Oxidative stress via hydrogen peroxide and menadione does not induce the secretion of IGFBP-5 in primary rat hepatocytes

Conference abstract describing how oxidative stress via hydrogen peroxide and menadione does not induce the secretion of IGFBP-5 in primary rat hepatocytes. Presented at the 2010 annual congress of the british toxicology societ

Stochastic control in microscopic nonequilibrium systems

Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the thermodynamic costs of nonequilibrium processes would illuminate the design principles for efficient microscopic machines. Considerable effort has gone into finding and classifying the deterministic control protocols that drive a system rapidly between states at minimum energetic cost. But for autonomous microscopic systems, driving processes are themselves stochastic. Here we generalize a linear-response framework to incorporate such protocol variability, deriving a lower bound on the work that is realized at finite protocol duration, far from the quasistatic limit. Our findings are confirmed in model systems. This theory provides a thermodynamic rationale for rapid operation, independent of functional incentives.Comment: 11 pages, 4 figure

Insulin-like growth factor binding protein-5 as a biomarker for detection of early liver disease

Study identifying an Insulin-like growth factor binding protein-5 as a biomarker for detection of early liver disease presented at the annual congress of the british toxicology societ

Optimal Control of the F1{_1}-ATPase Molecular Motor

F$_{1}$-ATPase is a rotary molecular motor that \emph{in vivo} is subject to strong nonequilibrium driving forces. There is great interest in understanding the operational principles governing its high efficiency of free-energy transduction. Here we use a near-equilibrium framework to design a non-trivial control protocol to minimize dissipation in rotating F$_{1}$ to synthesize ATP. We find that the designed protocol requires much less work than a naive (constant-velocity) protocol across a wide range of protocol durations. Our analysis points to a possible mechanism for energetically efficient driving of F$_{1}$ \emph{in vivo} and provides insight into free-energy transduction for a broader class of biomolecular and synthetic machines.Comment: 7 pages + SI, Minor revisio

Hidden energy flows in strongly coupled nonequilibrium systems

Quantifying the flow of energy within and through fluctuating nanoscale systems poses a significant challenge to understanding microscopic biological machines. A common approach involves coarse-graining, which allows a simplified description of such systems. This has the side effect of inducing so-called hidden contributions (due to sub-resolution dynamics) that complicate the resulting thermodynamics. Here we develop a thermodynamically consistent theory describing the nonequilibrium excess power internal to autonomous systems, and introduce a phenomenological framework to quantify the hidden excess power associated with their operation. We confirm our theoretical predictions in numerical simulations of a minimal model for both a molecular transport motor and a rotary motor.Comment: 14 pages, 3 figure

Magnetic tracing of fine-sediment over pool-riffle morphology

Field studies documenting fine-sediment (< 2 mm) transport in gravel-bed rivers are rare. For the first time in a fluvial environment, a technique that enhances the magnetic susceptibility of sand is used to trace its longitudinal dispersion and storage. This paper describes the methodology behind the artificial magnetic enhancement of iron-stained sand, and presents the results from sand tracing exercises conducted on two gravel-bed channels with pool-riffle morphology; one unregulated and sinuous in nature (site A), the other regulated and straight (site B), both situated on the River Rede Northumberland, UK. Two tonnes of magnetically enhanced tracer sand was introduced to site A and four tonnes to site B, to provide information on fine-sediment storage dynamics, interaction of fines with the stream bed, and rates of movement, expressed as virtual velocity (Vi). Sand transport pathways appeared to differ between the reaches; for site A, sand storage was found on bars and riffle margins with no storage or signs of transport through pools, and in contrast pool storage of tracer was a key feature shown at site B. Topographic forcing may cause differences in sediment sorting at site A; topographic highs tend to have low sand transport rates with sand grains becoming congested in these areas, whereas topographic lows show higher transport rates resulting in greater dispersion. Supply limitation of sand on the falling limb of the hydrograph may also become an issue in the topographic lows at this site. Hydrograph differences between the regulated and unregulated reaches could also play a role; however this could not be quantified in this study. There was no evidence of sand infiltration into the bed at site A; however marginal evidence for infiltration into the near-surface (0–15 cm) substrate voids was found at site B. The general lack of evidence for significant infiltration may reflect limited availability of void space in substrate framework gravels. Tracer sand was transported over the bed surface, with little vertical interaction with the substrate, despite periods of gravel mobilisation at site A. Vi over the study duration for site A was 2.28 m day− 1, and 0.28 m day− 1 for site B. These values are greater than those calculated using existing predictive equations developed from gravel tracer data, possibly reflecting differences in the mode of transport between bedload and saltation load

Multiplexed FBG sensor recorded in multimode microstructured polymer optical fibre

Fibre Bragg gratings have been inscribed in multimode microstructured polymer optical fibre (POF), with a core size of 50μm. The microstructured POF (mPOF) consists of a three ring hole structure and is made purely from poly(methyl methacrylate) (PMMA). In comparison to silica fibre, POF has a much smaller Young's modulus and a much greater breaking strain; additionally multimode fibre holds advantages of ease of handling and launching conditions. A linear strain sensitivity of 1.32 ± 0.01pm/με has been measured in the range 0 to 2% strain. The fibre drawing process leads to a degree of molecular alignment along the fibre axis. This alignment can be thermally annealed out; this can induce a permanent blue shift in the Bragg wavelength of a grating fabricated prior to annealing by up to 20 nm. Utilising this, wavelength demultiplexed gratings can be fabricated using a single phase mask. As an illustration of this we present for the first time wavelength division multiplexing of the spectral response of three Bragg gratings in POF within the C-band region. Complementing this work, a technique of splicing mPOF to step index silica fibre is described using UV curing optical adhesive, allowing characterisation of Bragg gratings fabricated in this fibre