158 research outputs found
Tracer particle diffusion in a system with hardcore interacting particles
In this study, inspired by the work of K. Nakazato and K. Kitahara [Prog.
Theor. Phys. 64, 2261 (1980)], we consider the theoretical problem of tracer
particle diffusion in an environment of diffusing hardcore interacting crowder
particles. The tracer particle has a different diffusion constant from the
crowder particles. Based on a transformation of the generating function, we
provide an exact formal expansion for the tracer particle probability density,
valid for any lattice in the thermodynamic limit. By applying this formal
solution to dynamics on regular Bravais lattices we provide a closed form
approximation for the tracer particle diffusion constant which extends the
Nakazato and Kitahara results to include also b.c.c. and f.c.c. lattices.
Finally, we compare our analytical results to simulations in two and three
dimensions.Comment: 28 pages with appendix, 5 figure. To appear in JSTA
Fitting a function to time-dependent ensemble averaged data
Time-dependent ensemble averages, i.e., trajectory-based averages of some
observable, are of importance in many fields of science. A crucial objective
when interpreting such data is to fit these averages (for instance, squared
displacements) with a function and extract parameters (such as diffusion
constants). A commonly overlooked challenge in such function fitting procedures
is that fluctuations around mean values, by construction, exhibit temporal
correlations. We show that the only available general purpose function fitting
methods, correlated chi-square method and the weighted least squares method
(which neglects correlation), fail at either robust parameter estimation or
accurate error estimation. We remedy this by deriving a new closed-form error
estimation formula for weighted least square fitting. The new formula uses the
full covariance matrix, i.e., rigorously includes temporal correlations, but is
free of the robustness issues, inherent to the correlated chi-square method. We
demonstrate its accuracy in four examples of importance in many fields:
Brownian motion, damped harmonic oscillation, fractional Brownian motion and
continuous time random walks. We also successfully apply our method, weighted
least squares including correlation in error estimation (WLS-ICE), to particle
tracking data. The WLS-ICE method is applicable to arbitrary fit functions, and
we provide a publically available WLS-ICE software.Comment: 47 pages (main text: 15 pages, supplementary: 32 pages
I arbetarens trÀdgÄrd
Mot bakgrund av att mycket lite trĂ€dgĂ„rdshistorisk forskning Ă€gnats Ă„t de lĂ€gre samhĂ€llsklassernas trĂ€dgĂ„rdar fokuserar den hĂ€r studien pĂ„ just det. Studien har genomförts genom bearbetning och analys av information hĂ€mtad ifrĂ„n litteratur, bild-, ritnings- och minnesarkiv samt intervjuer av sakkunniga och trĂ€dgĂ„rdsĂ€gare. En fallstudie av tre vĂ€lbevarade trĂ€dgĂ„rdar i omrĂ„det TivolivĂ„ngen pĂ„ HöganĂ€s Ăvre har genomförts för att analysera och dokumentera nĂ„gra av de sista exemplaren av gamla arbetartrĂ€dgĂ„rdar i HöganĂ€s.
HöganÀs var en utprÀglad gruv- och bruksort under nÀra 200 Är. Ur gruvorna hÀmtades stenkol och lera som exporterades eller förÀdlades till en mÀngd olika keramiska bruksprodukter. HöganÀsbolaget var tidigt ute med att bygga arbetarbostÀder och att erbjuda egnahemslÄn Ät arbetare sÄ att de sjÀlva skulle kunna bygga sig ett eget hem och förbÀttra sin livssituation. Redan de allra första arbetarlÀngorna, vid 1700-talets slut, hade smÄ trÀdgÄrdar dÀr arbetarna kunde odla mat för husbehov, vilket var livsavgörande för mÄnga. Att HöganÀs sÄ tidigt utvecklade ett engagemang för arbetarnas levnadsförhÄllanden springer ur influenser frÄn England som tidigt fick fÀste pÄ orten genom engelsmannen och gruvingenjören Thomas Stawford.
I trÀdgÄrdarna frÄn 1900-talets första hÀlft odlade man frÀmst nyttovÀxter och man sÄg till att maximera odlingsytan, exempelvis genom att plantera frukttrÀd i grönsakslandet. Men trÀdgÄrdarna fyllde ocksÄ en viktig funktion som en plats för ÄterhÀmtning och njutning. I de hÀckomgÀrdade trÀdgÄrdarna, fanns ofta en bÀnk och nÄgra enstaka vÀldoftande blommande buskar eller en klÀtterros. TrÀdgÄrdarnas disposition och vÀxtmaterial har stora likheter med tidens rÄdande trÀdgÄrdsideal för egnahemstrÀdgÄrdar. Arbetarna odlade inte bara i den egna trÀdgÄrdstÀppan utan Àven var helst det fanns möjlighet, exempelvis uppe pÄ bergbunkarna dÀr jordmassor frÄn gruvorna lades upp.
