Brown, W.M., Hughes, C.J., Plotnikov, M. Method and apparatus for data-ready memory operations. 6/30/2017. US2017040512.

Raman, K. Brown, W.M., Malladi, R.K., Semin, A. Dynamically predict and enhance energy efficiency. 3/3/2017. US20180253288.

Brown, W.M., Ould-Ahmed-Vall, E. Instruction and logic for partial reduction operations. 8/11/2016. US2016060951.

Brown, W.M., Raman, K. Instructions for dual destination type conversion, mixed precision accumulation, and mixed precision atomic memory operations. 6/30/2020. US-10698685B2.

Brown, W.M., Schulz, R., Raman, K. Apparatus and Method for Loop Flattening and Reduction in a Single Instruction Multiple Data Pipeline. 9/10/2019. US-10409601.

Brown, W.M., Ould-Ahmed-Vall, E. Systems, apparatuses, and methods for cumulative summation. 5/2/2019. US-10296342.

Brown, W.M., Ould-Ahmed-Vall, E. Systems, apparatuses, and methods for cumulative product. 10/2/2018. US-10089110.

Thompson, A.P., Aktulga, H.M., Berger, R.B., Dan, S., Brown, W.M., Crozier, P.S., in't Veld, P.J.; Kohlmeyer, A., Moore, S.G., Nguyen, T.D. LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications. 2022. 108171

Brown, W.M.*, Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

Sankaran, R.*, Angel, J., Brown, W.M. Genetic Algorithm based Task Reordering to Improve the Performance of Batch Scheduled Massively Parallel Scientific Applications. Concurrency and Computation, Practice and Experience. 2015. 27: p. 4763-4783.

Wayne, J.*, Archibald, R., Berrill, M., Brown, W.M., Eisenback, M., Grout, R., Larkin, J., Levesque, J., Messer, B., Norman, M., Philip, B., Sankaran, R., Tharrington, A., Turner, J. Accelerated Application Development: The ORNL Titan Experience. Computers and Electrical Engineering. 2015. 46: p. 123-138.

Nguyen, T. D.*, Carrillo, J.-M. Y., Matheson, M. A., Brown, W.M.*, Rupture Mechanism of liquid crystal thin films realized by large-scale molecular simulations. Nanoscale. 2014. 6: p. 3083-3096.

Brown, W.M.*, Masako, Y. Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials. Computer Physics Communications. 2013. 184: p. 2785-2793. (preprint)

Carrillo, J.-M. Y.*, Kumar, R.*, Goswami, G., Sumpter, B., Brown, W.M., New Insights into Dynamics and Morphology of P3HT:PCBM Active Layers in Bulk Heterojunctions. Physical Chemistry Chemical Physics. 2013. 15: p. 17873-17882.

Ahn, S., Pickel, D., Kochemba, W., Chen, J., Uhrig, D., Hinestrosa, J. P., Carrillo, J.-M., Shao, M., Do, C., Messman, J., Brown, W.M., Sumpter, B., Kilbey, S. M.* Poly(3-hexylthiophene) Molecular Bottlebrushes via Ring-Opening Metathesis Polymerization: Macromolecular Architecture Enhanced Aggregation. ACS Macro Letters. 2013. 2: p. 761–765.

Nguyen, T.D., Carrillo, J.-M., Dobrynin, A.V., Brown, W.M.^* A Case Study of Truncated Electrostatics for Simulation of Polyelectrolyte Brushes on GPU Accelerators. Journal of Chemical Theory and Computation. 2013. 9: p. 73–83.

Carrillo, J.-M., Brown, W.M., Dobrynin, A.V.^* Explicit Solvent Simulations

of Friction between Brush Layers of Charged and Neutral Bottle-Brush Macromolecules. Macromolecules. 2012. 45: p. 8880–8891.

Brown, W.M.^*, Kohlmeyer, A. Plimpton, S.J., Tharrington, A.N. Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh. Computer Physics Communications. 2012. 183: p. 449-459.(preprint)

Brown, W.M.^*, Wang, P. Plimpton, S.J., Tharrington, A.N. Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces.Computer Physics Communications. 2011. 182: p. 898-911. (preprint)

Brown, W.M.^*, Thompson, A.P., Schultz, P.A. Efficient Hybrid Evolutionary Optimization of Interatomic Potential Models. Journal of Chemical Physics. 2010. 132: p. 024108 (1-10).

