Associate Professor

Welty Faculty Fellow

Associate Head for Undergraduate Programs

School of Mechanical, Industrial, and Manufacturing Engineering

Oregon State University

Associate Editor-in-Chief,

email ⋅ mastadon

Filter by publication topic.

Cantera ChemKED GPUs Monte Carlo ODEs atmospheric chemistry biogeochemistry chemical kinetics computational fluid dynamics diffusion direct numerical simulation domain decomposition exascale experimental measurements feedstock to function finite element analysis integrators linear algebra live fuels machine learning manufacturing model reduction neutron transport nuclear reactors numerical methods ocean parameter databases reduction algorithms smoldering sustainable aviation fuels swept rule turbulence turbulent flames vacuum arc remelting vectorization wildfire

Skyler Kern, Mary E. McGuinn, Katherine M. Smith, Nadia Pinardi, Kyle E. Niemeyer, Nicole S. Lovenduski, Peter Hamlington (2024)

Computationally efficient parameter estimation for high-dimensional ocean biogeochemical models

*Geoscientific Model Development*

Shows a method for optimizing parameters for biogeochemical models based on ocean observations.

Computationally efficient parameter estimation for high-dimensional ocean biogeochemical models

Shows a method for optimizing parameters for biogeochemical models based on ocean observations.

Joanna Morgan, Ilham Variansyah, Samuel Pasmann, Kayla B. Clements, Braxton Cuneo, Alexander Mote, Charles Goodman, Caleb Shaw, Jordan Northrop, Rohan Pankaj, Ethan Lame, Benjamin Whewell, Ryan McClarren, Todd S. Palmer, Lizhong Chen, Dmitriy Anistratov, C. T. Kelley, Camille Palmer, Kyle E. Niemeyer (2024)

Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development

*Journal of Open Source Software*

Introduces MC/DC, a Python-based software package for modeling transient (i.e., time-dependent) neutron transport that performs well on exascale-class high-performance computing systems.

Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development

Introduces MC/DC, a Python-based software package for modeling transient (i.e., time-dependent) neutron transport that performs well on exascale-class high-performance computing systems.

Joanna Morgan, Alexander Mote, Samuel L. Pasmann, Gavin Ridley, Todd S. Palmer, Kyle E. Niemeyer, Ryan McClarren (2024)

The Monte Carlo Computational Summit - October 25 & 26, 2023 - Notre Dame, Indiana, USA

*Journal of Computational and Theoretical Transport*

Summarizes discussions held at the 2023 Monte Carlo Computational Summit.

The Monte Carlo Computational Summit - October 25 & 26, 2023 - Notre Dame, Indiana, USA

Summarizes discussions held at the 2023 Monte Carlo Computational Summit.

Diba Behnoudfar, Kyle E. Niemeyer (2024)

A physics-based ignition model with detailed chemical kinetics for live fuel burning studies

*Combustion and Flame*

Introduces a physics-based model for simulating ignition of live fuels (like trees and shrubs), that considers detailed models for fuel chemistry.

A physics-based ignition model with detailed chemical kinetics for live fuel burning studies

Introduces a physics-based model for simulating ignition of live fuels (like trees and shrubs), that considers detailed models for fuel chemistry.

Benjamin D. Smucker, W. Jayani Jayasuriya, Kyle E. Niemeyer, David Blunck (2024)

Influence of lignin on smoldering propagation

*Combustion and Flame*

Uses experiments and simulations to show how greater amounts of lignin in woody fuels slows down smouldering combustion.

Influence of lignin on smoldering propagation

Uses experiments and simulations to show how greater amounts of lignin in woody fuels slows down smouldering combustion.

Kyle E. Niemeyer, Meegan Kelly (2023)

Right Onsite: Accelerating deployment of onsite clean energy technology in the industrial sector

*2023 ACEEE Summer Study on Energy Efficiency in Industry*

Discusses the current state of onsite clean energy systems in the US industrial sector, needs and barriers, and strategies the US Department of Energy is taking to accelerate adoption.

Right Onsite: Accelerating deployment of onsite clean energy technology in the industrial sector

Discusses the current state of onsite clean energy systems in the US industrial sector, needs and barriers, and strategies the US Department of Energy is taking to accelerate adoption.

Parker Johnson, Michael Zingale, Eric T. Johnson, Alexander Smith, Kyle E. Niemeyer (2023)

A Fully Explicit Integrator for Modeling Astrophysical Reactive Flows

*Research Notes of the AAS*

Shows the Runge-Kutta-Chebyshev method efficiently integrates reactions in astrophysical reactive flows, such as simulations of X-ray bursts.

