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1. The 2023 Release of Cloudy

   Chatzikos, Marios; Bianchi, Stefano; Camilloni, F; Chakraborty, Priyanka; Gunasekera, Chamani M; Guzman, Francisco; Milby, Jonathan S; Sarkar, Arnab; Shaw, Gargi; van_Hoof, Peter A_M; et al (October 2023, Revista mexicana de astronomía y astrofísica)

   We describe the 2023 release of the spectral synthesis code Cloudy. Since the previous major release, migrations of our online services motivated us to adopt git as our version control system. This change alone led us to adopt an annual release scheme, accompanied by a short release paper, the present being the inaugural. Significant changes to our atomic and molecular data have improved the accuracy of Cloudy predictions: we have upgraded our instance of the Chianti database from version 7 to 10; our H- and He-like collisional rates to improved theoretical values; our molecular data to the most recent LAMDA database, and several chemical reaction rates to their most recent UDfA and KiDA values. Finally, we describe our progress on upgrading Cloudy's capabilities to meet the requirements of the X-ray microcalorimeters aboard the upcoming XRISM and Athena missions, and outline future developments that will make Cloudy of use to the X-ray community. 

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2. Simulation files for "Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm"

   https://doi.org/10.5281/zenodo.14855068  

   Comer, Jeffrey (February 2025, Zenodo)

   This is the simulation data set for the manuscript: Arvelo DM, Comer J, Schmit J, Garcia R (2024) Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm. ACS Nano 18:18683–18692. https://doi.org/10.1021/acsnano.4c05689 This data set includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. LAMMPS input files for the ReaxFF simulations are also included. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or LAMMPS data), force field parameter files (in CHARMM format or ReaxFF format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD or LAMMPS log files, and output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled with a stride of 100 to 20 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included. Version: 1.0. Figure5AC: Simulation of pentadecane on a 5 chains/nm^2 OTS layer. Figure5B_FigureS7: Calculation of force profile for an SiO2 tip asperity model using adaptive biasing force. Systems: octane with 5 chains/nm^2 OTS, octane with 4 chains/nm^2 OTS, decane with 5 chains/nm^2 OTS, water with 5 chains/nm^2 OTS. FigureS6: Simulations showing the effect of octadecane on the structure of the OTS layer for 3 and 5 chains/nm^2 densities. FigureS8: Calculation of the adsorption free energy of tetracosane (C24) at the OTS–water interface using ABF. FigureS9: Python script for estimating the critical concentration to form an alkane layer at the OTS–water interface using the mean-field Ising model. FigureS10: ReaxFF simulation and modeling to create the silanol-terminated amorphous silica model of an AFM tip asperity. FigureS11: Molecular dynamics simulations showing spontaneous assembly of twelve or twenty-four tetracosane (C24) molecules at the interface between water and the alkyl groups of an OTS-conjugated silica surface. 

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3. Molecular Dynamics Simulation of a Designed Cyclic Peptide Bound to CTLA4

   https://doi.org/10.5281/zenodo.7186684  

   Thakkar, Ravindra; Comer, Jeffrey (October 2022, RSC medicinal chemistry)

   This data set for the manuscript entitled "Computational Design of a Cyclic Peptide that Inhibits the CTLA4 Immune Checkpoint Pathway" includes all files needed to run and analyze the simulations of a designed cyclic peptide (Peptide 16) bound to CTLA4 in the putative most stable binding configuration, which is detailed in Figure 6 of the paper. These files include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. These scripts and their output are also included. Version: 1.0 Conventions Used in These Files =============================== Structure Files ---------------- - ctla4_P16_wat.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.) - ctla4_P16.pdb (initial coordinates before equilibration) - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl) - rest*.pdb (same as the above pdb files, but atoms have been marked for restraints in NAMD. These files are generated by doPrep.sh, with restraints applied to different atoms.) Force Field Parameters ---------------------- CHARMM format parameter files: - par_all36m_prot.prm (CHARMM36m FF for proteins) - toppar_water_ions_prot.str (CHARMM water and ions with NBFIX parameters needed for protein and others commented out) Template NAMD Configuration Files --------------------------------- These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory): - template_min.namd (minimization) - template_rest.namd (NPT equilibration with different parts of the protein restrained) - template_prod.namd (for the long production simulations) Minimization ------------- - namd/min_*.0.namd Restraints ------------- - namd/rest_*.0.namd (both CTLA4 binding site and peptide atoms are restrained) - namd/rest_*.1.namd (CA atoms of CTLA4 and all atoms of the peptide are restrained) - namd/rest_*.2.namd (all atoms of only the peptide are restrained) - namd/rest_*.3.namd (only CA atoms of only the peptide are restrained) - namd/rest_*.4.namd (no atoms are restrained) Production ------------- - namd/pro_*.{D,E,F}.0.namd Analysis ------------- - interaction.sh (Shell script for running analysis with VMD) - calcSeparationNearestAtom.tcl (Calculate the separation between two selections, taking the shortest distance between any pair of atoms spanning the two selections. Accounts for (orthogonal) periodic boundary conditions.) - useful.tcl (VMD Tcl script with a library of useful procs, used by the script above) - sep_*.dat (Output of the above analysis containing rows with two columns: time in nanoseconds and minimum distance in Å) Scripts ------- Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. 

