共查询到20条相似文献,搜索用时 15 毫秒
1.
Kuo-Yuan Hwa Boopathi Subramani Kay-Hooi Khoo 《Soft Computing - A Fusion of Foundations, Methodologies and Applications》2012,16(3):381-391
Protein xylosyltransferases are the group of enzymes which are involved in transferring xylose from UDP-d-xylose to serine residue in a protein. These enzymes are commonly found in multicellular organisms and in some unicellular
organisms. Previously we had identified the xylosyltransferase (XT) genes in EST sequence of a unicellular organism Trichomonas vaginalis through in silico approach based on the sequence homology. To corroborate if these genes are putative XT genes, we designed a workflow based
on the sequence characteristics of xylosyltransferase, to verify if any of the putative XT gene sequences have sequence motifs.
The XT genes in T. vaginalis predicted by Hidden Markov Model (HMM) were further analyzed with PfamHMM to identify if each putative sequence belongs to
a known protein family, with TMHMM to examine whether the predicted XTs are Golgi xylosyltransferases and with MEME to find
out the conserved motifs. The results confirmed our earlier study that these XTs are related to N-linked XTs in plants. To
confirm the in silico results further, we analyzed the N-linked glycans of T. vaginalis and the empirical data also confirmed the computational analysis. 相似文献
2.
How multicellular creatures can be developed from single cells into multicellular forms is a basic question in research into
artificial life. In this paper, we propose a possible anser to that question by developing multicellular digital organisms
from singe-cell digital organisms. We have done experiments on a computer. First we defined a model of a single-cell organism
which has open-ended evolvability and a self-replicating mechanism, so these single-cell digital organisms can develop into
multicellular creatures which have better adaptability than single-cell ones under certain environments. The phenomena of
cellular differentiation and cell self-organization were observed during the development of the multicellular digital organisms.
This work was presented in part at the Fourth International Symposium on Artificial Life and Robotics, Oita, Japan, January
19–22, 1999 相似文献
3.
A. N. Subochev 《Automation and Remote Control》2010,71(1):116-127
We consider the problem of collective choice in a tournament, i.e., when the majority relation, which plays the role of the
collective preference system on this set of alternatives, can be represented by a complete asymmetric oriented graph. We compare
three solutions of the collective choice problem: minimal dominating, uncovered, and minimal weakly stable sets. We construct
generalizations of the minimal dominating set and find out, with their help, how the system of dominating sets looks like
in the general case. We formulate a criterion that determines whether an alternative belongs to a minimal weakly stable set.
We find out how minimal weakly stable sets relate to uncovered sets. Based on the notion of stability of an alternative and
the set of alternatives we construct generalizations for the notions of uncovered and weakly stable sets—the classes of k-stable alternatives and k-stable sets. We prove inclusion relations between these classes. 相似文献
4.
Artificial life ("Alife") is purported to subsume real life, but in practice life-as-it-could-be is not based on life-as-we-know-it, but rather on life-as-we-don't-know-it. In terms of developmental biology, this means that we have yet to decide which of numerous paradigms for the embryogenesis of organisms is correct, if any. Two paradigms are compared and contrasted: positionalinformation and differentiation waves.These provide very different models for the nascent field of embryonics, the construction of computers and robots based on ideas from embryology. The behavioral component of Alife is usually thought about in terms of neural networks. Yet bacteria, single-cell ciliates such as Paramecium, and multicellular organisms, such as the ciliated placazoan Trichoplax adhaerens, have reasonably rich behavioral repertoires without nervous systems at all. It is therefore suggested that if Alife is to imitate and go beyond real life, then simulations of these organisms may be the place to begin. 相似文献
5.
6.
Philippe Huneman 《Minds and Machines》2008,18(4):493-520
I investigate the relationship between adaptation, as defined in evolutionary theory through natural selection, and the concept
of emergence. I argue that there is an essential correlation between the former, and “emergence” defined in the field of algorithmic
simulations. I first show that the computational concept of emergence (in terms of incompressible simulation) can be correlated
with a causal criterion of emergence (in terms of the specificity of the explanation of global patterns). On this ground,
I argue that emergence in general involves some sort of selective processes. Finally, I show that a second criterion, concerning
novel explanatory regularities following the emergence of a pattern, captures the robustness of emergence displayed by some
cases of emergence (according to the first criterion). Emergent processes fulfilling both criteria are therefore exemplified
in evolutionary biology by some so-called “innovations”, and mostly by the new units of fitness or new kinds of adaptations (like sexual reproduction, multicellular organisms, cells, societies) sometimes called “major transitions
in evolution”, that recent research programs (Maynard-Smith and Szathmary 1995; Michod 1999) aims at explaining.
