Potential-based Methods Research Articles

Impact of Fe-impurity centers on phonon subsystem of wurtzite-type ZnO

The paper addresses the question of the structural and vibrational properties of Fe-doped ZnO in the wurtzite structure with a lattice without an inversion center. The ZnO crystals containing Fe impurities in different charged states are studied by means of density functional theory (DFT) and potential-based methods. A first-principles simulation is performed to determine the local atomic configurations near the considered defects. The DFT results are compared with those obtained using the shell model. Both approaches give a similar pattern of lattice distortion around the Fe-impurity centers occupying cation sites in the isoelectronic charge state Fe2＋ and single-positive-charge state Fe3＋. The phonon local symmetrized densities of states projected onto the displacement of ions surrounding the defects are calculated by a well-established recursion method. The frequencies of defect vibrations of various symmetry types induced by Fe impurities are determined. The calculations made it possible to interpret the structure of the phonon sideband accompanying the zero-phonon line in polarized emission spectra attributed to the Fe3＋ intracenter transitions, as well as to estimate the role of Fe ions in the formation of observed peaks.

Structural and vibrational properties of wurtzite ZnO with oxygen-deficient defects: ab initio and potential-based calculations.

The structural and vibrational properties of the ZnO wurtzite phase with oxygen vacancies in different charged states are studied using first-principles and potential-based methods. The calculations based on density-functional theory are performed to determine the atomic configurations around defects. The DFT results are discussed and compared with those obtained using the static lattice method in the traditional shell model. Both computational approaches predict the same character of crystal lattice relaxation around oxygen vacancies. The phonon local symmetrized densities of states are calculated using the Green function method. The frequencies of localized vibrations of various symmetry types induced by oxygen vacancies in neutral and positively charged states are determined. The calculation results allow estimating the effect of oxygen vacancies on the formation of the intense Raman peak.

Physics and Accuracy of Dual-Solver Simulations of Rotors in Ground Effect

To characterize the interactions between rotorcraft and ground obstacles when tackling modern and emerging problems such as shipboard landings and urban air mobility, first-principles computational models offer the ability to perform design and analytical studies while resolving detailed flow features. However, the cost of Navier–Stokes methods with very high resolution is, for the most part, only tractable for research use cases. Conversely, midfidelity potential-based methods are cost-effective but may not capture important physics that occur near the rotor blades. Hybrid approaches that couple Navier–Stokes and potential solvers have recently been developed, which provide the ability to resolve complex physics with a Navier–Stokes solution while employing a potential solver to resolve far-wake effects for which it is well-suited. This research discusses the impact of new improvements to and best practices for the hybrid Navier–Stokes/free-wake solver OVERFLOW-CHARM applied to rotors in ground effect. Predictions of rotor performance and flow features are compared with experimental data for microscale and subscale rotors. Rotor performance is predicted within 6% of a conventional computational fluid dynamics simulation at approximately 20% of the computational cost and predicted flow features correlate well to experimental flow visualization.

Investigation on flutter stability of the DLR-F19/SACCON configuration

In the present work, flutter stability studies of an unmanned flying-wing configuration are presented. For this purpose, different fidelity modeling methods (DLM, CFD-Euler and CFD-RANS) are considered. The dependence of flutter speeds on altitude and Mach number is examined, showing that aerodynamic potential-based methods cannot predict aerodynamic phenomena such as flow detachment occurring at high angles of attack. In this respect, it is important that flutter investigations industry-oriented calculation methods are compared with the results obtained by high-fidelity CFD methods.

Brain-mechanistic responses to varying difficulty levels of approximate solutions to arithmetic problems.

Approximate strategies are crucial in daily human life. The studies on the “difficulty effect” seen in approximate complex arithmetic have long been neglected. Here, we aimed to explore the brain mechanisms related to this difficulty effect in the case of complex addition, using event-related potential-based methods. Following previous path-finding studies, we used the inequality paradigm and different split sizes to induce the use of two approximate strategies for different difficulty levels. By comparing dependent variables from the medium- and large-split conditions, we anticipated being able to dissociate the effects of task difficulty based on approximate strategy in electrical components. In the fronto−central region, early P2 (150–250 ms) and an N400-like wave (250–700 ms) were significantly different between different difficulty levels. Differences in P2 correlated with the difficulty of separation of the approximate strategy from the early physical stimulus discrimination process, which is dominant before 200 ms, and differences in the putative N400 correlated with different difficulties of approximate strategy execution. Moreover, this difference may be linked to speech processing. In addition, differences were found in the fronto-central region, which may reflect the regulatory role of this part of the cortex in approximate strategy execution when solving complex arithmetic problems.

