Updated on 03-07-2010
Research
Projects Organization
XIAOHUA WANG
INVESTIGATION of
the DYNAMICS of
CONFINED FLUID-LIKE FILMS using
SHEAR-FORCE/ACOUSTIC
NEAR-FIELD MICROSCOPY (SANM)
Implications to Nanotribology, protein
folding/unfolding
I.
HANDS-ON TASKS:
I.1. Using the commercial AFM:
- Implementation in
lithography-mode. (Document
detailed procedure.)
-
Measurement of the AFM-cantilever spring constant
(using the Park-AFM
software, correlation with the
theoretically
calculated values.)
- Drive the Park-AFM
externally (for obtaining
images using an AFM probe as well as with a TF probe)
- Implementation of a
humidity-controlled
small chamber (enclosing just the scanning stage.)
- Implement Dip Pen
Nanolithography (for
triggering mechanical swelling of polymer films using electric fields.)
References
[1.1] C.
Maedler, S. Chada, X. Cui, M. Taylor, M. Yan, and A. La Rosa, “Creation
of nanopatterns by local protonation of
P4VP
via
dip pen nanolithography.”
J. Appl. Phys.
104,
014311 (2008).
[I.2]
C. Huang, G. Jiang,
and R. Advincula, "Electrochemical
Cross-Linking and Patterning of NanostructuredPolyelectrolyte-Carbazole
Precursor Ultrathin Films," Macromolecules
41, 4661-4670 (2008).
I.2. Using the homemade microscope stages
- Approaching-retraction
curves
monitored by tunneling, acoustic, and
tuning fork
signals.
It involves the use of
silicon-substrates and tapered-probes coated with hydrophobic and
hydrophilic
polymer films.
- Fabrication of probes of
different geometries (sharp and chubby) and materials (tungsten and
gold)
- SEM images of the
homemade probes (using the
ISI-130 system available in the lab.)
II. RESEARCH SCOPE:
Investigation
of the
dynamics of confined mesoscopic fluid-like films [Ref II.1]
at the nanometer scale
using acousto/shear-force scanning
microscopy
[Ref II.2]
II.1
TECHNOLOGICAL and SCIENTIFIC BACKGROUND (Why is the thesis topic
important, what type of
problems it aims to
contribute in their solution, ... etc. See Ref II.1)
II.1.A
Mesoscopic fluid-like
films
Surfaces
are involved in the strikingly different
dynamics that emerge from adsorbed mesoscopic fluids. Shear
viscosity
is
enhanced, viscoelastic relaxation times
are prolonged, and fluid phase transitions to solid or liquid are seen
to be
induced
by
confinement. Ref [A.1], [A.,3], [A.,4] But, what
determines such behavior? What is the molecular organization of the
adsorbed
mesoscopic liquid layer that leads to the
observed differences in dynamics
compared to the bulk? What are the dynamics of liquids
in intimate contact with
a solid boundary? Which aspects of the
behavior of a mesoscopic liquid can be attributed to confinement
alone? These
questions identify some of the unresolved issues associated with
surface
phenomena. Additionally, there is evidence
that surfaces and
interfaces modify the relaxation rate
towards equilibrium of polymeric films when cooled to temperatures
below the
glass transition temperature; understanding the glassy state and its
associated
phenomena are also central
challenges in condensed matter physics. Ref [A.5] This
thesis aims at
characterizing surface,
interfaces, and the dynamics of
confined
mesoscopic fluids using the novel
Shear-force/Ultrasonic technique.
References:
[A.1]
S.
Granick, “Motions
and Relaxations of Confined
Liquids,” Science 253, 1374-1379
(1991).
[A.2] A. La Rosa, "An
investigation of the dynamics of confined fluid-like films under
shear-forces at the nanometer scale."
[A.3]
M.
Urbakh, J. Klafter, D. Gourdon, and J. Israelachvili, “The
nonlinear nature of friction,” Nature
430, 525-528 (2004).
[II.4]
J. Klein and E. Kumacheva, "Confinement
induced phase transition in simple liquids," Science 269, 816 (1995).
[A.5]
R. D. Priestley, C. J. Ellison, L. J.
Broadbelt, and J. M. Torkelson; “Structural Relaxation of Polymer
Glasses at
Surfaces,
Interfaces
and in Between,” Science
309, 456 (2005)
[A.6]
S. Davy, M. Spajer, and
D. Courjon, "Influence of the water on the shear foce damping in
near-field microscopy,"
Appl.
Phys. Lett. 73, 2594
(1998).
[A-7]
Maria-Pilar bernal, et al, "Theoretical and experimental study of the
forces between SNOM probes and chemically treated
AFM cantilevers," Proceeding of the
IEEE 88,1460 (2000).
[A-8]
S.
Biggs and P. Mulvaney, Measuring of forces between
gold surfaces in water by_AFM, J. Chem.
Phys. 100, 8501 (1994).
A long range attraction is seen,
consistent with
the large Hamaker constant for goldlwater/gold. Within the
Derjaguin
approximation,
the
force F between the sphere of radius R and the plate at a separation D,
due to
van der Waals forces,
is
given by F/R= -A(D)/6D*D, where
A(D) is the
Hamaker function at a separation D, obtained from Lifschitz theory.