相似文献
Philippe HunemanEmail: |
7.
The present study has numerically investigated two-dimensional electroosmotic flows in a microchannel with dielectric walls
of rectangle-waved surface roughness to understand the roughness effect. For the study, numerical simulations are performed
by employing the Nernst–Planck equation for the ionic species and the Poisson equation for the electric potential, together
with the traditional Navier–Stokes equation. Results show that the steady electroosmotic flow and ionic-species transport
in a microscale channel are well predicted by the Poisson–Nernst–Planck model and depend significantly on the shape of surface
roughness such as the amplitude and periodic length of wall wave. It is found that the fluid flows along the surface of waved
wall without involving any flow separation because of the very strong normal component of EDL (electric double layer) electric
field. The flow rate decreases exponentially with the amplitude of wall wave, whereas it increases linearly with the periodic
length. It is mainly due to the fact that the external electric-potential distribution plays a crucial role in driving the
electroosmotic flow through a microscale channel with surface roughness. Finally, the present results using the Poisson–Nernst–Planck
model are compared with those using the traditional Poisson–Boltzmann model which may be valid in these scales. 相似文献
8.
The codeword design problem is an important problem in DNA computing and its applications. Several theoretical analyses as
well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. These solutions have,
in turn, suggested new applications to DNA-based indexing and natural language processing, in addition to the obvious applications
to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of DNA-based
indexing for biological applications and show that DNA noncrosshybridizing (nxh) sets can be successfully applied to infer
ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides
selected so as to minimize crosshybridization. These phylogenies are solidly established and well accepted in biology. The
new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it is
demonstrated that DNA indexing does provide novel and principled insights into the phylogenesis of organisms hitherto inaccessible
by current methods, such as a prediction of the origin of the Salmonella plasmid 50 as being acquired horizontally, likely
from some bacteria somewhat related to Yesinia. Finally, DNA indexing can be scaled up to newly available universal DNA chips readily available both in vitro and in silico. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in DNA
spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform biomarker reference
system, a veritable and comprehensive “Atlas of Life”, as it is or as it could be on earth. 相似文献
9.
Lee Spector Jon Klein Chris Perry Mark Feinstein 《Genetic Programming and Evolvable Machines》2005,6(1):111-125
We demonstrate the emergence of collective behavior in two evolutionary computation systems, one an evolutionary extension
of a classic (highly constrained) flocking algorithm and the other a relatively un-constrained system in which the behavior
of agents is governed by evolved computer programs. The first system demonstrates the evolution of a form of multicellular
organization, while the second demonstrates the evolution of a form of altruistic food sharing. In this article we describe
both systems in detail, document the emergence of collective behavior, and argue that these systems present new opportunities
for the study of group dynamics in an evolutionary context. We also provide a brief overview of the breve simulation environment in which the systems were produced, and of breve’s facilities for the rapid, exploratory development of visualization strategies for artificial life. 相似文献
10.
Fluidic flow and species transport in integrated microfluidic devices can readily be simulated with computational fluid dynamics.
Nevertheless, the common practice to evaluate the solution accuracy is to decrease the discretization size (i.e., mesh size)
until the value of the quantity of interest (termed “output” here-in) does not change within a fixed tolerance. For systems
of partial differential equations such as the ones needed to be solved for electro-osmotic flows, this procedure is inappropriate
due to the resulting large computation cost when dealing with finer discretizations. Furthermore, in a design environment,
when investigating many geometries and flow configurations, the numerical uncertainty in the output may not allow the designer
to select the best design. In this paper, we present a numerical technique that is particularly appropriate to provide certainty
information for outputs of electro-osmotic microflows. The method uses an a-posteriori error estimation technique termed the
bound method to provide fast, inexpensive, and reliable bounds to the “output”, therefore, alleviating the need to systematically run
different meshes. To demonstrate the usefulness of the bound method, the electro-osmotic flow applied to the cross-intersection
in microchannel configuration is analyzed. The bound method presented in this paper is also extend to use an adaptive refinement
strategy to sharpen the bounds, the direct equilibrating strategy to calculate the ‘hybrid-flux’ very efficiently, and parallel
local computations to speed up the fine h-mesh computations. 相似文献
11.
