Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Assessment of the effectiveness of the guard ring in obtaining a uni-directional flow in an in situ water permeability test

The non-destructive evaluation of the water permeability of concrete structures is a long standing challenge, principally due to the difficulty of achieving a uni-direction flow for computing the water permeability coefficient. The use of a guard ring (GR) was originally proposed for the in situ sorptivity test, but little information can be found for the water permeability test. In this study, the effect of a GR was carefully examined through the flow simulation, which was verified by carrying out experiments. It was observed that the GR can confine the flow near the surface, but cannot achieve a uni-directional flow across the whole depth of flow. To achieve a better performance, it is essential to consider the effects of the size of the inner seal and the GR and the significant interaction between these two. The analysis of the experimental data has indicated that the GR influences the flow for porous concretes, but there is no significant effect for dense concretes. Further investigation, validated using the flow-net theory, has shown a strong correlation between the water permeability coefficients obtained with the GR (K w-GR) and without it (K w-No GR), suggesting that one dimensional flow is not essential for interpreting data for site tests. Another practical issue was that more than 30 % of the tests with GR failed due to the difficulty of achieving a good seal between the inner and the outer chambers. Based on the work reported in this paper, a new water permeability test is proposed.

Quantitative Analysis of Fault and Fracture Systems and their Impact on Groundwater Flow in Irish Bedrock Aquifers

Fault and fracture systems are the most important store and pathway for groundwater in Ireland’s bedrock aquifers, either directly as conductive flow structures, or indirectly as the locus for the development of dolomitised limestone and karst. This article presents the preliminary results of a study involving the quantitative analysis of fault and fracture systems in the broad range of Irish bedrock types and a consideration of their impact on groundwater flow. The principal aims of the project are to develop generic conceptual models for different fault/fracture systems in different lithologies and at different depths, and to link them to observed groundwater behaviour. Here we briefly describe the geometrical characteristics of the main post-Devonian fault/fracture systems controlling groundwater flow from field observations at outcrops, quarries and mines. The structures range from Lower Carboniferous normal faults through to Variscan-related faults and veins, with the most recent structures including Tertiary strike-slip faults and ubiquitous uplift-related joint systems. The geometrical characteristics of different fault/fracture systems combined with observations of groundwater behaviour in both quarry and mine localities, can be linked to general flow and transport conceptualisations of Irish fractured bedrock. Most importantly they also provide a basis for relating groundwater flow to particular fault/fracture systems and their expression with depth and within different lithological sequences, as well as their regional variability.

Contractile properties of human renal cell carcinoma recruited arteries and their response to nicotinamide

Background and purpose: The manipulation of tumour blood supply and thus oxygenation is a potentially important strategy for improving the treatment of solid tumours by radiation. Increased knowledge about the characteristics that distinguish the tumour vasculature from its normal counterparts may enable tumour blood flow to be more selectively modified, Nicotinamide (NA) causes relaxation of preconstricted normal and tumour-supply arteries in rats. It has also been shown to affect microregional blood flow in human tumours. Direct effects of NA on human tumour supply arteries have not previously been reported. This paper describes our evaluation of the effects of NA on two parameters: 'spontaneous', oscillatory contractile activity and agonist (phenylephrine)-induced constriction in the arteries supplying human renal cell carcinomas.

Materials and methods: Isolated renal cell carcinoma feeder vessels were perfused in an organ bath with the alpha(1)-adrenoceptor agonist phenylephrine (PE). When the arteries had reached a plateau of constriction, nicotinamide (8.2 mM) was added to the perfusate and changes in perfusion pressure were measured.

Results: PE (10 mu M) induced a sustained constriction in the majority of the renal cell carcinoma feeder vessels examined, demonstrating that they retain contractile characteristics, at least in response to this alpha(1)-adrenoceptor agonist. In combination with NA (8.2 mM) the constriction was significantly attenuated in half of the preparations. In addition, seven arteries exhibited spontaneous contractile activity which was significantly attenuated by NA in six of them.

Conclusions: NA can significantly attenuate both 'spontaneous' and agonist-induced constrictions in tumour-recruited human arteries, though not all arteries are sensitive. Published by Elsevier Science Ireland Ltd.

The Impact of Extension and Ecosystem Services on Smallholders’ Credit Constraint.

