PNNL

Derek Hopkins is a senior computer scientist with the Instrument Development Lab team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. An accomplished software developer, Hopkins’ software is widely used throughout PNNL and by Environmental and Molecular Science Laboratory users.  

Hopkins’s modular software design has enabled widespread adoption of software based on a common, robust backplane to interface hardware and automate scientific experiments. His software has been used to integrate systems as diverse as specialized surface science instruments, automated liquid chromatography systems, mass spectrometers, an R&D 100 award-winning combined confocal and magnetic resonance microscope, a micro-pulse light detection and ranging system, and an automation for a custom solar spectrometer used in atmospheric chemistry research. 

• Laboratory automation and process control 
• STORM microscope 
• Identification friend or foe  
• Waste tank mixing project 

• BS in Computer Science, Arkansas State University, 1991 
• BS in Engineering Physics-Computer Applications, Southeast Missouri State University, 1987 

• Key Contributor Award, PNNL (2002, 2005, 2011) 
• Software Creator Award, PNNL (1996, 2002, 2011) 
• Outstanding Performance Award, PNNL (2000, 2001, 2004, 2006, 2007, 2008) 
• Cover Feature, Scientific Computing and Instrumentation Journal, (2004, 2005) 
• Finalist, National Instruments Paper Contest, NIWeek (2003) 

2025

• Kaspar T.C., S.M. Akers, H.W. Sprueill, A.H. Ter-Petrosyan, J.A. Bilbrey, D.F. Hopkins, and A.V. Harilal, et al. 2025. "Machine-learning-enabled on-the-fly analysis of RHEED patterns during thin film deposition by molecular beam epitaxy." Journal of Vacuum Science & Technology A: International Journal Devoted to Vacuum, Surfaces, and Films 43, no. 3:Art. No. 032702. PNNL-SA-206700. doi:10.1116/6.0004493

2024

• Olszta M.J., K.H. Yano, D.F. Hopkins, K.R. Fiedler, J.V. Haag, and I.J. van Rooyen. 2024. TiltEM User Manual. PNNL-36495. Richland, WA: Pacific Northwest National Laboratory. TiltEM User Manual

2023

• Fiedler K.R., M.J. Olszta, K.H. Yano, C.M. Doty, D.F. Hopkins, S.M. Akers, and S.R. Spurgeon. 2023. "Evaluating Stage Motion for Automated Electron Microscopy." Microscopy and Microanalysis 29, no. 6:1931-1939. PNNL-SA-180645. doi:10.1093/micmic/ozad108

2022

• Olszta M.J., D.F. Hopkins, K.R. Fiedler, M.T. Oostrom, S.M. Akers, and S.R. Spurgeon. 2022. "An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics." Microscopy and Microanalysis 28, no. 5:1611 - 1621. PNNL-SA-166931. doi:10.1017/S1431927622012065

2013

• Denslow K.M., J.R. Bontha, H.E. Adkins, J.W. Jenks, D.F. Hopkins, M.G. Thien, and S.E. Kelly, et al. 2013. "System Performance Testing of the Pulse-Echo Ultrasonic Instrument for Critical Velocity Determination during Hanford Tank Waste Transfer Operations - 13584." In Annual Waste Management Symposium (WM2013): International Collaboration and Continuous Improvement, February 24-28, 2013, Phoenix, Arizona, 7, 5916-5938. Tempe, Arizona:WM Symposia. PNNL-SA-92964.

2012

• Denslow K.M., J.R. Bontha, H.E. Adkins, J.W. Jenks, C.A. Burns, P.P. Schonewill, and D.F. Hopkins, et al. 2012. "Continued Evaluation of the Pulse-Echo Ultrasonic Instrument for Critical Velocity Determination during Hanford Tank Waste Transfer Operations." In Waste Managemetn Symposium (WM 2012): Improving the Future in Waste Management, February 26-March 1, 2012, Phoenix, Arizona, Paper No. 12518. Tuscson, Arizona:Waste Management Symposia Inc. PNNL-SA-85110.

