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