Patrick D. Shipman
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View article: A New Formulation and Code to Compute Aerodynamic Roughness Length for Gridded Geometry—Tested on Lidar-Derived Snow Surfaces
A New Formulation and Code to Compute Aerodynamic Roughness Length for Gridded Geometry—Tested on Lidar-Derived Snow Surfaces Open
The roughness of the Earth’s surface dictates the nature of air flow across it. Detailed meteorological data that are necessary to access the aerodynamic roughness (z0) are not widely collected and, as such, the geometry of a surface can b…
View article: A Geometric-based Aerodynamic Roughness Length Formulation and Code Applied to Lidar-derived Snow Surfaces
A Geometric-based Aerodynamic Roughness Length Formulation and Code Applied to Lidar-derived Snow Surfaces Open
The roughness of the Earth’s surface dictates the nature of air flow across it. During some parts of the year, a large portion of the Earth’s surface is snow covered, and the roughness of the snow surface varies over the snow season and ov…
View article: Spatially Extended Dislocations Produced by the Dispersive Swift-Hohenberg Equation
Spatially Extended Dislocations Produced by the Dispersive Swift-Hohenberg Equation Open
Motivated by previous results showing that the addition of a linear dispersive term to the two-dimensional Kuramoto-Sivashinsky equation has a dramatic effect on the pattern formation, we study the Swift-Hohenberg equation with an added li…
View article: Estimating reaction parameters in mechanism‐enabled population balance models of nanoparticle size distributions: A Bayesian inverse problem approach
Estimating reaction parameters in mechanism‐enabled population balance models of nanoparticle size distributions: A Bayesian inverse problem approach Open
In order to quantitatively predict nano‐ as well as other particle‐size distributions, one needs to have both a mathematical model and estimates of the parameters that appear in these models. Here, we show how one can use Bayesian inversio…
View article: Determining the contributions of protein synthesis and breakdown to muscle atrophy requires non‐steady‐state equations
Determining the contributions of protein synthesis and breakdown to muscle atrophy requires non‐steady‐state equations Open
Background Ageing and cachexia cause a loss of muscle mass over time, indicating that protein breakdown exceeds protein synthesis. Deuterium oxide (D 2 O) is used for studies of protein turnover because of the advantages of long‐term label…
View article: National Estimates of Prevalence, Time-Trend, and Correlates of Smoking in US People Living with HIV (NHANES 1999–2016)
National Estimates of Prevalence, Time-Trend, and Correlates of Smoking in US People Living with HIV (NHANES 1999–2016) Open
Objective Approximately one in four deaths among people living with HIV (PLWH) in the United States can be attributed to cigarette smoking. Using a nationally representative sample of PLWH, this study examines the prevalence, time-trends, …
View article: Phase-Diffusion Equations for the Anisotropic Complex Ginzburg-Landau Equation
Phase-Diffusion Equations for the Anisotropic Complex Ginzburg-Landau Equation Open
The anisotropic complex Ginzburg-Landau equation (ACGLE) describes slow modulations of patterns in anisotropic spatially extended systems near oscillatory (Hopf) instabilities with zero wavenumbers. Traveling wave solutions to the ACGLE be…
View article: Particle Size Distributions via Mechanism-Enabled Population Balance Modeling
Particle Size Distributions via Mechanism-Enabled Population Balance Modeling Open
Mechanism-enabled population balance modeling (ME-PBM) was recently defined as the use of experimentally established (i.e., disproof-based, deliberately minimalistic, and pseudo-elementary step-based) mechanisms as more rigorous input for …
View article: Dust Effects on Ir(0)<sub>n</sub> Nanoparticle Formation Nucleation and Growth Kinetics and Particle Size-Distributions: Analysis by and Insights from Mechanism-Enabled Population Balance Modeling
Dust Effects on Ir(0)<sub>n</sub> Nanoparticle Formation Nucleation and Growth Kinetics and Particle Size-Distributions: Analysis by and Insights from Mechanism-Enabled Population Balance Modeling Open
The effects of microfiltration removal of filterable dust on nanoparticle formation kinetics and particle-size distribution, in a polyoxometalate polyanion (P2W15Nb3O629-)-stabilized Ir(0)n nanoparticle formation system, are analyzed by th…
View article: Mechanism-Enabled Population Balance Modeling of Particle Formation en Route to Particle Average Size and Size Distribution Understanding and Control
Mechanism-Enabled Population Balance Modeling of Particle Formation en Route to Particle Average Size and Size Distribution Understanding and Control Open
The concept of Mechanism-Enabled Population Balance Modeling (ME-PBM) is reported, illustrated by its application to a prototype Ir(0)n nanoparticle formation reaction. ME-PBM is defined herein as the use of now available, experimentally e…
View article: Julia and Mandelbrot Sets for Dynamics over the Hyperbolic Numbers
Julia and Mandelbrot Sets for Dynamics over the Hyperbolic Numbers Open
Julia and Mandelbrot sets, which characterize bounded orbits in dynamical systems over the complex numbers, are classic examples of fractal sets. We investigate the analogs of these sets for dynamical systems over the hyperbolic numbers. H…
View article: Julia and Mandelbrot sets for dynamics over the hyperbolic numbers
Julia and Mandelbrot sets for dynamics over the hyperbolic numbers Open
