User’s Guide to ADMB2R: A Set of AD Model Builder Output Routines Compatible with the R Statistics Language

ADMB2R is a collection of AD Model Builder routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 ADMB2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the ADMB2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer ADMB2R to others in the hope that they will find it useful. (PDF contains 30 pages)

Keeping Research Data Safe: a cost model and guidance for UK universities (KRDS1)

This study has investigated the medium to long term costs to Higher Education Institutions (HEIs) of the preservation of research data and developed guidance to HEFCE and institutions on these issues. It has provided an essential methodological foundation on research data costs for the forthcoming HEFCE-sponsored feasibility study for a UK Research Data Service.It will also assist HEIs and funding bodies wishing to establish strategies and TRAC costings for long-term data management and archiving. The rising tide of digital research data raises issues relating to access, curation and preservation for HEIs and within the UK a growing number of research funders are now implementing policies requiring researchers to submit data management, preservation or data sharing plans with their funding applications.

An agent-based multi-scale wind generation model

(EuroPES 2009)

Scale-similarity model for Lagrangian velocity correlations in isotropic and stationary turbulence

A scale-similarity model for Lagrangian two-point, two-time velocity correlations LVCs in isotropic turbulence is developed from the Kolmogorov similarity hypothesis. It is a second approximation to the isocontours of LVCs, while the Smith-Hay model is only a first approximation. This model expresses the LVC by its space correlation and a dispersion velocity. We derive the analytical expression for the dispersion velocity from the Navier-Stokes equations using the quasinormality assumption. The dispersion velocity is dependent on enstrophy spectra and shown to be smaller than the sweeping velocity for the Eulerian velocity correlation. Therefore, the Lagrangian decorrelation process is slower than the Eulerian decorrelation process. The data from direct numerical simulation of isotropic turbulence support the scale-similarity model: the LVCs for different space separations collapse into a universal form when plotted against the separation axis defined by the model.

A surface energy model and application to mechanical behavior analysis of single crystals at sub-micron scale

Size effects of mechanical behaviors of materials are referred to the variation of the mechanical behavior due to the sample sizes changing from macroscale to micro-/nanoscales. At the micro-/nanoscale, since sample has a relatively high specific surface area (SSA) (ratio of surface area to volume), the surface although it is often neglected at the macroscale, becomes prominent in governing the energy effect, although it is often neglected at the macroscale, becomes prominent in governing the mechanical behavior. In the present research, a continuum model considering the surface energy effect is developed through introducing the surface energy to total potential energy. Simultaneously, a corresponding finite element method is developed. The model is used to analyze the axial equilibrium strain problem for a Cu nanowire at the external loading-free state. As another application of the model, from dimensional analysis, the size effects of uniform compression tests on the microscale cylinder specimens for Ni and Au single crystals are analyzed and compared with experiments in literatures. (C) 2009 Elsevier B.V. All rights reserved.

A Trabecular Bone Explant Model of Osteocyte–Osteoblast Co-Culture for Bone Mechanobiology

The osteocyte network is recognized as the major mechanical sensor in the bone remodeling process, and osteocyte-osteoblast communication acts as an important mediator in the coordination of bone formation and turnover. In this study, we developed a novel 3D trabecular bone explant co-culture model that allows live osteocytes situated in their native extracellular matrix environment to be interconnected with seeded osteoblasts on the bone surface. Using a low-level medium perfusion system, the viability of in situ osteocytes in bone explants was maintained for up to 4 weeks, and functional gap junction intercellular communication (GJIC) was successfully established between osteocytes and seeded primary osteoblasts. Using this novel co-culture model, the effects of dynamic deformational loading, GJIC, and prostaglandin E-2 (PGE(2)) release on functional bone adaptation were further investigated. The results showed that dynamical deformational loading can significantly increase the PGE(2) release by bone cells, bone formation, and the apparent elastic modulus of bone explants. However, the inhibition of gap junctions or the PGE(2) pathway dramatically attenuated the effects of mechanical loading. This 3D trabecular bone explant co-culture model has great potential to fill in the critical gap in knowledge regarding the role of osteocytes as a mechano-sensor and how osteocytes transmit signals to regulate osteoblasts function and skeletal integrity as reflected in its mechanical properties.

