Spatial Coarse Research Articles

Intraneural stimulation elicits discrimination of textural features by artificial fingertip in intact and amputee humans.

Restoration of touch after hand amputation is a desirable feature of ideal prostheses. Here, we show that texture discrimination can be artificially provided in human subjects by implementing a neuromorphic real-time mechano-neuro-transduction (MNT), which emulates to some extent the firing dynamics of SA1 cutaneous afferents. The MNT process was used to modulate the temporal pattern of electrical spikes delivered to the human median nerve via percutaneous microstimulation in four intact subjects and via implanted intrafascicular stimulation in one transradial amputee. Both approaches allowed the subjects to reliably discriminate spatial coarseness of surfaces as confirmed also by a hybrid neural model of the median nerve. Moreover, MNT-evoked EEG activity showed physiologically plausible responses that were superimposable in time and topography to the ones elicited by a natural mechanical tactile stimulation. These findings can open up novel opportunities for sensory restoration in the next generation of neuro-prosthetic hands.

OpenPSTD: The open source pseudospectral time-domain method for acoustic propagation

An open source implementation of the Fourier pseudospectral time-domain (PSTD) method for computing the propagation of sound is presented, which is geared towards applications in the built environment. Being a wave-based method, PSTD captures phenomena like diffraction, but maintains efficiency in processing time and memory usage as it allows to spatially sample close to the Nyquist criterion, thus keeping both the required spatial and temporal resolution coarse. In the implementation it has been opted to model the physical geometry as a composition of rectangular two-dimensional subdomains, hence initially restricting the implementation to orthogonal and two-dimensional situations. The strategy of using subdomains divides the problem domain into local subsets, which enables the simulation software to be built according to Object-Oriented Programming best practices and allows room for further computational parallelization. The software is built using the open source components, Blender, Numpy and Python, and has been published under an open source license itself as well. For accelerating the software, an option has been included to accelerate the calculations by a partial implementation of the code on the Graphical Processing Unit (GPU), which increases the throughput by up to fifteen times. The details of the implementation are reported, as well as the accuracy of the code. Program summaryProgram title: openPSTD v1.1 (v1.0 is the version without the GPU acceleration)Catalogue identifier: AFAA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAA_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, version 3No. of lines in distributed program, including test data, etc.: 45339No. of bytes in distributed program, including test data, etc.: 4139815Distribution format: tar.gzProgramming language: Python (as comes with Blender 2.72).Computer: Variable.Operating system: Windows, Linux, Mac OS X.RAM: From 250 MB for a typical geometry up to 1 GB for large geometries (with about 4M grid points)Classification: 4.3, 12.External routines: Blender 2.72, NumPy, SciPy, PyFFT, PyOpenCL, PyCUDANature of problem: Sound propagationSolution method: Fourier pseudospectral time-domain methodRestrictions: Structured grid, two dimensions, real-valued boundary conditions onlyUnusual features: Implementation of code using Blender/Python including GPU acceleration; subdomain modelling within Fourier pseudospectral methodRunning time: Depending on the dimension of the problem, calculation times take minutes up to hours

Connecting complexity with spectral entropy using the Laplace transformed solution to the fractional diffusion equation

Analytical solutions to the fractional diffusion equation are often obtained by using Laplace and Fourier transforms, which conveniently encode the order of the time and the space derivatives (α and β) as non-integer powers of the conjugate transform variables (s, and k) for the spectral and the spatial frequencies, respectively. This study presents a new solution to the fractional diffusion equation obtained using the Laplace transform and expressed as a Fox’s H-function. This result clearly illustrates the kinetics of the underlying stochastic process in terms of the Laplace spectral frequency and entropy. The spectral entropy is numerically calculated by using the direct integration method and the adaptive Gauss–Kronrod quadrature algorithm. Here, the properties of spectral entropy are investigated for the cases of sub-diffusion and super-diffusion. We find that the overall spectral entropy decreases with the increasing α and β, and that the normal or Gaussian case with α=1 and β=2, has the lowest spectral entropy (i.e., less information is needed to describe the state of a Gaussian process). In addition, as the neighborhood over which the entropy is calculated increases, the spectral entropy decreases, which implies a spatial averaging or coarse graining of the material properties. Consequently, the spectral entropy is shown to provide a new way to characterize the temporal correlation of anomalous diffusion. Future studies should be designed to examine changes of spectral entropy in physical, chemical and biological systems undergoing phase changes, chemical reactions and tissue regeneration.

