This readme.txt file was updated on 2023-11-14 by Madeline Murphy ------------------- General Information ------------------- Data used in the case studies in Murphy et. al Catalytic Resonance Theory: Circumfluence of Programmable Catalytic Loops Principal Investigator Contact Information Name: Paul Dauenhauer University of Minnesota hauer@umn.edu Room 484 421 Washington Avenue SE Minneapolis, MN 55455 Co-investigator Contact Information: Madeline Murphy University of Minnesota murp1677@umn.edu Help with script writing: Sallye Gathmann University of Minnesota gathm005@umn.edu Chris Bartel University of Minnesota cbartel@umn.edu Date Published or finalized for release: 2023-11-16 Date of data collection: 2023-06-04 -- 2023-08-30 -------------------- Overview of the data -------------------- This data bank includes a csv file [CaseStudy_Parameters.csv] containing all the Parameter inputs for simulations ran in Julia using the script CaseStudy_LoopSimulation.jl [in the folder Murphy_Loop_JuliaCodes.zip]. Each simulation outputs two sets of data. The raw data from the simulation for time, surface coverages, rates, and catalyst states were exported to its own csv titled RawData_Simulation(Batch ID).(Job ID).csv, where Batch ID denotes the figure number the data appears in and Job ID specifies the input parameter set. Data is also exported to CaseStudy_Outputs.csv which stores the simulation identification, input parameters, and output parameter(loopTOF). In Figure 6, the behavior of a system with a programmable catalyst including 3 distinct states was explored. These simulations were ran using the script 3State_LoopSimulation.jl [in the folder Murphy_Loop_3State_JuliaCodes.zip]. Scripts written in Julia 1.9.0 and all relevant data files included for the case studies including in Catalytic Resonance Theory: Circumfluence of Programmable Catalytic Loops. Batch scripts used to submit the files to run through the Minnesota Supercomputing Institute's slurm workload manager are also included. -------------------------- SHARING/ACCESS INFORMATION -------------------------- Murphy, Madeline A; Gathmann, Sallye R; Bartel, Chris. (2023). Data for Catalytic Resonance Theory: Circumfluence of Programmable Catalytic Loops. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/cng1-fb88. Licenses/restrictions placed on the data: CC0 1.0 Universal Links to publications that cite or use the data: Preprint: https://doi.org/10.26434/chemrxiv-2023-xmb84 Peer review: under review Data was derived using the following Julia files to run simulations of the reaction on a dynamic catalyst surface (All included in Murphy_Loop_JuliaCodes.zip) : - CaseStudy_LoopSimulation.jl - CycleBaseFuncts.jl - Callbacks.jl - Plots.jl To run simulation using a programmable catalyst with three states, the following Julia files were used (All included in Murphy_Loop_3State_JuliaCodes.zip) : - 3State_LoopSimulation.jl - 123_Callbacks.jl - 132_Callbacks.jl - CycleBaseFuncts.jl Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List Murphy_Loop_JuliaCodes.zip Zip File containing all Julia scripts used to run simulations with two distinct catalyst states 12.34Kb application/zip Murphy_Loop_3State_JuliaCodes.zip Zip File containing all Julia scripts used to run simulations with three distinct catalyst states 10.76Kb application/zip DynamicLoop-CaseStudy.slurm Batch script used to submit batches of simulations with two distinct catalyst states as a single job to the Minnesota Supercomputing Institute. 908bytes Unknown DynamicLoop-CaseStudy-3State.slurm Batch script used to submit batches of simulations with three distinct catalyst states as a single job to the Minnesota Supercomputing Institute. 908bytes Unknown Input and Output definitions.pdf Input and output definitions 581.6Kb PDF CaseStudyData.zip Zip file containing all simulation results and figures. 396.8Mb application/zip General Data: (Included in CaseStudyData.zip) A. Filename: CaseStudy_Parameters.csv Description: Parameter inputs for the case studies explored in Figures 02-05 of Murphy et. al Catalytic Resonance Theory: Circumfluence of Programmable Catalytic Loops B. Filename: CaseStudy_Outputs.csv Description: Parameter inputs and resulting loop TOF output for the case studies explored in Figures 02-05 of Murphy et. al Catalytic Resonance Theory: Circumfluence of Programmable Catalytic Loops Raw Data: (Included in CaseStudyData.zip) Raw simulation data, stored as CSV files, for time, surface coverages of A*, B*, and C*, instantaneous rates of elementary reaction 1, 2, and 3, and catalyst state. Figure 02: Inducing a positive loop TOF about the reactive loop. Data includes the same chemistry parameter, varying the frequency and amplitude of oscillation to explore the effects of dynamics on the rate of circumfluence clockwise about the loop. A. Filename: RawData_Simulation2.1.csv B. Filename: RawData_Simulation2.2.csv C. Filename: RawData_Simulation2.3.csv D. Filename: RawData_Simulation2.4.csv E. Filename: RawData_Simulation2.5.csv F. Filename: RawData_Simulation2.6.csv G. Filename: RawData_Simulation2.7.csv H. Filename: RawData_Simulation2.8.csv I. Filename: RawData_Simulation2.9.csv J. Filename: RawData_Simulation2.10.csv