On formal credit markets, access to formal credit and reasonable credit terms of smallholder farmers
in rural sub-Saharan Africa is limited due to adverse selection. Financial institutions operating in
rural areas often cannot distinguish between borrowers (farmers) that are creditworthy and those that
are not, thus, allocate limited resource to agriculture to reduce credit risk. In the presence of limited business quality signaling by smallholder farmers, financial institutions shall demand for collateral and/or offer unfavorable contract terms. Moreover, agricultural productivity of rural sub-Saharan
Africa, dominated by subsistence or small-scale farmers, is also negatively impacted by the adverse
effect of climate change. A strategy that may make the farming practices of smallholder farmer’s
climate resilient and profitable may also improve smallholder farmer's access to formal credit. This
study investigates to what extent participating in ecosystem and extension services (EES) programs
signals business quality of smallholders, thus granting them credit accessibility. We collected data
on 210 smallholder farmers in 2013, comprising farmers that receive payments for ecosystem
services (PES) and farm management training from the International Small Group Tree Planting
Program (TIST) Kenya to test the aforementioned theory empirically. We use game theory,
particularly a screening and sorting model, to illustrate the prospects for farmers with EES to access
formal credit and to improve their credit terms given that they receive PES and banking services
training. Furthermore, the PES’ long term duration (10 – 30 years) generates stable cash-flow which
may be perceived as collateral substitute. Results suggest that smallholder farmers in the TIST
program were less likely to be credit constraint compared to non-TIST farmers. Distance to market,
education, livestock and farm income are factors that determine access to credit from microfinance
institutions in rural Kenya. Amongst farmers that have obtained loans, those keeping business records
enjoy more favorable formal credit conditions. These farmers were observed to pay ca. 5 percent less
interest rate in microfinance charges. For TIST farmers, this type of farm management practices may
be attributed to the banking services and other training they receive within the program. While the
availability of classical collateral (farmlands) and PES may reduce interest rate, the latter was found
to be statistically insignificant. This research underlines the importance of an effective extension
services in rural areas of developing countries and the need to improve gains from conservation
agriculture and ensuing PES. The benefits associated with EES and PES may encompass agricultural
financing.

Relative Contribution of P5 and Hap Surface Proteins to Nontypable Haemophilus influenzae Interplay with the Host Upper and Lower Airways

Nontypable Haemophilus influenzae (NTHi) is a major cause of opportunistic respiratory tract disease, and initiates infection by colonizing the nasopharynx. Bacterial surface proteins play determining roles in the NTHi-airways interplay, but their specific and relative contribution to colonization and infection of the respiratory tract has not been addressed comprehensively. In this study, we focused on the ompP5 and hap genes, present in all H. influenzae genome sequenced isolates, and encoding the P5 and Hap surface proteins, respectively. We employed isogenic single and double mutants of the ompP5 and hap genes generated in the pathogenic strain NTHi375 to evaluate P5 and Hap contribution to biofilm growth under continuous flow, to NTHi adhesion, and invasion/phagocytosis on nasal, pharyngeal, bronchial, alveolar cultured epithelial cells and alveolar macrophages, and to NTHi murine pulmonary infection. We show that P5 is not required for bacterial biofilm growth, but it is involved in NTHi interplay with respiratory cells and in mouse lung infection. Mechanistically, P5NTHi375 is not a ligand for CEACAM1 or α5 integrin receptors. Hap involvement in NTHi375-host interaction was shown to be limited, despite promoting bacterial cell adhesion when expressed in H. influenzae RdKW20. We also show that Hap does not contribute to bacterial biofilm growth, and that its absence partially restores the deficiency in lung infection observed for the ΔompP5 mutant. Altogether, this work frames the relative importance of the P5 and Hap surface proteins in NTHi virulence.

Behaviour-time budget and functional habitat use of a free-ranging European badger (Meles meles)

Background: The European badger (Melesmeles) is involved in the maintenance of bovine tuberculosis infection and onward spread to cattle. However, little is known about how transmission occurs. One possible route could be through direct contact between infected badgers and cattle. It is also possible that indirect contact between cattle and infected badger excretory products such as faeces or urine may occur either on pasture or within and around farm buildings. A better understanding of behaviour patterns in wild badgers may help to develop biosecurity measures to minimise direct and indirect contact between badgers and cattle. However, monitoring the behaviour of free-ranging badgers can be logistically challenging and labour intensive due to their nocturnal and semi-fossorial nature.We trialled a GPS and tri-axial accelerometer-equipped collar on a free-ranging badger to assess its potential value to elucidate behaviour-time budgets and functional habitat use. Results: During the recording period between 16:00 and 08:00 on a single night, resting was the most commonly identified behaviour (67.4%) followed by walking (20.9%), snuffling (9.5%) and trotting (2.3%).When examining accelerometer data associated with each GPS fix and habitat type (occurring 2 min 30 s before and after), walking was themost common behaviour in woodland (40.3%) and arable habitats (53.8%), while snuffling was themost common behaviour in pasture (61.9%). Several nocturnal resting periods were also observed. The total distance travelled was 2.28 km. Conclusions: In the present report, we demonstrate proof of principle in the application of a combined GPS and accelerometer device to collect detailed quantitative data on wild badger behaviour. Behaviour-time budgets allow us to investigate how badgers allocate energy to different activities and how thismight change with disease status. Such information could be useful in the development of measures to reduce opportunities for onward transmission of bovine tuberculosis from badgers to cattle.