Micro–macro transition and simplified contact models for wet granular materials

Wet granular materials in a quasistatic steady-state shear flow have been studied with discrete particle simulations. Macroscopic quantities, consistent with the conservation laws of continuum theory, are obtained by time averaging and spatial coarse graining. Initial studies involve understanding the effect of liquid content and liquid properties like the surface tension on the macroscopic quantities. Two parameters of the liquid bridge contact model have been identified as the constitutive parameters that influence the macroscopic rheology (i) the rupture distance of the liquid bridge model, which is proportional to the liquid content, and (ii) the maximum adhesive force, as controlled by the surface tension of the liquid. Subsequently, a correlation is developed between these microparameters and the steady-state cohesion in the limit of zero confining pressure. Furthermore, as second result, the macroscopic torque measured at the walls, which is an experimentally accessible parameter, is predicted from our simulation results with the same dependence on the microparameters. Finally, the steady- state cohesion of a realistic non-linear liquid bridge contact model scales well with the steady-state cohesion for a simpler linearized irreversible contact model with the same maximum adhesive force and equal energy dissipated per contact.

Thermal Ground State and Nonthermal Probes

The Euclidean formulation of SU(2) Yang-Mills thermodynamics admits periodic, (anti)self-dual solutions to the fundamental, classical equation of motion which possess one unit of topological charge: (anti)calorons. A spatial coarse graining over the central region in a pair of such localised field configurations with trivial holonomy generates an inert adjoint scalar fieldϕ, effectively describing the pure quantum part of the thermal ground state in the induced quantum field theory. Here we show for the limit of zero holonomy how (anti)calorons associate a temperature independent electric permittivity and magnetic permeability to the thermal ground state ofSU2CMB, the Yang-Mills theory conjectured to underlie the fundamental description of thermal photon gases.

One-loop photon–photon scattering in a thermal, deconfining SU(2) Yang–Mills plasma

For a deconfining thermal SU(2) Yang–Mills plasma we discuss the role of (anti)calorons in introducing non-thermal behavior effectively described in terms of Planck’s quantum of action ħ. This non-thermality cancels exactly between the ground-state estimate and its free quasiparticle excitations. Kinematic constraints in 4-vertex scattering and the counting of radial loop variables versus the number of independent constraints on them are re-visited. Next, we consider thermal 2→2 one-loop scattering of the modes remaining massless upon the (anti)caloron induced adjoint Higgs mechanism (thermal ground state after spatial coarse graining). Starting with stringent analytical arguments, we are able to exclude the contribution to photon–photon scattering from diagrams containing at least one three-vertex and, in a next step, a vast majority of all possible configurations involving two four-vertices. By numerical analysis we show that the remaining contribution of the overall S channel is severely suppressed compared those of the T and U channels, meaning that the creation of a pair of massive vector modes by a pair of photons and vice versa practically does not occur in the Yang–Mills plasma. For the T and U channels the domain of loop integration represents less than 10−7 times the volume of the unconstrained integration region. The thus introduced photon–photon correlation should affect the Cosmic Microwave Background’s polarization at low redshift. An adaption of the here-developed methods to the analysis of irreducible bubble diagrams could prove the conjecture of hep-th/0609033 on the termination of the loop expansion of thermodynamical quantities at a finite irreducible order.

The influence of non-climate predictors at local and landscape resolutions depends on the autecology of the species

Species distribution models have come under criticism for being too simplistic for making robust future forecasts, partly because they assume that climate is the main determinant of geographical range at large spatial extents and coarse resolutions, with non-climate predictors being important only at finer scales. We suggest that this paradigm might be obscured by species movement patterns. To explore this we used contrasting kangaroo (family Macropodidae) case studies: two species with relatively small, stable home ranges (Macropus giganteus and M. robustus) and three species with more extensive, adaptive ranging behaviour (M. antilopinus, M. fuliginosus and M. rufus). We predicted that non-climate predictors will be most influential to model fit and predictive performance at local spatial resolution for the former species and at landscape resolution for the latter species. We compared residuals autocovariate – boosted regression tree (RAC-BRT) model statistics with and without species-specific non-climate predictors (habitat, soil, fire, water and topography), at local- and landscape-level spatial resolutions (5 and 50 km). As predicted, the influence of non-climate predictors on model fit and predictive performance (compared with climate-only models) was greater at 50 compared with 5 km resolution for M. rufus and M. fuliginosus and the opposite trend was observed for M. giganteus. The results for M. robustus and M. antilopinus were inconclusive. Also notable was the difference in inter-scale importance of climate predictors in the presence of non-climate predictors. In conclusion, differences in autecology, particularly relating to space use, may contribute to the importance of non-climate predictors at a given scale, not model scale per se. Further exploration of this concept across a range of species is encouraged and findings may contribute to more effective conservation and management of species at ecologically meaningful scales.

