3,653 research outputs found
Hydrodynamic models of a cepheid atmosphere
A method for including the solution of the transfer equation in a standard Henyey type hydrodynamic code was developed. This modified Henyey method was used in an implicit hydrodynamic code to compute deep envelope models of a classical Cepheid with a period of 12(d) including radiative transfer effects in the optically thin zones. It was found that the velocity gradients in the atmosphere are not responsible for the large microturbulent velocities observed in Cepheids but may be responsible for the occurrence of supersonic microturbulence. It was found that the splitting of the cores of the strong lines is due to shock induced temperature inversions in the line forming region. The adopted light, color, and velocity curves were used to study three methods frequently used to determine the mean radii of Cepheids. It is concluded that an accuracy of 10% is possible only if high quality observations are used
Enhanced Operational Semantics in Systems Biology
We are faced with a great challenge: the cross-fertilization between the fields of formal methods for concurrency, in the computer science domain, and systems biology in the biological realm
Percolation of satisfiability in finite dimensions
The satisfiability and optimization of finite-dimensional Boolean formulas
are studied using percolation theory, rare region arguments, and boundary
effects. In contrast with mean-field results, there is no satisfiability
transition, though there is a logical connectivity transition. In part of the
disconnected phase, rare regions lead to a divergent running time for
optimization algorithms. The thermodynamic ground state for the NP-hard
two-dimensional maximum-satisfiability problem is typically unique. These
results have implications for the computational study of disordered materials.Comment: 4 pages, 4 fig
Subtropical Real Root Finding
We describe a new incomplete but terminating method for real root finding for
large multivariate polynomials. We take an abstract view of the polynomial as
the set of exponent vectors associated with sign information on the
coefficients. Then we employ linear programming to heuristically find roots.
There is a specialized variant for roots with exclusively positive coordinates,
which is of considerable interest for applications in chemistry and systems
biology. An implementation of our method combining the computer algebra system
Reduce with the linear programming solver Gurobi has been successfully applied
to input data originating from established mathematical models used in these
areas. We have solved several hundred problems with up to more than 800000
monomials in up to 10 variables with degrees up to 12. Our method has failed
due to its incompleteness in less than 8 percent of the cases
The Combinatorial World (of Auctions) According to GARP
Revealed preference techniques are used to test whether a data set is
compatible with rational behaviour. They are also incorporated as constraints
in mechanism design to encourage truthful behaviour in applications such as
combinatorial auctions. In the auction setting, we present an efficient
combinatorial algorithm to find a virtual valuation function with the optimal
(additive) rationality guarantee. Moreover, we show that there exists such a
valuation function that both is individually rational and is minimum (that is,
it is component-wise dominated by any other individually rational, virtual
valuation function that approximately fits the data). Similarly, given upper
bound constraints on the valuation function, we show how to fit the maximum
virtual valuation function with the optimal additive rationality guarantee. In
practice, revealed preference bidding constraints are very demanding. We
explain how approximate rationality can be used to create relaxed revealed
preference constraints in an auction. We then show how combinatorial methods
can be used to implement these relaxed constraints. Worst/best-case welfare
guarantees that result from the use of such mechanisms can be quantified via
the minimum/maximum virtual valuation function
Turbulence-plankton interactions : a new cartoon
Author Posting. © John Wiley & Sons, 2009. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Marine Ecology 30 (2009): 133-150, doi:10.1111/j.1439-0485.2009.00288.x.Climate change will alter turbulence intensity, motivating greater attention to mechanisms of
turbulence effects on organisms. Many analytic and analog models used to simulate and assess
effects of turbulence on plankton rely on a one-dimensional simplification of the dissipative
scales of turbulence, i.e., simple, steady, uniaxial shears, as produced in Couette vessels. There
shear rates are constant and spatially uniform, and hence so is vorticity. Studies in such Couette
flows have greatly informed, spotlighting stable orientations of nonspherical particles and
predictable, periodic, rotational motions of steadily sheared particles in Jeffery orbits that steepen
concentration gradients around nutrient-absorbing phytoplankton and other chemically (re)active
particles. Over the last decade, however, turbulence research within fluid dynamics has focused
on the structure of dissipative vortices in space and time and on spatially and temporally varying
2
vorticity fields in particular. Because steadily and spatially uniformly sheared flows are
exceptional, so therefore are stable orientations for particles in turbulent flows. Vorticity
gradients, finite net diffusion of vorticity and small radii of curvature of streamlines are
ubiquitous features of turbulent vortices at dissipation scales that are explicitly excluded from
simple, steady Couette flows. All of these flow components contribute instabilities that cause
rotational motions of particles and so are important to simulate in future laboratory devices
designed to assess effects of turbulence on nutrient uptake, particle coagulation and predatorprey
encounter in the plankton. The Burgers vortex retains these signature features of turbulence