Arbuscular mycorrhizal fungal hyphae reduce soil erosion by surface water flow in a greenhouse experiment

The role of arbuscular mycorrhizal fungi (AMF) in resisting surface flow soil erosion has never been tested experimentally. We set up a full factorial greenhouse experiment using Achillea millefolium with treatments consisting of addition of AMF inoculum and non-microbial filtrate, non-AMF inoculum and microbial filtrate, AMF inoculum and microbial filtrate, and non-AMF inoculum and non-microbial filtrate (control) which were subjected to a constant shear stress in the form of surface water flow to quantify the soil detachment rate through time. We found that soil loss can be explained by the combined effect of roots and AMF extraradical hyphae and we could disentangle the unique effect of AMF hyphal length, which significantly reduced soil loss, highlighting their potential importance in riparian systems.

Investigation of the effects of flow conditions at rotor inlet on mixed flow turbine performance for automotive applications

Current trends in the automotive industry have placed increased importance on engine downsizing for passenger vehicles. Engine downsizing often results in reduced power output and turbochargers have been relied upon to restore the power output and maintain drivability. As improved power output is required across a wide range of engine operating conditions, it is necessary for the turbocharger to operate effectively at both design and off-design conditions. One off-design condition of considerable importance for turbocharger turbines is low velocity ratio operation, which refers to the combination of high exhaust gas velocity and low turbine rotational speed. Conventional radial flow turbines are constrained to achieve peak efficiency at the relatively high velocity ratio of 0.7, due the requirement to maintain a zero inlet blade angle for structural reasons. Several methods exist to potentially shift turbine peak efficiency to lower velocity ratios. One method is to utilize a mixed flow turbine as an alternative to a radial flow turbine. In addition to radial and circumferential components, the flow entering a mixed flow turbine also has an axial component. This allows the flow to experience a non-zero inlet blade angle, potentially shifting peak efficiency to a lower velocity ratio when compared to an equivalent radial flow turbine.
This study examined the effects of varying the flow conditions at the inlet to a mixed flow turbine and evaluated the subsequent impact on performance. The primary parameters examined were average inlet flow angle, the spanwise distribution of flow angle across the inlet and inlet flow cone angle. The results have indicated that the inlet flow angle significantly influenced the degree of reaction across the rotor and the turbine efficiency. The rotor studied was a custom in-house design based on a state-of-the-art radial flow turbine design. A numerical approach was used as the basis for this investigation and the numerical model has been validated against experimental data obtained from the cold flow turbine test rig at Queen’s University Belfast. The results of the study have provided a useful insight into how the flow conditions at rotor inlet influence the performance of a mixed flow turbine.

Interaction between Mycobacterium avium subsp. paratuberculosis and environmental protozoa

Background: Interactions between Mycobacterium avium subsp. paratuberculosis (Map) and free-living protozoa in water are likely to occur in nature. The potential impact of ingestion of Map by two naturally occurring Acanthamoeba spp. on this pathogen's survival and chlorine resistance was investigated. Results: Between 4.6 and 9.1% of spiked populations of three Map strains (NCTC 8578, B2 and ATCC 19698), which had been added at a multiplicity of infection of 10: 1, were ingested by Acanthamoeba castellanii CCAP 1501/1B and A. polyphaga CCAP 1501/3B during co-culture for 3 h at 25 C. Map cells were observed to be present within the vacuoles of the amoebae by acid-fast staining. During extended co-culture of Map NCTC 8578 at 25 degrees C for 24 d with both A. castellanii and A. polyphaga Map numbers did not change significantly during the first 7 days of incubation, however a 1-1.5 log(10) increase in Map numbers was observed between days 7 and 24 within both Acanthamoeba spp. Ingested Map cells were shown to be more resistant to chlorine inactivation than free Map. Exposure to 2 mu g/ml chlorine for 30 min resulted in a log(10) reduction of 0.94 in ingested Map but a log(10) reduction of 1.73 in free Map (p <0.001). Conclusion: This study demonstrated that ingestion of Map by and survival and multiplication of Map within Acanthamoeba spp. is possible, and that Map cells ingested by amoebae are more resistant to inactivation by chlorine than free Map cells. These findings have implications with respect to the efficacy of chlorination applied to Map infected surface waters.