K. Filename: RawData_Simulation2.11.csv L. Filename: RawData_Simulation2.12.csv M. Filename: RawData_Simulation2.13.csv N. Filename: RawData_Simulation2.14.csv O. Filename: RawData_Simulation2.15.csv P. Filename: RawData_Simulation2.1_SC2.csv initial surface coverage: [0.8, 0.1, 0.1] Q. Filename: RawData_Simulation2.1_SC3.csv initial surface coverage: [0.5, 0.2, 0.3] R. Filename: RawData_Simulation2.1_SC4.csv initial surface coverage: [0.1, 0.8, 0.1] S. Filename: RawData_Simulation2.3_SC2.csv initial surface coverage: [0.0, 1.0, 0.0] T. Filename: RawData_Simulation2.3_SC3.csv initial surface coverage: [0.0, 0.0, 1.0] U. Filename: RawData_Simulation2.3_SC4.csv initial surface coverage: [0.8, 0.1, 0.1] Figure 03: Inducing a negative loop TOF about the reactive loop. Data includes the same chemistry parameter, varying the frequency and amplitude of oscillation to explore the effects of dynamics on the rate of circumfluence counterclockwise about the loop. A. Filename: RawData_Simulation3.1.csv B. Filename: RawData_Simulation3.2.csv C. Filename: RawData_Simulation3.3.csv D. Filename: RawData_Simulation3.4.csv E. Filename: RawData_Simulation3.5.csv F. Filename: RawData_Simulation3.6.csv G. Filename: RawData_Simulation3.7.csv H. Filename: RawData_Simulation3.8.csv I. Filename: RawData_Simulation3.9.csv J. Filename: RawData_Simulation3.10.csv K. Filename: RawData_Simulation3.11.csv L. Filename: RawData_Simulation3.12.csv M. Filename: RawData_Simulation3.13.csv N. Filename: RawData_Simulation3.14.csv O. Filename: RawData_Simulation3.15.csv Figure 04: Catalyst surface poisoning. A steady state solution of one surface species covering the entire catalyst surface. A. Filename: RawData_Simulation4.1.csv B. Filename: RawData_Simulation4.2.csv C. Filename: RawData_Simulation4.3.csv Figure 05: Oscillation between surface species B* and C* in resonance with oscillation between catalyst states 1 and 2. No loop TOF is observed. A. Filename: RawData_Simulation5.1.csv B. Filename: RawData_Simulation5.2.csv C. Filename: RawData_Simulation5.3.csv D. Filename: RawData_Simulation5.4.csv E. Filename: RawData_Simulation5.5.csv F. Filename: RawData_Simulation5.6.csv Figure 06: Using a 3 state programmable catalyst to observe both positive loop turnover frequency and negative loop turnover frequency. A. Filename: RawData_Simulation6.1.csv B. Filename: RawData_Simulation6.2.csv C. Filename: RawData_Simulation6.3.csv D. Filename: RawData_Simulation6.4.csv E. Filename: RawData_Simulation6.5.csv F. Filename: RawData_Simulation6.6.csv G. Filename: RawData_Simulation6.7.csv H. Filename: RawData_Simulation6.8.csv Figure 07: Using a programmable catalyst with the same three states as in Figure 6, but isolating the program to using only two of the states. A. Filename: RawData_Simulation7.1.csv B. Filename: RawData_Simulation7.2.csv C. Filename: RawData_Simulation7.3.csv Individual Figures: (Included in CaseStudyData.zip) The individual panels included in each figure generated in Julia 1.9.0 depicting the raw data above and stored as TIFF files. Figure 02: Inducing a positive loop TOF about the reactive loop. Data includes the same chemistry parameter, varying the frequency and amplitude of oscillation to explore the effects of dynamics on the rate of circumfluence clockwise about the loop. A. Filename: Figure2b.tiff B. Filename: Figure2c.tiff C. Filename: Figure2d.tiff D. Filename: Figure2e.tiff E. Filename: Figure2f.tiff F. Filename: Figure2g.tiff G. Filename: Figure2h.tiff H. Filename: Figure2i.tiff I. Filename: Figure2j.tiff Figure 03: Inducing a negative loop TOF about the reactive loop. Data includes the same chemistry parameter, varying the frequency and amplitude of oscillation to explore the effects of dynamics on the rate of circumfluence counterclockwise about the loop. A. Filename: Figure3a.tiff B. Filename: Figure3b.tiff C. Filename: Figure3c.tiff D. Filename: Figure3d.tiff E. Filename: Figure3e.tiff F. Filename: Figure3f.tiff G. Filename: Figure3g.tiff Figure 04: Catalyst surface poisoning. A steady state solution of one surface species covering the entire catalyst surface. A. Filename: Figure4a.tiff B. Filename: Figure4b.tiff C. Filename: Figure4c.tiff D. Filename: Figure4d.tiff E. Filename: Figure4e.tiff F. Filename: Figure4f.tiff Figure 05: Oscillation between surface species B* and C* in resonance with oscillation between catalyst states 1 and 2. No loop TOF is observed. A. Filename: Figure5a.tiff B. Filename: Figure5b.tiff C. Filename: Figure5c.tiff D. Filename: Figure5d.tiff E. Filename: Figure5e.tiff F. Filename: Figure5f.tiff G. Filename: Figure5g.tiff H. Filename: Figure5h.tiff Figure 06: Using a 3 state programmable catalyst to observe both positive loop turnover frequency and negative loop turnover frequency. A. Filename: Figure6b.tiff B. Filename: Figure6c.tiff C. Filename: Figure6c_zoom.tiff D. Filename: Figure6d.tiff E. Filename: Figure6f.tiff F. Filename: Figure6g.tiff G. Filename: Figure6g_zoom.tiff H. Filename: Figure6h.tiff Figure 07: Using a programmable catalyst with the same three states as in Figure 6, but isolating the program to using only two of the states. A. Filename: Figure7b.tiff B. Filename: Figure7d.tiff C. Filename: Figure7f.tiff