Gray, Genetha A.^*, Williams, P.J., Brown, W.M., Faulon, J.-L., Sale, K.S. Disparate Data Fusion for Protein Phosphorylation Prediction. Annals of Operations Research.2010. 174: p. 219-235.

Brown, W.M.^*, Petersen, M.K., Plimpton, S.J., Grest, G.S. Liquid Crystal Nanodroplets in Solution. Journal of Chemical Physics. 2009. 130: p. 044901 (1-7).

Brown, W.M.^*, Martin, S., Pollock, S.N., Coutsias, E.A., Watson, J.-P. Algorithmic Dimensionality Reduction for Molecular Structure Analysis. Journal of Chemical Physics. 2008. 129: p. 064118 (1-13).

Brown, W.M.^*, Sasson, A., Bellew, D.R., Hunsaker, L.A., Martin, S., Leitao, A., Deck, L.M., Vander Jagt, D. L., Oprea, T.I. Efficient Calculation of Molecular Properties from Simulation using Kernel Molecular Dynamics. Journal of Chemical Information and Modeling, 2008. 48: p. 1626-1637.

Brown, W.M.^*, Martin, S., Rintoul, M.D., Faulon, J.L. Designing Novel Polymers with Targeted Properties using the Signature Molecular Descriptor. Journal of Chemical Information and Modeling, 2006. 46: p. 826-835.

Brown, W. M.^* and Backer, A. Optimal Neuronal Tuning for Finite Stimulus Spaces. Neural Computation, 2006. 18: p. 1511-1526.

Brown, W. M., Martin, S.^*, Strauss, C., and Faulon, J.L. Prediction of Beta-Strand Packing Interactions Using the Signature Product. Journal of Molecular Modeling, 2006. 12: p. 355-361..

Faulon, J.L., Brown, W. M., Martin, S., Faulon, J.L.^* Reverse Engineering Chemical Structures from Molecular Descriptors: How Many Solutions? Journal of Computer-Aided Molecular Design, 2005. 19: p. 637-650.

Brown, W. M.^*, Faulon, JL., Sale, K. A Deterministic Algorithm for Constrained Enumeration of Transmembrane Protein Folds. Computational Biology and Chemistry, 2005. 29: p. 143-150.

Sillerud, L.O.^*, Burks, E.J., Brown, W.M., Brown, D.C., and Larson, R.S. NMR Solution Structure of a Potent Peptide Inhibitor of Integrin-based Cell Adhesion Produced by Homologous Amino Acid Substitution. Journal of Peptide Research, 2004. 64: p. 127-140.

Brown, W.M.^* and Vander Jagt, D.L. Creating Artificial Binding Pocket Boundaries to Improve the Efficiency of Flexible Ligand Docking. Journal of Chemical Information and Computer Science, 2004. 44: p. 1412-1422.

Brown, W.M., Hoard, A.,Vanderjagt, T.A., Hunsaker, L.A., Deck, L.M., Royer, R.E., Piper, R.C., Dame, J., Makler, D.L., and Vander Jagt, D.L.^* Comparative structural analysis and kinetic properties of lactate dehydrogenases from four species of human malarial parasites. Biochemistry, 2004. 43: p. 6219-6229.

Vander Jagt, D.L.^*, Hunsaker, L.A., Young, B.S. and Brown, W.M. Aldo-Keto Reductase-Catalyzed Detoxication of Endogenous Aldehydes Associated with Diabetic Complications. American Chemical Society Series, 2004. 865: p. 23-35.

Brown, W.M., Hunsaker, L.A., Deck, J.A., Royer, R.E. and Vander Jagt, D.L.^* 17-Beta-Hydroxysteroid Dehydrogenase Type 1: Computational Design of Active Site Inhibitors Targeted to the Rossmann Fold. Chemico-Biological Interactions, 2003. 143: p. 481-491.

Stoddard Hatch, M., Brown, W.M., Deck, J.A., Hunsaker, L.A., Deck, L.M. and Vander Jagt, D.L^*. Inhibition of Yeast Lipase (Crl1) and Cholesterol Esterase (Crl3) by 6-Chloro-2-Pyrones: Comparison with Porcine Cholesterol Esterase. Biochim Biophys Acta, 2002. 1596(2): p. 381-91.