A Fully Explicit Integrator for Modeling Astrophysical Reactive Flows

Shows the Runge-Kutta-Chebyshev method efficiently integrates reactions in astrophysical reactive flows, such as simulations of X-ray bursts.

Anthony S. Walker, Raymond L. Speth, Kyle E. Niemeyer (2023)

Generalized preconditioning for accelerating simulations with large kinetic models

*Proceedings of the Combustion Institute*

Extends a method to speed up chemistry simulations in Cantera, by preconditioning and sparse linear algebra operations.

Generalized preconditioning for accelerating simulations with large kinetic models

Extends a method to speed up chemistry simulations in Cantera, by preconditioning and sparse linear algebra operations.

Ilham Variansyah, Joanna Morgan, Jordan Northrop, Kyle E. Niemeyer, Ryan G. McClarren (2023)

Development of MC/DC: a performant, scalable, and portable Python-based Monte Carlo neutron transport code

*International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering*

Verifies and demonstrates MC/DC (Monte Carlo Dynamic Code) code for simulating transient neutron transport.

Development of MC/DC: a performant, scalable, and portable Python-based Monte Carlo neutron transport code

Verifies and demonstrates MC/DC (Monte Carlo Dynamic Code) code for simulating transient neutron transport.

Joanna Morgan, Travis J. Trahan, Timothy P. Burke, Colin J. Josey, Kyle E. Niemeyer (2023)

Hybrid-Delta Tracking on a Structured Mesh in MCATK

*International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering*

Demonstrates performance of hybrid delta tracking for surfaces in the Monte Carlo Application Toolkit.

Hybrid-Delta Tracking on a Structured Mesh in MCATK

Demonstrates performance of hybrid delta tracking for surfaces in the Monte Carlo Application Toolkit.

Joanna Morgan, Ilham Variansyah, Todd S. Palmer, Kyle E. Niemeyer (2023)

Exploring One-Cell Inversion Method for Transient Transport on GPU

*International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering*

Introduces a new iterative scheme for deterministic neutron transport modeling, one-cell inversion, that offers high performance on GPUs.

Exploring One-Cell Inversion Method for Transient Transport on GPU

Introduces a new iterative scheme for deterministic neutron transport modeling, one-cell inversion, that offers high performance on GPUs.

W. Jayani Jayasuriya, Tejas C. Mulky, Kyle E. Niemeyer (2022)

Smouldering combustion in cellulose and hemicellulose mixtures: Examining the roles of density, fuel composition, oxygen concentration, and moisture content

*Combustion Theory and Modelling*

Examines the roles of some key physical parameters on smoldering combustion in cellulose and hemicelluose mixtures, relevant to fuels in wildland fires; shows how fuel composition changes critical moisture content of ignition and extincion.

Smouldering combustion in cellulose and hemicellulose mixtures: Examining the roles of density, fuel composition, oxygen concentration, and moisture content

Examines the roles of some key physical parameters on smoldering combustion in cellulose and hemicelluose mixtures, relevant to fuels in wildland fires; shows how fuel composition changes critical moisture content of ignition and extincion.

Aaron J. Fillo, Peter Hamlington, Kyle E. Niemeyer (2022)

Assessing diffusion model impacts on enstrophy and flame structure in turbulent lean premixed flames

*Combustion Theory and Modelling*

Shows that choice of diffusion model noticably impacts both turbulence dynamics (shown with the enstrophy, or vorticity magnitude) and flame structure.

Assessing diffusion model impacts on enstrophy and flame structure in turbulent lean premixed flames

Shows that choice of diffusion model noticably impacts both turbulence dynamics (shown with the enstrophy, or vorticity magnitude) and flame structure.

Ana E. Comesana, Tyler T. Huntington, Corinne D. Scown, Kyle E. Niemeyer, Vi Rapp (2022)

A systematic method for selecting molecular descriptors as features when training models for predicting physiochemical properties

*Fuel*

Presents a new approach for identifying which pieces of information about molecules should be used when training machine-learning models to predict properties, and demonstrates models for predicting properties relevant to biofuels.

A systematic method for selecting molecular descriptors as features when training models for predicting physiochemical properties

Presents a new approach for identifying which pieces of information about molecules should be used when training machine-learning models to predict properties, and demonstrates models for predicting properties relevant to biofuels.

Nicholas Curtis, Kyle E. Niemeyer, Chih-Jen Sung (2022)

Accelerating reactive-flow simulations using vectorized chemistry integration

*Computer Physics Communications*

Presents an approach to reducing the cost of simulating reacting fluid flows using vectorization of the chemistry integration.