Two-Dimensional Hillslope Scale Soil Erosion Model

On a hillslope, overland flow first generates sheet erosion and then, with increasing flux, it causes rill erosion. Sheet erosion (interrill erosion) and rill erosion are commonly observed to coexist on hillslopes. Great differences exist between both the intensities and incidences of rill and interrill erosion. In this paper, a two-dimensional rill and interrill erosion model is developed to simulate the details of the soil erosion process on hillslopes. The hillslope is treated as a combination of a two-dimensional interrill area and a one-dimensional rill. The rill process, the interrill process, and the joint occurrence of rill and interrill areas are modeled, respectively. Thus, the process of sheet flow replenishing rill flow with water and sediment can be simulated in detail, which may possibly render more truthful results for rill erosion. The model was verified with two sets of data and the results seem good. Using this model, the characteristics of soil erosion on hillslopes are investigated. Study results indicate that (1) the proposed model is capable of describing the complex process of interrill and rill erosion on hillslopes; (2) the spatial distribution of erosion is simulated on a simplified two-dimensional hillslope, which shows that the distribution of interrill erosion may contribute to rill development; and (3) the quantity of soil eroded increases rapidly with the slope gradient, then declines, and a critical slope gradient exists, which is about 15-20 degrees for the accumulated erosion amount.

A Dynamic Model For Ice-Induced Vibration Of Structures

A dynamic model for the ice-induced vibration (IIV) of structures is developed in the present study. Ice properties have been taken into account, such as the discrete failure, the dependence of the crushing strength on the ice velocity, and the randomness of ice failure. The most important prediction of the model is to capture the resonant frequency lock-in, which is analog to that in the vortex-induced vibration. Based on the model, the mechanism of resonant IIV is discussed. It is found that the dependence of the ice crushing strength on the ice velocity plays an important role in the resonant frequency lock-in of IIV. In addition, an intermittent stochastic resonant vibration is simulated from the model. These predictions are supported by the laboratory and field observations reported. The present model is more productive than the previous models of IIV.

A Mechanical Model For The Quantification Of The Effect Of Laser Quenching On Ctod In Steels

The technology of laser quenching is widely used to improve the surface properties of steels in surface engineering. Generally, laser quenching of steels can lead to two important results. One is the generation of residual stress in the surface layer. In general, the residual stress varies from the surface to the interior along the quenched track depth direction, and the residual stress variation is termed as residual stress gradient effect in this work. The other is the change of mechanical properties of the surface layer, such as the increases of the micro-hardness, resulting from the changes of the microstructure of the surface layer. In this work, a mechanical model of a laser-quenched specimen with a crack in the middle of the quenched layer is developed to quantify the effect of residual stress gradient and the average micro-hardness over the crack length on crack tip opening displacement (CTOD). It is assumed that the crack in the middle of the quenched layer is created after laser quenching, and the crack can be a pre-crack or a defect due to some reasons, such as a void, cavity or a micro-crack. Based on the elastic-plastic fracture mechanics theory and using the relationship between the micro-hardness and yield strength, a concise analytical solution, which can be used to quantify the effect of residual stress gradient and the average micro-hardness over the crack length resulting from laser quenching on CTOD, is obtained. The concise analytical solution obtained in this work, cannot only be used as a means to predict the crack driving force in terms of the CTOD, but also serve as a baseline for further experimental investigation of the effect after laser-quenching treatment on fracture toughness in terms of the critical CTOD of a specimen, accounting for the laser-quenching effect. A numerical example presented in this work shows that the CTOD of the quenched can be significantly decreased in comparison with that of the unquenched. (C) 2008 Elsevier B.V. All rights reserved.