Husen uppfördes av material som HöganÀsbolaget producerade och Àven i trÀdgÄrden anvÀndes olika restprodukter frÄn bruket. Keramiskt material i gÄngar, som planteringskÀrl och kantstöd Àr, tillsammans med stenkolsbodarna dÀr lönekolet förvarades, starkt utmÀrkande drag för arbetarnas trÀdgÄrdar i HöganÀs. De flesta ursprungliga trÀdgÄrdarna vid arbetarbostÀderna har förÀndrats eller försvunnit men Àn finns ett fÄtal vÀlbevarade trÀdgÄrdar kvar. Dessa trÀdgÄrdar Àr viktiga representanter för den unika trÀdgÄrdskultur som rÄtt i HöganÀs i över 200 Är och bör betraktas som en del av det lokala kulturarvet
Aging dynamics in interacting many-body systems
Low-dimensional, complex systems are often characterized by logarithmically
slow dynamics. We study the generic motion of a labeled particle in an ensemble
of identical diffusing particles with hardcore interactions in a strongly
disordered, one-dimensional environment. Each particle in this single file is
trapped for a random waiting time with power law distribution
, such that the values are
independent, local quantities for all particles. From scaling arguments and
simulations, we find that for the scale-free waiting time case ,
the tracer particle dynamics is ultra-slow with a logarithmic mean square
displacement (MSD) . This extreme
slowing down compared to regular single file motion is due to the high likelihood that the labeled
particle keeps encountering strongly immobilized neighbors. For the case
we observe the MSD scaling , where we recover Harris law
.Comment: 5 pages, 4 figure
Synergistic interaction in simultaneous exposure to Streptomyces californicus and Stachybotrys chartarum.
The microbial exposure associated with health complaints in moldy houses consists of a heterogeneous group of components, including both living and dead bacteria, fungi, and their metabolites and active compounds. However, little is known about the interactions between different microbes and their metabolites, although the cytotoxicity and inflammatory potential of certain individual microbes have been reported. In this study, we investigated the inflammatory responses of mouse RAW264.7 macrophages after exposure to six indoor air microbes (Aspergillus versicolor, Penicillium spinulosum, Stachybotrys chartarum, Bacillus cereus, Mycobacterium terrae, and Pseudomonas fluorescens) alone and together with the actinomycete Streptomyces californicus. The production of nitric oxide, levels of the proinflammatory cytokines tumor necrosis factor alpha (TNF-alpha) and interleukin-6 (IL-6), and cytotoxicity were measured. The coexposure to Sta. chartarum and Str. californicus caused a synergistic increase in the production of IL-6 but not other cytokines. In further experiments, the metabolites from Sta. chartarum or from closely related fungi (atranones B and E, satratoxin G, trichodermin, 7-alpha-hydroxytrichodermol, staplabin, and SMTP-7) and the known fungal toxins sterigmatocystin, citrinin, and ochratoxin A were each tested with Str. californicus. The testing revealed a synergistic response in TNF-alpha and IL-6 production after coexposure to Str. californicus with both trichodermin and 7-alpha-hydroxytrichodermol. Finally, the synergistic inflammatory response caused by Str. californicus and trichodermin together was studied by analyzing for the presence of nuclear factor-kappa-B (NF-kappa-B) in nuclear extracts of the exposed cells. The exposure to Str. californicus induced the binding of NF-kappa-B proteins to the NF-kappa-B consensus sequence as well as to the natural NF-kappa-B site of the IL-6 promoter. Adding trichodermin to the exposure did not increase the DNA binding
Phototropins maintain robust circadian oscillation of PSII operating efficiency under blue light
The circadian system allows plants to coordinate metabolic and physiological functions with predictable environmental variables such as dusk and dawn. This endogenous oscillator is comprised of biochemical and transcriptional rhythms that are synchronized with a plant's surroundings via environmental signals, including light and temperature. We have used chlorophyll fluorescence techniques to describe circadian rhythms of PSII operating efficiency (FqâČ/FmâČ) in the chloroplasts of Arabidopsis thaliana. These FqâČ/FmâČ oscillations appear to be influenced by transcriptional feedback loops previously described in the nucleus, and are induced by rhythmic changes in photochemical quenching over circadian time. Our work reveals that a family of blue photoreceptors, phototropins, maintain robust rhythms of FqâČ/FmâČ under constant blue light. As phototropins do not influence circadian gene expression in the nucleus our imaging methodology highlights differences between the modulation of circadian outputs in distinct subcellular compartments
A constitutively active allele of phytochrome B maintains circadian robustness in the absence of light