Magneto-hydrodynamics (MHD) provides a convenient, programmable means for propelling liquids and controlling fluid flow in
microfluidic devices without a need for mechanical pumps and valves. When the magnetic field is uniform and the electric field
in the electrolyte solution is confined to a plane that is perpendicular to the direction of the magnetic field, the Lorentz
body force is irrotational and one can define a “Lorentz” potential. Since the MHD-induced flow field under these circumstances
is identical to that of pressure-driven flow, one can utilize the large available body of knowledge about pressure-driven
flows to predict MHD flows and infer MHD flow patterns. In this note, we prove the equivalence between MHD flows and pressure-driven
flows under certain conditions other than flow in straight conduits with rectangular cross sections. We determine the velocity profile and the
efficiency of MHD pumps, accounting for current transport in the electrolyte solutions. Then, we demonstrate how data available
for pressure-driven flow can be utilized to study various MHD flows, in particular, in a conduit patterned with pillars such
as may be useful for liquid chromatography and chemical reactors. In addition, we examine the effect of interior obstacles
on the electric current flow in the conduit and show the existence of a particular pillar geometry that maximizes the current. 相似文献
12.
We propose a solution of the multiprocessor scheduling problem based on applying a relatively new metaheuristic technique,
called Generalized Extremal Optimization (GEO). GEO is inspired by a simple coevolutionary model known as the Bak–Sneppen
model. The model describes an ecosystem consisting of N species. Evolution in this model is driven by a process in which the weakest species in the ecosystem, together with its
nearest neighbors, is always forced to mutate. This process shows the characteristics of a phenomenon called punctuated equilibrium,
which is observed in evolutionary biology. We interpret the multiprocessor scheduling problem in terms of the Bak–Sneppen
model and apply the GEO algorithm to solve the problem. We show that the proposed optimization technique is simple and yet
outperforms genetic algorithm-based and swarm algorithm-based approaches to the multiprocessor scheduling problem. 相似文献
13.
14.
Scientific literature with rich metadata can be represented as a labeled directed graph. This graph representation enables
a number of scientific tasks such as ad hoc retrieval or named entity recognition (NER) to be formulated as typed proximity queries in the graph. One popular proximity measure is called Random Walk with Restart (RWR), and much work has been done on the supervised learning of RWR measures by associating each edge label with a parameter.
In this paper, we describe a novel learnable proximity measure which instead uses one weight per edge label sequence: proximity is defined by a weighted combination of simple “path experts”, each corresponding to following a particular sequence
of labeled edges. Experiments on eight tasks in two subdomains of biology show that the new learning method significantly
outperforms the RWR model (both trained and untrained). We also extend the method to support two additional types of experts
to model intrinsic properties of entities: query-independent experts, which generalize the PageRank measure, and popular entity experts which allow rankings to be adjusted for particular entities that are especially important. 相似文献
15.
Andreas Lund Ingvill Rasmussen 《International Journal of Computer-Supported Collaborative Learning》2008,3(4):387-412
Using Vygotsky’s notion of double stimulation as an analytical tool, we discuss the complex relationship between tasks, tools,
and agency in CSCL environments. Empirically we examine how learners in a Norwegian senior high school class learning English
as a foreign language approach and respond to an open-ended and collectively oriented task using a wiki. Our findings show
that collectively oriented knowledge and language production takes place locally in small groups as well as in the larger
collective of the class, and that learners find it difficult to maintain awareness of both levels of activity. However, when
facing a breakdown in the wiki application, learners sustained strategies that carried many of the characteristics of collective
production. We argue that there is a need to further theorize the task-tool relationship in activities involving collective
knowledge production and that we need to align pedagogical as well as technological designs in order to give support for such
efforts. 相似文献
16.
