zenowrapper

zenowrapper

Description

ZenoWrapper - Hydrodynamic Property Calculations for Molecular Systems

ZenoWrapper provides a Python interface to the NIST ZENO software for computing hydrodynamic, electronic, and geometric properties of molecular structures from MD simulations. This package integrates ZENO’s Monte Carlo algorithms with MDAnalysis, enabling high-throughput analysis of biomolecular trajectories.

Key Applications

Compute essential physical properties for understanding molecular behavior in solution:

• Diffusion coefficients - predict translational mobility and transport rates

• Sedimentation coefficients - analyze molecular mass and shape from ultracentrifugation

• Intrinsic viscosity - determine solution behavior and polymer characterization

• Hydrodynamic radius - estimate effective molecular size in solution

• Friction coefficients - quantify resistance to motion through solvent

• Gyration tensor - characterize molecular shape and anisotropy

Scientific Impact

These properties are critical for:

• Comparing simulation predictions with experimental measurements (AUC, DLS, etc.)

• Characterizing protein complexes, polymers, and nanoparticles

• Validating force field accuracy in solution conditions

• Predicting macromolecular behavior in crowded cellular environments

Algorithm

ZENO employs two complementary Monte Carlo methods:

1. Walk-on-Spheres (exterior): Solves Laplace’s equation to compute electrical properties (capacitance, polarizability) and hydrodynamic properties via electrostatic-hydrodynamic analogy

2. Interior Sampling: Estimates geometric properties (volume, gyration tensor) by random point sampling within the molecular volume

These algorithms provide rigorous statistical uncertainties for all computed properties.

References

• ZENO Documentation: https://zeno.nist.gov/

• Calculations: https://zeno.nist.gov/Calculations.html

• Output Properties: https://zeno.nist.gov/Output.html

• Douglas, J.F. et al. (2017) J. Res. NIST 122: https://doi.org/10.6028/jres.122.020

Usage Example

import MDAnalysis as mda
from zenowrapper import ZenoWrapper

# Load system
u = mda.Universe('protein.pdb', 'trajectory.dcd')

# Define VdW radii by atom type
type_radii = {
    'C': 1.70, 'N': 1.55, 'O': 1.52, 'S': 1.80,
    'H': 1.20, 'P': 1.80
}

# Initialize analysis
zeno = ZenoWrapper(
    u.select_atoms('protein'),
    type_radii=type_radii,
    n_walks=1000000,           # exterior calculation
    n_interior_samples=100000,  # interior calculation
    temperature=298.15,         # K, for diffusion coefficient
    viscosity=0.01,            # poise (water at 20°C)
    mass=50000.0,              # Da
    buoyancy_factor=0.73,      # typical for proteins in water
    length_units='A'           # Angstroms
)

# Run over trajectory frames
zeno.run(start=0, stop=100, step=1, verbose=True)

# Access results (each is a Property object with .values and .variance arrays)
print(f"Hydrodynamic radius: {zeno.results.hydrodynamic_radius.values.mean():.2f} Å")
print(f"Diffusion coefficient: {zeno.results.diffusion_coefficient.values.mean():.2e}")
print(f"Volume: {zeno.results.volume.values.mean():.2f} ų")

main	Hydrodynamic Property Calculations Using ZENO Monte Carlo Methods