Work Description

Title: A Microscopic Theory of Entropic Bonding – Energy/Simulation Scripts with Representative Data Open Access Deposited

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Attribute Value
Methodology
  • Simulation data were collected by running the included simulation scripts using the HOOMD-Blue v2.9 simulation engine ( http://glotzerlab.engin.umich.edu/hoomd-blue/index.html). Theoretical calculations for wavefunctions and subsequent lattice energies are computed using the included energy calculation script. Briefly, wavefunctions are computed by constructing a fine meshgrid in xyz that spans the system size and evaluating the pseudoparticle density at each point as defined by our developed theory. Lattice energy are then determined via integration across this xyz grid weighted by the appropriate Hamiltonian describing particle-particle interactions. All energy calculation codes are written in matlab/octave and are stored as “.m” files.
Description
  • The goal of this project is to develop a first principle driven approach for predicting the self-assembly behavior of entropically driven crystallization. We first developed a set of mean-field theoretical framework that captures the relevant energetic contributions to the assembly process and then evaluate relevant terms within our framework to determine the excess free energy of formation for each lattice (matlab/octave codes). We then validate theoretical predictions of relevant features like shape and bonding orbitals using standard MD simulations using HOOMD-Blue (simulation scripts).

  • This research was supported by the Office of the Undersecretary of Defense for Research and Engineering (OUSD(R&E)), Newton Award for Transformative Ideas during the COVID-19 Pandemic, Award number HQ00342010030.
Creator
Depositor
  • thiv@umich.edu
Contact information
Discipline
Funding agency
  • Department of Defense (DOD)
ORSP grant number
  • AWD016127
Keyword
Citations to related material
  • Vo, T., & Glotzer, S. C. (2021). Microscopic Theory of Entropic Bonding for Colloidal Crystal Prediction. ArXiv:2107.02081 [Cond-Mat]. http://arxiv.org/abs/2107.02081
Resource type
Last modified
  • 11/19/2022
Published
  • 10/17/2022
Language
DOI
  • https://doi.org/10.7302/1b70-7970
License
To Cite this Work:
Vo, T., Glotzer, S. C. (2022). A Microscopic Theory of Entropic Bonding – Energy/Simulation Scripts with Representative Data [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/1b70-7970

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Files (Count: 7; Size: 858 MB)

Thumbnailthumbnail-column Title Original Upload Last Modified File Size Access Actions
readme.txt 2021-07-21 2021-07-21 4.56 KB Open Access
AIChE_Annual_Meeting_11_16_2020.pdf 2021-07-21 2021-07-21 39.5 MB Open Access
PP_sims_signac.zip 2021-07-21 2021-07-21 3.94 MB Open Access
entropic_bond_signac.zip 2021-07-21 2021-07-21 58.4 KB Open Access
energy_calculator.zip 2021-07-21 2021-07-21 49.9 MB Open Access
PP_simulations.zip 2021-07-21 2021-07-21 764 MB Open Access
metadata.txt 2021-07-21 2021-07-21 2.34 KB Open Access

Project Description:

This project aims to develop a framework for predicting the assembly behavior for entropically driven self-assembly of hard polyhedra. Briefly, we first develop a psuedoparticle (pP) ansatz that facilitates the quantification of emergent directional attractions between hard polyhedra upon crowding. We then employ pP to quantitatively map out regions of interactions between neighboring polyhedra and develop a set of eigenvalue solvers to determine configurations that maximizes interactions between polyhedra. These calculations are subsequently extended to enable the input of test crystal in order to compute the excess free energy of formation of polyhedra occupying lattice sites of differing crystal structures, thereby facilitating the determination of the most thermodynamically stable lattice.

Here, we included sample scripts for both lattice predictions as well as MD simulations of pP that verifies the presence of "shape" and "bonding orbitals" as predicted by theory. Lattice energy calculations are written in MATLAB and MD simulations employ the usage of the HOOMD-Blue simulation engine. Sample data outputs are provided for a diamond lattice (lattice energy) and singe/binary NP orbital formations (MD simulations).

Link to paper describing the theory/simulations:

Vo, T., & Glotzer, S. C. (2021). Microscopic Theory of Entropic Bonding for Colloidal Crystal Prediction. ArXiv:2107.02081 [Cond-Mat]. http://arxiv.org/abs/2107.02081

Short description of files:

*All energy calculations codes are ".m" files that can be run in either matlab or octave environments*

*All simulation scripts are for use with HOOMD-Blue v 2.9*

File: AIChE_Annual_Meeting_11_16_2020.pptx: AIChE conference presentation of theory

Folder: PP_sims_signac - signac project folder with JSON files describing PP simulation parameters

Folder: entropic_bond_signac - signac project folder with JSON files describing entropic bond calculation parameters

Folder: energy_calculator

Subfolder: lattice_files
all relevant lattices tested for shapes studied organized by shape name
Order of columns: x y z quaternion (q1, q2, q3, q4)
Subfolder: shape_files
all vertices of shapes used in calculations (tetrahedron varies truncation so that is organized into its own subfolder)
Order of columns: x y z
Subfolder: polyhedron_functions
basis functions for shape manipulations, add to path before running

Files:
calc_rscale.m: compute relative scaling distances between shapes
gen_kernel_evaluator.m: compute shape kernel for use in calculations
parameterize_shape.m: working function to generate shape grid for use in gen_kenel_evaluator
sample_diamond_energy.m: code that computes sample entropic bond energy
change name of lattice_type and pts_shape where indicated in code to switch testing for different shapes/lattices
cubic_wavefunction.txt: sample output of wavefunction for cubic diamond
hexagonal_wavefunction.txt: sample output of wavefunction for hexagonal diamond
trunc_tetra.txt: shape vertices input for calculations
cubicdiamond.txt: cubic diamond lattice coordinate inputs for calculations
hexagonaldiamond.txt: hexagonal diamond lattice coordinate inputs for calculations

Folder: PP_simulations

Subfolder: simulation_codes
sample_sims_unary.py: HOOMD-Blue script for single NP within sea of PP for orbital visualization
sample_sims_binary.py: HOOMD-Blue script for two NP within sea of PP for orbital visualization

Subfolder: sample_results
Folders
cube: sample result for single cube NP
prism6: sample result for single hexagonal prism NP
tetrahedron: sample result for single tetrahedron NP
dodecahedron: sample result for single dodecahedron NP
cube_binary: sample result for binary cube NP
prism6_binary: sample result for binary hexagonal prism NP
tetrahedron_binary: sample result for binary tetrahedron NP
dodecahedron_binary: sample result for binary dodecahedron NP

Files:
Tetrahedronorbital_full.txt: theory orbital output for tetrahedron
Order of columns: x, y, z, 1st orbital value, 2nd orbital value, 3rd orbital value, 4th orbital value
Cubeorbital_full.txt: theory orbital output for cube
Order of columns: x, y, z, 1st orbital value, 2nd orbital value, 3rd orbital value, 4th orbital value
Dodecahedronorbital_full.txt: theory orbital output for dodecahedron
Order of columns: x, y, z, 1st orbital value, 2nd orbital value, 3rd orbital value, 4th orbital value
Prism6orbital_full.txt: theory orbital output for hexagonal prism
Order of columns: x, y, z, 1st orbital value, 2nd orbital value, 3rd orbital value, 4th orbital value

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