Accelerating reactive-flow simulations using vectorized chemistry integration

Presents an approach to reducing the cost of simulating reacting fluid flows using vectorization of the chemistry integration.

Joanna Morgan, Todd S. Palmer, Kyle E. Niemeyer (2022)

Explorations of Python-Based Automatic Hardware Code Generation for Neutron Transport Applications

*Transactions of the American Nuclear Society*

Examines techniques for using Python libraries to easily parallelize a Monte Carlo neutron transport solver on large-scale high performance computing systems.

Explorations of Python-Based Automatic Hardware Code Generation for Neutron Transport Applications

Examines techniques for using Python libraries to easily parallelize a Monte Carlo neutron transport solver on large-scale high performance computing systems.

Joanna Morgan, Alex Long, Kendra Long, Kyle E. Niemeyer (2022)

Novel MC TRT Method: Vectorizable Variance Reduction for Energy Spectra

*Transactions of the American Nuclear Society*

Presents a method for reducing the statistical variance in thermal radiation transport solver to better-resolve energy spectra at lower computational cost.

Novel MC TRT Method: Vectorizable Variance Reduction for Energy Spectra

Presents a method for reducing the statistical variance in thermal radiation transport solver to better-resolve energy spectra at lower computational cost.

Katherine M. Smith, Skyler Kern, Peter Hamlington, Marco Zavatarelli, Nadia Pinardi, Emily Klee, Kyle E. Niemeyer (2021)

BFM17 v1.0: Reduced-Order Biogeochemical Flux Model for Upper Ocean Biophysical Simulations

*Geoscientific Model Development*

Presents a novel reduced model for biogeochemistry that can be used in expensive, highly accurate simulations of the upper ocean.

BFM17 v1.0: Reduced-Order Biogeochemical Flux Model for Upper Ocean Biophysical Simulations

Presents a novel reduced model for biogeochemistry that can be used in expensive, highly accurate simulations of the upper ocean.

Anthony S. Walker, Kyle E. Niemeyer (2021)

Applying the swept rule for solving two-dimensional partial differential equations on heterogeneous architectures

*Mathematical and Computational Applications*

Extends the swept rule for domain decomposition to working on heterogeneous combinations of CPUs and GPUs, for solving two-dimensional partial differential equations.

Applying the swept rule for solving two-dimensional partial differential equations on heterogeneous architectures

Extends the swept rule for domain decomposition to working on heterogeneous combinations of CPUs and GPUs, for solving two-dimensional partial differential equations.

Aaron J. Fillo, Jason Schlup, Guillaume Blanquart, Kyle E. Niemeyer (2021)

Assessing the impact of multicomponent diffusion in direct numerical simulations of premixed, high-Karlovitz, turbulent flames

*Combustion and Flame*

Shows that the choice of diffusion model matters in simulations of turbulent flames, comparing the commonly used mixture-averaged model to the accurate but more expensive multicomponent model.

Assessing the impact of multicomponent diffusion in direct numerical simulations of premixed, high-Karlovitz, turbulent flames

Shows that the choice of diffusion model matters in simulations of turbulent flames, comparing the commonly used mixture-averaged model to the accurate but more expensive multicomponent model.

Dan Magee, Anthony S. Walker, Kyle E. Niemeyer (2021)

Applying the swept rule for solving explicit partial differential equations on heterogeneous computing systems

*Journal of Supercomputing*

Extends the swept rule for domain decomposition to working on heterogeneous combinations of CPUs and GPUs, and shows that the method can lead to performance benefits or downsides depending on the configuration.

Applying the swept rule for solving explicit partial differential equations on heterogeneous computing systems

Extends the swept rule for domain decomposition to working on heterogeneous combinations of CPUs and GPUs, and shows that the method can lead to performance benefits or downsides depending on the configuration.

Aaron J. Fillo, Jason Schlup, Guillaume Beardsell, Guillaume Blanquart, Kyle E. Niemeyer (2020)

A fast, low-memory, and stable algorithm for implementing multicomponent transport in direct numerical simulations

*Journal of Computational Physics*

Introduces a method for efficiently implementing accurate multicomponent diffusion models in high-fidelity computational fluid dynamics simulations of reacting turbulent flows.

A fast, low-memory, and stable algorithm for implementing multicomponent transport in direct numerical simulations

Introduces a method for efficiently implementing accurate multicomponent diffusion models in high-fidelity computational fluid dynamics simulations of reacting turbulent flows.