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4. DFTB based models of gas molecules adsorbed in functionalized carbophenes

   https://doi.org/10.17632/BXKBBS2553.3  

   Junkermeier, Chad E; Junkermeier, Chad; Kobobel, Jedediah; Lavarez, Kat; Adra, Martin; Diaz, Valeria; Yang, Jirui; Psofogiannakis, George; Paupitz, Ricardo (January 2024, Mendeley Data)

   Molecular data of functionalized carbophenes, gas molecules, and gas molecules adsorbed by functionalized carbophenes. All data was produced using density functional tight-binding theory. The data is divided into three text files, each containing the data in the edn extensible data format. A fourth file is an example job script used for creating a DFTB+ input file and running the code on the Mana cluster at the University of Hawaiʻi at Mānoa. Version 1 of this data contained incorrect adsorption energies of CO2 molecules into the pores of the functionalized carbophenes. The errors came from accidentally using the total energy of CO2 as computed in DFTB+ using Universal Force Field parameters for the long-range energy corrections. In contrast, the data set used DFTB+ with Grimme’s D3 dispersion corrections. In Version 2, we corrected the adsorption energy values in the Gas_molecules_in_functionalized_carbophenes.txt records. The file Gas_molecules.txt now includes records for N2 and O2 which were used in computing the formation energies recorded in Gas_molecules_in_functionalized_carbophenes.txt. In creating producing Version 2, we accidentally missed five records. In Version 3, we added those five records back into Gas_molecules_in_functionalized_carbophenes.txt. 

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5. Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.5281/zenodo.6426152  

   Comer, Jeffrey; Thakkar, Ravindra; Velásquez-Silva, Astrid; Miranda-Carvajal, Ingrid (January 2022, Zenodo)

   {"Abstract":["This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.<\/p>\n\nVersion: 2.0<\/p>\n\nChanges versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.<\/p>\n\n\nConventions Used in These Files\n===============================<\/p>\n\nStructure Files\n----------------\n- graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)<\/p>\n\n- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)\n- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)\n- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)\n- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)\n- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)<\/p>\n\nForce Field Parameters\n----------------------\nCHARMM format parameter files:\n- par_all36m_prot.prm (CHARMM36m FF for proteins)\n- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.\n- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)<\/p>\n\nTemplate NAMD Configuration Files\n---------------------------------\nThese contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):\n- template_min.namd (minimization)\n- template_eq.namd (NPT equilibration with lower graphene fixed)\n- template_abf.namd (for adaptive biasing force)<\/p>\n\nMinimization\n-------------\n- namd/min_*.0.namd<\/p>\n\nEquilibration\n-------------\n- namd/eq_*.0.namd<\/p>\n\nAdaptive biasing force calculations\n-----------------------------------\n- namd/eabfZRest7_graph_chp1404.0.namd\n- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)<\/p>\n\nLog Files\n---------\nFor each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.<\/p>\n\nSimulation Output\n-----------------\nThe simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.<\/p>\n\nScripts\n-------\nFiles with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.<\/p>\n\n\nCONTENTS\n========<\/p>\n\nThe directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.<\/p>\n\nSim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.<\/p>\n\nSim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 295 K.<\/p>\n\nSim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.<\/p>\n\nSim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).<\/p>\n\nSim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.<\/p>\n\nSim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene\u2013water interface in the initial configuration.<\/p>\n\nSim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.<\/p>\n\n <\/p>"],"Other":["This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030."]} 

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