ZenoWrapper: Accessing Hydrodynamic and Electronic Properties through MDAnalysis

ZENO computes hydrodynamic and electronic properties using numerical path integration techniques based on Brownian motion Monte Carlo methods. These methods provide stochastic solutions to elliptic partial differential equations, which represent the desired material properties or serve as intermediates for their computation. The mathematical framework maps these problems onto the electrostatic capacitance problem, where the stochastic solution corresponds to the probability of a random walk from infinity hitting the material's surface. ZENO employs the Walk-on-Spheres algorithm to efficiently simulate Brownian motion, enabling larger jumps compared to traditional Brownian dynamics techniques, significantly reducing computational cost. The ZENOWrapper package provides a Python interface to the ZENO computation engine, integrating it seamlessly with MDAnalysis. This integration automates the preparation of ZENO input files, execution of computations, and retrieval of results as Python objects. By accepting MDAnalysis Universe/AtomGroup objects and trajectory frames, ZENOWrapper enables hydrodynamic and transport property analyses to be conducted directly within MDAnalysis workflows, facilitating reproducible research. Additionally, ZENOWrapper bridges ZENO’s specialized input system with any simulation package supported by MDAnalysis. It also leverages MDAnalysis’ parallelization capabilities and compatibility with interactive molecular dynamics (IMD3), enhancing the efficiency and scalability of hydrodynamic property calculations for macromolecular systems.

[
  "006:55"
]

{
  "fn": "Debra Audus",
  "hasEmail": "mailto:debra.audus@nist.gov"
}

[
  {
    "title": "GitHub Link",
    "format": "This code is hosted on GitHub in a repository.",
    "accessURL": "https://github.com/usnistgov/zenowrapper",
    "description": "This is a link to the GitHub repository where the package, zenowrapper, is hosted."
  }
]

[
  "MDAnalysis",
  "hydrodynamic properties",
  "polymers",
  "simulations"
]

[
  "en"
]

[
  "006:045"
]

{
  "name": "National Institute of Standards and Technology",
  "@type": "org:Organization"
}

[
  "Materials:Materials characterization",
  "Materials:Modeling and computational material science",
  "Materials:Polymers"
]