and provides a simplified “cartoon” of vortex structure and dynamics that nevertheless obeys the
Navier-Stokes equations. Moreover, this idealization closely resembles many dissipative
vortices observed in both the laboratory and the field as well as in direct numerical simulations
of turbulence. It is simple enough to allow both simulation in numerical models and fabrication
of analog devices that selectively reproduce its features. Exercise of such numerical and analog
models promises additional insights into mechanisms of turbulence effects on passive trajectories
and local accumulations of both living and nonliving particles, into solute exchange with living
and nonliving particles and into more subtle influences on sensory processes and swimming
trajectories of plankton, including demersal organisms and settling larvae in turbulent bottom
boundary layers. The literature on biological consequences of vortical turbulence has focused
primarily on the smallest, Kolmogorov-scale vortices of length scale η. Theoretical dissipation
spectra and direct numerical simulation, however, indicate that typical dissipative vortices with
radii of 7η to 8η, peak azimuthal speeds of order 1 cm s-1 and lifetimes of order 10 s as a
minimum (and much longer for moderate pelagic turbulence intensities) deserve new attention in
studies of biological effects of turbulence.This research was supported by collaborative U.S. National Science Foundation grant (OCE-
0724744) to Jumars and Karp-Boss
Validation of the particle size distribution obtained with the laser in-situ scattering and transmission (LISST) meter in flow-through mode
High spatial and temporal resolution estimates of the particle size distribution (PSD) in the surface ocean can enable improved understanding of biogeochemistry and ecosystem dynamics. Oceanic PSD measurements remain rare due to the time-consuming, manual sampling methods of common particle sizing instruments. Here, we evaluate the utility of measuring particle size data at high spatial resolution with a commercially-available submersible laser di raction particle sizer (LISST-100X, Sequoia Scientific), operating in an automated mode with continuously flowing seawater. The LISST PSD agreed reasonably well with discrete PSD measurements obtained with a Coulter Counter and data from the flow-through sampling Imaging Flow-Cytobot, validating our methodology. Total particulate area and Volume derived from the LISST PSD agreed well with beam-attenuation and particulate organic carbon respectively, further validating the LISST PSD. Furthermore, When compared to the measured spectral characteristics of particulate beam attenuation, we find a significant correlation. However, no significant relationship between the PSD and spectral particulate backscattering was found
Scaling Limits for Internal Aggregation Models with Multiple Sources
We study the scaling limits of three different aggregation models on Z^d:
internal DLA, in which particles perform random walks until reaching an
unoccupied site; the rotor-router model, in which particles perform
deterministic analogues of random walks; and the divisible sandpile, in which
each site distributes its excess mass equally among its neighbors. As the
lattice spacing tends to zero, all three models are found to have the same
scaling limit, which we describe as the solution to a certain PDE free boundary
problem in R^d. In particular, internal DLA has a deterministic scaling limit.
We find that the scaling limits are quadrature domains, which have arisen
independently in many fields such as potential theory and fluid dynamics. Our
results apply both to the case of multiple point sources and to the
Diaconis-Fulton smash sum of domains.Comment: 74 pages, 4 figures, to appear in J. d'Analyse Math. Main changes in
v2: added "least action principle" (Lemma 3.2); small corrections in section
4, and corrected the proof of Lemma 5.3 (Lemma 5.4 in the new version);
expanded section 6.
Complex networks theory for analyzing metabolic networks
One of the main tasks of post-genomic informatics is to systematically
investigate all molecules and their interactions within a living cell so as to
understand how these molecules and the interactions between them relate to the
function of the organism, while networks are appropriate abstract description
of all kinds of interactions. In the past few years, great achievement has been
made in developing theory of complex networks for revealing the organizing
principles that govern the formation and evolution of various complex
biological, technological and social networks. This paper reviews the
accomplishments in constructing genome-based metabolic networks and describes
how the theory of complex networks is applied to analyze metabolic networks.Comment: 13 pages, 2 figure
Determining the Solution Space of Vertex-Cover by Interactions and Backbones
To solve the combinatorial optimization problems especially the minimal
Vertex-cover problem with high efficiency, is a significant task in theoretical
computer science and many other subjects. Aiming at detecting the solution
space of Vertex-cover, a new structure named interaction between nodes is
defined and discovered for random graph, which results in the emergence of the
frustration and long-range correlation phenomenon. Based on the backbones and
interactions with a node adding process, we propose an Interaction and Backbone
Evolution Algorithm to achieve the reduced solution graph, which has a direct
correspondence to the solution space of Vertex-cover. By this algorithm, the
whole solution space can be obtained strictly when there is no leaf-removal
core on the graph and the odd cycles of unfrozen nodes bring great obstacles to
its efficiency. Besides, this algorithm possesses favorable exactness and has
good performance on random instances even with high average degrees. The
interaction with the algorithm provides a new viewpoint to solve Vertex-cover,
which will have a wide range of applications to different types of graphs,
better usage of which can lower the computational complexity for solving
Vertex-cover
- …