Posterior probability and fluctuation theorem in stochastic processes

A generalization of fluctuation theorems in stochastic processes is proposed. The new theorem is written in terms of posterior probabilities, which are introduced via the Bayes theorem. In usual fluctuation theorems, a forward path and its time reversal play an important role, so that a microscopically reversible condition is essential. In contrast, the microscopically reversible condition is not necessary in the new theorem. It is shown that the new theorem adequately recovers various theorems and relations previously known, such as the Gallavotti-Cohen-type fluctuation theorem, the Jarzynski equality, and the Hatano-Sasa relation, when adequate assumptions are employed.Comment: 4 page

Regionalised impacts of climate change on flood flows: regionalising the flood response types in Britain. Milestone report 4. Revised November 2009

The primary objective of this project is to assess the suitability of current FCDPAG3 guidance given the advances in climate change science since its publication. PAG3 requires an allowance of 20% to be added to peak flows for any period between 2025 and 2115 for any location across Britain. This guidance was considered a precautionary value and its derivation reflected the evidence available at that time. FD2020 has been designed to increase this evidence base, and it is anticipated that the research will lead to the development of regional, rather than national, guidelines for changes to peak flows due to climate change. A scenario-neutral approach based on a broad sensitivity analysis to determine catchment response to changes in climate as chosen for FD2020. The method separates the climate change that a catchment may be exposed to (the hazard) from the catchment response (change in peak flows) to changes in the climate (the vulnerability). By combining current understanding of climate change likelihood (the ‘hazard’) with the vulnerability of a given catchment, it is possible to evaluate the risk of flood flow changes. The vulnerability of a catchment is to be characterised in two steps: first, the response of a set of catchments to a range of climatic changes are modelled, then analysed for similarity, and second the main responses are characterised according to catchment properties. This is possible by defining a sensitivity framework of changes to the mean and seasonality of precipitation and temperature and modelling the response of each catchment within this fixed framework. This milestone report describes the second step of the vulnerability assessment. This is achieved by identifying the relationships identified between a catchment’s characteristics (geographic, geologic or climatic) and the vulnerability of its flood peak to changes in the climate. The work follows the identification of nine flood response types for catchments in Britain, after a comprehensive ‘scenario-neutral’ sensitivity study based on 4,200 patterns of changes in rainfall, temperature and potential evaporation. These nine flood response types were found to fully describe the range of changes in flood peak obtained in 154 catchments, and represent five main families of behaviour from the most ‘damping’ (low vulnerability), through ‘neutral’, to the most ‘enhancing’ (high vulnerability) catchments. One of the response types, with a very damped response to changes in climate, was removed from the analysis, as the group was too small for a reliable model to be built; leaving eight flood response types to characterise. Using a hierarchical partitioning technique and digital catchment descriptors from the Flood Estimation Handbook and the Hydrometric Register databases, decision trees were identified to discriminate the flood response type from nine descriptors including mean annual rainfall, area, northing and easting, elevation, and measures of permeability and catchment losses. At the 2-year return period level, all eight flood response types could be discriminated. For changes in the 20- and 50-year return period floods, the flood response types had to be merged into four main categories before they could be discriminated by the catchment characteristics. This merging was also necessary to ensure that uncertainty due to the impact of seasonality in rainfall change was fully incorporated into the flood response types. For the most enhancing catchments (i.e. where the changes in flood peak are proportionally much greater than the maximum increases in rainfall), the difference between the mean annual rainfall and the losses in the catchment was found to be an important discriminatory factor. For changes in higher return period floods, mean annual rainfall was found to be less critical. Wetter catchments were found to be in general less enhancing than drier catchments. The decision trees were successful for between 67.5% and 84% of the study catchments, depending on the flood indicator. Amongst the misclassified catchments, a larger proportion was misclassified as more enhancing, resulting in a potential over-estimation of changes in flood peaks, or an over-precautionary assessment. When evaluating the ability to discriminate between the more general families of ‘resilient/damping catchments’ (i.e. associated with a damped flood response type), ‘neutral catchments’ and ‘vulnerable/enhancing catchments’ (i.e. associated with an enhanced response type), 80% of the catchments were found to be correctly classified across all four flood indicators. Large catchments seem to be slightly more difficult to classify, suggesting they might not be well represented by single value descriptors which smooth out spatial variations important in the response of the river to climatic changes. Following the decision trees (sets of partitioning rules and paths for each of the flood response types), it is possible to quickly identify, for any catchment (gauged or ungauged but with available descriptors), the expected flood response type in response to climate change. This regionalised vulnerability assessment can be used in combination with an evaluation of potential climatic changes (or the hazard) to provide a measure of the risk of changes in flood peaks. In particular, this framework will enable a quick update of the potential risk of changes in peak floods when new climate change projections become available, such as for example the UKCP09 scenarios, without the need to undertake an extensive hydrological modelling and impact study