The Doubly Conditioned Frequency Spectrum Does Not Distinguish between Ancient Population Structure and Hybridization

Distinguishing between hybridization and population structure in the ancestral species is a key challenge in our understanding of how permeable species boundaries are to gene flow. The doubly conditioned frequency spectrum (dcfs) has been argued to be a powerful metric to discriminate between these two explanations, and it was used to argue for hybridization between Neandertal and anatomically modern humans. The shape of the observed dcfs for these two species cannot be reproduced by a model that represents ancient population structure in Africa with two populations, while adding hybridization produces realistic shapes. In this letter, we show that this result is a consequence of the spatial coarseness of the demographic model and that a spatially structured stepping stone model can generate realistic dcfs without hybridization. This result highlights how inferences on hybridization between recently diverged species can be strongly affected by the choice of how population structure is represented in the underlying demographic model. We also conclude that the dcfs has limited power in distinguishing between the signals left by hybridization and ancient structure.

Radiation fields for nanoscale systems

Abstractmagnified imageFor a group of charged particles obeying quantum mechanics (QM) and interacting with an electromagnetic field, the charge, and current density in a pure state of the system are expressed in terms of the many‐body wave function. Using these as sources, the microscopic Maxwell equations can be written down for any given pure state of a many‐body system. By employing semi‐classical radiation theory (SCRT) with these sources, the microscopic Maxwell equations can be used to compute the strong radiation fields produced by interacting charged quantal particles. For a charged particle, three radiation fields involve only the vector potential A. This is another example demonstrating the observability of the vector potential. Five radiation fields are perpendicular to the canonical momentum of a single charged particle. For a group of charged particles, a new type of radiation field is predicted. This kind of radiation does not exist for a single charged particle. The macroscopic Maxwell equations are derived from the corresponding microscopic equations for a pure state by the Russakoff–Robinson procedure which requires only a spatial coarse graining. Because the sources of fields are also the responses of a system to an external field, one also has to give up the temporal coarse graining of the current density which is often supposed to be critical to the kinetic approach of conductivity.

Spatial surface coarseness analysis: technique for fingerprint spoof detection

Proposed is a technique for fingerprint spoof detection, the spatial surface coarseness analysis. This approach improves the wavelet analysis of the fingertip surface texture by introducing spatial features to the model. Thus, the accuracy of the fingerprint classification is increased to 70.09% compared with the original solution.

Comparing low‐frequency and intermittent variability in comprehensive climate models through nonlinear Laplacian spectral analysis

Nonlinear Laplacian spectral analysis (NLSA) is a recently developed technique for spatiotemporal analysis of high‐dimensional data, which represents temporal patterns via natural orthonormal basis functions on the nonlinear data manifold. Through such basis functions, determined efficiently via graph‐theoretic algorithms, NLSA captures intermittency, rare events, and other nonlinear dynamical features which are not accessible through linear approaches (e.g., singular spectrum analysis (SSA)). Here, we apply NLSA to study North Pacific SST monthly data from the CCSM3 and ECHAM5/MPI‐OM models. Without performing spatial coarse graining (i.e., operating in ambient‐space dimensions up to 1.6 × 105after lagged embedding), or seasonal‐cycle subtraction, the method reveals families of periodic, low‐frequency, and intermittent spatiotemporal modes. The intermittent modes, which describe variability in the Western and Eastern boundary currents, as well as variability in the subtropical gyre with year‐to‐year reemergence, are not captured by SSA, yet are likely to have high significance in a predictive context and utility in cross‐model comparisons.