Julia and Mandelbrot sets, which characterize bounded orbits in dynamical systems over the complex numbers, are classic examples of fractal sets. We investigate the analogs of these sets for dynamical systems over the hyperbolic numbers. H…
View article: Informing the structure of complex Hadamard matrix spaces using a flow
Informing the structure of complex Hadamard matrix spaces using a flow Open
A complex Hadamard matrix $ H $ may be isolated or may lie in a higher-dimensional space of Hadamards. We provide an upper bound for this dimension as the dimension of the center subspace of a gradient flow and apply the Center Manifold Th…
View article: Enhanced skeletal muscle regrowth and remodelling in massaged and contralateral non‐massaged hindlimb
Enhanced skeletal muscle regrowth and remodelling in massaged and contralateral non‐massaged hindlimb Open
Key points Muscle fibre cross sectional area is enhanced with massage in the form of cyclic compressive loading during regrowth after atrophy. Massage enhances protein synthesis of the myofibrillar and cytosolic, but not the mitochondrial …
View article: Formation of square lattices in coupled pattern-forming systems
Formation of square lattices in coupled pattern-forming systems Open
A wide variety of natural and labo-ratory systems can produce patterns of ripples, hexagons, or squares. The formation of stable square patterns from partial differential equation models requires specific cubic nonlinearities involving hig…
View article: Informing the structure of complex Hadamard matrix spaces using a flow
Informing the structure of complex Hadamard matrix spaces using a flow Open
The defect of a complex Hadamard matrix $H$ is an upper bound for the dimension of a continuous Hadamard orbit stemming from $H$. We provide a new interpretation of the defect as the dimension of the center subspace of a gradient flow and …
View article: Topological Analysis of Pattern-Forming Systems
Topological Analysis of Pattern-Forming Systems Open
A few basic motifs, such as hexagonal lattices, are prevalent in a wide variety of pattern-forming biological and other chemical and physical systems. These include phyllotaxis (the arrangement of elements such as leaves or seeds on plant…
View article: The role of water and fire in driving tree dynamics in Australian savannas
The role of water and fire in driving tree dynamics in Australian savannas Open
Summary Ecologists rely on models to explore tree compositional changes especially when occurring over decades or centuries. In this article, we construct a theoretical, mathematical model to investigate the long‐term relationships between…
View article: AusSavannaModel: Journal of Ecology (2016) article release
AusSavannaModel: Journal of Ecology (2016) article release Open
This release is meant to accompany the journal article "The role of water and fire in driving tree dynamics in Australian savannas" by Christopher Strickland, Adam C. Liedloff, Garry D. Cook, Gerhard Dangelmayr, and Patrick D. Shipman publ…
View article: Producing nanodot arrays with improved hexagonal order by patterning surfaces before ion sputtering
Producing nanodot arrays with improved hexagonal order by patterning surfaces before ion sputtering Open
When the surface of a nominally flat binary material is bombarded with a broad, normally incident ion beam, disordered hexagonal arrays of nanodots can form. Shipman and Bradley have derived equations of motion that govern the coupled dyna…
View article: Persistence Images: An Alternative Persistent Homology Representation.
Persistence Images: An Alternative Persistent Homology Representation. Open
Many datasets can be viewed as a noisy sampling of an underlying topological space. Topological data analysis aims to understand and exploit this underlying structure for the purpose of knowledge discovery. A fundamental tool of the discip…
View article: Persistence Images: A Stable Vector Representation of Persistent Homology
Persistence Images: A Stable Vector Representation of Persistent Homology Open
Many datasets can be viewed as a noisy sampling of an underlying space, and tools from topological data analysis can characterize this structure for the purpose of knowledge discovery. One such tool is persistent homology, which provides a…
View article: A Stochastically Driven Model for Savanna Water Resource Dynamics
A Stochastically Driven Model for Savanna Water Resource Dynamics Open
Modeling has become an essential part of understanding ecosystem dynamics, and within the savanna ecology community, models are used as a key tool to advance theories about the determinants of savanna as an ecological state between forest …
View article: Modeling the contribution of individual proteins to mixed skeletal muscle protein synthetic rates over increasing periods of label incorporation
Modeling the contribution of individual proteins to mixed skeletal muscle protein synthetic rates over increasing periods of label incorporation Open
Advances in stable isotope approaches, primarily the use of deuterium oxide ( 2 H 2 O), allow for long-term measurements of protein synthesis, as well as the contribution of individual proteins to tissue measured protein synthesis rates. H…
View article: Geometric methods in the study of the snow surface roughness
Geometric methods in the study of the snow surface roughness Open
The snow surface is very dynamic, and the roughness of the snowpack surface varies spatially and temporally. The snow surface roughness influences the movement of air across the snow surface as well as the resulting transfers of energy, an…