Lentiviral vectors with amplified beta cell-specific gene expression.

An important goal of gene therapy is to be able to deliver genes, so that they express in a pattern that recapitulates the expression of an endogenous cellular gene. Although tissue-specific promoters confer selectivity, in a vector-based system, their activity may be too weak to mediate detectable levels in gene-expression studies. We have used a two-step transcriptional amplification system to amplify gene expression from lentiviral vectors using the human insulin promoter. In this system, the human insulin promoter drives expression of a potent synthetic transcription activator (the yeast GAL4 DNA-binding domain fused to the activation domain of the Herpes simplex virus-1 VP16 activator), which in turn activates a GAL4-responsive promoter, driving the enhanced green fluorescent protein reporter gene. Vectors carrying the human insulin promoter did not express in non-beta-cell lines, but expressed in murine insulinoma cell lines, indicating that the human insulin promoter was capable of conferring cell specificity of expression. The insulin-amplifiable vector was able to amplify gene expression five to nine times over a standard insulin-promoter vector. In primary human islets, gene expression from the insulin-promoted vectors was coincident with insulin staining. These vectors will be useful in gene-expression studies that require a detectable signal and tissue specificity

Nonequilibrium work on spin glasses in longitudinal and transverse fields

We derive a number of exact relations between equilibrium and nonequilibrium quantities for spin glasses in external fields using the Jarzynski equality and gauge symmetry. For randomly-distributed longitudinal fields, a lower bound is established for the work done on the system in nonequilibrium processes, and identities are proven to relate equilibrium and nonequilibrium quantities. In the case of uniform transverse fields, identities are proven between physical quantities and exponentiated work done to the system at different parts of the phase diagram with the context of quantum annealing in mind. Additional relations are given, which relate the exponentiated work in quantum and simulated (classical) annealing. It is also suggested that the Jarzynski equality may serve as a guide to develop a method to perform quantum annealing under non-adiabatic conditions.Comment: 17 pages, 5 figures, submitted to JPS

Multi-core job submission and grid resource scheduling for ATLAS AthenaMP

AthenaMP is the multi-core implementation of the ATLAS software framework and allows the efficient sharing of memory pages between multiple threads of execution. This has now been validated for production and delivers a significant reduction on the overall application memory footprint with negligible CPU overhead. Before AthenaMP can be routinely run on the LHC Computing Grid it must be determined how the computing resources available to ATLAS can best exploit the notable improvements delivered by switching to this multi-process model. A study into the effectiveness and scalability of AthenaMP in a production environment will be presented. Best practices for configuring the main LRMS implementations currently used by grid sites will be identified in the context of multi-core scheduling optimisation

The length of time's arrow

An unresolved problem in physics is how the thermodynamic arrow of time arises from an underlying time reversible dynamics. We contribute to this issue by developing a measure of time-symmetry breaking, and by using the work fluctuation relations, we determine the time asymmetry of recent single molecule RNA unfolding experiments. We define time asymmetry as the Jensen-Shannon divergence between trajectory probability distributions of an experiment and its time-reversed conjugate. Among other interesting properties, the length of time's arrow bounds the average dissipation and determines the difficulty of accurately estimating free energy differences in nonequilibrium experiments

