Multiscale Computer Simulations
for Chemistry, Biology, Material
and Energy Sciences
Hao Hu
Department of Chemistry
The University of Hong Kong
HKU_Grid_2010
Summary of Ongoing GRIDPOINT Projects
• Dr. H. Hu
Computer Simulations of Biomolecular and Chemical
Processes for Medicinal and Material Sciences
• Prof. K. Y. Chan
Computation of Materials & Transport Related to Energy
Applications
HKU_Grid_2010
Enzyme: Extraordinary Catalyst for Life
HKU_Grid_2010
Enzyme: Target for Medicinal and Industrial
Research
• Many enzymes are key players in critical physiological
processes
– Target for drug design for cancer research
• Enzyme design for new chemistry
– New synthesis
– Energy research
HKU_Grid_2010
Methodology Developments for Simulating Enzymes
QM
MM
Combined Quantum
Mechanical / Molecular
Mechanical Method
Ultimate goal: Simulate bigger molecules,
at longer timescale, with better accuracy
Technical Challenges
Speeding up quantum mechanical calculation
Proper consideration of long-range forces
Sufficient sampling of enzyme conformations
HKU_Grid_2010
Simulating Enzymes Catalysis
HKU_Grid_2010
Simulation of Enzyme Catalysis
Chorismate mutase• Synthesis of Phe and Tyr
• Only exists in fungi, bacteria, and higher plant
• Target for fighting Tuberculosis, especially drug-resistant
Tuberculosis
HKU_Grid_2010
Simulation of Enzyme Catalysis
Aminoacyl-tRNA synthetaseActivation of amino acid
Amino acid + ATP ========> Aminoacyl-5‘AMP + PPi
Reaction mechanism is unclear
Evolution of the enzyme is interesting.
HKU_Grid_2010
Simulation of Enzyme Catalysis
Pin-1Catalyzes cis/trans isomerization of peptidyl-prolyl bond.
plays key roles in many important physiological/cellular processes
HKU_Grid_2010
Other Projects
• New methods for quantum chemistry calculations: linear-
scaling
• Enzyme design
• Molecular docking/design for drug discovery
• Multi-scale methods for the structure, dynamics, and
recognition of important giant biomolecular complexes
HKU_Grid_2010
Prof. K.Y. Chan’s Research
Computation of Materials & Transport
Related to Energy Applications
Collaborator: Dr. David Yu-Hang Chui,
now in Melbourne University
Multi-Scale Methodology:
Equilibrium Molecular Dynamics (EMD) Non-Equilibrium
Molecular Dynamics (NEMD) Car-Parrinello Molecular
Dynamics (CPMD) Monte Carlo (MC), Continuum
Mechanics
HKU_Grid_2010
Anode Electrode
H2 2H+ + 2e-
alcohols
glucose CO2 + H+ + 2e-
Liq. fuels
HKU Fuel Cell Cart
A DMFC powered
cellular phone fuel cell stack
TEM
Image of
Nano
Catalyst
Cathode Electrode:
½O2 + 2H+ + 2e- H2O
Molecular/
Atomic
Nanoscopic
Macroscopic
Structuring
System
Integrated
Devices
e-
H+
Bott
om
up r
esea
rch s
trat
egy
Nano Size
dependence
catalytic
activity
Cu, Fe, Pt, support
Mixed Nano
Metal/Metal Oxides:
Pt/Ru/Co/Sn/W
Mesoporous carbon
cationic, anionic, bipolar
nano polymeric-ceramic
membranes
SynthesisComputing / Modeling
HKU made
A single fuel cell
FuelOxidant
Properties
HKU_Grid_2010
Simulations and modelling help
to understand the formation and
properties of nanostructures
Chui and co-workers, 2004-now
Limitations in
characterization
lead to poor understanding
of nanostructures
Problem Tools
Nanostructuring of metals
HKU_Grid_2010
Combine classical and quantum calculations to investigate
the effect of shapes, sizes, and compositions
on the catalytic activity of nanoparticles.
to design a durable and more efficient nano-catalyst
for fuel cell applications.
Modelling core-shell Mixed Metal nanoparticles at HKU
Red - Pt Blue - Cu
Observed phase change in core/shell PtCu/Pt nanoparticles
Understand lattice strain control in core-shell structures.
The computational time : 2 hours on HKU Gridpoint
HKU_Grid_2010
Ionic Transport in Nanopores
Experiments
AC Impedance in
Nanoporous Electrodes
NEMD Simulations with AC
Electric Field applied
0 100 200 300 400 500 600 700 800
0
50
100
150
200
250
300
350
Z''
Z' / ohm
-0.24V
-0.19V
-0.14V
-0.09V
-0.04V
0.00 2.00 4.00 6.00 8.00
0.00
1.00
2.00
3.00
4.00 R=4.5Å
R=9Å
R=15Å
s" /W
-1m
-1
s ' /W-1
m-1
Tang, Szalai & Chan,
Nano LettersRen, Ding, Chan, & Wang, Chem Mater
0 20 40 60 80 100
-60
-40
-20
0
20
40
60
80
s' (W
-1cm
-1)
900 K
s"
(W-1cm
-1)
1273 K
1759 K
Zhang & Chan,
J. Phys Chem
YSZSPC/E Electrolyte
HKU_Grid_2010
The (Old) Ecologic System for Academic Research
Experiment
Theory
Industry
Money
HKU_Grid_2010
The (New) Ecologic System for Academic Research
Experiment
Theory
Industry
Simulation
& Modeling
Money ?
HKU_Grid_2010
Thank You