An Atomistic Fingerprint Algorithm for Learning Ab Initio Molecular Force Fields

Molecular fingerprints, i.e. feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the Density-Encoded Canonically Aligned Fingerprint (DECAF) fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over PCA-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the `distance' between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields, and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems

Locating bugs without looking back

Bug localisation is a core program comprehension task in software maintenance: given the observation of a bug, e.g. via a bug report, where is it located in the source code? Information retrieval (IR) approaches see the bug report as the query, and the source code files as the documents to be retrieved, ranked by relevance. Such approaches have the advantage of not requiring expensive static or dynamic analysis of the code. However, current state-of-the-art IR approaches rely on project history, in particular previously fixed bugs or previous versions of the source code. We present a novel approach that directly scores each current file against the given report, thus not requiring past code and reports. The scoring method is based on heuristics identified through manual inspection of a small sample of bug reports. We compare our approach to eight others, using their own five metrics on their own six open source projects. Out of 30 performance indicators, we improve 27 and equal 2. Over the projects analysed, on average we find one or more affected files in the top 10 ranked files for 76% of the bug reports. These results show the applicability of our approach to software projects without history

U-shaped fairings suppress vortex-induced vibrations for cylinders in cross-flow

We employ three-dimensional direct and large-eddy numerical simulations of the vibrations and flow past cylinders fitted with free-to-rotate U-shaped fairings placed in a cross-flow at Reynolds number 100 ⩽ Re ⩽ 10,000. Such fairings are nearly neutrally buoyant devices fitted along the axis of long circular risers to suppress vortex-induced vibrations (VIVs). We consider three different geometric configurations: a homogeneous fairing, and two configurations (denoted A and AB) involving a gap between adjacent segments. For the latter two cases, we investigate the effect of the gap on the hydrodynamic force coefficients and the translational and rotational motions of the system. For all configurations, as the Reynolds number increases beyond 500, both the lift and drag coefficients decrease. Compared to a plain cylinder, a homogeneous fairing system (no gaps) can help reduce the drag force coefficient by 15 % for reduced velocity U* = 4.65, while a type A gap system can reduce the drag force coefficient by almost 50 % for reduced velocity U* = 3.5, 4.65, 6, and, correspondingly, the vibration response of the combined system, as well as the fairing rotation amplitude, are substantially reduced. For a homogeneous fairing, the cross-flow amplitude is reduced by about 80 %, whereas for fairings with a gap longer than half a cylinder diameter, VIVs are completely eliminated, resulting in additional reduction in the drag coefficient. We have related such VIV suppression or elimination to the features of the wake flow structure. We find that a gap causes the generation of strong streamwise vorticity in the gap region that interferes destructively with the vorticity generated by the fairings, hence disorganizing the formation of coherent spanwise cortical patterns. We provide visualization of the incoherent wake flow that leads to total elimination of the vibration and rotation of the fairing–cylinder system. Finally, we investigate the effect of the friction coefficient between cylinder and fairing. The effect overall is small, even when the friction coefficients of adjacent segments are different. In some cases the equilibrium positions of the fairings are rotated by a small angle on either side of the centreline, in a symmetry-breaking bifurcation, which depends strongly on Reynolds number

U-shaped fairings suppress vortex-induced vibrations for cylinders in cross-flow

We employ three-dimensional direct and large-eddy numerical simulations of the vibrations and flow past cylinders fitted with free-to-rotate U-shaped fairings placed in a cross-flow at Reynolds number 100 ⩽ Re ⩽ 10,000. Such fairings are nearly neutrally buoyant devices fitted along the axis of long circular risers to suppress vortex-induced vibrations (VIVs). We consider three different geometric configurations: a homogeneous fairing, and two configurations (denoted A and AB) involving a gap between adjacent segments. For the latter two cases, we investigate the effect of the gap on the hydrodynamic force coefficients and the translational and rotational motions of the system. For all configurations, as the Reynolds number increases beyond 500, both the lift and drag coefficients decrease. Compared to a plain cylinder, a homogeneous fairing system (no gaps) can help reduce the drag force coefficient by 15 % for reduced velocity U* = 4.65, while a type A gap system can reduce the drag force coefficient by almost 50 % for reduced velocity U* = 3.5, 4.65, 6, and, correspondingly, the vibration response of the combined system, as well as the fairing rotation amplitude, are substantially reduced. For a homogeneous fairing, the cross-flow amplitude is reduced by about 80 %, whereas for fairings with a gap longer than half a cylinder diameter, VIVs are completely eliminated, resulting in additional reduction in the drag coefficient. We have related such VIV suppression or elimination to the features of the wake flow structure. We find that a gap causes the generation of strong streamwise vorticity in the gap region that interferes destructively with the vorticity generated by the fairings, hence disorganizing the formation of coherent spanwise cortical patterns. We provide visualization of the incoherent wake flow that leads to total elimination of the vibration and rotation of the fairing–cylinder system. Finally, we investigate the effect of the friction coefficient between cylinder and fairing. The effect overall is small, even when the friction coefficients of adjacent segments are different. In some cases the equilibrium positions of the fairings are rotated by a small angle on either side of the centreline, in a symmetry-breaking bifurcation, which depends strongly on Reynolds number

Spin correlations in the electron-doped high-transition-temperature superconductor Nd{2-x}Ce{x}CuO{4+/-delta}

