Exact and Approximate Stochastic Simulation of Intracellular Calcium Dynamics

In simulations of chemical systems, the main task is to find an exact or approximate solution of the chemical master equation (CME) that satisfies certain constraints with respect to computation time and accuracy. While Brownian motion simulations of single molecules are often too time consuming to represent the mesoscopic level, the classical Gillespie algorithm is a stochastically exact algorithm that provides satisfying results in the representation of calcium microdomains. Gillespie's algorithm can be approximated via the tau-leap method and the chemical Langevin equation (CLE). Both methods lead to a substantial acceleration in computation time and a relatively small decrease in accuracy. Elimination of the noise terms leads to the classical, deterministic reaction rate equations (RRE). For complex multiscale systems, hybrid simulations are increasingly proposed to combine the advantages of stochastic and deterministic algorithms. An often used exemplary cell type in this context are striated muscle cells (e.g., cardiac and skeletal muscle cells). The properties of these cells are well described and they express many common calcium-dependent signaling pathways. The purpose of the present paper is to provide an overview of the aforementioned simulation approaches and their mutual relationships in the spectrum ranging from stochastic to deterministic algorithms

Insulator-to-metal transition in sulfur-doped silicon

We observe an insulator-to-metal (I-M) transition in crystalline silicon doped with sulfur to non- equilibrium concentrations using ion implantation followed by pulsed laser melting and rapid resolidification. This I-M transition is due to a dopant known to produce only deep levels at equilibrium concentrations. Temperature-dependent conductivity and Hall effect measurements for temperatures T > 1.7 K both indicate that a transition from insulating to metallic conduction occurs at a sulfur concentration between 1.8 and 4.3 x 10^20 cm-3. Conduction in insulating samples is consistent with variable range hopping with a Coulomb gap. The capacity for deep states to effect metallic conduction by delocalization is the only known route to bulk intermediate band photovoltaics in silicon.Comment: Submission formatting; 4 journal pages equivalen

Anomalous f-electron Hall Effect in the Heavy-Fermion System CeTIn5_{5} (T = Co, Ir, or Rh)

The in-plane Hall coefficient $R_{H}(T)$ of CeRhIn$_{5}$, CeIrIn$_{5}$, and CeCoIn$_{5}$ and their respective non-magnetic lanthanum analogs are reported in fields to 90 kOe and at temperatures from 2 K to 325 K. $R_{H}(T)$ is negative, field-independent, and dominated by skew-scattering above $\sim$ 50 K in the Ce compounds. $R_{H}(H \to 0)$ becomes increasingly negative below 50 K and varies with temperature in a manner that is inconsistent with skew scattering. Field-dependent measurements show that the low-T anomaly is strongly suppressed when the applied field is increased to 90 kOe. Measurements on LaRhIn$_{5}$, LaIrIn$_{5}$, and LaCoIn$_{5}$ indicate that the same anomalous temperature dependence is present in the Hall coefficient of these non-magnetic analogs, albeit with a reduced amplitude and no field dependence. Hall angle ($\theta_{H}$) measurements find that the ratio $\rho_{xx}/\rho_{xy}=\cot(\theta_{H})$ varies as $T^{2}$ below 20 K for all three Ce-115 compounds. The Hall angle of the La-115 compounds follow this T-dependence as well. These data suggest that the electronic-structure contribution dominates the Hall effect in the 115 compounds, with $f$-electron and Kondo interactions acting to magnify the influence of the underlying complex band structure. This is in stark contrast to the situation in most $4f$ and $5f$ heavy-fermion compounds where the normal carrier contribution to the Hall effect provides only a small, T-independent background to $R_{H}.$Comment: 23 pages and 8 figure

Bog plant/lichen tissue nitrogen and sulfur concentrations as indicators of emissions from oil sands development in Alberta, Canada

