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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)

2
Computational nanoscience
Growth mechanism
Properties Structural, electronic, electrical,
optical, magnetic, etc.
Devices Nanoelectronics, nanosensors,
spintronics, etc.
3
Outline
  • Growth mechanism and properties of covalent
    nanostructures
  • Biodetection, nanomaterials for sensor
  • Sensitivity of CNTs CO, FAD and PPE
  • Biosensitivity of semiconductor Nanowires in
    progress

4
Outline
  • Growth mechanism and properties of covalent
    nanostructures
  • Biodetection, nanomaterials for sensor
  • Sensitivity of CNTs CO, FAD and PPE
  • Biosensitivity of semiconductor Nanowires in
    progress

5
OAG vs VLS
6
Oxide assisted growth (OAG)Adv. Mat. 15, 635
(2003).
Si SiO2 or SiO
  • Laser ablation
  • Thermal evaporation

Substrate
7
PRL93, 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

8
Oxide-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

9
Chemical Stability
Can H-Passivated Si nanostructure Surfaces be
achieved using HF-etching?
10
Chemical 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
11
Chemical 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
12
Chemical Stability
D.D.D. Ma et al. Science 299 (2003) 1874
13
Chemical Stability
Treated surface stable for days in air
D.D.D. Ma et al. Science 299 (2003) 1874
14
Megnetism of BN nanotubes doped with C
C
C C C C C
C
15
Electron Transport
  • Reported nanodevices made of
  • metal nanodots
  • fullerences
  • carbon nanotubes

16
Electron 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)

17
The orthodox theory
  • For an elastic tunneling, transition rates

where the transmission coefficient takes
(WKB)
  • ab initio calculations for electronic structures.

18
Electron Transport
Conductance
I-V
PRB(2002) JPC(2004)
19
Optical properties
Theory (1) TD-DFTB (2) INDO/S-TDHF
20
Optical properties Si nanodot
unpublished
21
Optical 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.
22
Optical properties BN/CNT
PRB(2004), PRB(2005)
(4,4)
(7,0)
(5,3)
23
Outline
  • Growth mechanism and properties of covalent
    nanostructures
  • Biodetection, nanomaterials for sensor
  • Sensitivity of CNTs CO, FAD and PPE
  • Biosensitivity of semiconductor Nanowires in
    progress

24
Biodetection
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.
25
Nanomaterials 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)
26
Status
  • 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.

27
Outline
  • Growth mechanism and properties of covalent
    nanostructures
  • Biodetection, nanomaterials for sensor
  • Sensitivity of CNTs CO, FAD and PPE
  • Biosensitivity of semiconductor Nanowires in
    progress

28
Transport 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.

29
Theory
Where µL, µR are the electronic chemical
potential of the left and right electrode.
30
Models
One molecule and five molecular have been studied
in this work
31
Results
Current-Voltage characteristic
(O end points to the tube)
32
(C end points to the tube)
33
(No Transcript)
34
Summary
  • 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.

35
FAD 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).

36
Examples 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.
37
Interactions 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.

38
Computation
  • 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.

39
FAD Models
40
Optimized structure of FAD adsorbed on CNT
41
Energy (eV)
DOS of pure (5,5) carbon nanotube (magenta color)
and FAD adsorbed on (5,5) carbon nanotube (blue
color)
42
Energy (eV)
PDOS of O atoms and C atoms of flavin and adenine
group
43
I-V of FAD and GOx adsorbed on SWNT/GCE (From
Nanotechnology 13 (2002) 559564).
44
Absorption spectrum of FAD. Green curve the gas
state FAD blue curve the FAD adsorbed on CNT.
45
Summary
  • 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.

46
PPE 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
47
Experiment
The 1HNMR spectrum of 1a-SWNTsHiPco supports a
strong p-pinteraction between 1a and the
nanotube.
48
The optical spectroscopy supports a significant p
- p interaction between the polymer and the
nanotube.
49
PPE adsorption on CNT
PPE1-SWNTsHiPco
PPE2-SWNTsHiPco
50
Results
Theory TDDFTB
51
Results
52
Summary
  • 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.

53
Problems of CNT sensor
  • Metallic and semiconducting
  • Lack of flexible methods for the modification of
    NT surface

54
Outline
  • Growth mechanism and properties of covalent
    nanostructures
  • Biodetection, nanomaterials for sensor
  • Sensitivity of CNTs CO, FAD and PPE
  • Biosensitivity of semiconductor Nanowires in
    progress

55
Biosensitivity 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

56
Experiment
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.
57
Model
  • 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.

58
Theory
Implementation of linear-scaling approach in DFT
based NEGF method (with Duke group)
59
Acknowledgements
  • CityU C.S. Lin, Y.H. Qi, Y.J. Wang
  • Duke Prof. Weitao Yang
  • Germany Prof. Th. Fraueheim

60
Thank You!
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