid
group on three strands, and demonstrating a correspondence between the
invariants used to characterise these braids (a braid is a set of
non-intersecting curves, that connect one set of points with another set of
points), and quantities like electric charge, colour charge, and so on. In
this paper we show how to manipulate a modified form of framed braids to yield
an invariant standard form for sets of isomorphic braids, characterised by a
vector of real numbers. This will serve as a basis for more complete
discussions of quantum numbers in future work.Comment: 21 pages, 16 figure
Teleportation, Braid Group and Temperley--Lieb Algebra
We explore algebraic and topological structures underlying the quantum
teleportation phenomena by applying the braid group and Temperley--Lieb
algebra. We realize the braid teleportation configuration, teleportation
swapping and virtual braid representation in the standard description of the
teleportation. We devise diagrammatic rules for quantum circuits involving
maximally entangled states and apply them to three sorts of descriptions of the
teleportation: the transfer operator, quantum measurements and characteristic
equations, and further propose the Temperley--Lieb algebra under local unitary
transformations to be a mathematical structure underlying the teleportation. We
compare our diagrammatical approach with two known recipes to the quantum
information flow: the teleportation topology and strongly compact closed
category, in order to explain our diagrammatic rules to be a natural
diagrammatic language for the teleportation.Comment: 33 pages, 19 figures, latex. The present article is a short version
of the preprint, quant-ph/0601050, which includes details of calculation,
more topics such as topological diagrammatical operations and entanglement
swapping, and calls the Temperley--Lieb category for the collection of all
the Temperley--Lieb algebra with physical operations like local unitary
transformation
Robustness of Transcriptional Regulation in Yeast-like Model Boolean Networks
We investigate the dynamical properties of the transcriptional regulation of
gene expression in the yeast Saccharomyces Cerevisiae within the framework of a
synchronously and deterministically updated Boolean network model. By means of
a dynamically determinant subnetwork, we explore the robustness of
transcriptional regulation as a function of the type of Boolean functions used
in the model that mimic the influence of regulating agents on the transcription
level of a gene. We compare the results obtained for the actual yeast network
with those from two different model networks, one with similar in-degree
distribution as the yeast and random otherwise, and another due to Balcan et
al., where the global topology of the yeast network is reproduced faithfully.
We, surprisingly, find that the first set of model networks better reproduce
the results found with the actual yeast network, even though the Balcan et al.
model networks are structurally more similar to that of yeast.Comment: 7 pages, 4 figures, To appear in Int. J. Bifurcation and Chaos, typos
were corrected and 2 references were adde
Network growth models and genetic regulatory networks
We study a class of growth algorithms for directed graphs that are candidate
models for the evolution of genetic regulatory networks. The algorithms involve
partial duplication of nodes and their links, together with innovation of new
links, allowing for the possibility that input and output links from a newly
created node may have different probabilities of survival. We find some
counterintuitive trends as parameters are varied, including the broadening of
indegree distribution when the probability for retaining input links is
decreased. We also find that both the scaling of transcription factors with
genome size and the measured degree distributions for genes in yeast can be
reproduced by the growth algorithm if and only if a special seed is used to
initiate the process.Comment: 8 pages with 7 eps figures; uses revtex4. Added references, cleaner
figure
Tempo and Mode of Evolution in the Tangled Nature Model
We study the Tangled Nature model of macro evolution and demonstrate that the
co-evolutionary dynamics produces an increasingly correlated core of well
occupied types. At the same time the entire configuration of types becomes
increasing de-correlated. This finding is related to ecosystem evolution. The
systems level dynamics of the model is subordinated to intermittent transitions
between meta-stable states. We improve on previous studies of the statistics of
the transition times and show that the fluctuations in the offspring
probability decreases with number of transitions. The longtime adaptation, as
seen by an increasing population size is demonstrated to be related to the
convexity of the offspring probability. We explain how the models behaviour is
a mathematical reflection of Darwin's concept of adaptation of profitable
variations.Comment: 6 pages, 5 figure
State Concentration Exponent as a Measure of Quickness in Kauffman-type Networks
We study the dynamics of randomly connected networks composed of binary
Boolean elements and those composed of binary majority vote elements. We
elucidate their differences in both sparsely and densely connected cases. The
quickness of large network dynamics is usually quantified by the length of
transient paths, an analytically intractable measure. For discrete-time
dynamics of networks of binary elements, we address this dilemma with an
alternative unified framework by using a concept termed state concentration,
defined as the exponent of the average number of t-step ancestors in state
transition graphs. The state transition graph is defined by nodes corresponding
to network states and directed links corresponding to transitions. Using this
exponent, we interrogate the dynamics of random Boolean and majority vote
networks. We find that extremely sparse Boolean networks and majority vote
networks with arbitrary density achieve quickness, owing in part to long-tailed
in-degree distributions. As a corollary, only relatively dense majority vote
networks can achieve both quickness and robustness.Comment: 6 figure
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