George Weiss 《Mathematics of Control, Signals, and Systems (MCSS)》1991,4(2):193-203
We give an elementary proof of the well-known fact that shift-invariant operators onL
2[0, ∞) are represented by transfer functions which are bounded and analytic on the right open half-plane. We prove a generalization
to Banach space-valuedL
p
-functions, where 1≤p<∞. We show that the result no longer holds forp=∞.
This research was supported partially by the Weizmann Fellowship, and partially by the Air Force Office of Scientific Research
under Contract F49620-86-C-0111. 相似文献
17.
Masao Kubo Hiroshi Sato Takashi Matsubara Chris Melhuish 《Artificial Life and Robotics》2009,14(2):168-173
In this article, energy trophallaxis, i.e., distributed autonomous energy management methodology inspired by social insects
and bat behavior, and its advantages, are shown by a series of computer simulations to address the survivability of organized
groups of agents in a dynamic environment with uncertainty. The uncertainty of the agents’ organizational behavior is represented
by two Lévy distributions. By carefully controlling energy donation behavior based on these distributions, we can examine
the survivability of a larger group that traditional methods cannot analyze. As a result, even a small degree of friendship
throughout the organization makes the group’s survivability improve dramatically. 相似文献
18.
In this paper we study collective additive tree spanners for special families of graphs including planar graphs, graphs with bounded genus, graphs with bounded tree-width, graphs with bounded clique-width, and graphs with bounded chordality. We say that a graph G=(V,E) admits a system of μ collective additive tree r -spanners if there is a system $\mathcal{T}(G)In this paper we study collective additive tree spanners for special families of graphs including planar graphs, graphs with
bounded genus, graphs with bounded tree-width, graphs with bounded clique-width, and graphs with bounded chordality. We say
that a graph G=(V,E) admits a system of
μ
collective additive tree
r
-spanners if there is a system
T(G)\mathcal{T}(G)
of at most μ spanning trees of G such that for any two vertices x,y of G a spanning tree
T ? T(G)T\in\mathcal{T}(G)
exists such that d
T
(x,y)≤d
G
(x,y)+r. We describe a general method for constructing a “small” system of collective additive tree r-spanners with small values of r for “well” decomposable graphs, and as a byproduct show (among other results) that any weighted planar graph admits a system
of
O(?n)O(\sqrt{n})
collective additive tree 0-spanners, any weighted graph with tree-width at most k−1 admits a system of klog 2
n collective additive tree 0-spanners, any weighted graph with clique-width at most k admits a system of klog 3/2
n collective additive tree
(2w)(2\mathsf{w})
-spanners, and any weighted graph with size of largest induced cycle at most c admits a system of log 2
n collective additive tree
(2?c/2?w)(2\lfloor c/2\rfloor\mathsf{w})
-spanners and a system of 4log 2
n collective additive tree
(2(?c/3?+1)w)(2(\lfloor c/3\rfloor +1)\mathsf {w})
-spanners (here,
w\mathsf{w}
is the maximum edge weight in G). The latter result is refined for weighted weakly chordal graphs: any such graph admits a system of 4log 2
n collective additive tree
(2w)(2\mathsf{w})
-spanners. Furthermore, based on this collection of trees, we derive a compact and efficient routing scheme for those families
of graphs. 相似文献
19.
Kronecker's theorem is used to show that the irrational flows on then-dimensional torus are globally observed by a large class of continuous functions. These results are used to study the observability of Riccati flows on the Grassman manifolds.Supported in part by NASA Grant # NAG 2-203. 相似文献
20.
We consider an Eulerian predictor of optimal mixing appropriate for steady, three-dimensional channel flow of the type that
is commonly used in a variety of microfluidic mixing applications. This Eulerian indicator is applied to a kinematic model of the channel flow that allows one to control the flow structure of the secondary flows
and the number of distinct secondary flows. The cases of two and three distinct secondary flows are considered and the Eulerian
indicator predicts the optimal flow structure in the two secondary flow case and in the three secondary flow case that result
in the best mixing. Moreover, it is shown that the case of three secondary flows mixes “optimally” (i.e., faster and more
completely) than the case of two secondary flows. An explanation of this difference is given in terms of the Eulerian flow
structure. 相似文献