Mechanical Properties of the Poling Motion in Cross Country Skiing

Skate cross-country skiing is a unique gait with the skis acting as sliding limbs and poles acting as fixed limbs. As skiers increase their speed, the sliding limbs (skis) remain relatively unrestricted in their ability to generate forward impulse. The poles, however, are fixed and thus the poling action depends on the skier’s speed. Since muscles generate less force at higher shortening velocity (Hill, 1938), the arms become limited in their ability to generate force through the poles. Also, muscles ability to generate force depends on their length, or the configuration of joints the muscles cross (Gordon et al., 1966). Therefore, it might be expected that the forces of arm and trunk muscles contributing to the poling action change as a function of the poling cycle. The purpose of this study was to relate maximum isometric force of the muscles contributing to poling as a function of the poling cycle, and quantify the dynamic force of these muscles as a function of skiing speed. Maximal isometric force was measured at 11 points in the poling stride of ten nationally ranked skiers. Five of these subjects were also tested for their maximal dynamic poling force at skiing speeds ranging from 6 to 36 km/h, increasing by 6km/h increments. Maximal isometric poling force was maximal (223N) at 20% of the poling cycle. The component of the pole force in the direction of travel was highest (117N) at 30% of the poling cycle. Toward the end of the poling cycle, the propulsive force approaches the total force and the total force decreases to 50 N. The dynamic poling force was maximal for the two slowest speeds tested (236 N at 6km/h and 254 N at 12km/h), and then decreased force almost linearly with increasing speeds and reached 102 N at 36 km/h. The results of this study suggest that the propulsive forces in poling depend greatly on the position of arms and trunk and the speed of skiing

The expansion of thymopoiesis in neonatal mice is dependent on expression of high mobility group a 2 protein (Hmga2).

Cell number in the mouse thymus increases steadily during the first two weeks after birth. It then plateaus and begins to decline by seven weeks after birth. The factors governing these dramatic changes in cell production are not well understood. The data herein correlate levels of High mobility group A 2 protein (Hmga2) expression with these temporal changes in thymopoiesis. Hmga2 is expressed at high levels in murine fetal and neonatal early T cell progenitors (ETP), which are the most immature intrathymic precursors, and becomes almost undetectable in these progenitors after 5 weeks of age. Hmga2 expression is critical for the initial, exponential expansion of thymopoiesis, as Hmga2 deficient mice have a deficit of ETPs within days after birth, and total thymocyte number is repressed compared to wild type littermates. Finally, our data raise the possibility that similar events occur in humans, because Hmga2 expression is high in human fetal thymic progenitors and falls in these cells during early infancy

Contribution of the Upper-Body in Skate Cross-Country Skiing

The skate technique in cross-country skiing has a unique gait transition. Typically, skiers will use the two-skate technique at low speeds, transition to the one-skate technique at intermediate speeds, then return to the two-skate technique at high speeds. We hypothesize that this unique gait transition can be explained by differences in the contribution of the arms to propulsion and the associated metabolic cost of upper-body and arm work. In one-skate, poles are planted simultaneously with every skate stride, while in two-skate, poles are planted with every second skate stride (Smith, 2000). Using four trained cross-country ski racers, two separate tests were performed for each technique of skate skiing. First, subjects skied at 6, 15, and 30 km/h on a rollerski treadmill. During the entire test VO2, pole force, lactate, and video were recorded for one technique and repeated on another day using the second technique. In the second phase of testing, the poling motion only was simulated on a pole ergometer with subjects matching their stroke rate and poling forces using video and force feedback. Upper-body VO2 and lactate were measured and compared to the treadmill test values. The average metabolic cost associated with the upper-body work was 60% of the total metabolic cost when skiing on the treadmill. The upper-body metabolic cost was always higher for the one skate compared to the two skate technique. At slow speeds the difference between the two techniques was small (3%), but this difference increased at higher speeds from 10% at 15km/h to 14% at 30km/h. The poling motion associated with one-skate becomes more metabolically costly than two-skate as speed increases. A skier’s regressive transition from one-skate to two-skate at high speeds may be explained by a need to transfer impulse generation to the legs, since the sliding limbs remain effective at high speeds while the fixed limbs (poles) become less effective