Improved hydrodynamic analysis of marine propellers using a B-spline-based higher-order panel method

An improved hydrodynamic analysis of marine propellers based on a B-spline higher-order panel method is presented. The existing potential-based panel methods inevitably result in the degradation of the accuracy, especially near the trailing edge and the tip of the lift-generating surface. However, in the present method, the order of the B-splines used to represent body geometries and potentials can be increased without limit and, hence, solutions of any order can be obtained. In addition, the wake roll-up phenomenon of the propeller is adopted and its effects are investigated. The alignment procedure which satisfies the kinematic and dynamic boundary conditions on the shedding wake surface has been investigated by taking a close look at the case of marine propellers. In this work, we show that wake roll-up modeling gives improved results for the flow of extreme tip such as r/R = 0.99. The present method is validated by comparing it to the existing numerical and experimental results.

A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks.

Essential proteins are indispensable for cellular life. It is of great significance to identify essential proteins that can help us understand the minimal requirements for cellular life and is also very important for drug design. However, identification of essential proteins based on experimental approaches are typically time-consuming and expensive. With the development of high-throughput technology in the post-genomic era, more and more protein-protein interaction data can be obtained, which make it possible to study essential proteins from the network level. There have been a series of computational approaches proposed for predicting essential proteins based on network topologies. Most of these topology based essential protein discovery methods were to use network centralities. In this paper, we investigate the essential proteins' topological characters from a completely new perspective. To our knowledge it is the first time that topology potential is used to identify essential proteins from a protein-protein interaction (PPI) network. The basic idea is that each protein in the network can be viewed as a material particle which creates a potential field around itself and the interaction of all proteins forms a topological field over the network. By defining and computing the value of each protein's topology potential, we can obtain a more precise ranking which reflects the importance of proteins from the PPI network. The experimental results show that topology potential-based methods TP and TP-NC outperform traditional topology measures: degree centrality (DC), betweenness centrality (BC), closeness centrality (CC), subgraph centrality (SC), eigenvector centrality (EC), information centrality (IC), and network centrality (NC) for predicting essential proteins. In addition, these centrality measures are improved on their performance for identifying essential proteins in biological network when controlled by topology potential.

ChemInform Abstract: Lithium and Sodium Battery Cathode Materials: Computational Insights into Voltage, Diffusion and Nanostructural Properties

AbstractReview: DFT and atomistic potential‐based methods; 187 refs.

Electroarthrography provides a non-invasive streaming potential-based method for detecting natural and trypsin-induced cartilage degeneration in equine fetlock joints