Measurement and interpretation of the mid-infrared properties of single crystal and polycrystalline gold

The contribution of electron-phonon scattering and grain boundary scattering to the mid-IR (lambda = 3.392 mum) properties of An has been assessed by examining both bulk, single crystal samples-Au(1 1 1) and Au(1 1 0)-and thin film, polycrystalline An samples at 300 K and 100 K by means of surface plasmon polariton excitation. The investigation constitutes a stringent test for the in-vacuo Otto-configuration prism coupler used to perform the measurements, illustrating its strengths and limitations. Analysis of the optical response is guided by a physically based interpretation of the Drude model. Relative to the reference case of single crystal Au at 100 K (epsilon = - 568 + i17.5), raising the temperature to 300 K causes increased electron-phonon scattering that accounts for a reduction of similar to40 nm in the electron mean free path. Comparison of a polycrystalline sample to the reference case determines a mean free path due to grain boundary scattering of similar to 17 nm, corresponding to about half the mean grain size as determined from atomic force microscopy and indicating a high reflectance coefficient for the An grain boundaries. An analysis combining consideration of grain boundary scattering and the inclusion of a small percentage of voids in the polycrystalline film by means of an effective medium model indicates a value for the grain boundary reflection coefficient in the range 0.55-0.71. (C) 2005 Elsevier B.V. All rights reserved.

Calcium signaling in ocular arterioles

Local control of blood flow to the photoreceptors and associated neurons in the retina is largely achieved through changes in tone within the choroidal and retinal arterioles. This is primarily achieved through changes in [Ca2+] within the smooth muscle of these vessels, which regulates cell contraction and vascular constriction. Here we review some aspects of the cell physiology involved in these Ca2+-signaling processes, with particular emphasis on the molecular mechanisms involved. Ca2+-influx across the plasma membrane can occur via a variety of Ca2+-channels, including voltage-operated, store-operated, and receptor-operated channels. Ca2+ may also be released from intracellular stores via RyR-, or IP3R-gated channels in the SR membrane. Using high-speed confocal Ca2+-imaging, we have also demonstrated that the resulting signals are far from homogeneous, with spontaneous activity in retinal arterioles being characterized by both localized Ca2+-sparks and more global Ca2+-waves and oscillations. These signals may be specifically and differentially targeted, for example, to Ca2+-sensitive ion channels (stimulus-excitation coupling), or pathways regulating contraction (stimulus-contraction coupling). Exploring the role of changes in such targeting in disease states will provide exciting opportunities for future research.

International order flows: Explaining equity and exchange rate returns

Macroeconomic models of equity and exchange rate returns perform poorly at high frequencies. The proportion of daily returns that these models explain is essentially zero. Instead of relying on macroeconomic determinants, we model equity price and exchange rate behavior based on a concept from microstructure – order flow. The international order flows are derived from belief changes of different investor groups in a two-country setting. We obtain a structural relationship between equity returns, exchange rate returns and their relationship to home and foreign equity market order flow. To test the model we construct daily aggregate order flow data from 800 million equity trades in the U.S. and France from 1999 to 2003. Almost 60% of the daily returns in the S&P100 index are explained jointly by exchange rate returns and aggregate order flows in both markets. As predicted by the model, daily exchange rate returns and order flow into the French market have significant incremental explanatory power for the daily S&P returns. The model implications are also validated for intraday returns.

Validation study for prediction of iced aerofoil aerodynamics

Ice accretions can significantly change the aerodynamic performance of wings and rotor blades. Significant performance degradation can occur when ice accreations cause regions of separated flow, to predict this change implies, at a minimum, the solution of the Reynolds-Averaged Navier-Stokes equations. This paper presents validation for two generic cases involving the flow over aerofoil sections with added synthetic ice shapes. Results were obtained for two aerofoils, namely the NACA 23012 and a generic multi-element configuration. These results are compared with force and pressure coefficient measurements obtained in the NASA LTPT wind-tunnel for the NACA 23012, and force, PIV and boundary-layer measurements obtained at DNW for the multi-clement case. The level of agreement is assessed in the context of industrial requirements.

Nonconservative current-induced forces: A physical interpretation

We give a physical interpretation of the recently demonstrated non-conservative nature of interatomic forces in current-carrying nanostructures. We start from the analytical expression for the curl of these forces, and evaluate it for a point defect in a current-carrying system. We obtain a general definition of the capacity of electrical current flow to exert a non-conservative force, and thus do net work around closed paths, by a formal non-invasive test procedure. Second, we show that the gain in atomic kinetic energy in time, generated by non-conservative current-induced forces, is equivalent to the uncompensated stimulated emission of directional phonons. This connection with electron-phonon interactions quantifies explicitly the intuitive notion that non-conservative forces work by angular momentum transfer.