NERSCPowering Scientific Discovery Since 1974

Transport and Self-Assembly in Molecular Nanosystems

Key Challenges: Use classical molecular dynamics and coarse grain molecular dynamics to enable "bottom-up" material design of a wide variety of nanostructures possessing a wealth of unique properties.  The goal is to guide and inform synthetic investigations and understand molecular and electronic transport, self-assembly, catalysis, and other phenomena.  Ab-initio electronic structure and quantum transport methods are also used. The modeling often involves large systems (500,000 atoms) and cooperative use of several codes such as Gaussian and NAMD.  Free-energy calculations typically require good ensemble averaging and therefore, must be performed 10-15 times for each test case.

Why it Matters: This work has application in the design of nanomedicines - delivery of drugs by micelles.  This also includes systems capable of molecular-level mechanical functions.  A second area explores design of optimal functionalized nanopores from graphene monolayers and ion and molecular passage through the nanopores.  The resulting graphene sheets might be used for molecular detection, separation, desalination, and battery technologies.  At a more basic level the work seeks to mimic – inorganically – the behavior of proteins & cells.

Accomplishments: Simulations of water droplets on sheets of carbon atoms show that the sheets spontaneously fold or roll into three-dimensional shapes.  Other simultions showed that electron tunneling can drive nano-scale motors used in nanopropellers; that functionalized graphene-based nanopores can serve as ionic sieves; that nanodroplets can be dragged on the surface of carbon nanotubes; and that hydrated lipid micelles filled with hydrophobic molecules of preferred sizes and amounts can be self-assembled on the surfaces of carbon nanotubes.  This work uses NERSC-provided software packages - an extensive NERSC effort to provide over 13 million lines of software so scientist/customers can focus more on discovery than on compiling code.

Investigator: Petr Král (University of Illinois at Chicago)

More Information: See, for example, Journal of the American Chemical Society, 133 (16), pp 6146–6149 (2011).  Movies from some of the simulations and additional info are available on Prof. Král's web site.

Below: A galery of nanostructures studied by Prof. Král and his group at NERSC.  From left to right on the top row: a graphene stripe spontaneously slides and wraps around a nanodroplet of water; two example highly-selective nanosieves that enable chemical ion separation; and a molecular propeller formed by a carbon nanotube rotor with attached aromatic blades that rotates driven by electron tunneling.  On the bottom row: two snapshots showing controlled self-assembly of micelles filled with a hydrophobic molecule on a carbon nanotubes.

About NERSC and Berkeley Lab
The National Energy Research Scientific Computing Center (NERSC) is the primary high-performance computing facility for scientific research sponsored by the U.S. Department of Energy's Office of Science. Located at Lawrence Berkeley National Laboratory, the NERSC Center serves more than 6,000 scientists at national laboratories and universities researching a wide range of problems in combustion, climate modeling, fusion energy, materials science, physics, chemistry, computational biology, and other disciplines. Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the U.S. DOE Office of Science. »Learn more about computing sciences at Berkeley Lab.