Curriculum Vitae
A PDF is available upon request.
Nicholas A. Danes
Computational Scientist
- Denver, CO
- ndanes@mines.edu
- hello@ndanes.com
- ndanes.com
Summary
Computational scientist with over 10 years combined experience in industry and academia:
- Extensive background in the implementation of computational algorithms within existing finite element method codes for mathematical modeling coupled to CFD; modifying computational physics methods with innovative extensions using object oriented and distributed-memory parallel programming
- Experience with developing, building, benchmarking and running codes on high performance computing (HPC) clusters
- On and off-site technical customer support for HPC applications, modeling & simulation projects
- Excellent teamwork through interpersonal communication and interdisciplinary collaboration with experimentalists, mathematicians and engineers
- Flexibility in completing self-conducted review to learn new tools for a project, whether it be a programming language, numerical method or modeling program
Education
Colorado School of Mines, PhD in Computational & Applied Mathematics December 2019
PhD Advisor: Dr. Karin Leiderman
- Dissertation: Computational modeling of extravascular platelet aggregation under flow
- MATH440 - Parallel Scientific Computing
Ph.D., Applied Mathematics (Continued at Mines) August 2013 - July 2016 August 2013 - July 2016
University of California, Merced, Left to Colorado School of Mines Research: Computational Model of Extravascular Platelet Aggregation Advisor: Dr. Karin Leiderman
California State University, Bakersfield, BS in Mathematics - Applied June 2013
- 3.82 GPA, Magna Cum Laude
- Minor in Computer Science
Work Experience
Computational Scientist
Colorado School of Mines, Information Technology (IT)
August 2020 – Present
- Member of the Research Computing (RC) group under IT where main duties include:
+ Supporting HPC users on technical and non-technical issues with research computing
+ Building, porting and scaling applications & software libraries on Mines’ HPC cluster systems
+ Lead on developing and providing new technical information & user guides for Mines HPC users via RC Mines website
+ Providing per-semester training workshops on Intro to HPC & Intro to MPI using Python
- Fostering community through “Tech Talk Tuesdays” monthly meetings
Computational Engineer I
Ball Aerospace & Technologies
September 2019 – August 2020
- Utilized massively parallel coupled multi-physics codes for modeling and simulation
- Aided in code development of a Python written model using object-oriented principles with user documentation in a version control environment (git)
- Conducted parallel scaling studies on massively parallel coupled multiphysics codes to benchmark runtimes and identify solver bottlenecks for specific modeling problems
- Built scientific computing (MPI-enabled) libraries from source on workstation and high-performance computing clusters; provided user documentation on successful builds
- Collaborated with a team of Ball engineers and sub-contractors to develop and verify/validate coupled multiphysics codes
Research Experience
Graduate Student Researcher
Colorado School of Mines, Department of Applied Mathematics & Statistics
University of California, Merced, Department of Applied Mathematics
August 2016 – 2019
August 2014 – 2016
Advisor: Dr. Karin Leiderman | Funding: NIH R01HL120728
- Developed and validated a 2D computational model of extravascular platelet aggregation within the FEniCS software suite; model involves solving a large system of partial differential equations to account for fluid dynamics & platelet aggregation
- Code development includes novel changes to existing numerical algorithms; solved using multiple processing cores on Colorado School of Mines‘ “Mio” high performance computing cluster
- Compared and cross-validated model outputs with microfluidic experiments and reduced-order mathematical models
- Wrote technical reports, papers and presented research at major conferences
Research Intern
National Renewable Energy Lab (NREL), Computational Science Center
June – August 2017
Mentors: Drs. H. Sitarman, J. Stickel & M. A. Sprague | Funding: NSF DMS-155122
- Implemented, and validated a 3D model of lignocellulosic biomass conversion into an existing CFD code
- Simulations of model were run using the NREL high performance computing cluster “Peregine”
- Presented work at the 2017 APS-DFD conference
- Edited and reviewed manuscript submitted for publication
Undergraduate Researcher
California State University, Chico
June – August 2012
Mentor: Dr. Sergei Fomin | Funding: NSF DMS-1156612 Chico, CA
- Used a combination of perturbation methods, asymptotic analysis and numerical simulation to study rimming flow inside a cylinder
- Collaborated with a teacher and other undergraduate math students with research, writing and presentations
Awards
- GRADS Poster Award Spring 2017
- Colorado School of Mines
- Poster Title: Toward A Mathematical Model of Hemostasis
- Awarded 1st place in Session I of the College of Engineering & Computational Science Division
- Research Fellowship Summer 2014
- University of California Merced, School of Natural Sciences
- Mathematics Chair Award 2013
- California State University, Bakersfield, Department of Mathematics
- Jazz Festival Scholarship 2012
- California State University, Bakersfield, Department of Mathematics
Publications
Link, K.G., Sorrells, M.G., Danes, N.A., Neeves, K.B., Leiderman, K. and Fogelson, A.L., 2020. A mathematical model of platelet aggregation in an extravascular injury under flow. Multiscale modeling & simulation, 18(4), pp.1489-1524.
