Transcript Slide Show - Stevens Institute of Technology

Zeno Site- Website Providing a
Computational Algorithm for the
Computation of Transport Properties of
Nanoparticles, Polymers and Complex
Biological Structures
Marc Mansfield
Eunhee Kang
Jack F. Douglas
Stevens Institute
(Stevens doctoral student)
Polymers Division, NIST
Objective:
Provide algorithm (Zeno) for calculating the
Stokes friction coefficient, electrostatic capacity,
intrinsic viscosity, intrinsic conductivity and
electrical polarizability of essentially arbitrarilyshaped 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
Scientific Principle of Program:
The Zeno computational method
involves enclosing an arbitraryshaped 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:
Project Status - New
 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)
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
Dumbbell
RH
[]
L/D
L/D
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 where
ensembles of objects must be generated
and sampled
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
Zeno
RH (nm)
10 nm
Watts et al., Biochemistry
41, 12662 (2002)
Mussachio et al.,
Mol. Cell 3 , 761 (1999)
Hydro
ring 11.3
11.1
cage 33.3
N/A
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)