Vander Jagt, D.L.^*, Hassebrook, R.K., Hunsaker, L.A., Brown, W.M. and Royer, R.E. Metabolism of the 2-Oxoaldehyde Methylglyoxal by Aldose Reductase and by Glyoxalase-I: Roles for Glutathione in Both Enzymes and Implications for Diabetic Complications. Chemico-Biological Interactions, 2001. 130(1-3): p. 549-562.

Brown, W. M.^*, Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. High Performance Computing, Networking, Storage and Analysis, SC16: International Conference for. IEEE. 2016. p. 82-95.

Brown, W. M.^*, Nguyen, T.D., Fuentes-Cabrera, M., Fowlkes, J. D., Rack, P. D., Berger, M., Bland, A. S. An Evaluation of Molecular Dynamics Performance on the Hybrid Cray XK6 Supercomputer. Proceedings of the ICCS Workshop on Large Scale Computational Physics. 2012. Published in Procedia Computer Science, 2012. 9 p. 186-195.

Martin, S.^*, Brown, W.M., Klavans, R. Boyack, K.W. OpenOrd: An Open-Source Toolbox for Large Graph Layout. Proceedings of the Visualization and Data Analysis Conference, 2011. Published in SPIE-IS&T, 2011. 7868. p. 786806-1-11.

Martin, S.^*, Brown, W.M., Faulon, J.-L., Weis, D., Visco, D. Inverse Design of Large Molecules using Linear Diophantine Equations. Proceedings of the 2005 IEEE Computational Systems Biology Conference, 2005. p. 11-16.

Brown, W.M.*, Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., “Optimizing Classical Molecular Dynamics in LAMMPS,” in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.

Martin, S., Brown, W.M., Faulon, J.-L., “Using Product Kernels to Predict Protein Interactions,” in Advances in Biochemical Engineering/Biotechnology: Protein-Protein Interactions, H. Seitz and M. Werther, Eds., Springer-Verlag.

Crozier, P.S., Agarwal, P.K., Alam, S.R., Brown, W.M., Hampton, S.S., Plimpton, S.J., Tharrington, A.N., Trott, C.R., Wang, P. Winterfeld, L. Harnessing GPU speed to accelerate LAMMPS particle simulations. SAND Reports, 2010. p. 1-69.

Brown, W.M., Thompson, A.P., Watson, J-P., Schultz, P.A. Bridging Scales from Ab Initio Models to Predictive Empirical Models for Complex Materials. SAND Reports, 2008. 6454: p. 1-57.

Grest, G. S., Brown, W. M., Lechman, J. B., Petersen, M. K., Plimpton, S. J., Schunk, P. R. Nanoparticle Flow, Ordering, and Self-Assembly. SAND Reports,2008. 6516: p. 1-29.

Martin, S., Brown, W.M., Klavans, R., Boyack, K.W., DrL: Distributed Recursive (Graph) Layout. SAND Reports, 2008. 2936: p. 1-10.

Brown, W.M., Davidson, G.S. Interactomes to Biological Phase Space: a call to begin thinking at a new level in computational biology. SAND Reports, 2007. 6278: p. 1-30.

May, E.E., Johnston, A.M., Watson, J.P., Hart, W.E., Brown, W.M. Deciphering the Genetic Regulatory Code Using an Inverse Error Control Coding Framework. SAND Reports, 2005. 1029: p. 1-41.

Brown, W.M., Faulon, J.L., Gray, G.A., Hunt, T.W., Schoeniger, J.S.,Shirley, D., Slepoy, A., Young, M.M., Sale, K.L. Model-Building Codes for Membrane Proteins. SAND Reports, 2004. 6383: p. 1-75.

Wang, P., Brown, W.M., Crozier, P.S. Efficient Short-Range Force Calculations on GPUs. SAND Reports, 2010. 4080C: p. 1-7.

Wagner, G.J., Deng, J., Erickson, L.C., Plimpton, S.J., Thompson, A.P., Zhou, X., Zimmerman, J.A., Brown, W.M. Accelerated Molecular Dynamics and Equation-Free Methods for Simulating Diffusion in Solids. SAND Reports, 2011. 6659: p. 1-146.