Rolf Sander, Andreas Baumgaertner, David Cabrera-Perez, Franziska Frank, Sergey Gromov, Jens-Uwe Grooß, Hartwig Harder, Vincent Huijnen, Patrick Jöckel, Vlassis A. Karydis, Kyle E. Niemeyer, Andrea Pozzer, Hella Riede, Martin G. Schultz, Domenico Taraborrelli, Sebastian Tauer (2019)

The community atmospheric chemistry box model CAABA/MECCA-4.0

*Geoscientific Model Development*

Presents an updated version of a model for atmospheric chemistry, including the capability of reducing the model using a method adapted from the combustion literature.

The community atmospheric chemistry box model CAABA/MECCA-4.0

Presents an updated version of a model for atmospheric chemistry, including the capability of reducing the model using a method adapted from the combustion literature.

Jeffrey F. Glusman, Kyle E. Niemeyer, Amanda S. Makowiecki, Nicholas T. Wimer, Caelan Lapointe, Gregory B. Rieker, Peter Hamlington, John W. Daily (2019)

Reduced Gas-Phase Kinetic Models for Burning of Douglas Fir

*Frontiers in Mechanical Engineering*

Presents and validates a reduced model for simulating burning of Douglas Fir trees.

Reduced Gas-Phase Kinetic Models for Burning of Douglas Fir

Presents and validates a reduced model for simulating burning of Douglas Fir trees.

Phillip Mestas, Parker Clayton, Kyle E. Niemeyer (2019)

pyMARS: automatically reducing chemical kinetic models in Python

*Journal of Open Source Software*

Presents a new Python-based open-source software package for automatically reducing chemical kinetic models, pyMARS.

pyMARS: automatically reducing chemical kinetic models in Python

Presents a new Python-based open-source software package for automatically reducing chemical kinetic models, pyMARS.

Katherine M. Smith, Peter Hamlington, Kyle E. Niemeyer, Baylor Fox-Kemper, Nicole S. Lovenduski (2019)

Effects of Langmuir turbulence on upper ocean carbonate chemistry

*Journal of Advances in Modeling Earth Systems*

Shows that carbonate chemistry and turbulent mixing in the upper ocean interact, and time-dependent chemistry needs to be considered for accurate simulations.

Effects of Langmuir turbulence on upper ocean carbonate chemistry

Shows that carbonate chemistry and turbulent mixing in the upper ocean interact, and time-dependent chemistry needs to be considered for accurate simulations.

Benjamin D. Smucker, Tejas C. Mulky, Daniel A. Cowan, Kyle E. Niemeyer, David Blunck (2019)

Effects of fuel content and density on the smoldering characteristics of cellulose and hemicellulose

*Proceedings of the Combustion Institute*

A companion paper to our computational study, experimentally studies smoldering in mixtures of cellulose and hemicellulose, using both horizontal spread and downward spread, to identify controlling parameters.

Effects of fuel content and density on the smoldering characteristics of cellulose and hemicellulose

A companion paper to our computational study, experimentally studies smoldering in mixtures of cellulose and hemicellulose, using both horizontal spread and downward spread, to identify controlling parameters.

Tejas C. Mulky, Kyle E. Niemeyer (2019)

Computational study of the effects of density, fuel content, and moisture content on smoldering propagation of cellulose and hemicellulose mixtures

*Proceedings of the Combustion Institute*

Uses computational modeling to study how changes in important physical properties, including fuel composition, affect smoldering in mixtures of cellulose and hemicellulose.

Computational study of the effects of density, fuel content, and moisture content on smoldering propagation of cellulose and hemicellulose mixtures

Uses computational modeling to study how changes in important physical properties, including fuel composition, affect smoldering in mixtures of cellulose and hemicellulose.

Shane Daly, Khang Tran, Kyle E. Niemeyer, William J. Cannella, Christopher Hagen (2019)

Predicting fuel low-temperature combustion performance using Fourier-transform infrared absorption spectra of neat hydrocarbons

*Fuel*

Builds on our previously demonstrated work, trains a model using infrared spectra to predict the performance of fuels in low-temperature combustion engines.

Predicting fuel low-temperature combustion performance using Fourier-transform infrared absorption spectra of neat hydrocarbons

Builds on our previously demonstrated work, trains a model using infrared spectra to predict the performance of fuels in low-temperature combustion engines.

