1,314 research outputs found
Elasticity of Semiflexible Biopolymer Networks
We develop a model for gels and entangled solutions of semiflexible
biopolymers such as F-actin. Such networks play a crucial structural role in
the cytoskeleton of cells. We show that the rheologic properties of these
networks can result from nonclassical rubber elasticity. This model can explain
a number of elastic properties of such networks {\em in vitro}, including the
concentration dependence of the storage modulus and yield strain.Comment: Uses RevTeX, full postscript with figures available at
http://www.umich.edu/~fcm/preprints/agel/agel.htm
Punctuated equilibria and 1/f noise in a biological coevolution model with individual-based dynamics
We present a study by linear stability analysis and large-scale Monte Carlo
simulations of a simple model of biological coevolution. Selection is provided
through a reproduction probability that contains quenched, random interspecies
interactions, while genetic variation is provided through a low mutation rate.
Both selection and mutation act on individual organisms. Consistent with some
current theories of macroevolutionary dynamics, the model displays
intermittent, statistically self-similar behavior with punctuated equilibria.
The probability density for the lifetimes of ecological communities is well
approximated by a power law with exponent near -2, and the corresponding power
spectral densities show 1/f noise (flicker noise) over several decades. The
long-lived communities (quasi-steady states) consist of a relatively small
number of mutualistically interacting species, and they are surrounded by a
``protection zone'' of closely related genotypes that have a very low
probability of invading the resident community. The extent of the protection
zone affects the stability of the community in a way analogous to the height of
the free-energy barrier surrounding a metastable state in a physical system.
Measures of biological diversity are on average stationary with no discernible
trends, even over our very long simulation runs of approximately 3.4x10^7
generations.Comment: 20 pages RevTex. Minor revisions consistent with published versio
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Sensitivity of polar stratospheric ozone loss to uncertainties in chemical reaction kinetics
The impact and significance of uncertainties in model calculations of stratospheric ozone loss resulting from known uncertainty in chemical kinetics parameters is evaluated in trajectory chemistry simulations for the Antarctic and Arctic polar vortices. The uncertainty in modeled ozone loss is derived from Monte Carlo scenario simulations varying the kinetic (reaction and photolysis rate) parameters within their estimated uncertainty bounds. Simulations of a typical winter/spring Antarctic vortex scenario and Match scenarios in the Arctic produce large uncertainty in ozone loss rates and integrated seasonal loss. The simulations clearly indicate that the dominant source of model uncertainty in polar ozone loss is uncertainty in the Cl2O 2 photolysis reaction, which arises from uncertainty in laboratory-measured molecular cross sections at atmospherically important wavelengths. This estimated uncertainty in JCl 2O2 from laboratory measurements seriously hinders our ability to model polar ozone loss within useful quantitative error limits. Atmospheric observations, however, suggest that the Cl2O2 photolysis uncertainty may be less than that derived from the lab data. Comparisons to Match, South Pole ozonesonde, and Aura Microwave Limb Sounder (MLS) data all show that the nominal recommended rate simulations agree with data within uncertainties when the Cl2O2 photolysis error is reduced by a factor of two, in line with previous in situ ClOx measurements. Comparisons to simulations using recent cross sections from Pope et al. (2007) are outside the constrained error bounds in each case. Other reactions producing significant sensitivity in polar ozone loss include BrO + ClO and its branching ratios. These uncertainties challenge our confidence in modeling polar ozone depletion and projecting future changes in response to changing halogen emissions and climate. Further laboratory, theoretical, and possibly atmospheric studies are needed
Dynamics in online social networks
An increasing number of today's social interactions occurs using online
social media as communication channels. Some online social networks have become
extremely popular in the last decade. They differ among themselves in the
character of the service they provide to online users. For instance, Facebook
can be seen mainly as a platform for keeping in touch with close friends and
relatives, Twitter is used to propagate and receive news, LinkedIn facilitates
the maintenance of professional contacts, Flickr gathers amateurs and
professionals of photography, etc. Albeit different, all these online platforms
share an ingredient that pervades all their applications. There exists an
underlying social network that allows their users to keep in touch with each
other and helps to engage them in common activities or interactions leading to
a better fulfillment of the service's purposes. This is the reason why these
platforms share a good number of functionalities, e.g., personal communication
channels, broadcasted status updates, easy one-step information sharing, news
feeds exposing broadcasted content, etc. As a result, online social networks
are an interesting field to study an online social behavior that seems to be
generic among the different online services. Since at the bottom of these
services lays a network of declared relations and the basic interactions in
these platforms tend to be pairwise, a natural methodology for studying these
systems is provided by network science. In this chapter we describe some of the
results of research studies on the structure, dynamics and social activity in
online social networks. We present them in the interdisciplinary context of
network science, sociological studies and computer science.Comment: 17 pages, 4 figures, book chapte
Percolation model for structural phase transitions in LiHIO mixed crystals
A percolation model is proposed to explain the structural phase transitions
found in LiHIO mixed crystals as a function of the
concentration parameter . The percolation thresholds are obtained from Monte
Carlo simulations on the specific lattices occupied by lithium atoms and
hydrogen bonds. The theoretical results strongly suggest that percolating
lithium vacancies and hydrogen bonds are indeed responsible for the solid
solution observed in the experimental range .Comment: 4 pages, 2 figure
Effects of epidemic threshold definition on disease spread statistics
We study the statistical properties of the SIR epidemics in heterogeneous
networks, when an epidemic is defined as only those SIR propagations that reach
or exceed a minimum size s_c. Using percolation theory to calculate the average
fractional size of an epidemic, we find that the strength of the
spanning link percolation cluster is an upper bound to .