s / Osteoarthritis and Cartilage 21 (2013) S63–S312 S103 177 ELECTROARTHROGRAPHY PROVIDES A NON-INVASIVE STREAMING POTENTIAL-BASED METHOD FOR DETECTING NATURAL AND TRYPSIN-INDUCED CARTILAGE DEGENERATION IN EQUINE FETLOCK JOINTS A. Changoor y, M. Hoba y, M. Garon z, E. Quenneville z, K. Gordon y, M.D. Buschmann x, P. Savard x, M.B. Hurtig y. yUniv. of Guelph, Guelph, ON, Canada; zBiomomentum Inc., Laval, QC, Canada; x Ecole Polytechnique Montreal, Montreal, QC, Canada Purpose: Electroarthrography (EAG) is a new technology capable of measuring cartilage streaming potentials non-invasively through electrodes contacting the skin surrounding a diarthrodial joint. Streaming potentials are produced during cartilage compression and directly reflect cartilage composition, structure and load bearing properties. Study objectives were to assess EAG sensitivity to naturally occurring and trypsin-induced cartilage degradation, as well as to compare EAG to direct measurements of cartilage streaming potentials and biomechanical properties. Methods: Distal forelimbs were collected from one horse exhibiting natural cartilage degradation (ICRS Grade 2) and one horse with normal cartilage (ICRS Grade 0). EAG was performed on the fetlock (metacarpophalangeal) joint during simulated physiological loading using gold-plated disk electrodes attached to skin at 8 sites around the fetlock (Fig.1) and EAG signals were acquired at 600 Hz. Cartilage degradation was induced in the right fetlock of the normal horse by intraarticular Fig. 1. EAG during A) standing and B) walking on the same fetlock preand posttrypsin and from a fetlock exhibiting natural cartilage degradation (ICRS score of 2). Two electrodes were placed at the anterior interface between the cannon/phalanx, one medial (CH1) and one lateral (CH2). Four electrodes were placed at interfaces between the medial cannon/phalanx (CH3), medial sesamoid/cannon (CH4), lateral sesamoid/ cannon/phalanx (CH5), and lateral sesamoid/cannon. Two electrodes were placed on the phalanx beneath the articulation, one medial (CH7) and one lateral (CH8). * indicates statistically significant (p<0.05) differences between control and both trypsin treated and natural degraded fetlocks. # indicates p<0.05 between control and naturally degraded fetlocks. injection of 0.5% w/v trypsin in Tris buffer and incubation at 37 C for 3 hours. EAG coefficients (mV/kN) were calculated by fitting EAG signals from each electrode to the measured load. Joints were then disarticulated and direct measurements of cartilage streaming potentials made at 75 sites with the Arthro-BST; an arthroscopic device that records streaming potentials during manual cartilage indentation through an array of 37 microelectrodes (5 microelectrodes/mm^2). The device calculates a quantitative parameter (QP) corresponding to the number of microelectrodes in contact with cartilage when the sum of potentials reaches 100mV. Cartilage disks were then isolated for testing in unconfined compression geometry. Each disk was subjected to five stress relaxation ramps of 2% strain. The fibril-network-reinforced biphasic model was used to obtain fibril modulus (Ef), matrix modulus (Em) and hydraulic permeability (k). Results: EAG coefficients were significantly reduced (p<0.05) following trypsin degradation of cartilage in all but two electrodes during standing and one during walking (Fig. 1). Joints with natural cartilage degradation also produced lower (p<0.05) EAG coefficients compared to normal control cartilage and were lower than that observed in the trypsin treated explant (Fig. 1). Significantly elevated QP, indicating lower cartilage stiffness, were observed after treatment with trypsin on both the phalanx (p<10^-5, n1⁄435) and cannon (p<10^-5, n1⁄440) (Fig. 2). QP measured in naturally degraded joints were higher (p<10^-5, n1⁄435 phalanx, n1⁄440 cannon) compared to controls and were similar to trypsin treated cartilage in the phalanx (p1⁄40.12, n1⁄435) but not the cannon (p1⁄40.0016, n1⁄440) (Fig. 2). Compared to controls, trypsin treatment reduced Em, representing proteoglycan matrix stiffness (p1⁄40.005, n1⁄46), but did not significantly alter Ef, representing collagen network stiffness (p1⁄40.15, n1⁄46), or k (p1⁄40.24, n1⁄46). Naturally degraded cartilage had similar Ef (p1⁄40.06, n1⁄46) and k (p1⁄40.23, n1⁄46) compared to trypsin treated but had significantly higher Em (p1⁄40.04, n1⁄46). Conclusions: Externally measured EAG was sensitive to cartilage degradation (Fig. 1) and reflected direct measurements of cartilage streaming potentials (Fig. 2). Biomechanical tests detected proteoglycan changes but were generally less sensitive to cartilage degradation compared to Arthro-BST and EAG, which are both streaming potentialbased methods. Trypsin produced cartilage changes similar to naturally occurring degradation observed in early OA, but less pronounced. These data demonstrate the potential for non-invasive EAG to provide a sensitive diagnostic of cartilage health that may contribute to the early detection and treatment of OA and other degenerative joint diseases. Fig. 2. Spatially resolved QP mapping of the articular surfaces from the fetlock joint obtained with the Arthro-BST. QP at each site ( ) are an average of three measurements. The QP scale is inversely proportional to cartilage stiffness so that higher values represent softer or degraded cartilage. Control and naturally degraded joint surfaces are from left fetlocks while trypsin treated joint surfaces are from a right fetlock. Note that the QP scales for the phalanx and cannon are different.

A comparison of the performance of three visual evoked potential-based methods to estimate visual acuity