Arfon M. Smith, Kyle E. Niemeyer, Daniel S. Katz, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn D. Huff, Christopher R. Madan, Abigail Cabunoc Mayes, Kevin M. Moerman, Pjotr Prins, Karthik Ram, Ariel Rokem, Tracy K. Teal, Roman Valls Guimera, Jacob T. Vanderplas (2018)

Journal of Open Source Software (JOSS): design and first-year review

*PeerJ Computer Science*

Describes the motivation, design, and progress of the Journal of Open Source Software (JOSS), which is a free and open-access journal that publishes articles describing research software.

Journal of Open Source Software (JOSS): design and first-year review

Describes the motivation, design, and progress of the Journal of Open Source Software (JOSS), which is a free and open-access journal that publishes articles describing research software.

Daniel S. Katz, Kyle E. Niemeyer, Sandra Gesing, Lorraine Hwang, Wolfgang Bangerth, Simon Hettrick, Ray Idaszak, Jean Salac, Neil Chue Hong, Santiago Núñez-Corrales, Alice Allen, R. Stuart Geiger, Jonah Miller, Emily Chen, Anshu Dubey, Patricia Lago (2018)

Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)

*Journal of Open Research Software*

Records and discusses the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4).

Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)

Records and discusses the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4).

Daniel S. Katz, Gabrielle Allen, Lorena A. Barba, Devin R. Berg, Holly Bik, Carl Boettiger, Christine L. Borgman, C. Titus Brown, Stuart Buck, Randy Burd, Anita de Waard, Martin Paul Eve, Brian E. Granger, Josh Greenberg, Adina Howe, Bill Howe, May Khanna, Timothy L. Killeen, Matthew Mayernik, Erin McKiernan, Chris Mentzel, Nirav Merchant, Kyle E. Niemeyer, Laura Noren, Sarah M. Nusser, Daniel A. Reed, Edward Seidel, MacKenzie Smith, Jeffrey R. Spies, Matt Turk, John D. Van Horn, Jay Walsh (2018)

The principles of tomorrow's university

*F1000Research*

Discusses and summarizes the activities of a workshop on imagining the university of tomorrow, focused on open scholarly research.

The principles of tomorrow's university

Discusses and summarizes the activities of a workshop on imagining the university of tomorrow, focused on open scholarly research.

Devin R. Berg, Kyle E. Niemeyer (2018)

The case for openness in engineering research

*F1000Research*

Reviews benefits and possible downsides of open science in engineering research, making the case that a culture of openness and sharing in the engineering community can help drive societal development.

The case for openness in engineering research

Reviews benefits and possible downsides of open science in engineering research, making the case that a culture of openness and sharing in the engineering community can help drive societal development.

Miguel Soler, Kyle E. Niemeyer (2018)

Analysis of an approach for detecting arc positions during vacuum arc remelting based on magnetic flux density measurements

*Journal of Manufacturing Science and Engineering*

Examines the assumptions made in a commercially used method for detecting the locations of electrical arcs in vacuum arc remelting furnaces, which are used to produce high-grade metal ingots.

Analysis of an approach for detecting arc positions during vacuum arc remelting based on magnetic flux density measurements

Examines the assumptions made in a commercially used method for detecting the locations of electrical arcs in vacuum arc remelting furnaces, which are used to produce high-grade metal ingots.

Shane Daly, Kyle E. Niemeyer, William R. Cannella, Christopher Hagen (2018)

FACE gasoline surrogates formulated by an enhanced multivariate optimization framework

*Energy & Fuels*

FACE gasoline surrogates formulated by an enhanced multivariate optimization framework

Dan Magee, Kyle E. Niemeyer (2018)

Accelerating solutions of one-dimensional unsteady PDEs with GPU-based swept time-space decomposition

*Journal of Computational Physics*

Implements a recent domain decomposition scheme on GPUs, the swept time-space decomposition rule, and analyzes its performance for solving one-dimensional partial differential equations.

Accelerating solutions of one-dimensional unsteady PDEs with GPU-based swept time-space decomposition

Implements a recent domain decomposition scheme on GPUs, the swept time-space decomposition rule, and analyzes its performance for solving one-dimensional partial differential equations.

Christopher P. Stone, Andrew T. Alferman, Kyle E. Niemeyer (2018)

Accelerating finite-rate chemical kinetics with coprocessors: Comparing vectorization methods on GPUs, MICs, and CPUs

*Computer Physics Communications*

Accelerating finite-rate chemical kinetics with coprocessors: Comparing vectorization methods on GPUs, MICs, and CPUs

Nicholas Curtis, Kyle E. Niemeyer, Chih-Jen Sung (2018)

Using SIMD and SIMT vectorization to evaluate sparse chemical kinetic Jacobian matrices and thermochemical source terms

*Combustion and Flame*

Presents an updated version of the pyJac software for generating analytical Jacobian matrices, featuring alternate formulations that allow for sparse linear algebra operations and vectorized evaluation.

