Marc Mansfield Stevens Institute Eunhee Kang (Stevens doctoral student)

1. Zeno Site- Website Providing a Computational Algorithm for the Computation of Transport Properties of Nanoparticles, Polymers and Complex Biological Structures Marc MansfieldStevens Institute Eunhee Kang(Stevens doctoral student) Jack F. DouglasPolymers Division, NIST

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 accuracyMain TargetCustomers: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 ZenoThe most widely accepted computational method for calculating the intrinsic viscosity and hydrodynamic radius of complex macromolecular structures is a program called HydroZeno outperforms this program in a variety of ways

6. Tests of Zeno1) Zeno permits greater flexibility in defining particle geometryIn 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. D L 2) Tests of Hydro and Zeno against exactly solvable models indicate that Zeno is more accurate Dumbbell RH [] L/D L/D

8. 3) Zeno is computationally faster and is completely parallelHydro computational times O(n3)Zeno computational times O(n) where n is the number of body elementsThis is a factor for complex bodies where n is large and for random objects whereensembles of objects must be generated and sampled

9. 10 nm 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 Zeno Hydro RH (nm) ring 11.3 11.1 cage 33.3 N/A Watts et al., Biochemistry 41, 12662 (2002) Mussachio et al., Mol. Cell3 , 761 (1999) 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 computations3) Extend calculations to second virial coefficient (Ray Mountain)