Increasing gaseous emissions of nitrogen (N) and sulfur (S) associated with oil sands development in northern Alberta (Canada) has led to changing regional wet and dry N and S deposition regimes. We assessed the potential for using bog plant/lichen tissue chemistry (N and S concentrations, C:N and C:S ratios, in 10 plant/lichen species) to monitor changing atmospheric N and S deposition through sampling at five bog sites, 3-6 times per growing season from 2009 to 2016. During this 8-year period, oil sands N emissions steadily increased, while S emissions steadily decreased. We examined the following: (1) whether each species showed changes in tissue chemistry with increasing distance from the Syncrude and Suncor upgrader stacks (the two largest point sources of N and S emissions); (2) whether tissue chemistry changed over the 8 year period in ways that were consistent with increasing N and decreasing S emissions from oil sands facilities; and (3) whether tissue chemistry was correlated with growing season wet deposition of NH4+-N, NO3--N, or SO42--S. Based on these criteria, the best biomonitors of a changing N deposition regime were Evernia mesomorpha, Sphagnum fuscum, and Vaccinium oxycoccos. The best biomonitors of a changing S deposition regime were Evernia mesomorpha, Cladonia mitis, Sphagnum fuscum, Sphagnum capillifolium, Vaccinium oxycoccos, and Picea mariana. Changing N and S deposition regimes in the oil sands region appear to be influencing N and S cycling in what once were pristine ombrotrophic bogs, to the extent that these bogs may effectively monitor future spatial and temporal patterns of deposition

Low contrast visual acuity testing is associated with cognitive performance in multiple sclerosis: a cross-sectional pilot study

Background: Cognitive impairment and visual deterioration are two key clinical symptoms in MS and affect 50 to 80% of patients. Little is known about the influence of cognitive impairment on visual tests recommended for MS such as low contrast sensitivity testing. Our objective was to investigate whether low contrast sensitivity testing is influenced by cognitive impairment in multiple sclerosis (MS) patients. Methods: Cross-sectional study including 89 patients with relapsing-remitting MS. All patients received cognitive evaluation using Rao’s Brief Repeatable Battery of Neuropsychological Testing (BRB-N). Visual assessments included low contrast sensitivity (CS) by functional acuity contrast testing and high contrast visual acuity (VA) using ETDRS charts. Retinal morphology as visual impairment correlate was measured using retinal nerve fiber layer (RNFL) thickness by optical coherence tomography. Results: In combined analyses using generalized estimating equation models, Paced Auditory Serial Addition Test (PASAT) and RNFL as well as and the Symbol Digit Modalities Test (SDMT) and RNFL predicted CS. To further control for a potential influence of the anterior visual system we performed partial correlation analyses between visual function and cognitive function test results but controlling for RNFL. Even when controlling for RNFL, CS was associated with PASAT performance and SDMT performance. Conclusion: Our data show that: a) cognitive impairment and performance in visual function tests such as low contrast sensitivity testing are associated; b) the main cognitive domains correlating with visual test performance are information processing speed and, to a lesser degree, memory; This preliminary data needs to be substantiated in further studies investigating patients with a higher cognitive burden, healthy controls and in longitudinal settings

Experimental nitrogen addition alters structure and function of a boreal bog: critical load and thresholds revealed

Bogs and fens cover 6% and 21%, respectively, of the 140,329 km2 Oil Sands Administrative Area in northern Alberta. Development of the oil sands has led to increasing atmospheric N deposition, with values as high as 17 kg N.ha-1yr-1; regional background deposition is N.ha-1yr-1. Bogs, being ombrotrophic, may be especially susceptible to increasing N deposition. To examine responses to N deposition, over five years, we experimentally applied N (as NH4NO3) to a bog near Mariana Lake, Alberta, unaffected by oil sands activities, at rates of 0, 5, 10, 15, 20, and 25 kg N.ha-1yr-1, plus controls (no water or N addition). Increasing N addition: (1) stimulated N2 fixation at deposition .ha-1yr-1, and progressively inhibited N2 fixation as N deposition increased above this level; (2) had no effect on Sphagnum fuscum net primary production (NPP) in years 1, 2, and 4, but inhibited S. fuscum NPP in years 3 and 5; (3) stimulated dominant shrub and Picea mariana NPP; (4) led to increased root biomass and production; (5) changed Sphagnum species relative abundance (decrease in S. fuscum, increase in S. magellanicum, no effect on S. angustifolium); (6) led to increasing abundance of Rhododendron groenlandicum and Andromeda polifolia, and to vascular plants in general; (7) led to increasing shrub leaf N concentrations in Andromeda polifolia, Chamaedaphne calyculata, Vaccinium oxycoccos, V. vitis-idaea, and Picea mariana; (8) stimulated cellulose decomposition, with no effect on S. fuscum peat or mixed vascular plant litter decomposition; (9) had no effect on net N mineralization rates or on porewater NH4+-N, NO3--N, or DON concentrations; and (10) had minimal effects on peat microbial community composition. Increasing experimental N addition led to a switch from new N being taken up primarily by Sphagnum to being taken up primarily by shrubs. As shrub growth and cover increase, Sphagnum abundance and NPP decrease. Because inhibition of N2 fixation by increasing N deposition plays a key role in bog structural and functional responses, we recommend a N deposition critical load of 3 kg N.ha-1yr-1 for northern Alberta bogs