Earthquakes of the Nepal Himalaya : towards a physical model of the seismic cycle

Home to hundreds of millions of souls and land of excessiveness, the Himalaya is also the locus of a unique seismicity whose scope and peculiarities still remain to this day somewhat mysterious. Having claimed the lives of kings, or turned ancient timeworn cities into heaps of rubbles and ruins, earthquakes eerily inhabit Nepalese folk tales with the fatalistic message that nothing lasts forever. From a scientific point of view as much as from a human perspective, solving the mysteries of Himalayan seismicity thus represents a challenge of prime importance. Documenting geodetic strain across the Nepal Himalaya with various GPS and leveling data, we show that unlike other subduction zones that exhibit a heterogeneous and patchy coupling pattern along strike, the last hundred kilometers of the Main Himalayan Thrust fault, or MHT, appear to be uniformly locked, devoid of any of the “creeping barriers” that traditionally ward off the propagation of large events. The approximately 20 mm/yr of reckoned convergence across the Himalaya matching previously established estimates of the secular deformation at the front of the arc, the slip accumulated at depth has to somehow elastically propagate all the way to the surface at some point. And yet, neither large events from the past nor currently recorded microseismicity nearly compensate for the massive moment deficit that quietly builds up under the giant mountains. Along with this large unbalanced moment deficit, the uncommonly homogeneous coupling pattern on the MHT raises the question of whether or not the locked portion of the MHT can rupture all at once in a giant earthquake. Univocally answering this question appears contingent on the still elusive estimate of the magnitude of the largest possible earthquake in the Himalaya, and requires tight constraints on local fault properties. What makes the Himalaya enigmatic also makes it the potential source of an incredible wealth of information, and we exploit some of the oddities of Himalayan seismicity in an effort to improve the understanding of earthquake physics and cipher out the properties of the MHT. Thanks to the Himalaya, the Indo-Gangetic plain is deluged each year under a tremendous amount of water during the annual summer monsoon that collects and bears down on the Indian plate enough to pull it away from the Eurasian plate slightly, temporarily relieving a small portion of the stress mounting on the MHT. As the rainwater evaporates in the dry winter season, the plate rebounds and tension is increased back on the fault. Interestingly, the mild waggle of stress induced by the monsoon rains is about the same size as that from solid-Earth tides which gently tug at the planets solid layers, but whereas changes in earthquake frequency correspond with the annually occurring monsoon, there is no such correlation with Earth tides, which oscillate back-and-forth twice a day. We therefore investigate the general response of the creeping and seismogenic parts of MHT to periodic stresses in order to link these observations to physical parameters. First, the response of the creeping part of the MHT is analyzed with a simple spring-and-slider system bearing rate-strengthening rheology, and we show that at the transition with the locked zone, where the friction becomes near velocity neutral, the response of the slip rate may be amplified at some periods, which values are analytically related to the physical parameters of the problem. Such predictions therefore hold the potential of constraining fault properties on the MHT, but still await observational counterparts to be applied, as nothing indicates that the variations of seismicity rate on the locked part of the MHT are the direct expressions of variations of the slip rate on its creeping part, and no variations of the slip rate have been singled out from the GPS measurements to this day. When shifting to the locked seismogenic part of the MHT, spring-and-slider models with rate-weakening rheology are insufficient to explain the contrasted responses of the seismicity to the periodic loads that tides and monsoon both place on the MHT. Instead, we resort to numerical simulations using the Boundary Integral CYCLes of Earthquakes algorithm and examine the response of a 2D finite fault embedded with a rate-weakening patch to harmonic stress perturbations of various periods. We show that such simulations are able to reproduce results consistent with a gradual amplification of sensitivity as the perturbing period get larger, up to a critical period corresponding to the characteristic time of evolution of the seismicity in response to a step-like perturbation of stress. This increase of sensitivity was not reproduced by simple 1D-spring-slider systems, probably because of the complexity of the nucleation process, reproduced only by 2D-fault models. When the nucleation zone is close to its critical unstable size, its growth becomes highly sensitive to any external perturbations and the timings of produced events may therefore find themselves highly affected. A fully analytical framework has yet to be developed and further work is needed to fully describe the behavior of the fault in terms of physical parameters, which will likely provide the keys to deduce constitutive properties of the MHT from seismological observations.