Danes, N.A. and Leiderman, K., 2019. A density‐dependent FEM‐FCT algorithm with application to modeling platelet aggregation. International journal for numerical methods in biomedical engineering, 35(9), p.e3212.
Sitaraman, H., Danes, N., Lischeske, J.J., Stickel, J.J. and Sprague, M.A., 2019. Coupled CFD and chemical-kinetics simulations of cellulosic-biomass enzymatic hydrolysis: Mathematical-model development and validation. Chemical Engineering Science, 206, pp.348-360.
Schoeman, R.M., Rana, K., Danes, N., Lehmann, M., Di Paola, J.A., Fogelson, A.L., Leiderman, K. and Neeves, K.B., 2017. A microfluidic model of hemostasis sensitive to platelet function and coagulation. Cellular and molecular bioengineering, 10, pp.3-15.
Fomin, S., Shankar, R., Danes, N., Yasuda, A. and Chugunov, V., 2014. Rimming flow of a weakly elastic fluid. Theoretical and Computational Fluid Dynamics, 28, pp.485-498.
Mentoring
- Undergraduate Research Mentor, Topic: Mathematical modeling of blood coagulation Fall 2018
- Mentor for Community College Research Workshop (Colorado School of Mines) June 2018
Conferences & Presentations
- SIAM Life Sciences, Minneapolis, MN August 2018
- Presentation: A Mathematical Model of Extravascular Platelet Aggregation
- Siession: Multiscale Modeling of Biomechanical and Biochemical Systems - Part II of II
- WCCMXIII & PANACM II, New York City, NY July 2018
- Presentation: A Mathematical Model of Extravascular Platelet Aggregation
- Session: Computational Multiphysics Modeling Of Cardiovascular Systems
- Colorado School of Mines GRADS, Golden, CO April 2018
- Presentation: A computational model of platelet aggregation under flow
- 70th Annual Meeting of APS-DFD, Denver, CO November 2017
- Presentation: A coupled CFD and two-phase substrate kinetic model for enzymatic hydrolysis of lignocellulose
- Session: Reacting Flows: General I
- Co-Author(s): Drs. Jonathan Stickel, Michael A. Sprague, Hariswaran Sitaraman
- Other: Student Volunteer
- SIAM Central States, Colorado State University, Fort Collins, CO September-October 2017
- Presentation: Toward a Mathematical Model of Hemostasis
- Session: Mathematically-based Insights into Health and Disease
- RMFM Research Symposium, CU Boulder, Boulder, CO August 2017
- Presentation: Toward a Mathematical Model of Hemostasis
- Session: Biology, Surfaces and Droplets
- Math Bio Alumni Conference, University of Utah, Salt Lake City, UT July 2017
- Poster: Toward A Mathematical Model of Hemostasis
- SIAM Dynamical Systems, Snowbird, UT May 2017
- Presentation: A Computational Model of Hemostasis
- Session: Mathematical Model of Physiology and Medicine - Part II
- Colorado School of Mines GRADS, Golden, CO April 2017
- Poster: Toward A Mathematical Model of Hemostasis
- SIAM Computational Science & Engineering, Atlanta, GA Feburary-March 2017
- Poster: Toward A Mathematical Model of Hemostasis
- SIAM Life Sciences, Boston, MA July 2016
- Co-organizer of Minisymposium: Mathematical Models of Coagulation
- Presentation: Pressure Boundary Conditions in a Computational Bleeding Chip Model
- Computational Biofluids in Physiology, University of Utah, Salt Lake City, UT May 2015
- Poster: A Mathematical Model of Factor Xa Regulation by Rivaroxaban
Teaching Experience
- Teaching Assistant - January 2016 - May 2016
- Instructor: Karin Leiderman
- University of California, Merced, Department of Applied Mathematics
- Ran the discussion section for Numerical Analysis I. Met with students once a week to discuss practical implementations of programs using Matlab, as well as graded homeworks and exams.