High-transition-temperature (high-Tc) superconductivity develops near antiferromagnetic phases, and it is possible that magnetic excitations contribute to the superconducting pairing mechanism. To assess the role of antiferromagnetism, it is essential to understand the doping and temperature dependence of the two-dimensional antiferromagnetic spin correlations. The phase diagram is asymmetric with respect to electron and hole doping, and for the comparatively less-studied electron-doped materials, the antiferromagnetic phase extends much further with doping [1, 2] and appears to overlap with the superconducting phase. The archetypical electron-doped compound Nd{2-x}Ce{x}CuO{4\pm\delta} (NCCO) shows bulk superconductivity above x \approx 0.13 [3, 4], while evidence for antiferromagnetic order has been found up to x \approx 0.17 [2, 5, 6]. Here we report inelastic magnetic neutron-scattering measurements that point to the distinct possibility that genuine long-range antiferromagnetism and superconductivity do not coexist. The data reveal a magnetic quantum critical point where superconductivity first appears, consistent with an exotic quantum phase transition between the two phases [7]. We also demonstrate that the pseudogap phenomenon in the electron-doped materials, which is associated with pronounced charge anomalies [8-11], arises from a build-up of spin correlations, in agreement with recent theoretical proposals [12, 13].Comment: 5 pages, 4 figure

Room temperature plasmon laser by total internal reflection

Plasmon lasers create and sustain intense and coherent optical fields below light's diffraction limit with the unique ability to drastically enhance light-matter interactions bringing fundamentally new capabilities to bio-sensing, data storage, photolithography and optical communications. However, these important applications require room temperature operation, which remains a major hurdle. Here, we report a room temperature semiconductor plasmon laser with both strong cavity feedback and optical confinement to 1/20th of the wavelength. The strong feedback arises from total internal reflection of surface plasmons, while the confinement enhances the spontaneous emission rate by up to 20 times.Comment: 8 Page, 2 Figure

Impact of a brief group intervention to enhance parenting and the home learning environment for children aged 6-36 months: A cluster randomised controlled trial

This is the final version of the article. Available from the publisher via the DOI in this record.This study evaluated the effectiveness of a group parenting intervention designed to strengthen the home learning environment of children from disadvantaged families. Two cluster randomised controlled superiority trials were conducted in parallel and delivered within existing services: a 6-week parenting group (51 locations randomised; 986 parents) for parents of infants (aged 6-12 months), and a 10-week facilitated playgroup (58 locations randomised; 1200 parents) for parents of toddlers (aged 12-36 months). Each trial had three conditions: intervention (smalltalk group-only); enhanced intervention with home coaching (smalltalk plus); and 'standard'/usual practice controls. Parent-report and observational measures were collected at baseline, 12 and 32 weeks follow-up. Primary outcomes were parent verbal responsivity and home learning activities at 32 weeks. In the infant trial, there were no differences by trial arm for the primary outcomes at 32 weeks. In the toddler trial at 32-weeks, participants in the smalltalk group-only trial showed improvement compared to the standard program for parent verbal responsivity (effect size (ES) = 0.16; 95% CI 0.01, 0.36) and home learning activities (ES = 0.17; 95% CI 0.01, 0.38) but smalltalk plus did not. For the secondary outcomes in the infant trial, several initial differences favouring smalltalk plus were evident at 12 weeks, but not maintained to 32 weeks. For the toddler trial, differences in secondary outcomes favouring smalltalk plus were evident at 12 weeks and maintained to 32 weeks. These trials provide some evidence of the benefits of a parenting intervention focused on the home learning environment for parents of toddlers but not infants. TRIAL REGISTRATION: 8 September 2011; ACTRN12611000965909 .This research was commissioned and funded by the Victorian Government Department of Education and Early Childhood Development (DEECD), and designed and conducted at the Parenting Research Centre. NH, EW, SB, AS, MT, MY and JN were employees of the Parenting Research Centre when this study was conducted. EW was part-funded by the Centre for Research Excellence in Child Language at Murdoch Childrens Research Institute (NHMRC grant 1023493). NH, EW, SB and JN are funded by the Australian Communities Foundation (Coronella sub-fund) at La Trobe University. OU is supported by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care South West Peninsula at the Royal Devon and Exeter NHS Foundation Trust. Views expressed are those of the authors and not necessarily those of DEECD, NIHR, NHS or the Department of Health

Solar powered biohydrogen production requires specific localization of the hydrogenase

This work was supported by BBSRC Grant (BB/G021856/1) to SJB, PJN and CWM. We acknowledge support from the U.S. DoE, Biological and Environmental Research Program to MB, the U.S. DoE Fuel Cell Technologies Office (contract number DE-AC36-08-GO28308) to CAE and EPSRC (EP/F00270X/1) to MB and PJN

Formal and model driven design of the bright light therapy system Luxamet

Seasonal depression seriously diminishes the quality of life for many patients. To improve their condition, we propose LUXAMET, a bright light therapy system. This system has the potential to relieve patients from some of the symptoms caused by seasonal depression. The system was designed with a formal and model driven design methodology. This methodology enabled us to minimize systemic hazards, like blinding patients with an unhealthy dose of light. This was achieved by controlling race conditions and memory leaks, during design time. We prove that the system specification is deadlock as well as livelock free and there are no invariant violations. These proofs, together with the similarity between specification model and implementation code, make us confident that the implemented system is a reliable tool which can help patients during seasonal depression