Large-eddy simulations of fully developed turbulent channel and pipe flows with smooth and rough walls

Studies in turbulence often focus on two flow conditions, both of which occur frequently in real-world flows and are sought-after for their value in advancing turbulence theory. These are the high Reynolds number regime and the effect of wall surface roughness. In this dissertation, a Large-Eddy Simulation (LES) recreates both conditions over a wide range of Reynolds numbers Re_τ = O(10²)-O(10⁸) and accounts for roughness by locally modeling the statistical effects of near-wall anisotropic fine scales in a thin layer immediately above the rough surface. A subgrid, roughness-corrected wall model is introduced to dynamically transmit this modeled information from the wall to the outer LES, which uses a stretched-vortex subgrid-scale model operating in the bulk of the flow. Of primary interest is the Reynolds number and roughness dependence of these flows in terms of first and second order statistics. The LES is first applied to a fully turbulent uniformly-smooth/rough channel flow to capture the flow dynamics over smooth, transitionally rough and fully rough regimes. Results include a Moody-like diagram for the wall averaged friction factor, believed to be the first of its kind obtained from LES. Confirmation is found for experimentally observed logarithmic behavior in the normalized stream-wise turbulent intensities. Tight logarithmic collapse, scaled on the wall friction velocity, is found for smooth-wall flows when Re_τ ≥ O(10⁶) and in fully rough cases. Since the wall model operates locally and dynamically, the framework is used to investigate non-uniform roughness distribution cases in a channel, where the flow adjustments to sudden surface changes are investigated. Recovery of mean quantities and turbulent statistics after transitions are discussed qualitatively and quantitatively at various roughness and Reynolds number levels. The internal boundary layer, which is defined as the border between the flow affected by the new surface condition and the unaffected part, is computed, and a collapse of the profiles on a length scale containing the logarithm of friction Reynolds number is presented. Finally, we turn to the possibility of expanding the present framework to accommodate more general geometries. As a first step, the whole LES framework is modified for use in the curvilinear geometry of a fully-developed turbulent pipe flow, with implementation carried out in a spectral element solver capable of handling complex wall profiles. The friction factors have shown favorable agreement with the superpipe data, and the LES estimates of the Karman constant and additive constant of the log-law closely match values obtained from experiment.

I. Application of multi-Regge theory to production processes. II. High energy model for proton-proton scattering

This dissertation consists of two parts. The first part presents an explicit procedure for applying multi-Regge theory to production processes. As an illustrative example, the case of three body final states is developed in detail, both with respect to kinematics and multi-Regge dynamics. Next, the experimental consistency of the multi-Regge hypothesis is tested in a specific high energy reaction; the hypothesis is shown to provide a good qualitative fit to the data. In addition, the results demonstrate a severe suppression of double Pomeranchon exchange, and show the coupling of two "Reggeons" to an external particle to be strongly damped as the particle's mass increases. Finally, with the use of two body Regge parameters, order of magnitude estimates of the multi-Regge cross section for various reactions are given.

The second part presents a diffraction model for high energy proton-proton scattering. This model developed by Chou and Yang assumes high energy elastic scattering results from absorption of the incident wave into the many available inelastic channels, with the absorption proportional to the amount of interpenetrating hadronic matter. The assumption that the hadronic matter distribution is proportional to the charge distribution relates the scattering amplitude for pp scattering to the proton form factor. The Chou-Yang model with the empirical proton form factor as input is then applied to calculate a high energy, fixed momentum transfer limit for the scattering cross section, This limiting cross section exhibits the same "dip" or "break" structure indicated in present experiments, but falls significantly below them in magnitude. Finally, possible spin dependence is introduced through a weak spin-orbit type term which gives rather good agreement with pp polarization data.

The DICER Model: Methodological Issues and Initial Results

31 p.

