Zhang YL, Hu B, Teng Y, Tu K, Zhu C (2019) A library of BASIC scripts of reaction rates for geochemical modeling using PHREEQC. Computers & Geosciences
Title:
A library of BASIC scripts of rate equations for geochemical modeling using PHREEQC
Polly, P.D. and A. Goswami. 2010. Modularity for Mathematica, Version 1.0. Goswami, A. & Polly, P. D. 2010 Methods for studying morphological integration, modularity and covariance evolution. In Quantitative Methods in Paleobiology. Paleontological Society Short Course, October 30th, 2010, vol. The Paleontological Society Papers (ed. J. Alroy & G. Hunt), pp. 213-243. Chicago: The Paleontological Society.
Polly, P. D. 2012. Geometric morphometrics for Mathematica. Version 9.0. Department of Geological Sciences, Indiana University: Bloomington, Indiana. http://mypage.iu.edu/~pdpolly/Software.html
Title:
Geometric Morphometrics for Mathematica (Ver. 9.0)
Polly, P. D. 2012. Phylogenetics for Mathematica. Version 2.1. Department of Geological Sciences, Indiana University: Bloomington, Indiana. http://mypage.iu.edu/~pdpolly/Software.html
To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D.
MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 100 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size.
Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
Data variables can be found in Yanites, 2018 Journal of Geophysical Research: Earth Surface as well as in the model code uploaded to the Community Surface Dynamic Modeling System infrastructure.
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Data scripts for modeling dynamic width and slope evoluton of actively eroding rivers
A single ".ova" file encompassing an Ubuntu-based (v. 16.04) virtual machine (VM). This VM is the "artifact" used in the artifact evaluation of the corresponding PPoPP17 paper. It contains the complete software, such as example programs and benchmark programs, necessary to reproduce the results of the paper. Scripts are included in the virtual machine to automatically run benchmarks and compare their results. Download the VM by clicking the link below under "Link(s) to data and video for this item."
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Bundled VM artifact to accompany paper entitled SC-Haskell: Sequential Consistency in Languages That Minimize Mutable Shared Heap
Download the software applications used for the 2015 Student Cluster Competition by clicking the URLs below: HPC Repast (4 MB); MILC (2 GB); Trinity (64 GB); WRF (5 GB). Note that download times may vary and that due to its size the Trinity file could take several hours.
