mnflow 0.0.1.1

A package for micro/nanoflow

mnFlow

Single DLD	Parallelized DLD

[!TIP] The manual and tutorials can be accessed from the documentation, generated from /docs.

Introduction

Micro-nanoflow (mnFlow) library is aimed at providing the community with tools for design and modeling of micro-nanofluidic chips. The current focus of the project is on Deterministic Lateral Displacement (DLD) structures. In particular, the DLD design automation (DDA) tool aims at automating the entire process of design and production of computer-aided design (CAD) files for DLD-based micro-nanofluidic chips. The produced CAD files can be used for computational modeling, optimization, and manufacturing of DLD devices.

Usage

Installation

To use mnFlow, first install it using pip (preferably in a virtual environment using venv):

python -m pip install mnflow

Getting Started

Let us design a DLD structure with critical diameter of d_c=10.0 (microns) and periodicity of Np=10. The channel is vertical by default. In this example, we pass rot_last=90 to apply a 90-degree rotation to form a horizontal channel (for better arrangement in this document). Finally, we pass opt_save_image=True to save an image of the layout. Here, is the final script:

from mnflow.mfda.cad.dld.theme.block import DLD
dld = DLD(
    d_c=10.0,
    Np=10,
    rot_last=90,
    opt_save_image=True,
)

Output:

----------------------------------------
core.DLD___Np:10_Nw:8_gap_w:21.571_pitch_w:43.142_gap_a:21.571_pitch_a:43.142_height:86.284_boundary_treatment:pow_3
block.DLD___num_unit:9_opt_mirror:False_array_counts:[1, 1]_opt_mirror_before_array:[False, False]
----------------------------------------
{'Np': 10,
 'Nw': 8,
 'area': 1781004.4974180001,
 'bb': [(-3861.227, -113.554), (21.571, 345.137)],
 'count of 1D arrays of core.DLD': 1,
 'd_c': 9.999999999999998,
 'lx': 3882.798,
 'ly': 458.69100000000003,
 'performance': {'Flow rate @ 1 bar/area (micro-liter/min/mm-sq)': 715.9902222759154,
                 'die area (mm-sq)': 1.7810044974180002,
                 'gap over crit. dia.': 2.1571083717157262,
                 'volumetric flow rate at 1 bar (micro-liter/min)': 1275.1818059807188},
 'resistance (Pa.sec/m^3)': 4705211423076.657,
 'volumetric flow rate at 1 bar (m^3/sec)': 2.1253030099678647e-08,
 'volumetric flow rate at 1 bar (milli-liter/hr)': 76.51090835884312}

Output layout:

At this point, you should have a few files created in your working directory automatically: layout files in gds and png formats.

If that is the case, and if the layout is similar to the output layout presented above, and if the log you see after executing the script matches that shown above, the package should have been installed properly.

How to contribute code

Follow these steps to submit your code contribution.

Step 1. Open an issue

Before making any changes, we recommend opening an issue (if one doesn't already exist) and discussing your proposed changes. This way, we can give you feedback and validate the proposed changes.

Step 2. Make code changes

To make code changes, you need to fork the repository.

Step 3. Create a pull request

Once the change is ready, open a pull request from your branch in your fork to the dev branch of this repository.

Step 4. Review

Work with reviewers to apply any changes that may be necessary.

Step 5. Merge

Once the change is approved, we will merge the changes into the repository.

Acknowledgments

This project utilizes the packages mentioned in the following. We gratefully acknowledge their contributions to this project.

• klayout: For creating CAD layouts.
• numpy: For numerical computations.
• pillow: For creating image of layouts.
• scipy: For solving equations.
• matplotlib: For data visualization
• black, flake8, and isort: For linting and formatting codes.
• git and pre-commit: For revision control and pre-commit hooks, respectively.
• sphinx, and sphinx-rtd-theme: For creating docs.
• pytest, and pytest-cov: For creating test cases.

Citation

If you use this work in your research, please cite the relevant works associated with it as listed in the following.

Original paper

A. Mehboudi, S. Singhal, and S.V. Sreenivasan, A universal framework for design and manufacture of deterministic lateral displacement chips, Lab on a Chip, 2024. DOI: 10.1039/D4LC00838C

BibTeX entry:

@article{mehboudi_universal_2024,
  title = {A Universal Framework for Design and Manufacture of Deterministic Lateral Displacement Chips},
  author = {Mehboudi, Aryan and Singhal, Shrawan and Sreenivasan, S.V.},
  year = {2024},
  month = dec,
  journal = {Lab on a Chip},
  publisher = {The Royal Society of Chemistry},
  issn = {1473-0189},
  doi = {10.1039/D4LC00838C}
}

Zenodo Archive

A. Mehboudi, mnFlow: A package for micro/nanoflow, Zenodo, 2024. DOI: 10.5281/zenodo.14357811

BibTeX entry:

@misc{mehboudi_mnflow_2024,
  title = {{{mnFlow}}: {{A}} Package for Micro/Nanoflow},
  shorttitle = {{{mnFlow}}},
  author = {Mehboudi, Aryan},
  year = {2024},
  month = dec,
  publisher = {Zenodo},
  doi = {10.5281/ZENODO.14357811},
  url = {https://zenodo.org/doi/10.5281/zenodo.14357811},
  abstract = {Micro-nanoflow (mnFlow) package is aimed at providing the community with tools for design and modeling of micro-nanofluidic chips.},
  copyright = {GNU Affero General Public License v3.0 only}
}