For small values of s_c, is no longer a good approximation, and
the average fractional size has to be computed directly. The value of s_c for
which is a good approximation is found to depend on the
transmissibility T of the SIR. We also study Q, the probability that an SIR
propagation reaches the epidemic mass s_c, and find that it is well
characterized by percolation theory. We apply our results to real networks
(DIMES and Tracerouter) to measure the consequences of the choice s_c on
predictions of average outcome sizes of computer failure epidemics.Comment: 12 pages, 8 figure
Self-optimization, community stability, and fluctuations in two individual-based models of biological coevolution
We compare and contrast the long-time dynamical properties of two
individual-based models of biological coevolution. Selection occurs via
multispecies, stochastic population dynamics with reproduction probabilities
that depend nonlinearly on the population densities of all species resident in
the community. New species are introduced through mutation. Both models are
amenable to exact linear stability analysis, and we compare the analytic
results with large-scale kinetic Monte Carlo simulations, obtaining the
population size as a function of an average interspecies interaction strength.
Over time, the models self-optimize through mutation and selection to
approximately maximize a community fitness function, subject only to
constraints internal to the particular model. If the interspecies interactions
are randomly distributed on an interval including positive values, the system
evolves toward self-sustaining, mutualistic communities. In contrast, for the
predator-prey case the matrix of interactions is antisymmetric, and a nonzero
population size must be sustained by an external resource. Time series of the
diversity and population size for both models show approximate 1/f noise and
power-law distributions for the lifetimes of communities and species. For the
mutualistic model, these two lifetime distributions have the same exponent,
while their exponents are different for the predator-prey model. The difference
is probably due to greater resilience toward mass extinctions in the food-web
like communities produced by the predator-prey model.Comment: 26 pages, 12 figures. Discussion of early-time dynamics added. J.
Math. Biol., in pres
Superconducting zero temperature phase transition in two dimensions and in the magnetic field
We derive the Ginzburg-Landau-Wilson theory for the superconducting phase
transition in two dimensions and in the magnetic field. Without disorder the
theory describes a fluctuation induced first-order quantum phase transition
into the Abrikosov lattice. We propose a phenomenological criterion for
determining the transition field and discuss the qualitative effects of
disorder. Comparison with recent experiments on MoGe films is discussed.Comment: 7 pages, 2 figure
Multiple functional self-association interfaces in plant TIR domains
The self-association of Toll/interleukin-1 receptor/resistance protein (TIR) domains has been implicated in signaling in plant and animal immunity receptors. Structure-based studies identified different TIR-domain dimerization interfaces required for signaling of the plant nucleotide-binding oligomerization domain-like receptors (NLRs) L6 from flax and disease resistance protein RPS4 from Arabidopsis. Here we show that the crystal structure of the TIR domain from the Arabidopsis NLR suppressor of npr1-1, constitutive 1 (SNC1) contains both an L6-like interface involving helices alpha D and alpha E (DE interface) and an RPS4-like interface involving helices alpha A and alpha E (AE interface). Mutations in either the AE- or DE-interface region disrupt cell-death signaling activity of SNC1, L6, and RPS4 TIR domains and full-length L6 and RPS4. Self-association of L6 and RPS4 TIR domains is affected by mutations in either region, whereas only AE-interface mutations affect SNC1 TIR-domain self-association. We further show two similar interfaces in the crystal structure of the TIR domain from the Arabidopsis NLR recognition of Peronospora parasitica 1 (RPP1). These data demonstrate that both the AE and DE self-association interfaces are simultaneously required for self-association and cell-death signaling in diverse plant NLRs.11139Ysciescopu
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