Title: Towards design of nanosensor for biodetection through computation
1- Towards design of nanosensor for biodetection
through computation - R. Q. Zhang (???)
- City University of Hong Kong
- Yantai Workshop (May 22-25)
2Computational nanoscience
Growth mechanism
Properties Structural, electronic, electrical,
optical, magnetic, etc.
Devices Nanoelectronics, nanosensors,
spintronics, etc.
3Outline
- Growth mechanism and properties of covalent
nanostructures - Biodetection, nanomaterials for sensor
- Sensitivity of CNTs CO, FAD and PPE
- Biosensitivity of semiconductor Nanowires in
progress
4Outline
- Growth mechanism and properties of covalent
nanostructures - Biodetection, nanomaterials for sensor
- Sensitivity of CNTs CO, FAD and PPE
- Biosensitivity of semiconductor Nanowires in
progress
5OAG vs VLS
6Oxide assisted growth (OAG)Adv. Mat. 15, 635
(2003).
Si SiO2 or SiO
- Laser ablation
- Thermal evaporation
Substrate
7PRL93, 095503 (2004)
DFT-PBE-GGA (DZP) Trouiller and Martins MD 500 K
for 2 ps B3LYP/6-31G
- Energetics and dynamics (SiO)n for n5 contain a
sp3 Si core - Reactivity gt combination
- O migration
8Oxide-assisted SiNW nucleation mechanism
Mater. Sci. Engin. C, 16, 31(2001) PRB (2002),
PRL 93, 095503 (2004)
- High chemical reactivity gt small gt large
clusters - When ngt5, a sp3 Si core appears, surrounded by
SiO2 - Reconstruction and O migration gt Nuclei and
precursors Si nanostructures - Crystallographic dependence
9Chemical Stability
Can H-Passivated Si nanostructure Surfaces be
achieved using HF-etching?
10Chemical Stability
Size dependent oxidation
-
1
5
TS
Appl. Phys. Lett., 88(22), 4223-5 (June 3 2002).
Reactants
-
2
5
Products
SinHm H2O
SinHm-1OH H2
IC
-
3
5
lnk
-
4
5
Si2H6-SiH2 H2O ? Si5H10-SiH2
H2O ? Si9H14-SiH2 H2O. SiH3-SiH3
H2O ? Si4H9-SiH3 H2O ?
Si10H15-SiH3 H2O.
-
5
5
-
6
5
Total rate constants (cm3 mol-1 s-1) at 1 atm
-
7
5
1000/T
2
.
0
2
.
5
3
.
0
3
.
5
4
.
0
11Chemical Stability
SiH3-SiH3 H2O Si4H9-SiH3 H2O Si10H15-SiH3
H2O.
- SiH2 terminated surface is relatively stable.
- Size-dependent reactivity with respect to
oxidation. - It is possible to fabricate nonreactive, stable
nanodevices.
lnk
Si2H6-SiH2 H2O Si5H10-SiH2 H2O
Si9H14-SiH2 H2O.
Number of Si atoms
12Chemical Stability
D.D.D. Ma et al. Science 299 (2003) 1874
13Chemical Stability
Treated surface stable for days in air
D.D.D. Ma et al. Science 299 (2003) 1874
14Megnetism of BN nanotubes doped with C
C
C C C C C
C
15Electron Transport
- Reported nanodevices made of
- metal nanodots
- fullerences
- carbon nanotubes
16Electron Transport
- Theories of I-V characteristics and Coulomb
staircase of nanostructure - (1) Classical capacity theory
- (2) The orthodox theory
- a semi-classical approach based on quantum-
mechanical electronic structures - (3) Non-equilibrium Green-function method
- (4)
17The orthodox theory
- For an elastic tunneling, transition rates
where the transmission coefficient takes
(WKB)
- ab initio calculations for electronic structures.
18Electron Transport
Conductance
I-V
PRB(2002) JPC(2004)
19Optical properties
Theory (1) TD-DFTB (2) INDO/S-TDHF
20Optical properties Si nanodot
unpublished
21Optical properties Si nanodot
Electronic coherent density matrix plots of
hydrogenated silicon clusters (a) Ground state
of Si123H100. (b) First excited state of
Si17H36. (c) First excited state density matrix
of Si59H60. (d) First excited state density
matrix of Si123H100.
22Optical properties BN/CNT
PRB(2004), PRB(2005)
(4,4)
(7,0)
(5,3)
23Outline
- Growth mechanism and properties of covalent
nanostructures - Biodetection, nanomaterials for sensor
- Sensitivity of CNTs CO, FAD and PPE
- Biosensitivity of semiconductor Nanowires in
progress
24Biodetection
Signal transduction methods optical,
radioactive, electrochemical, piezoelectric,
magnetic, micromechanical, and mass
spectrometric. Requirements for a successful
biosensor sensitivity, selectivity, detection
limit, stability, and response time. Problems
remain Most sensors fail to meet the
requirements and thus remain mostly laboratory
curiosities.
25Nanomaterials for Sensor
Advantage high aspect ratio and quantum
effects Focused well-defined and functionalised
Examples (1) nanoparticles, (2) porous
silicon, (3) CNTs, (4) semiconductor
nanowires (a few, including one from CityU)
26Status
- More and more experimental works appeared
- Relevant theoretical works are too few
conformations functionalization adsorption
transport properties - Much in demand reliable calculations on the
transport and optical properties of
nanostructured materials functionalised with
biomolecules.
