614 research outputs found
Does the Mind Extend Out into the World
The extended mind debate juggles the possibilities of whether or not the mind extends out into the world. Today, with the rise in technology, we have an additional claim that our tools are responsible for extending our minds. The internet, smart phones, and other tools give us a foothold in the extended mind debate by providing real world examples of how our mind is perceived as extending out into the world. In discovering where the divide between mind and environment exists we can come up with a conclusion whether or not the mind truly extends out into the world
Pattern Formation in the Inhomogeneous Cooling State of Granular Fluids
We present results from comprehensive event-driven (ED) simulations of
nonlinear pattern formation in freely-evolving granular gases. In particular,
we focus on the the morphologies of density and velocity fields in the
inhomogeneous cooling state (ICS). We emphasize the strong analogy between the
ICS morphologies and pattern formation in phase ordering systems with a
globally conserved order parameter.Comment: 11 pages, 4 figures. to appear in Europhys. Let
Indeterminacy, Memory, and Motion in a Simple Granular Packing
We apply two theoretical and two numerical methods to the problem of a disk
placed in a groove and subjected to gravity and a torque. Methods assuming
rigid particles are indeterminate -- certain combinations of forces cannot be
calculated, but only constrained by inequalities. In methods assuming
deformable particles, these combinations of forces are determined by the
history of the packing. Thus indeterminacy in rigid particles becomes memory in
deformable ones. Furthermore, the torque needed to rotate the particle was
calculated. Two different paths to motion were identified. In the first,
contact forces change slowly, and the indeterminacy decreases continuously to
zero, and vanishes precisely at the onset of motion, and the torque needed to
rotate the disk is independent of method and packing history. In the second
way, this torque depends on method and on the history of the packing, and the
forces jump discontinuously at the onset of motion.Comment: 11 pages, 7 figures, submitted to Phys Rev
Force-induced desorption of a linear polymer chain adsorbed on an attractive surface
We consider a model of self-avoiding walk on a lattice with on-site repulsion
and an attraction for every vertex of the walk visited on the surface to study
force-induced desorption of a linear polymer chain adsorbed on an attractive
surface and use the exact enumeration technique for analyzing how the critical
force for desorption depends on the temperature. The curve
gives the boundary separating the adsorbed phase from the desorbed phase. Our
results show that in two dimensions where surface is a line the force
increases monotonically as temperature is lowered and becomes almost constant
at very low temperatures. In case of three-dimensions we, however, find
re-entrance, i. e. goes through a maximum as temperature is lowered.
The behaviour of the polymer chain at different values of temperature and force
is examined by calculating the probability distribution of the height from the
surface of the vertex at which external force is applied.Comment: Preprint 15 pages with 8figures and two tables. The file table-2d.ps
and table-3d.ps lists C_N(Ns,h) for given N with all possible Ns and h in two
and three dimension
On the accuracy of language trees
Historical linguistics aims at inferring the most likely language
phylogenetic tree starting from information concerning the evolutionary
relatedness of languages. The available information are typically lists of
homologous (lexical, phonological, syntactic) features or characters for many
different languages.
From this perspective the reconstruction of language trees is an example of
inverse problems: starting from present, incomplete and often noisy,
information, one aims at inferring the most likely past evolutionary history. A
fundamental issue in inverse problems is the evaluation of the inference made.
A standard way of dealing with this question is to generate data with
artificial models in order to have full access to the evolutionary process one
is going to infer. This procedure presents an intrinsic limitation: when
dealing with real data sets, one typically does not know which model of
evolution is the most suitable for them. A possible way out is to compare
algorithmic inference with expert classifications. This is the point of view we
take here by conducting a thorough survey of the accuracy of reconstruction
methods as compared with the Ethnologue expert classifications. We focus in
particular on state-of-the-art distance-based methods for phylogeny
reconstruction using worldwide linguistic databases.
In order to assess the accuracy of the inferred trees we introduce and
characterize two generalizations of standard definitions of distances between
trees. Based on these scores we quantify the relative performances of the
distance-based algorithms considered. Further we quantify how the completeness
and the coverage of the available databases affect the accuracy of the
reconstruction. Finally we draw some conclusions about where the accuracy of
the reconstructions in historical linguistics stands and about the leading
directions to improve it.Comment: 36 pages, 14 figure
The anisotropy of granular materials
The effect of the anisotropy on the elastoplastic response of two dimensional
packed samples of polygons is investigated here, using molecular dynamics
simulation. We show a correlation between fabric coefficients, characterizing
the anisotropy of the granular skeleton, and the anisotropy of the elastic
response. We also study the anisotropy induced by shearing on the subnetwork of
the sliding contacts. This anisotropy provides an explanation to some features
of the plastic deformation of granular media.Comment: Submitted to PR
Stretching of a polymer below the Theta point
The unfolding of a polymer below the point when pulled by an
external force is studied both in d=2 on the lattice and in off lattice.
A ground state analysis of finite length chains shows that the globule unfolds
via multiple steps, corresponding to transitions between different minima, in
both cases. In the infinite length limit, these intermediate minima have a
qualitative effect only in . The phase diagram in d=2 is determined using
transfer matrix techniques. Energy-entropy and renormalization group arguments
are given which predict a qualitatively correct phase diagram and a change of
the order of the transition from d=2 to d=3.Comment: 4 pages, 3 eps figure
Fast computation of distance estimators
BACKGROUND: Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n(3)). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n(2). Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications. RESULTS: We give an advanced algorithm for Computing the number of mutational events between DNA sequences which is significantly faster than both Phylip and Paup. Moreover, we give a new method for estimating pairwise distances between sequences which contain ambiguity Symbols. This new method is shown to be more accurate as well as faster than earlier methods. CONCLUSION: Our novel algorithm for Computing distance estimators provides a valuable tool in phylogeny reconstruction. Since the running time of our distance estimation algorithm is comparable to that of most distance methods, the previous bottleneck is removed. All distance methods, such as NJ, require a distance matrix as input and, hence, our novel algorithm significantly improves the overall running time of all distance methods. In particular, we show for real world biological applications how the running time of phylogeny reconstruction using NJ is improved from a matter of hours to a matter of seconds
The molecular epidemiology of human immunodeficiency virus type 1 in six cities in Britain and Ireland
The authors sequenced the p17 coding regions of the gag gene from 211 patients infected either through injecting drug use (IDU) or by sexual intercourse between men from six cities in Scotland, N. England, N. Ireland, and the Republic of Ireland. All sequences were of subtype 5. Phylogenetic analysis revealed substantial heterogeneity in the sequences from homosexual men. In contrast, sequence from over 80% of IDUs formed a relatively tight cluster, distinct both from those of published isolates and of the gay men. There was no large-scale clustering of sequences by city in either risk group, although a number of close associations between pairs of individuals were observed. From the known date of the HIV-1 epidemic among IDUs in Edinburgh, the rate of sequence divergence at synonymous sites is estimated to be about 0.8%. On this basis it has been estimated that the date of divergence of the sequences among homosexual men to be about 1975, which may correspond to the origin of the B subtype epidemic
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