The sensitivity of the circadian system to light allows entrainment of the clock, permitting coordination of plant metabolic function and flowering time across seasons. Light affects the circadian system via both photoreceptors, such as phytochromes and cryptochromes, and sugar production by photosynthesis. In the present study, we introduce a constitutively active version of phytochrome B-Y276H (YHB) into both wild-type and phytochrome null backgrounds of Arabidopsis (Arabidopsis thaliana) to distinguish the effects of photoreceptor signaling on clock function from those of photosynthesis. We find that the YHB mutation is sufficient to phenocopy red light input into the circadian mechanism and to sustain robust rhythms in steady-state mRNA levels even in plants grown without light or exogenous sugars. The pace of the clock is insensitive to light intensity in YHB plants, indicating that light input to the clock is constitutively activated by this allele. Mutation of YHB so that it is retained in the cytoplasm abrogates its effects on clock function, indicating that nuclear localization of phytochrome is necessary for its clock regulatory activity. We also demonstrate a role for phytochrome C as part of the red light sensing network that modulates phytochrome B signaling input into the circadian system. Our findings indicate that phytochrome signaling in the nucleus plays a critical role in sustaining robust clock function under red light, even in the absence of photosynthesis or exogenous sources of energy
Survey context and question wording affects self reported annoyance due to road traffic noise: a comparison between two cross-sectional studies
<p>Abstract</p> <p>Background</p> <p>Surveys are a common way to measure annoyance due to road traffic noise, but the method has some draw-backs. Survey context, question wording and answer alternatives could affect participation and answers and could have implications when comparing studies and/or performing pooled analyses. The aim of this study was to investigate the difference in annoyance reporting due to road traffic noise in two types of surveys of which one was introduced broadly and the other with the clearly stated aim of investigating noise and health.</p> <p>Methods</p> <p>Data was collected from two surveys carried out in the municipality of Malmö, southern Sweden in 2007 and 2008 (n = 2612 and n = 3810). The first survey stated an aim of investigating residential environmental exposure, especially noise and health. The second survey was a broad public health survey stating a broader aim. The two surveys had comparable questions regarding noise annoyance, although one used a 5-point scale and the other a 4-point scale. We used geographic information systems (GIS) to assess the average road and railway noise (L<sub>Aeq,24h</sub>) at the participants' residential address. Logistic regression was used to calculate odds ratios for annoyance in relation to noise exposure.</p> <p>Results</p> <p>Annoyance at least once a week due to road traffic noise was significantly more prevalent in the survey investigating environment and health compared to the public health survey at levels > 45 dB(A), but not at lower exposure levels. However no differences in annoyance were found when comparing the extreme alternatives "never" and "every day". In the study investigating environment and health, "Noise sensitive" persons were more likely to readily respond to the survey and were more annoyed by road traffic noise compared to the other participants in that survey.</p> <p>Conclusions</p> <p>The differences in annoyance reporting between the two surveys were mainly due to different scales, suggesting that extreme alternatives are to prefer before dichotomization when comparing results between the two. Although some findings suggested that noise-sensitive individuals were more likely to respond to the survey investigating noise and health, we could not find convincing evidence that contextual differences affected either answers or participation.</p
Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System
A wide range of organisms features molecular machines, circadian clocks,
which generate endogenous oscillations with ~24 h periodicity and thereby
synchronize biological processes to diurnal environmental fluctuations.
Recently, it has become clear that plants harbor more complex gene regulatory
circuits within the core circadian clocks than other organisms, inspiring a
fundamental question: are all these regulatory interactions between clock genes
equally crucial for the establishment and maintenance of circadian rhythms? Our
mechanistic simulation for Arabidopsis thaliana demonstrates that at least half
of the total regulatory interactions must be present to express the circadian
molecular profiles observed in wild-type plants. A set of those essential
interactions is called herein a kernel of the circadian system. The kernel
structure unbiasedly reveals four interlocked negative feedback loops
contributing to circadian rhythms, and three feedback loops among them drive
the autonomous oscillation itself. Strikingly, the kernel structure, as well as
the whole clock circuitry, is overwhelmingly composed of inhibitory, rather
than activating, interactions between genes. We found that this tendency
underlies plant circadian molecular profiles which often exhibit
sharply-shaped, cuspidate waveforms. Through the generation of these cuspidate
profiles, inhibitory interactions may facilitate the global coordination of
temporally-distant clock events that are markedly peaked at very specific times
of day. Our systematic approach resulting in experimentally-testable
predictions provides insights into a design principle of biological clockwork,
with implications for synthetic biology.Comment: Supplementary material is available at the journal websit
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