Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using the AM1-BCC charge model against measurements (specifically bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive, and discuss the extent of available data. The results of this benchmark highlight a general problem with fixed-charge forcefields in the representation low dielectric environments such as those seen in binding cavities or biological membranes

Unsteady wake modelling for tidal current turbines

The authors present a numerical model for three-dimensional unsteady wake calculations for tidal turbines. Since wakes are characterised by the shedding of a vortex sheet from the rotor blades, the model is based on the vorticity transport equations. A vortex sheet may be considered a jump contact discontinuity in tangential velocity with, in inviscid hydrodynamic terms, certain kinematic and dynamic conditions across the sheet. The kinematic condition is that the sheet is a stream surface with zero normal fluid velocity; the dynamic condition is that the pressure is equal on either side of the sheet. The dynamic condition is explicitly satisfied at the trailing edge only, via an approximation of the Kutta condition. The shed vorticity is the span-wise derivative of bound circulation, and the trailed vorticity is the time derivative of bound circulation, and is convected downstream from the rotors using a finite-volume solution of vorticity transport equations thus satisfying the kinematic conditions. Owing to an absence in the literature of pressure data for marine turbines, results from the code are presented for the NREL-UAE Phase IV turbine. Axial flow cases show a close match in pressure coefficients at various spanwise stations; however, yawed flow cases demonstrate the shortcomings of a modelling strategy lacking viscosity

A two-step hybrid approach for modeling the nonlinear dynamic response of piezoelectric energy harvesters

An effective hybrid computational framework is described here in order to assess the nonlinear dynamic response of piezoelectric energy harvesting devices. The proposed strategy basically consists of two steps. First, fully coupled multiphysics finite element (FE) analyses are performed to evaluate the nonlinear static response of the device. An enhanced reduced-order model is then derived, where the global dynamic response is formulated in the state-space using lumped coefficients enriched with the information derived from the FE simulations. The electromechanical response of piezoelectric beams under forced vibrations is studied by means of the proposed approach, which is also validated by comparing numerical predictions with some experimental results. Such numerical and experimental investigations have been carried out with the main aim of studying the influence of material and geometrical parameters on the global nonlinear response. The advantage of the presented approach is that the overall computational and experimental efforts are significantly reduced while preserving a satisfactory accuracy in the assessment of the global behavior

Joint perceptual decision-making: a case study in explanatory pluralism.

Traditionally different approaches to the study of cognition have been viewed as competing explanatory frameworks. An alternative view, explanatory pluralism, regards different approaches to the study of cognition as complementary ways of studying the same phenomenon, at specific temporal and spatial scales, using appropriate methodological tools. Explanatory pluralism has been often described abstractly, but has rarely been applied to concrete cases. We present a case study of explanatory pluralism. We discuss three separate ways of studying the same phenomenon: a perceptual decision-making task (Bahrami et al., 2010), where pairs of subjects share information to jointly individuate an oddball stimulus among a set of distractors. Each approach analyzed the same corpus but targeted different units of analysis at different levels of description: decision-making at the behavioral level, confidence sharing at the linguistic level, and acoustic energy at the physical level. We discuss the utility of explanatory pluralism for describing this complex, multiscale phenomenon, show ways in which this case study sheds new light on the concept of pluralism, and highlight good practices to critically assess and complement approaches

Four-dimensional Cone Beam CT Reconstruction and Enhancement using a Temporal Non-Local Means Method