Adaptive partitioning of real-time tasks on multiple processors

This paper presents a new algorithm for scheduling real-time tasks on multiprocessor/multicore systems. This new algorithm is based on combining EDF scheduling with a migration strategy that moves tasks only when needed. It has been evaluated through an extensive set of simulations that showed good performance when compared with global or partitioned EDF: a worst-case utilisation bound similar to partitioned EDF for hard real-time tasks, and a tardiness bound similar to global EDF for soft real-time tasks. Therefore, the proposed scheduler is effective for dealing with both soft and hard real-time workloads

First-principles theory of ferroelectric phase transitions for perovskites: The case of BaTiO3

We carry out a completely first-principles study of the ferroelectric phase transitions in BaTiO$_3$. Our approach takes advantage of two features of these transitions: the structural changes are small, and only low-energy distortions are important. Based on these observations, we make systematically improvable approximations which enable the parameterization of the complicated energy surface. The parameters are determined from first-principles total-energy calculations using ultra-soft pseudopotentials and a preconditioned conjugate-gradient scheme. The resulting effective Hamiltonian is then solved by Monte Carlo simulation. The calculated phase sequence, transition temperatures, latent heats, and spontaneous polarizations are all in good agreement with experiment. We find the transitions to be intermediate between order-disorder and displacive character. We find all three phase transitions to be of first order. The roles of different interactions are discussed.Comment: 33 pages latex file, 9 figure

Phase transitions in BaTiO3_3 from first principles

We develop a first-principles scheme to study ferroelectric phase transitions for perovskite compounds. We obtain an effective Hamiltonian which is fully specified by first-principles ultra-soft pseudopotential calculations. This approach is applied to BaTiO$_3$, and the resulting Hamiltonian is studied using Monte Carlo simulations. The calculated phase sequence, transition temperatures, latent heats, and spontaneous polarizations are all in good agreement with experiment. The order-disorder vs.\ displacive character of the transitions and the roles played by different interactions are discussed.Comment: 13 page

The influence of ‘topic and resource’ on some aspects of social theorising

Developments in sociological theory since the 1960s have been responses to disciplinary problems rather than changes in fashion. The problem of topic and resource—where sociology has to use everyday understandings and practices as study resources even though they are legitimate topics of enquiry—has been an important and sometimes neglected spur to many of these developments. The turn to discourse, conversation analysis and the rise of Bourdieu's reflexivity are all attempts to address the problem, but each is shown to be unsatisfactory in different ways. In summary, they seek to address the issue as requiring either a principled methodological or a principled theoretical solution, and neither approach is capable of comprehensively addressing the matter. It is argued that these ‘solutions’ depend, in turn, on one of two particular construals of what the ‘problem’ consists in, neither of which is necessary or coherent. Each, it is argued, depends on a philosophical trick: making language out to need formal improvement (the Bertrand Russell trick) or introducing inappropriate scepticism to everyday life (the René Descartes trick). It is suggested that treating topic and resource not as a problem but as something which opens up new areas of investigation successfully deflates the issue and avoids unnecessary theoretical and methodological contortions