Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Large eddy simulations in low-pressure turbines: Effect of wakes at elevated free-stream turbulence

The transition of a separated shear layer over a flat plate, in the presence of periodic wakes and elevated free-stream turbulence (FST), is numerically investigated using Large Eddy Simulation (LES). The upper wall of the test section is inviscid and specifically contoured to impose a streamwise pressure distribution over the flat plate to simulate the suction surface of a low-pressure turbine (LPT) blade. Two different distributions representative of a 'high-lift' and an 'ultra high-lift' turbine blade are examined. Results obtained from the current LES compare favourably with the extensive experimental data previously obtained for these configurations. The LES results are then used to further investigate the flow physics involved in the transition process.In line with experimental experience, the benefit of wakes and FST obtained by suppressing the separation bubble, is more pronounced in 'ultra high-lift' design when compared to the 'high-lift' design. Stronger 'Klebanoff streaks' are formed in the presence of wakes when compared to the streaks due to FST alone. These streaks promoted much early transition. The weak Klebanoff streaks due to FST continued to trigger transition in between the wake passing cycles.The experimental inference regarding the origin of Klebanoff streaks at the leading edge has been confirmed by the current simulations. While the wake convects at local free-stream velocity, its impression in the boundary layer in the form of streaks convects much slowly. The 'part-span' Kelvin-Helmholtz structures, which were observed in the experiments when the wake passes over the separation bubble, are also captured. The non-phase averaged space-time plots manifest that reattachment is a localized process across the span unlike the impression of global reattachment portrayed by phase averaging. © 2013 Elsevier Inc.

Label-free detection of human prostate-specific antigen (hPSA) using film bulk acoustic resonators (FBARs)

Label-free detection of cancer biomarkers using low cost biosensors has promising applications in clinical diagnostics. In this work, ZnO-based thin film bulk acoustic wave resonators (FBARs) with resonant frequency of ∼1.5 GHz and mass sensitivity of 0.015 mg/m2 (1.5 ng/cm2) have been fabricated for their deployment as biosensors. Mouse monoclonal antibody, anti-human prostate-specific antigen (Anti-hPSA) has been used to bind human prostate-specific antigen (hPSA), a model cancer used in this study. Ellipsometry was used to characterize and optimise the antibody adsorption and antigen binding on gold surface. It was found that the best amount of antibody at the gold surface for effective antigen binding is around 1 mg/m2, above or below which resulted in the reduced antigen binding due to either the limited binding sites (below 1 mg/m2) or increased steric effect (above 1 mg/m2). The FBAR data were in good agreement with the data obtained from ellipsometry. Antigen binding experiments using FBAR sensors demonstrated that FBARs have the capability to precisely detect antigen binding, thereby making FBARs an attractive low cost alternative to existing cancer diagnostic sensors. © 2013 Elsevier B.V.

Modelling of free-space optoelectronic switching with MPLS for storage area networks (SANs)

Low-cost optical switches based on SLMs have conventionally been considered unsuitable for packet switching due to slow reconfiguration time. In this paper, we demonstrate that the constraint of SLM reconfiguration time in a hybrid three-stage electronic/optical switching node architecture can be compensated through the utilization of MPLS label switching mechanism to achieve the best performance for SAN applications. © 2012 SEE.

Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

Physiological responses to capture and handling of free-ranging male Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis)

We captured free-ranging male Yangtze finless porpoises over three seasons and assayed leukocytes and serum biochemistry to investigate physiological responses to the capture and handlings. Serum thyroid hormones (THs) declined sharply in those porpoises compared with hormone variation in a captive male finless porpoise. Hypernatremia and hypokalemia were also significant in the free-ranging animals suggesting that conservation of serum sodium might be acutely vital for this freshwater subspecies. The animals captured in spring showed more significant neutrophilia and eosinopenia than those captured in autumn suggesting that they may be more affected by capture during the breeding season. Furthermore, physical examination of porpoises when out of the water was apparently stressful, particularly when they were kept out of the water for longer periods. However, an increase in circulating THs may be an adaptive response to accommodate these short-term stresses.

FEC-free 50 m 1.5 Gb/s plastic optical fibre link using CAP modulation for home networks

LED-based carrierless amplitude and phase modulation is investigated for a multi-gigabit plastic optical fibre link. An FPGA-based 1.5 Gbit/s error free transmission over 50 m standard SI-POF using CAP64 is achieved, providing 2.9 dB power margin without forward error correction. © 2012 Optical Society of America.