Four-dimensional Cone Beam Computed Tomography (4D-CBCT) has been developed to provide respiratory phase resolved volumetric imaging in image guided radiation therapy (IGRT). Inadequate number of projections in each phase bin results in low quality 4D-CBCT images with obvious streaking artifacts. In this work, we propose two novel 4D-CBCT algorithms: an iterative reconstruction algorithm and an enhancement algorithm, utilizing a temporal nonlocal means (TNLM) method. We define a TNLM energy term for a given set of 4D-CBCT images. Minimization of this term favors those 4D-CBCT images such that any anatomical features at one spatial point at one phase can be found in a nearby spatial point at neighboring phases. 4D-CBCT reconstruction is achieved by minimizing a total energy containing a data fidelity term and the TNLM energy term. As for the image enhancement, 4D-CBCT images generated by the FDK algorithm are enhanced by minimizing the TNLM function while keeping the enhanced images close to the FDK results. A forward-backward splitting algorithm and a Gauss-Jacobi iteration method are employed to solve the problems. The algorithms are implemented on GPU to achieve a high computational efficiency. The reconstruction algorithm and the enhancement algorithm generate visually similar 4D-CBCT images, both better than the FDK results. Quantitative evaluations indicate that, compared with the FDK results, our reconstruction method improves contrast-to-noise-ratio (CNR) by a factor of 2.56~3.13 and our enhancement method increases the CNR by 2.75~3.33 times. The enhancement method also removes over 80% of the streak artifacts from the FDK results. The total computation time is ~460 sec for the reconstruction algorithm and ~610 sec for the enhancement algorithm on an NVIDIA Tesla C1060 GPU card.Comment: 20 pages, 3 figures, 2 table

Design Principles for Plasmonic Nanoparticle Devices

For all applications of plasmonics to technology it is required to tailor the resonance to the optical system in question. This chapter gives an understanding of the design considerations for nanoparticles needed to tune the resonance. First the basic concepts of plasmonics are reviewed with a focus on the physics of nanoparticles. An introduction to the finite element method is given with emphasis on the suitability of the method to nanoplasmonic device simulation. The effects of nanoparticle shape on the spectral position and lineshape of the plasmonic resonance are discussed including retardation and surface curvature effects. The most technologically important plasmonic materials are assessed for device applicability and the importance of substrates in light scattering is explained. Finally the application of plasmonic nanoparticles to photovoltaic devices is discussed.Comment: 29 pages, 15 figures, part of an edited book: "Linear and Non-Linear Nanoplasmonics

SpECTRE: A Task-based Discontinuous Galerkin Code for Relativistic Astrophysics

We introduce a new relativistic astrophysics code, SpECTRE, that combines a discontinuous Galerkin method with a task-based parallelism model. SpECTRE's goal is to achieve more accurate solutions for challenging relativistic astrophysics problems such as core-collapse supernovae and binary neutron star mergers. The robustness of the discontinuous Galerkin method allows for the use of high-resolution shock capturing methods in regions where (relativistic) shocks are found, while exploiting high-order accuracy in smooth regions. A task-based parallelism model allows efficient use of the largest supercomputers for problems with a heterogeneous workload over disparate spatial and temporal scales. We argue that the locality and algorithmic structure of discontinuous Galerkin methods will exhibit good scalability within a task-based parallelism framework. We demonstrate the code on a wide variety of challenging benchmark problems in (non)-relativistic (magneto)-hydrodynamics. We demonstrate the code's scalability including its strong scaling on the NCSA Blue Waters supercomputer up to the machine's full capacity of 22,380 nodes using 671,400 threads.Comment: 41 pages, 13 figures, and 7 tables. Ancillary data contains simulation input file

Effect of van der Waals interaction strength and nanocluster size on the dynamical and mechanical properties of 1,4-cis-polybutadiene melts

Using molecular dynamics simulations, we have investigated the effect of embedding nanoclusters of radius 3-7 Å on the dynamical and mechanical properties of 1,4-cispolybutadiene melts. To see the effect of polymer-nanocluster interaction strength on the bulk modulus, the van der Waals interactions (vdW) between the polymer chain and nanocluster have been varied from weak to very stong while keeping polymer-polymer and nanocluster-nanocluster interactions constant. The modulus depends on the interaction strength, but not on nanocluster size. Residence time of chains on the surface of the nanocluster (τr) has an increasing trend that reaches to a plateau as the vdW strength is increased. τr also doubles from 100 ps to 200 ps as the nanocluster size is increased from 3 to 7 Å. Our findings give clues on how the properties of polymeric materials may be controlled by nanoparticles of different chemistry and size