- Held office hours weekly to assist students with homework and general lecture questions.
- Teaching Assistant - August 2014 - December 2014
- Instructor: Francois Blanchette
- University of California, Merced, Department of Applied Mathematics
- Ran the discussion section for Numerical Analysis I. Met with students once a week to discuss practical implementations of programs using Matlab, as well as graded homeworks and exams.
- Held office hours weekly to assist students with homework and general lecture questions.
- Teaching Assistant - January 2014 - May 2014
- Instructor: Dimitrios Mitsotakis
- University of California, Merced, Department of Applied Mathematics - Ran the discussion section for Numerical Analysis I. Met with students once a week to discuss practical implementations of programs using Matlab, as well as graded homeworks and exams. - Held office hours weekly to assist students with homework and general lecture questions.
- Teaching Assistant - August 2013 - December 2013
- Instructor: Alexander Yatskar
- University of California, Merced, Department of Applied Mathematics
- Ran the discussion section for Calculus II for the Physical Sciences and Engineering. Assisted students with weekly worksheet/lab sessions, answered questions in class, held weekly office hours, graded and proctored exams. T
- Teaching Assistant June 2013 - August 2013
- Instructor: Haik Stephanian
- University of California, Merced, Department of Applied Mathematics
- Ran the discussion section for Vector Calculus. Assisted students with bi-weekly worksheet/lab sessions, answered questions in class, held weekly office hours, and graded homework and exams.
- Teaching Assistant April 2013 - June 2013
- Instructor: Rebecca Larson
- California State University Bakersfield, Department of Mathematics
- Assisted professor in grading homework, quizzes, and labs for her Calculus III for Engineering course.
- Led the lab section of the course to serve as a in-class tutor for students.
- Teaching Assistant September 2012 - March 2013
- Instructor: Yangsuk Ko
- California State University Bakersfield, Department of Mathematics
- Assisted professor in grading homework, quizzes, and labs for his Calculus I and Calculus II for Engineering courses.
- Led the lab section of the course to serve as a in-class tutor for students.
- Mathematics Tutor September 2011 - June 2013
- California State University, Bakersfield, Department of Mathematics
- Tutored students taking undergraduate courses in Finite Math, Pre-Calculus, Trigonometry, Statis- tics, and Single/Multivariable Calculus through an on-campus mathematics tutoring center
- California State University, Bakersfield, Department of Mathematics
Skills
Computer Skills
| Proficient | HTML, CSS, Markdown, Git, C/C++, Bash |
|---|---|
| Intermediate | Matlab, LaTeX, Fortran 77/90, Nek5000, Paraview, MPI, Slurm, Linux |
| Advanced | Python (NumPy, SciPy, PETSc4Py, Matplotlib), FEniCS |
Math
- Numerical Solution of Ordinary & Partial Differential Equations, Numerical Anaylsis, Computational Fluid Dynamics, Linear Algebra
Other
- Formal presentations to groups and/or conferences, technical writing
- Interdisciplinary communication for research projects, papers, and presentations
Professional Memberships
- Association for Computing Machinery (ACM)
- 2020 to Present