Using SIMD and SIMT vectorization to evaluate sparse chemical kinetic Jacobian matrices and thermochemical source terms

Presents an updated version of the pyJac software for generating analytical Jacobian matrices, featuring alternate formulations that allow for sparse linear algebra operations and vectorized evaluation.

Sai Krishna Sirumalla, Morgan Mayer, Kyle E. Niemeyer, Richard West (2018)

Assessing impacts of discrepancies in model parameters on autoignition model performance: A case study using butanol

*Combustion and Flame*

Shows that discrepancies between parameters in chemical kinetic models found across the literature can lead to significantly different outcomes, and calls for concerted efforts to compile all kinetic models, parameters, and experimental measurements into shared databases.

Assessing impacts of discrepancies in model parameters on autoignition model performance: A case study using butanol

Shows that discrepancies between parameters in chemical kinetic models found across the literature can lead to significantly different outcomes, and calls for concerted efforts to compile all kinetic models, parameters, and experimental measurements into shared databases.

Bryan Weber, Kyle E. Niemeyer (2018)

ChemKED: A human- and machine-readable data standard for chemical kinetics experiments

*International Journal of Chemical Kinetics*

Introduces the ChemKED file standard for describing fundamental combustion experiments, along with a Python-based software package for validating and working with files.

ChemKED: A human- and machine-readable data standard for chemical kinetics experiments

Introduces the ChemKED file standard for describing fundamental combustion experiments, along with a Python-based software package for validating and working with files.

Jonathan P. Tennant, Jonathan M. Dugan, Daniel Graziotin, Damien C. Jacques, François Waldner, Daniel Mietchen, Yehia Elkhatib, Lauren B. Collister, Christina K. Pikas, Tom Crick, Paola Masuzzo, Anthony Caravaggi, Devin R. Berg, Kyle E. Niemeyer, Tony Ross-Hellauer, Sara Mannheimer, Lillian Rigling, Daniel S. Katz, Bastian Greshake Tzovaras, Josmel Pacheco-Mendoza, Nazeefa Fatima, Marta Poblet, Marios Isaakidis, Dasapta Erwin Irawan, Sébastien Renaut, Christopher R. Madan, Lisa Matthias, Jesper Nørgaard Kjær, Daniel Paul O'Donnell, Cameron Neylon, Sarah Kearns, Manojkumar Selvaraju, Julien Colomb (2017)

A multi-disciplinary perspective on emergent and future innovations in peer review

*F1000 Research*

Examines models for peer review across the systems of scholarly communication, and proposes potential new models that resolve technical and social issues inherent to the status quo.

A multi-disciplinary perspective on emergent and future innovations in peer review

Examines models for peer review across the systems of scholarly communication, and proposes potential new models that resolve technical and social issues inherent to the status quo.

Xin Hui, Kyle E. Niemeyer, Kyle B. Brady, Chih-Jen Sung (2017)

Reduced chemistry for butanol isomers at engine-relevant conditions

*Energy & Fuels*

Presents and analyzes reduced chemical kinetic models for the four isomers of butanol. Discusses some issues related to pressure-dependent reactions made using the logarithmic pressure interpolation approach.

Reduced chemistry for butanol isomers at engine-relevant conditions

Presents and analyzes reduced chemical kinetic models for the four isomers of butanol. Discusses some issues related to pressure-dependent reactions made using the logarithmic pressure interpolation approach.

Shyam Menon, Himakar Ganti, Kyle E. Niemeyer, Christopher Hagen (2017)

Effects of oil and water contamination on natural gas engine combustion processes

*Journal of Natural Gas Science and Engineering*

Investigates the effects of upstream conditions of natural gas on conditions in an internal combustion engine, finding that water does not have an impact but oil contamination can play a larger role.

Effects of oil and water contamination on natural gas engine combustion processes

Investigates the effects of upstream conditions of natural gas on conditions in an internal combustion engine, finding that water does not have an impact but oil contamination can play a larger role.

Kyle E. Niemeyer, Nicholas Curtis, Chih-Jen Sung (2017)

pyJac: Analytical Jacobian generator for chemical kinetics

*Computer Physics Communications*

Presents the pyJac software package for automatically generating analytical Jacobian matrices for chemical kinetic models, which can be used to speed up simulations.

pyJac: Analytical Jacobian generator for chemical kinetics

Presents the pyJac software package for automatically generating analytical Jacobian matrices for chemical kinetic models, which can be used to speed up simulations.

