Deformation Dynamics of Nanopores upon Water Imbibition: Molecular Dynamics simulations

This dataset contains configuration files and results of Molecular Dynamics simulations investigating the imbibition dynamics of water into MCM-41 nanopores and the resulting deformation dynamics of the MCM-41 pore matrix. During the spontaneous imbibition process of liquids into the nanopores, the pore matrix solid deforms due to a superposition of the Laplace pressure effect and the surface stress release (Bangham effect). The two effects responsible for the deformation are proportional to the imbibition dynamics, which can be described by the Lucas-Washburn equation. For more details see https://doi.org/10.1073/pnas.2318386121.

### Molecular Dynamics Simulation
The molecular dynamics simulation studies of water imbibition in MCM-41 nanopores were performed using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1] https://www.lammps.org. The configuration files to run a simulation of water imbibition into silica nanopores (MCM-41) are provided in the md-config folder. The MCM-41 pore matrix is derived of the MCM-41 structure (the mcm-41.cif file) developed by Ugliengo et al. [2] by converting the structure to a LAMMPS file, breaking the symmetry of the porous matrix in axial direction and protonating the surface. The original coordinates of the MCM-structure, also in the form of a LAMMPS file with unbroken symmetry, are available at https://doi.org/10.13140/RG.2.2.19035.99361 under a CC-BY license. The silica-silica interactions are modeled by a modified Demiralp potential [3]. The water-silica interactions are modeled as described in [4, 5] and the water-water interactions are modelled with the TIP4P/2005 water model [6]. For more details see [doi.org/10.1073/pnas.2318386121](https://doi.org/10.1073/pnas.2318386121) and the SI therein. To perform an imbibition simulation the LAMMPS simulation has to be executed with the "system.in" as input file. In addition, a number of time steps must be provided so that the water reservoir is integrated in order to make the individual imbibition simulations independent. Assuming the LAMMPS executable is named "lmp" the command to run an imbibition simulation with initial 100 timesteps of water reservoir integration would be:
```lmp -in system.in -var randomize_run 100```

[1] LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, S. J. Plimpton, Comp Phys Comm, 271 (2022) 10817.

[2] Ugliengo, Piero, et al. "Realistic models of hydroxylated amorphous silica surfaces and MCM‐41 mesoporous material simulated by large‐scale periodic B3LYP calculations." Advanced Materials 20.23 (2008): 4579-4583.

[3] Meißner RH, Schneider J, Schiffels P, Colombi Ciacchi L (2014) Computational prediction of
circular dichroism spectra and quantification of helicity loss upon peptide adsorption on silica.
Langmuir 30(12):3487–3494.

[4] Cole DJ, Payne MC, Csányi G, Spearing SM, Ciacchi LC (2007) Development of a classical
force field for the oxidized Si surface: Application to hydrophilic wafer bonding. Journal of
Chemical Physics 127(20):204704.

[5] Butenuth A, et al. (2012) Ab initio derived force-field parameters for molecular dynamics
simulations of deprotonated amorphous-SiO2/water interfaces. physica status solidi (b)
249(2):292–305.

[6] Abascal JL, Vega C (2005) A general purpose model for the condensed phases of water:
TIP4P/2005. The Journal of Chemical Physics 123(23):234505.

### Simulation Results Datasets
The datasets in the md-results folder are the results of 20 independent molecular dynamics imbibtion simulations using the provided configuration files. The used timestep variable "randomize_run" was 20, 40, ..., 400. The simulations were performed with the LAMMPS version (23 Jun 2022 - Update 4) with the included KSPACE, MOLECULE and RIGID packages.

The included files are:

#### analysis.ipynb
The Jupyter notebook analysis.ipynb contains the analysis performed on the simulation data to obtain the imbibition and strain dynamics results as published in [doi.org/10.1073/pnas.2318386121](https://doi.org/10.1073/pnas.2318386121).

#### calc-long-strain.py
The Python script calc-long-strain.py extracts the longitudinal induced strain from the solid pore matrix output from the imbibition simulation runs as mcm_position.data. The script produces the long-cauchy-strain.csv file used in the Jupyter Notebook.

#### boxinfo{#}.data in the boxinfo folder
The boxinfo{#}.data files contain the extensions of the orthogonal MD simulation box for every 10 simulation time steps for each simulation number #. This information is used to determine the imbibition dynamics and the induced strain lateral to the cylindrical pore.

| Column Name | Description |
| ----------- | ----------- |
| timestep | Time step of the simulation |
| Lx | Extension of the simulation box in x direction (lateral to cylindrical pore) |
| Ly | Extension of the simulation box in y direction (lateral to cylindrical pore) |
| Lz | Extension of the simulation box in z direction (longitudinal to cylindrical pore) |

#### long-cauchy-strain.csv

The longitudinal pore matrix strain is provided in the long-cauchy-strain.csv file. The Cauchy strain is calculated between two groups of atoms in the pore solid at the axial ends of the pore matrix of 5 nm (see [doi.org/10.1073/pnas.2318386121](https://doi.org/10.1073/pnas.2318386121) and SI). It contains 5 columns.

| Column Name | Description |
| ----------- | ----------- |
| simnum | Number of conducted simulation |
| timestep | Timestep of the simulation |
| strain_mean | Mean of the Cauchy strain |
| strain_sq_dev | The squared standard devation of the strain |
| strain_count | The number of z difference components of atom used to calculate the strain |

#### relaxed_system.data

The initial LAMMPS configuration file relaxed_system.data used to compute the imbibition dynamics from.