Corrigendum on Seasonal and Spatial Coarse Particle Elemental Concentrations in the Los Angeles Area

Corrigendum on Seasonal and Spatial Coarse Particle Elemental Concentrations in the Los Angeles Area

Seasonal and Spatial Coarse Particle Elemental Concentrations in the Los Angeles Area

The concentrations of trace metals and elements in the coarse fraction of atmospheric particulate matter (CPM, particles smaller than 10 and larger than 2.5 μm in diameter, PM10–2.5) and their spatial and temporal trends were investigated in the greater Los Angeles area. Ten distinct sampling sites were chosen to encompass a variety of CPM sources, including urban, rural, coastal, inland, and near-freeway sites. Time-integrated 24-h CPM samples were collected at each location once a week, for an entire year, from April 2008 to March 2009, to characterize drivers of the seasonal and spatial patterns of the CPM trace metal content. Metals were quantified using sector-field inductively coupled plasma mass spectrometry (SF-ICP-MS). Trace metals in CPM displayed distinct seasonal and temporal variations, and a principal component analysis (PCA) was performed to aid the identification of the CPM sources underlying these variations. The probable sources of each principal component were identified using elemental...

Targeting the conformational transitions of MDM2 and MDMX: Insights into key residues affecting p53 recognition

The oncogenic proteins MDM2 and MDMX have distinct and critical roles in the control of the activity of the p53 tumor suppressor protein. Recently, we have used spatial coarse graining simulations to analyze the conformational transitions manifest in the p53 recognition of MDM2 and MDMX. These conformational movements are different between MDM2 and MDMX and unveil the presence of conserved and nonconserved interactions in the p53 binding cleft that may be exploited in the design of selective and dual modulators of the oncogenic proteins. In this study, we investigate the conformational profiles of apo- and p53-bound states of MDM2 and MDMX using molecular dynamic simulations along a time scale of 60 ns. The analysis of the trajectories is instrumental to discuss energetical and conformational aspects of p53 recognition and to point out specific key residues whose conformational shifts have crucial roles in affecting the apo- and p53-bound states of MDM2 and MDMX. Among these, in particular, linear discriminant analyses identify diverse conformations of Y99/Y100 (MDMX/MDM2) as markers of the apo- and p53-bound states of the oncogenic proteins. The results of this study shed further light on different p53 recognition in MDM2 and MDMX and may prove useful for the design and identification of new potent and selective synthetic modulators of p53-MDM2/MDMX interactions.

Molecular docking and spatial coarse graining simulations as tools to investigate substrate recognition, enhancer binding and conformational transitions in indoleamine-2,3-dioxygenase (IDO)

Indoleamine 2,3-dioxygenase (IDO) is an heme-containing enzyme involved in the regulation of important immunological responses and neurological processes. The enzyme catalyzes the oxidative cleavage of the pyrrole ring of the indole nucleus of tryptophan (Trp) to yield N-formylkynurenine, that is the initial and rate limiting step of the kynurenine pathway. Some indole derivatives have been reported to act as effectors of the enzyme by enhancing its catalytic activity. On the basis of the recent availability of the crystal structure of IDO, in this work we investigate substrate recognition and enhancer binding to IDO using molecular docking experiments. In addition, conformational transitions of IDO in response to substrate and enhancer binding are studied using coarse graining simulations with the program FIRST. The results enable us to identify (i) the binding site of enhancer modulators; (ii) the motion of an electrostatic gate that regulates the access of the substrate to the catalytic site of the enzyme; (iii) the movement of the anchoring region of a hairpin loop that may assist the shuttle of substrates/products to/from the catalytic site of IDO. These data, combined with available site-directed mutagenesis experiments, reveal that conformational transitions of IDO in response to substrate and enhancer binding are controlled by distinct combination of two conformational states (open and close) of the above structural motifs. On this basis, a molecular mechanism regarding substrate recognition and activity enhancement by indole derivatives is proposed.

Evaluation of national and global LAI products derived from optical remote sensing instruments over Canada

