High-throughput molecular simulations and machine learning (ML) have been implemented to adequately screen a large number of metal−organic frameworks (MOFs) for applications involving adsorption. Grand canonical Monte Carlo (GCMC) simulations have proven effective in calculating the adsorption capacity at given pressures and temperatures, but they can require expensive computational resources. While they can be resource-efficient, ML models can require large datasets, creating a need for algorithms that can efficiently characterize adsorption; active learning (AL) can play a very important role in this regard. In this work, we make use of Gaussian process regression (GPR) to model pure component adsorption of nitrogen at 77 K from 10−5 to 1 bar, methane at 298 K from 10 −5 to 100 bar, carbon dioxide at 298 K from 10−5 to 100 bar, and hydrogen at 77 K from 10−5 to 100 bar on PCN-61, MgMOF-74, DUT-32, DUT-49, MOF-177, NU-800, UiO-66, ZIF-8, IRMOF-1, IRMOF-10, and IRMOF-16. The GPR model requires an initial training of the model with an initial dataset, the prior one, and, in this study of evaluating AL, we make use of three different prior selection schemes. Each prior scheme is updated with a sampling point resulting from the GP model uncertainties. This protocol continues until a maximum GPR relative error of 2% is attained. We make a recommendation on the best prior selection scheme for the total 44 adsorbate−adsorbent pairs primarily making use of the mean absolute error and the total amount of points required for convergence of the model. To further evaluate the AL framework, we apply the BET consistency criteria on the simulated and GP nitrogen isotherms and compare the resulting surface areas.
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Sequential design of adsorption simulations in metal–organic frameworks
The large number of possible structures of metal–organic frameworks (MOFs) and their limitless potential applications have motivated molecular modelers and researchers to develop methods and models to efficiently assess MOF performance. Some of the techniques include large-scale high-throughput molecular simulations and machine learning models. Despite those advances, the number of possible materials and the potential conditions that could be used still pose a formidable challenge for model development requiring large data sets. Therefore, there is a clear need for algorithms that can efficiently explore the spaces while balancing the number of simulations with prediction accuracy. Here, we present how active learning can sequentially select simulation conditions for gas adsorption, ultimately resulting in accurate adsorption predictions with an order of magnitude lower number of simulations. We model adsorption of pure components methane and carbon dioxide in Cu–BTC. We employ Gaussian process regression (GPR) and use the resulting uncertainties in the predictions to guide the next sampling point for molecular simulation. We outline the procedure and demonstrate how this model can emulate adsorption isotherms at 300 K from 10 −6 to 300 bar (methane)/100 bar (carbon dioxide). We also show how this procedure can be used for predicting adsorption on a temperature–pressure phase space for a temperature range of 100 to 300 K, and pressure range of 10 −6 to 300 bar (methane)/100 bar (carbon dioxide).
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- Award ID(s):
- 1941596
- NSF-PAR ID:
- 10315108
- Date Published:
- Journal Name:
- Molecular Systems Design & Engineering
- ISSN:
- 2058-9689
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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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.
Version: 2.0
Changes 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.
Conventions Used in These Files
===============================Structure Files
----------------
- 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.)- graph_*.pdb or sol_*.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)
- 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)
- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)
- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)Force Field Parameters
----------------------
CHARMM format parameter files:
- par_all36m_prot.prm (CHARMM36m FF for proteins)
- 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.
- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included 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_eq.namd (NPT equilibration with lower graphene fixed)
- template_abf.namd (for adaptive biasing force)Minimization
-------------
- namd/min_*.0.namdEquilibration
-------------
- namd/eq_*.0.namdAdaptive biasing force calculations
-----------------------------------
- namd/eabfZRest7_graph_chp1404.0.namd
- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)Log Files
---------
For 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.Simulation Output
-----------------
The 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.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. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.
CONTENTS
========The 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.
Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.
Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.
Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.
Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.
Sim_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.
Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).
Sim_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.
Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.
Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.
Sim_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.
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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Abstract Geological storage of carbon dioxide (CO2) in depleted gas reservoirs represents a cost-effective solution to mitigate global carbon emissions. The surface chemistry of the reservoir rock, pressure, temperature, and moisture content are critical factors that determine the CO2 adsorption capacity and storage mechanisms. Shale-gas reservoirs are good candidates for this application. However, the interactions of CO2 and organic content still need further investigation. The objectives of this paper are to (i) experimentally investigate the effect of pressure and temperature on the CO2 adsorption capacity of activated carbon, (ii) quantify the nanoscale interfacial interactions between CO2 and the activated carbon surface using Monte Carlo molecular modeling, and (iii) quantify the correlation between the adsorption isotherms of activated carbon-CO2 system and the actual carbon dioxide adsorption on shale-gas rock at different temperatures and geochemical conditions. Activated carbon is used as a proxy for kerogen. The objectives aim at obtaining a better understanding of the behavior of CO2 injection and storage into shale-gas formations.
We performed experimental measurements and Grand Canonical Monte Carlo (GCMC) simulations of CO2 adsorption onto activated carbon. The experimental work involved measurements of the high-pressure adsorption capacity of activated carbon using pure CO2 gas. Subsequently, we performed a series of GCMC simulations to calculate CO2 adsorption capacity on activated carbon to validate the experimental results. The simulated activated carbon structure consists of graphite sheets with a distance between the sheets equal to the average actual pore size of the activated carbon sample. Adsorption isotherms were calculated and modeled for each temperature value at various pressures.
The adsorption of CO2 on activated carbon is favorable from the energy and kinetic point of view. This is due to the presence of a wide micro to meso pore sizes that can accommodate a large amount of CO2 particles. The results of the experimental work show that excess adsorption results for gas mixtures lie in between the results for pure components. The simulation results agree with the experimental measurements. The strength of CO2 adsorption depends on both surface chemistry and pore size of activated carbon. Once strong adsorption sites within nanoscale network are established, gas adsorption even at very low pressure is governed by pore width rather than chemical composition. The outcomes of this paper provides new insights about the parameters affecting CO2 adsorption and storage in shale-gas reservoirs, which is critical for developing standalone representative models for CO2 adsorption on pure organic carbon.
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The characterization of petrophysical and geomechanical properties of source rocks presents inherent challenges due to lithology heterogeneity, lamination, distribution of organic matter, and presence of fractures. Organic-rich shales also present some distinctive features that make hydrocarbon production and CO2 geological storage unique in these rocks. The objective of this paper is to quantify and model the deformational behavior of carbon-based compounds due to changes of stress and pressure that happen simultaneously with gas adsorption and desorption processes. We designed an experimental procedure that consists of: (1) compaction of organic-rich grains/powder under oedometric conditions, (2) measurement of poromechanical properties in the absence of adsorption effects using helium in a triaxial cell through independent changes of confining pressure and pore pressure, (3) measurement of the adsorption strain, and stress for methane (CH4). An adsorptive-poromechanical model permits explaining the experimental data, discriminating between the strain/stress caused by poroelastic response from the adsorption-induced strain/stress, and measuring the poroelastic-sorption properties of the organic-rich compound. We applied this procedure to activated carbon and measured skeletal volumetric modulus ranging from 11.8 to 16.6 GPa and skeletal adsorption stress of ~100 MPa for CH4 at 7 MPa of adsorbate pressure. The proposed procedure and model are useful to explain and predict the unique properties of carbon-based adsorbents which can be extended to kerogen, a critical component in source rocks.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D1ME00138H