Nicholas Curtis, Kyle E. Niemeyer, Chih-Jen Sung (2017)

An investigation of GPU-based stiff chemical kinetics integration methods

*Combustion and Flame*

Studies the performance on GPUs of multiple integration algorithms for stiff chemical kinetics, building on an earlier study of simpler algorithms that can only handle moderate stiffness.

An investigation of GPU-based stiff chemical kinetics integration methods

Studies the performance on GPUs of multiple integration algorithms for stiff chemical kinetics, building on an earlier study of simpler algorithms that can only handle moderate stiffness.

Arfon M Smith, Daniel S Katz, Kyle E. Niemeyer, FORCE11 Software Citation Working Group (2016)

Software Citation Principles

*PeerJ Computer Science*

Presents a consolidated set of principles for citing software in scholarly studies, to encourage broad adoption of a consistent policy for software citation across disciplines and venues.

Software Citation Principles

Presents a consolidated set of principles for citing software in scholarly studies, to encourage broad adoption of a consistent policy for software citation across disciplines and venues.

Daniel S. Katz, Sou-Cheng T. Choi, Kyle E. Niemeyer, James Hetherington, Frank Löffler, Dan Gunter, Ray Idaszak, Steven R. Brandt, Mark A. Miller, Sandra Gesing, Nick D. Jones, Nic Weber, Suresh Marru, Gabrielle Allen, Birgit Penzenstadler, Colin C. Venters, Ethan Davis, Lorraine Hwang, Ilian Todorov, Abani Patra, Miguel de Val-Borro (2016)

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

*Journal of Open Research Software*

Records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3).

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

Records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3).

Kyle E. Niemeyer, Arfon M Smith, Daniel S Katz (2016)

The challenge and promise of software citation for credit, identification, discovery, and reuse

*Journal of Data and Information Quality*

Presents the challenge of software citation as a method to ensure credit for and identification, discovery, and reuse of software in scientific and engineering research. Also discusses related work and key challenges/research directions.

The challenge and promise of software citation for credit, identification, discovery, and reuse

Presents the challenge of software citation as a method to ensure credit for and identification, discovery, and reuse of software in scientific and engineering research. Also discusses related work and key challenges/research directions.

Shane Daly, Kyle E. Niemeyer, William J. Cannella, Christopher Hagen (2016)

Predicting fuel research octane number using Fourier-transform infrared absorption spectra of neat hydrocarbons

*Fuel*

Presents a statistical model for accurately predicting the octane numbers of practical gasoline fuels, using their infrared spectra. Showed that models can be developed using neat fuels and their blends for broad applicability.

Predicting fuel research octane number using Fourier-transform infrared absorption spectra of neat hydrocarbons

Presents a statistical model for accurately predicting the octane numbers of practical gasoline fuels, using their infrared spectra. Showed that models can be developed using neat fuels and their blends for broad applicability.

Kyle E. Niemeyer, Shane Daly, William J. Cannela, Christopher Hagen (2015)

A novel fuel performance index for LTC engines based on operating envelopes in light-duty driving cycle simulations

*Journal of Engineering for Gas Turbines and Power*

Presents a new metric for quantifying the performance of fuels for low-temperature combustion engines, that uses simulations of a light-duty vehicle over standard driving cycle and the associated engine operating envelope.

A novel fuel performance index for LTC engines based on operating envelopes in light-duty driving cycle simulations

Presents a new metric for quantifying the performance of fuels for low-temperature combustion engines, that uses simulations of a light-duty vehicle over standard driving cycle and the associated engine operating envelope.

Kyle E. Niemeyer, Chih-Jen Sung (2015)

Reduced chemistry for a gasoline surrogate valid at engine-relevant conditions

*Energy & Fuels*

Demonstrates a multi-stage approach to reducing chemical kinetic models, and uses it to produce separate reduced models for gasoline surrogate fuels for spark-ignition engine and low-temperature compression-ignition engine simulations.

Reduced chemistry for a gasoline surrogate valid at engine-relevant conditions

Demonstrates a multi-stage approach to reducing chemical kinetic models, and uses it to produce separate reduced models for gasoline surrogate fuels for spark-ignition engine and low-temperature compression-ignition engine simulations.

Kyle E. Niemeyer, Shane Daly, William J. Cannela, Christopher Hagen (2015)

Investigation of the LTC fuel performance index for oxygenated reference fuel blends

*Fuel*

Extends the study of our LTC fuel performance index to consider fuel blends with oxygenated components like ethanol.