27Outline
- Growth mechanism and properties of covalent
nanostructures - Biodetection, nanomaterials for sensor
- Sensitivity of CNTs CO, FAD and PPE
- Biosensitivity of semiconductor Nanowires in
progress
28Transport CO/NO on CNT
- Background
- Experiment conductance decreases when exposed to
water vapor. - Theory the I-V characteristics of different type
of nanotube response differently to the adsorbed
H2O. - Our work CO, NO etc. on CNT using a DFT based
non-equilibrium Green functions (NEGF) method.
29Theory
Where µL, µR are the electronic chemical
potential of the left and right electrode.
30Models
One molecule and five molecular have been studied
in this work
31Results
Current-Voltage characteristic
(O end points to the tube)
32(C end points to the tube)
33(No Transcript)
34Summary
- When the O end is attached to the NT, the effect
is negligible - when the C end is attached to the NT surface, the
effect of adsorption is significant.
35FAD adsorption on carbon nanotube
- Background
- Flavin adenine dinucleotide (FAD) is the redox
active group of flavoenzymes (?????). - It catalyses important biological redox reactions
and the flavoenzyme glucose oxidase (GOx).
36Examples of FAD in biosystem
The bend of the isoalloxazine ring of FAD in the
active site of wild-type POX (2).
Electron density map of the region of the protein
(white) bound with flavin.
37Interactions with CNTs
- The combination of SWNT with redox active enzymes
would be expected to offer - an excellent and convenient platform for a
fundamental understanding of biological redox
reactions - the development of reagentless biosensors and
nanobiosensors.
38Computation
- DFTB and DFT
- (5,5) nanotube and FAD molecule was optimized by
DFTB. - The dispersion energy is taken into account.
Optical absorption spectrum is calculated by
TDDFTB method. (C.S. Lin et al., JPC(B) 2005) - DOS was calculated by DFT method.
39FAD Models
40Optimized structure of FAD adsorbed on CNT
41Energy (eV)
DOS of pure (5,5) carbon nanotube (magenta color)
and FAD adsorbed on (5,5) carbon nanotube (blue
color)
42Energy (eV)
PDOS of O atoms and C atoms of flavin and adenine
group
43I-V of FAD and GOx adsorbed on SWNT/GCE (From
Nanotechnology 13 (2002) 559564).
44Absorption spectrum of FAD. Green curve the gas
state FAD blue curve the FAD adsorbed on CNT.
45Summary
- FAD contributes more in DOS at Fermi energy. The
enhanced electron transfer is responsible for the
I-V increase in experiment. - It is predicted that the FAD absorption spectrum
does not change when FAD is adsorbed on CNT.
46PPE adsorption on CNT
1a ploy phenylenethynylene (PPE)
PPEs are excellent sensors for land mine
detection.
PPEs can also applied as light-emitting
devices , or in binary PPE / polyethylene
mixtures as sheet polarizers in LC displays
47Experiment
The 1HNMR spectrum of 1a-SWNTsHiPco supports a
strong p-pinteraction between 1a and the
nanotube.
48The optical spectroscopy supports a significant p
- p interaction between the polymer and the
nanotube.
49PPE adsorption on CNT
PPE1-SWNTsHiPco
PPE2-SWNTsHiPco
50Results
Theory TDDFTB
51Results
52Summary
- The calculated adsorption spectrum of PPE vs
experimental value 447nm vs 439nm. - A result of p - p interactions between the SWNTs
and the fully conjugated PPE backbone. - The adsorption spectrum of SWNTs/PPE 750nm lt
band-to-band transitions of pure SWNTs. - The binding energies independent of the diameter
of CNTs. - No covalent interaction, between (n, n) SWNTs and
PPE. They are combined by p - p interactions and
Van der Waals attraction.
53Problems of CNT sensor
- Metallic and semiconducting
- Lack of flexible methods for the modification of
NT surface
54Outline
- Growth mechanism and properties of covalent
nanostructures - Biodetection, nanomaterials for sensor
- Sensitivity of CNTs CO, FAD and PPE
- Biosensitivity of semiconductor Nanowires in
progress
55Biosensitivity of Semiconductor Nanowires
- Semiconductor nanowires (SCNWs) gt the
fundamental building blocks of future electronic,
photonic and sensing devices. - oxide-assisted growth
- various applications
- biosensing devices
- modelling design
56Experiment
Glucose oxidase (40?L) detections (I-V
characteristics) using SiNWs curve (a) 40?L HF
treated SiNWs, curve (b) 20?L HF treated SiNWs
plus 20?L water, and curve (c) 40?L SiNWs.
57Model
- A SiNW adsorbed with some glucose molecules is
sandwiched between two electrodes. - A gate voltage is applied to tune the
conductance. - Solvent effect is included.
58Theory
Implementation of linear-scaling approach in DFT
based NEGF method (with Duke group)
59Acknowledgements
- CityU C.S. Lin, Y.H. Qi, Y.J. Wang
- Duke Prof. Weitao Yang
- Germany Prof. Th. Fraueheim
60Thank You!