Leaf area index (LAI) is an important surface variable for monitoring the status of vegetation and as input in a number of ecosystem process models. There are currently several coarse-resolution LAI maps over Canada, including a Canada Centre for Remote Sensing ten-day, 1-km resolution, Canada-wide product based on SPOT-4 VEGETATION (VGT), a MODIS eight-day, 1-km resolution, global product and a monthly, 7-km resolution, global map produced using POLDER-1. These products are difficult to validate because of their large spatial extent and coarse resolution. In this study we use in situ LAI measurements collected over a wide range of forest types and ecological zones in Canada to derive 30-m resolution reference LAI maps based on robust error-in-measurement regressions to Landsat Enhanced Thematic Mapper Plus vegetation indices. The reference maps and LAI products were aggregated to a coarser resolution (3 km for MODIS and VGT and 7 km for POLDER) before comparison to account for registration errors, and variability in sensor projected point spread functions. Spatially corresponding aggregated pixels with both high-quality reference and coarse scale LAI retrievals were compared. The comparison shows reasonable agreement (biases less than 25% or one LAI) between the VGT and reference LAI. The MODIS LAI product showed weak correlations (R2<0.25) over all sites at the scale of comparison and typically overestimated reference LAI in mixed forests by approximately 200%. The POLDER LAI product, only available in June 1997, showed almost no correlation to the summer reference LAI datasets. It underestimated reference LAI for an early growing season with an extent, in some cases, greater than the seasonal differences in LAI. This independent validation of three large area LAI products suggests that there may be substantial biases due to the lack of regional tuning of retrieval algorithms. These biases are far larger than the uncertainties in the reference-based LAI scenes in the case of the MODIS product. This suggests that reliable LAI maps may require regional calibration to meet the Global Terrestrial Observing System mapping requirements of plusmn15% uncertainties

Numerical analysis of the averaged flow field in a turbulent lattice Boltzmann simulation

A direct numerical simulation of a turbulent flow field with a lattice BGK method is presented. A spatial coarse graining of the numerical results is compared with the expected LBGK dynamics for a flow field on a reduced lattice size. This comparison permits to exhibit subgrid properties of the fluid which are not resolved on the coarse lattice. As expected from existing subgrid models, an effective viscosity can be measured that increases when the lattice is coarse grained. Turbulence models based on an effective viscosity are particularly interesting in a lattice Boltzmann simulation, due to the linearity of the propagation operator.

Contrasting rooting patterns of some arid-zone fruit tree species from Botswana – I. Fine root distribution

Spatial coarse root distribution of the in situ grown species Strychnos cocculoides Bak., Strychnos spinosa Lam. (Loganiaceae), Vangueria infausta Burch. (Rubiaceae) and Grewia flava DC. (Tiliaceae) was investigated. The woody roots provide the scaffolding for fine roots, and thus underpin potential competition with fine roots of other species. We developed a method for quantitative description of spatial patterns of coarse roots and correlated fine root distribution with the spatial arrangement of the coarse root systems. In order to estimate different exploration and exploitation strategies, we used the spatial distribution of structural roots within the individual soil volumes (ISV) of each root system, and compared the results with other published parameters. We defined a new parameter, “generalized efficiency of exploitation” GEE(φ), unifying different notions from the literature. Among all the investigated species and dependent on the considered parameter, either Vangueria infausta or Grewia flava had the highest mean values of exploration, hence they could clearly be separated from both Strychnos species. For the exploitation indices, no significant differences were found. However, the generalized efficiency of exploitation GEE(φ) was again different between the species. For correlations between coarse and fine roots, the restriction to the ISV was useful to increase the strength of correlations.

A Heterogeneous Coarse Mesh Transport Method

A method to solve the neutron transport equation on a grid with arbitrarily large spatial coarse meshes (elements) is developed. The method, which is based on a variational principle, uses discontinuous trial functions to derive a set of integral equations. The trial functions are constructed from surface Green's functions for each unique coarse mesh (e.g., fuel assembly) in the system. The theoretical approach is validated numerically for three multigroup, slab geometry problems, with the angular dependence treated by the discrete ordinates (SN) method. In this case, the fine-mesh results are reproduced by the coarse-mesh method. #Current address: Dan Ilas, Ph.D., Nuclear Science Center, Louisiana State University, Baton Rouge, Louisiana, USA

Spatial and temporal coarse graining for dispersion in randomly packed spheres.

The propagator for molecular displacements P(zeta, t) and its first three cumulants were measured for Stokes flow in monodisperse bead packs with different sphere sizes d and molecular diffusion coefficients D(m). We systematically varied the normalized mean displacement <zeta>/d and diffusion length L(D)=sqrt[2D(m)t]/d. The experimental results map onto each other with this scaling. For L(D)/d<0.2 the propagator remains non-Gaussian, and thus an advection diffusion equation is not obeyed, for mean displacements measured up to <zeta>>10d. A Gaussian shape is approached for large mean displacements when L(D)>0.3d.