2010

• Baker E.S., E.A. Livesay, D.J. Orton, R.J. Moore, W.F. Danielson, D.C. Prior, and Y.M. Ibrahim, et al. 2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." Journal of Proteome Research 9, no. 2:997-1006. PNNL-SA-67461. doi:10.1021/pr900888b
• Bamberger J.A., M.S. Greenwood, B.D. Lawler, S.K. Sundaram, E.B. Baer, B.K. Hatchell, and D.F. Hopkins, et al. 2010. "EVALUATING CONCENTRATION PROFILES DURING UNSTEADY MIXING." In Proceedings of the ASME International Mechanical Engineering Congress and Exposition 2009 (IMECE2009), November 13-19, 2009, Lake Buena Vista, Florida, 8, 1-10. New York, New York:American Society of Mechanical Engineers. PNNL-SA-67923.

2008

• Livesay E.A., K. Tang, B.K. Taylor, M.A. Buschbach, D.F. Hopkins, B.L. Lamarche, and R. Zhao, et al. 2008. "Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses." Analytical Chemistry 80, no. 1:294-302. PNNL-SA-56532. doi:10.1021/ac701727r

2007

• Lamarche B.L., D.F. Hopkins, C.O. Hughes, T.P. McKenna, and E.W. Fulp. 2007. "A Network Layer for Teleoperations in High Speed Environments." In IEEE High-Speed Networks Workshop, 11-15. Piscataway, New Jersey:IEEE. PNNL-SA-54021. doi:10.1109/HSNW.2007.4290537

2005

• Perrine K.A., D.F. Hopkins, B.L. Lamarche, and M.B. Sowa. 2005. "Pixel Perfect." Scientific Computing & Instrumentation 22, no. 10:16-20. PNNL-SA-45704.
• Perrine K.A., D.F. Hopkins, B.L. Lamarche, S.E. Budge, and M.B. Sowa. 2005. "Pixel Perfect: a real-time image processing system for biology." Scientific Computing & Instrumentation 22, no. 10:16-20. PNNL-SA-46035.

2004

• Hopkins D.F., M.L. Alexander, K.R. Swanson, and M.A. Buschbach. 2004. "Control System for an Ion Trap Mass Spectrometer." Scientific Computing & Instrumentation. PNNL-SA-40943.

2002

• Majors P.D., K.R. Minard, E.J. Ackerman, G.R. Holtom, D.F. Hopkins, C.I. Parkinson, and T.J. Weber, et al. 2002. "A combined confocal and magnetic resonance microscope for biological studies." Review of Scientific Instruments 73, no. 12:4329-4338. PNNL-SA-37808.

2001

• Autrey T., N.S. Foster, D.F. Hopkins, and J.M. Price. 2001. "Tunable Ultraviolet Visible Photoacoustic Detection - Analysis of the Sensitivity and Selectivity Provided by a Xenon Flash Lamp." Analytica Chimica Acta 434, no. 2:217-222. PNNL-SA-33807.
• Holtom, G., B. Thrall, T. Weber, L. Zhu, D. Hopkins, C. Parkinson, S. Colson, J. Price, B. Y. Chin, A. Choi, and T. Risby. 2001. “Application of Coherent Anti-Stokes Raman Scattering (CARS) to Imaging Mammalian Cells: A Means for Gaining Molecular Selectivity in Multiphoton Imaging.” Proceedings of SPIE - The International Society for Optical Engineering 4262: 319-328. https://doi.org/10.1117/12.424571.  

• 1992 

• Bass, M. B., D. F. Hopkins, W. A. N. Jaquysh, and R. L. Ornstein. 1992. “A Method for Determining the Positions of Polar Hydrogens Added to a Protein Structure That Maximizes Protein Hydrogen Bonding.” Proteins: Structure, Function, and Bioinformatics 12 (3): 266-277. https://doi.org/10.1002/prot.340120305.