To compare visual acuities estimated by three methods of visual evoked potential (VEP) recordings to those obtained by two subjective measures [ETDRS and FrACT (Freiburg acuity test)]. Ten healthy subjects, aged between 26 and 67years (mean 43.5), were examined. Best-corrected acuity determined by the ETDRS was between 0.03 and -0.3 logMAR (mean -0.06). Sweep VEPs (sweepVEP), pattern appearance VEPs (pappVEP) and steady-state VEPs (ssVEP) were recorded with two electrode placements (10-20 and Laplace) with best optical correction and with artificially degraded vision using five Bangerter occlusion foils, reducing acuity to about 0.1, 0.22, 0.52, 0.7 and 1.0 logMAR (0.8, 0.6, 0.3, 0.2 and 0.1 decimal scale). Two runs were performed. ETDRS and FrACT acuities showed good agreement, even though ETDRS seemed to underestimate acuity compared with FrACT at higher acuities. Laplace derivation did not improve any of the VEP-estimated acuities over the 10-20. SweepVEP tended to overestimate lower FrACT acuities, but showed good repeatability. PappVEP placed FrACT acuities into correct or neighboring categories in 87% of cases. Average ssVEP acuity showed little difference to those of FrACT but variance was larger. ROC analysis for typical clinical application showed good performance for all three methods. The two subjective measurements of acuities are well correlated. Under the conditions of our experiment, sweepVEP results were less variable and had a better repeatability than ssVEP acuities, whose analysis, in contrast to sweepVEP, can be automated. PappVEP estimates, however, offer a viable alternative, that is, quicker but of lower performance regarding the detection of low acuity thresholds. All methods had a good performance regarding minimum acuity detection if an average of two runs is used.

HORIBALFRE program: Higher Order Residue Interactions Based ALgorithm for Fold REcognition.

Understanding the functional and structural implication of a protein encoded in novel genes using function association or fold recognition approaches remains to be a challenging task in the current era of genomes, metagenomes and personal genomes. In an attempt to enhance potential-based fold-recognition methods in recognizing remote homology between proteins, we propose a new approach "Higher Order Residue Interaction Based ALgorithm for Fold REcognition (HORIBALFRE)". Higher order residue interactions refer to a class of interactions in protein structures mediated by C(α) or C(β) atoms within a pre-defined distance cut-off. Higher order residue interactions (pairwise, triplet and quadruplet interactions) play a vital role in attaining the stable conformation of a protein structure. In HORIBALFRE, we incorporated the potential contributions from two body (pairwise) interactions, three body (triplet interactions) and four-body (quadruple interaction) interactions, to implement a new fold recognition algorithm. Core of HORIBALFRE algorithm includes the potentials generated from a library of protein structure derived from manually curated CAMPASS database of structure based sequence alignment. We used Fischer's dataset, with 68 templates and 56 target sequences, derived from SCOP database and performed one-against-all sequence alignment using TCoffee. Various potentials were derived using custom scripts and these potentials were incorporated in the HORIBALFRE algorithm. In this manuscript, we report outline of a novel fold recognition algorithm and initial results. Our results show that inclusion of quadruplet class of higher order residue interaction improves fold recognition.

Structure-Based Pharmacophores for Virtual Screening.

Pharmacophores describe the spatial arrangement of essential interactions in a receptor-ligand complex. Although highly established in ligand-based virtual screening, the application of pharmacophores for in absence of a ligand is more sophisticated. This article summarizes the recent approaches to derive and evaluate pharmacophore models using only limited information (e.g. a homology model of the binding site). A range of different methodologies including geometrical and/or potential-based methods and successes in the application to virtual screening problems are described. Advantages and current limitations of the state-of-the-art methods and future perspectives for development are discussed in this publication.

Combining initialization and solution inverse methods for inverse electrocardiography

Many methods have been developed over the last 25 years for the inverse problem of electrocardiography. The 2 main classes of such methods that have been of recent interest use 2 alternative equivalent source formulations. Activation-based methods were use as a source model a dipole layer on the heart surface with identical known transmembrane potential waveforms at each node. Potential-based methods use as a source model potential values at each time instant at each node on a closed surface surrounding the sources. The former is highly constrained, nonlinear, and nonconvex, whereas the latter is loosely constrained but linear. Recent interest in activation-based iterative solutions has focused on initialization. Much recent interest in potential-based solutions has focused on devising constraints, which impose physiologically meaningful waveform shapes. Here we describe work using one method to initialize a second for both formulations. For activation-based solutions, we initialize by embedding the solution set for the nonconvex optimization problem, which results from fixing waveforms and allowing only activation sample times to vary, into a less constrained solution set, thus formulating a convex problem. To do so, we replace the hard constraints on waveform shape by softer constraints. We solve this convex optimization problem combining constraints on the residual with the waveform shape constraints and imposing smoothness of the activation surface. The resulting optimal solution will not be a feasible set of activation waveforms, but we use it to obtain a good initialization for subsequent Newton-type iterations for the nonlinear, nonconvex problem. For the potential-based problem, we use a recent method from our group, Wavefront-Based Potential Reconstruction. Wavefront-Based Potential Reconstruction uses a constraint based on segmenting the reconstructed potentials from a previous iteration or time step into 3 spatial regions: activated, not yet activated, and transition. The first 2 are modeled as spatially constant, the third by a specified transition function. This constraint is used in a Tikhonov-like regularization, producing wavefronts without the typical regularized smoothing. Wavefront-Based Potential Reconstruction requires an initialization to remove reference drift to create the 3-region segmentation. We use a different potential-based method, the “isotropy method” from Huiskamp and Greensite, to estimate the required initialization parameters. In both cases, the combination of these 2 inversemethods shows, in simulations based on measured canine heart surface data and data from the ECGSim software package, improved results compared with standard approaches.

