1. 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

2. 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 accuracy Main 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

3. 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.

4. 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

5. 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

6. 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

7. 2) Tests of Hydro and Zeno against exactly solvable models indicate that Zeno is more accurate L D Dumbbell RHRH [][] L/D

8. 3) Zeno is computationally faster and is completely parallel Hydro computational times O(n 3 ) 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 where ensembles of objects must be generated and sampled

9. Impact: Provides useful tool for characterizing nanoparticle and biological structures Zeno’s test- it’s utilization and acceptance Recent case studies from NIH-LIMB: Cryptophycin-tubulin rings and clathrin cages R H (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

10. 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)