Effects of high-order laser distortion products in radio over free-space optical links

RoFSO links are found to be susceptible to high-order laser distortion making conventional SFDR ineffective as a performance indicator. For the first time, peak input power is demonstrated as a service-independent bound on dynamic range. © OSA/ CLEO 2011.

Aberration correction for free space optical communications using rectangular zernike modal wavefront sensing

A time multiplexed rectangular Zernike modal wavefront sensor based on a nematic phase-only liquid crystal spatial light modulator and specially designed for a high power two-electrode tapered laser diode which is a compact and novel free space optical communication source is used in an adaptive beam steering free space optical communication system, enabling the system to have 1.25 GHz modulation bandwidth, 4.6° angular coverage and the capability of sensing aberrations within the system and caused by atmosphere turbulence up to absolute value of 0.15 waves amplitude and correcting them in one correction cycle. Closed-loop aberration correction algorithm can be implemented to provide convergence for larger and time varying aberrations. Improvement of the system signal-to-noise-ratio performance is achieved by aberration correction. To our knowledge, it is first time to use rectangular orthonormal Zernike polynomials to represent balanced aberrations for high power rectangular laser beam in practice. © 2014 IEEE.

Relationships among the contents of total phenolics, soluble carbohydrate, and free amino acids of 15 aquatic macrophytes

In order to examine how carbon and nitrogen status of a macrophyte may affect its total phenolics (TP) production, the contents of free amino acids (FAA), soluble carbohydrate (SC) and TP were examined in leaves of seven submersed, four floating-leaved, and four emergent macrophytes. The floating-leaved and emergent macrophytes had much higher contents of SC and TP than the submersed macrophytes. The contents of FAA were not significantly different among the submersed, floating-leaved, and emergent macrophytes. Correlations among the contents of FAA, SC, and TP indicated that the production of TP was more dependent on the SC content than on the FAA content.

Radio over free space optical link using a directly modulated two-electrode high power tapered laser

The analog modulation performance of a high-power two-electrode tapered laser is investigated. A 25dB dynamic range for 2.4GHz 802.11g signals is achieved with a 26dB loss budget, showing a >1km free space range is possible. © 2010 Optical Society of America.

Free radical scavenging and antioxidant enzymes activation of polysaccharide extract from Nostoc sphaeroides

Nostoc sphaeroides Kuetzing has been used as a traditional medicine in China to treat a variety of ailments. This research identified the antioxidant activities of polysaccharide extract from Nostoc sphaeroides. The extract, which contains 46.2% carbohydrates, exhibited an effective scavenging capability on superoxide radical, hydroxyl radicals in non site-specific as well as site-specific assays, and also performed lipid peroxidation inhibition in a dose-dependent manner. Polysaccharide extract had no 1,1-diphenyl-2-picrylhydrazyl radical scavenging potential at all test concentrations. Activities of superoxide dismutase, catalase, and glutathione peroxidase in human embryo kidney 293 cells were increased effectively when Nostoc sphaeroides extract was applied. These results suggested that the use of N. sphaeroides in treating ailments may be based on the antioxidant capacities of polysaccharide composition.

Binder free three-dimensional sulphur/few-layer graphene foam cathode with enhanced high-rate capability for rechargeable lithium sulphur batteries.

A novel ultra-lightweight three-dimensional (3-D) cathode system for lithium sulphur (Li-S) batteries has been synthesised by loading sulphur on to an interconnected 3-D network of few-layered graphene (FLG) via a sulphur solution infiltration method. A free-standing FLG monolithic network foam was formed as a negative of a Ni metallic foam template by CVD followed by etching away of Ni. The FLG foam offers excellent electrical conductivity, an appropriate hierarchical pore structure for containing the electro-active sulphur and facilitates rapid electron/ion transport. This cathode system does not require any additional binding agents, conductive additives or a separate metallic current collector thus decreasing the weight of the cathode by typically ∼20-30 wt%. A Li-S battery with the sulphur-FLG foam cathode shows good electrochemical stability and high rate discharge capacity retention for up to 400 discharge/charge cycles at a high current density of 3200 mA g(-1). Even after 400 cycles the capacity decay is only ∼0.064% per cycle relative to the early (e.g. the 5th cycle) discharge capacity, while yielding an average columbic efficiency of ∼96.2%. Our results indicate the potential suitability of graphene foam for efficient, ultra-light and high-performance batteries.