Collective behavior of asperities as a model for friction and adhesion

Understanding friction and adhesion in static and sliding contact of surfaces is important in numerous physical phenomena and technological applications. Most surfaces are rough at the microscale, and thus the real area of contact is only a fraction of the nominal area. The macroscopic frictional and adhesive response is determined by the collective behavior of the population of evolving and interacting microscopic contacts. This collective behavior can be very different from the behavior of individual contacts. It is thus important to understand how the macroscopic response emerges from the microscopic one. In this thesis, we develop a theoretical and computational framework to study the collective behavior. Our philosophy is to assume a simple behavior of a single asperity and study the collective response of an ensemble. Our work bridges the existing well-developed studies of single asperities with phenomenological laws that describe macroscopic rate-and-state behavior of frictional interfaces. We find that many aspects of the macroscopic behavior are robust with respect to the microscopic response. This explains why qualitatively similar frictional features are seen for a diverse range of materials. We first show that the collective response of an ensemble of one-dimensional independent viscoelastic elements interacting through a mean field reproduces many qualitative features of static and sliding friction evolution. The resulting macroscopic behavior is different from the microscopic one: for example, even if each contact is velocity-strengthening, the macroscopic behavior can be velocity-weakening. The framework is then extended to incorporate three-dimensional rough surfaces, long- range elastic interactions between contacts, and time-dependent material behaviors such as viscoelasticity and viscoplasticity. Interestingly, the mean field behavior dominates and the elastic interactions, though important from a quantitative perspective, do not change the qualitative macroscopic response. Finally, we examine the effect of adhesion on the frictional response as well as develop a force threshold model for adhesion and mode I interfacial cracks.

A model for energy and morphology of crystalline grain boundaries with arbitrary geometric character

It has been well-established that interfaces in crystalline materials are key players in the mechanics of a variety of mesoscopic processes such as solidification, recrystallization, grain boundary migration, and severe plastic deformation. In particular, interfaces with complex morphologies have been observed to play a crucial role in many micromechanical phenomena such as grain boundary migration, stability, and twinning. Interfaces are a unique type of material defect in that they demonstrate a breadth of behavior and characteristics eluding simplified descriptions. Indeed, modeling the complex and diverse behavior of interfaces is still an active area of research, and to the author's knowledge there are as yet no predictive models for the energy and morphology of interfaces with arbitrary character. The aim of this thesis is to develop a novel model for interface energy and morphology that i) provides accurate results (especially regarding "energy cusp" locations) for interfaces with arbitrary character, ii) depends on a small set of material parameters, and iii) is fast enough to incorporate into large scale simulations.

In the first half of the work, a model for planar, immiscible grain boundary is formulated. By building on the assumption that anisotropic grain boundary energetics are dominated by geometry and crystallography, a construction on lattice density functions (referred to as "covariance") is introduced that provides a geometric measure of the order of an interface. Covariance forms the basis for a fully general model of the energy of a planar interface, and it is demonstrated by comparison with a wide selection of molecular dynamics energy data for FCC and BCC tilt and twist boundaries that the model accurately reproduces the energy landscape using only three material parameters. It is observed that the planar constraint on the model is, in some cases, over-restrictive; this motivates an extension of the model.

In the second half of the work, the theory of faceting in interfaces is developed and applied to the planar interface model for grain boundaries. Building on previous work in mathematics and materials science, an algorithm is formulated that returns the minimal possible energy attainable by relaxation and the corresponding relaxed morphology for a given planar energy model. It is shown that the relaxation significantly improves the energy results of the planar covariance model for FCC and BCC tilt and twist boundaries. The ability of the model to accurately predict faceting patterns is demonstrated by comparison to molecular dynamics energy data and experimental morphological observation for asymmetric tilt grain boundaries. It is also demonstrated that by varying the temperature in the planar covariance model, it is possible to reproduce a priori the experimentally observed effects of temperature on facet formation.

Finally, the range and scope of the covariance and relaxation models, having been demonstrated by means of extensive MD and experimental comparison, future applications and implementations of the model are explored.