Investigation of the LTC fuel performance index for oxygenated reference fuel blends

Extends the study of our LTC fuel performance index to consider fuel blends with oxygenated components like ethanol.

Kyle B Brady, Xin Hui, Kyle E. Niemeyer, Chih-Jen Sung (2015)

Counterflow ignition of n-butanol at atmospheric and elevated pressures

*Combustion and Flame*

Used a new experimental apparatus to study and investigate chemical kinetic models for n-butanol, identifying gaps in the current understanding of how the fuel reacts and ignites.

Counterflow ignition of n-butanol at atmospheric and elevated pressures

Used a new experimental apparatus to study and investigate chemical kinetic models for n-butanol, identifying gaps in the current understanding of how the fuel reacts and ignites.

Nicholas Curtis, Kyle E. Niemeyer, Chih-Jen Sung (2015)

An automated target species selection method for dynamic adaptive chemistry simulations

*Combustion and Flame*

Introduces a new method for automatically identifying important target species for use with dynamic algorithms to reduce chemical kinetic models on the fly.

An automated target species selection method for dynamic adaptive chemistry simulations

Introduces a new method for automatically identifying important target species for use with dynamic algorithms to reduce chemical kinetic models on the fly.

Fengquan Zhong, Sugang Ma, Xinyu Zhang, Chih-Jen Sung, Kyle E. Niemeyer (2015)

Development of efficient and accurate skeletal mechanisms for hydrocarbon fuels and kerosene surrogate

*Acta Mechanica Sinica*

Development of efficient and accurate skeletal mechanisms for hydrocarbon fuels and kerosene surrogate

Kyle E. Niemeyer, Chih-Jen Sung (2014)

Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs

*Journal of Computational Physics*

While integrating chemical kinetics usually requires complex implicit algorithms to handle stiffness, certain stabilized explicit methods can handle moderate levels of stiffness, and these algorithms also parallelize efficiently on GPUs.

Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs

While integrating chemical kinetics usually requires complex implicit algorithms to handle stiffness, certain stabilized explicit methods can handle moderate levels of stiffness, and these algorithms also parallelize efficiently on GPUs.

Kyle E. Niemeyer, Chih-Jen Sung (2014)

Mechanism reduction for multicomponent surrogates: a case study using toluene reference fuels

*Combustion and Flame*

When reducing chemical kinetic models for fuel blends, rather than a single fuel, additional care must be taken.

Mechanism reduction for multicomponent surrogates: a case study using toluene reference fuels

When reducing chemical kinetic models for fuel blends, rather than a single fuel, additional care must be taken.

Kyle E. Niemeyer, Chih-Jen Sung (2014)

Recent progress and challenges in exploiting graphics processors in computational fluid dynamics

*Journal of Supercomputing*

Surveys the history (up to that point) of using graphics processing units (GPUs) for performing computational fluid dynamics simulations.

Recent progress and challenges in exploiting graphics processors in computational fluid dynamics

Surveys the history (up to that point) of using graphics processing units (GPUs) for performing computational fluid dynamics simulations.

Kyle E. Niemeyer, Chih-Jen Sung (2011)

On the importance of graph search algorithms for DRGEP-based mechanism reduction methods

*Combustion and Flame*

Choosing an appropriate graph search algorithm makes a difference for kinetic model reduction methods based on graph theory for correctness and efficiency.

On the importance of graph search algorithms for DRGEP-based mechanism reduction methods

Choosing an appropriate graph search algorithm makes a difference for kinetic model reduction methods based on graph theory for correctness and efficiency.

Kyle E. Niemeyer, Chih-Jen Sung, Mandhapati P Raju (2010)

Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis

*Combustion and Flame*

Develops a new method for automatically reducing chemical kinetic models and applies it to large models for n-heptane, iso-octane, and n-decane.

Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis

Develops a new method for automatically reducing chemical kinetic models and applies it to large models for n-heptane, iso-octane, and n-decane.

Craig R. Slyfield, Kyle E. Niemeyer, EV Tkachenko, Ryan E Tomlinson, Grant G Steyer, CG Patthanacharoenphon, GJ Kazakia, David L Wilson, Christopher J Hernandez (2009)

Three-dimensional surface texture visualization of bone tissue through epifluorescence-based serial block face imaging

*Journal of Microscopy*

Developed a method to visualize the surfaces of bones, and create three-dimensional models, by processing high-resolution images taken as microscopic surfaces were ground away.

Three-dimensional surface texture visualization of bone tissue through epifluorescence-based serial block face imaging

Developed a method to visualize the surfaces of bones, and create three-dimensional models, by processing high-resolution images taken as microscopic surfaces were ground away.

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