Marc Mansfield Stevens Institute Eunhee Kang (Stevens doctoral

student) Jack F. Douglas Polymers Division, NIST

Zeno Site- Website Providing a Computational Algorithm for the

Computation of Transport Properties of Nanoparticles, Polymers and Complex

Biological Structures

Objective:Provide algorithm (Zeno) for calculating the Stokes friction coefficient, electrostatic capacity, intrinsic viscosity, intrinsic conductivity and electrical polarizability of essentially arbitrarily-shaped objects to unprecedented accuracyMain Target Customers:Material scientists and biologists interested in characterizing complex shaped nanoparticles (e.g., nanotubes) and basic biological structures (e.g., viruses, proteins, clathrin cages) based on transport and scattering measurements

Scientific Principle of Program:The Zeno computational method involves enclosing an arbitrary-shaped probed object within a sphere and launching random walks from this sphere. The probing trajectories either hit or return to the launch surface (‘loss’) as shown in the figure for a model soot particle aggregate, whereupon the trajectory is either terminated or reinitiated.

The fraction of random walk trajectories that hit the probed object determines its capacity C (hydrodynamic radius) and the electric polarizibility tensor and [] are estimated similarly.

Accomplishments:

Constructed website that makes Zeno available in an accessible format (well-documented Fortran program)- provides explanation of method principle and list of relevant references

Tested Zeno against competing programs

Established database for protein transport properties (Calculated properties 1 K proteins from the PDB and compared to measurement)

Project Status - New

Tests of Zeno

The most widely accepted computational method for

calculating the intrinsic viscosity and hydrodynamic radius of

complex macromolecular structures is a program called Hydro

Zeno outperforms this program in a variety of ways

Tests of Zeno 1) Zeno permits greater flexibility in defining particle geometry

In Hydro the particles must be built up from beads while Zeno allows for beads, cylinders, ellipsoids, surfaces with triangulated surfaces, etc. Allows physically more realistic modeling of particle structure

2) Tests of Hydro and Zeno against exactly solvable models indicate that Zeno is more accurate L

D

Dumbbell

RH []

L/DL/D

3) Zeno is computationally faster and is completely parallel

Hydro computational times O(n3)Zeno computational times O(n) where n is the number of body elements

This is a factor for complex bodies where n is large and for random objects whereensembles of objects must be generated and sampled

Impact: Provides useful tool for characterizing nanoparticle and biological structuresZeno’s test- it’s utilization and acceptanceRecent case studies from NIH-LIMB: Cryptophycin-tubulin rings and clathrin

cages RH (nm)

Zeno Hydro

10 nm

ring 11.3 11.1

cage 33.3 N/A

Mussachio et al., Mol. Cell 3 , 761 (1999)

Watts et al., Biochemistry 41, 12662 (2002) 7000 beads

Planned Improvements:1) Create database of calculated structures e.g., Perform calculations on all protein structures in PDB (12 K)

2) Develop web module for direct online Zeno computations

3) Extend calculations to second virial coefficient (Ray Mountain)