Calculation of nuclear magnetic resonance shielding constants using potential-based methods

We present the calculation of nuclear magnetic resonance shielding constants using a range of different methods. In particular we examine two new methods proposed by Yang and Wu which are based on the Kohn–Sham potential. The first is a method which reproduces an accurate input density (WY) and the second is an implementation of the optimised effective potential method. We find that these methods give results which are very similar to each other and when the methods are applied to a hybrid functional (e.g. B3LYP) we obtain good agreement with experiment.

A computer modelling study of the uptake and segregation of fluoride ions at the hydrated hydroxyapatite (0001) surface: introducing a Ca10(PO4)6(OH)2potential model

A combination of electronic structure calculations and interatomic potential-based methods are employed to study the uptake and segregation of fluoride ions from solution into the hydroxyapatite lattice. The hydroxyapatite potential model derived for this work accurately reproduces experimental properties and relative enthalpies of formation and is further validated by Density Functiontional Theory calculations of fluoride defects in bulk hydroxyapatite. Calculations of solid solutions of fluor- and hydroxy-apatite show that hydroxy groups are easily replaced by fluoride ions on thermodynamic grounds (ΔEx = −0.4 to −6.4 kJ mol−1), forming sheets of fluoride in the a/b plane. Molecular Dynamics simulations of the incorporation of fluoride into hydroxyapatite show that fluoride ions are also easily incorporated from solution into the surface of hydroxyapatite (ΔE = −193 kJ mol−1), but they do not segregate into the bulk crystal beyond approximately 10 A. The hydroxy-groups, which remain aligned in the c-direction in the bulk material, due to the formation of pairs of OH− groups, are found to reverse randomly in the surface region when a vacuum interface is introduced. This surface region shows considerable relaxation and reconstruction of the calcium and phosphate sub-lattices, leading to the disintegration of the OH− pairs and hence their re-orientation. However, when the vacuum is filled with water, the surface relaxation is less extensive and the hydroxy groups remain aligned, although surface OH− groups dissolve into the water. When surface OH− groups are replaced by fluoride ions, this fluoride remains in the crystal lattice and further anchors surface calcium ions. As such this surface fluoride prevents the onset of apatite dissolution, although the fluorapatite layer is only superficial.

Comparison of the Bulk and Surface Properties of Ceria and Zirconia by ab Initio Investigations

In this paper, we present quantum mechanical (QM) calculations, at a periodic Hartee−Fock (HF) level, on the bulk and surface properties of cubic CeO2 and ZrO2. We have investigated the M−O bonding features, and established the high degree of ionicity of both materials, which is greater for CeO2 than ZrO2. The calculated values for the C11, C12, and C44 elastic constants, are in close agreement with experiment; an extended oxygen basis set, containing d-orbital polarization functions, is essential to model accurately the symmetry lowering during the C44 distortion. In the surface studies, we have calculated the surface energies of the {011} and {111} faces of both ceria and zirconia. QM results are compared with interatomic potential-based (IP) methods to assess the accuracy of the latter. We found that IP methods provide a correct estimate of the surface relaxations and the correct order of stability of the two faces examined, with the energy difference between the {011} and the {111} surfaces being appr...

Improving spatial and temporal resolution in evoked EEG responses using surface Laplacians

Spline generated surface Laplacian temporal wave forms are presented as a method to improve both spatial and temporal resolution of evoked EEG responses. Middle latency and the N1 components of the auditory evoked response were used to compare potential-based methods with surface Laplacian methods in the time domain. Results indicate that surface Laplacians provide better estimates of underlying cortical activity than do potential wave forms. Spatial discrimination among electrode sites was markedly better with surface Laplacian than with potential wave forms. Differences in the number and latencies of peaks, and their topographic distributions, were observed for surface Laplacian, particularly during the time period encompassing the middle latency responses. Focal activities were observed in surface Laplacian wave forms and topographic maps which were in agreement with previous findings from auditory evoked response studies. Methodological issues surrounding the application of spline methods to the time domain are also discussed. Surface Laplacian methods in the time domain appear to provide an improved way for studying evoked EEG responses by increasing temporal and spatial resolution of component characteristics.