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 trädgård

Mot bakgrund av att mycket lite trädgårdshistorisk forskning ägnats åt de lägre samhällsklassernas trädgårdar fokuserar den här studien på just det. Studien har genomförts genom bearbetning och analys av information hämtad ifrån litteratur, bild-, ritnings- och minnesarkiv samt intervjuer av sakkunniga och trädgårdsägare. En fallstudie av tre välbevarade trädgårdar i området Tivolivången på Höganäs Övre har genomförts för att analysera och dokumentera några av de sista exemplaren av gamla arbetarträdgårdar i Höganäs. Höganäs var en utpräglad gruv- och bruksort under nära 200 år. Ur gruvorna hämtades stenkol och lera som exporterades eller förädlades till en mängd olika keramiska bruksprodukter. Höganäsbolaget var tidigt ute med att bygga arbetarbostäder och att erbjuda egnahemslån åt arbetare så att de själva skulle kunna bygga sig ett eget hem och förbättra sin livssituation. Redan de allra första arbetarlängorna, vid 1700-talets slut, hade små trädgårdar där arbetarna kunde odla mat för husbehov, vilket var livsavgörande för många. Att Höganäs så tidigt utvecklade ett engagemang för arbetarnas levnadsförhållanden springer ur influenser från England som tidigt fick fäste på orten genom engelsmannen och gruvingenjören Thomas Stawford. I trädgårdarna från 1900-talets första hälft odlade man främst nyttoväxter och man såg till att maximera odlingsytan, exempelvis genom att plantera fruktträd i grönsakslandet. Men trädgårdarna fyllde också en viktig funktion som en plats för återhämtning och njutning. I de häckomgärdade trädgårdarna, fanns ofta en bänk och några enstaka väldoftande blommande buskar eller en klätterros. Trädgårdarnas disposition och växtmaterial har stora likheter med tidens rådande trädgårdsideal för egnahemsträdgårdar. Arbetarna odlade inte bara i den egna trädgårdstäppan utan även var helst det fanns möjlighet, exempelvis uppe på bergbunkarna där jordmassor från gruvorna lades upp. Husen uppfördes av material som Höganäsbolaget producerade och även i trädgården användes olika restprodukter från bruket. Keramiskt material i gångar, som planteringskärl och kantstöd är, tillsammans med stenkolsbodarna där lönekolet förvarades, starkt utmärkande drag för arbetarnas trädgårdar i Höganäs. De flesta ursprungliga trädgårdarna vid arbetarbostäderna har förändrats eller försvunnit men än finns ett fåtal välbevarade trädgårdar kvar. Dessa trädgårdar är viktiga representanter för den unika trädgårdskultur som rått i Höganäs i över 200 år 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 $\tau$ with power law distribution $\psi(\tau)\simeq\tau^{-1- \alpha}$, such that the $\tau$ values are independent, local quantities for all particles. From scaling arguments and simulations, we find that for the scale-free waiting time case $0<\alpha<1$, the tracer particle dynamics is ultra-slow with a logarithmic mean square displacement (MSD) $\langle x^2(t)\rangle\simeq(\log t)^{1/2}$. This extreme slowing down compared to regular single file motion $\langle x^2(t)\rangle\simeq t^{1/2}$ is due to the high likelihood that the labeled particle keeps encountering strongly immobilized neighbors. For the case $1<\alpha<2$ we observe the MSD scaling $\langle x^2(t)\rangle\simeq t^{\gamma}$, where $\gamma2$ we recover Harris law $\simeq t^{1/2}$.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 (Fq′/Fm′) in the chloroplasts of Arabidopsis thaliana. These Fq′/Fm′ 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 Fq′/Fm′ 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_Aeq,24h) 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