II.1.B Basics of Intermolecular forces
-
Summarize Chapters 9, 10, and particularly 15, of Ref [B.1].
Highlight the concepts
of interfacial energy, surface
tension adhesion, cohesion, ...
Include concepts contrasting
intermolecular and intersurface forces
- Adhesion between
two rigid (incompressible) macroscopic spheres
Adhesion between spheres that deform elastically: the Hertz and
JKR models (the latter takes into account adhesion forces).
References:
[B.1] Jacob N. Israelachvili, Jacob N., " Intermolecular and surface
forces," Available at PSU Library: QD461 .I87 1991.
[B.2] C.
Rotsch, K. Jacobson, and M. Radmacher, “Dimensional and
mechanical dynamics of active and stable edges in motile
fibroblasts
investigated by using force microscopy,” Proc. Natl. Acad. Sci. USA 96,
921 (1999).
(It uses Hertzian model to calculate the Young modulus E of
fibroblasts.
This article may be useful to learn how to apply the
Hertz
model to obtain Young modulus values from approaching and
retraction curves data.)
II.1.C The Hydrophobic
and Hydrophilic Interactions
What are the hydrophobic
and hydrophilic interactions?
- Make a review summary of
Chapter 8 of Israelachvili's
book Ref
[C.1]
- In Israelachvili's book Ref [C.1] check
section 15.5 and, in particular, the 3rd
paragraph on page 329, where the author
highlights the potential
different molecular
rearrangements during the approaching and
retraction. The latter may account for the
cases where the Hertz and
JKR models (the latter
takes into account adhesion forces)
fail.
- In Ref [C. 1] check section 13.6
that makes reference to the "attractive hydrophobic forces".
Relevance of the hydrophobic
and hydrophilic interactions
Water at interfaces is
fundamental to
the understanding of wetting, foldin/unfolding of macromolecules,
tribology, chemical
reactivity and dynamics.
Hydrophobic
and hydrophilic interactions on amorphous and crystalline substrates
Amorphous polymer samples
In this thesis we are
preparing polymer samples with
well controlled hydrophobic and hydrophilic properties. [ Xiaohua,
Dr. Yan told me once that
her lab can even control the degree of hydrophobicity or
hydrophilicity. But I am not so sure.
Check with Suji if this is
correct. If so, it would be a good way to verify whether samples
of higher hydrophobicity or
hydrophilicity produce more
or less sound.)
Crystalline hydrophobic
graphite
For comparison purposes,
this thesis will include approaching/retraction curves using
commercially available hydrophobic
crystalline graphite samples
References:
[C.1] Jacob N.
Israelachvili, Jacob N., " Intermolecular and surface
forces," Available at PSU Library: QD461 .I87 1991.
[C.2]
Ding-Shyue Yang and Ahmed H. Zewail, “Ordered
water structure at hydrophobic graphite interfaces observed by 4D,
ultrafast electron
crystallography,” PNAS 106, 4122 (2009).
II.1.D Quantum phenomena
Include a perspective of future studies to your thesis theme:
Review the
Casimir-Lifshitz force subject.
References:
[D.1]
J. N. Munday, F. Capasso, and V. A. Parsegian, "Measured
long-range repulsive Casimir–Lifshitz forces," Nature 457,
170 (2009).
[D.2] Katharine
Sanderson, "Quantum
force gets repulsive," Nature
457, 156 ( 2007).
[D.3]
J. N. Munday, F. Capasso, V. Adrian Parsegian, and S.
M. Bezrukov, "Measurements of the Casimir-Lifshitz force in
fluids:
The effect of electrostatic forces, and Debye
screening," Physical Review A
78, 032109 (2008).
[D.4]
Philip Ball, "Fundamental physics feel the force," Nature
447, 772 ( 2007).
II.2
CHARACTERIZATION TOOLS
To study
such complex surface phenomena, this thesis will exploit the versatile
capabilities of the
Near-field Ultrasonic/Shear-force
Scanning Microscope (NSUM)
[Ref. II.10], a novel technique able to concurrently and
independently monitor the effects that fluid-mediated
interactions exert on both the microscope’s probe and the
sample to be analyzed.
Provide a
background of other techniques also being used to study
mesoscopic films, like for example, the Shear-force apparatus
References:
[II.10] A. H. La Rosa, R. Nordstrom, X. Cui, J.
McCollum,"The
Ultrasonic/shear-force microscope: Integrating ultrasonic sensing into
a
near-field scanning optical
microscopemicroscope," Rev.
Sci. Instrum. 76,
093707 (2005).
RODOLFO FERNANDEZ
DEVELOPMENT
of FAR- and NEAR-FIELD OPTO/ACOUSTO NANOIMAGING TOOLS
for BIO-MATERIALS CHARACTERIZATION at the MOLECULAR
LEVEL
Morphology, spectroscopy and single-molecule
optical
nano-localization
I. HANDS-ON TASKS
I.1 Developing acousto/electronic position-control feedback for
scanning probe microscopy
I.1A Implementation
of a (homemade) feedback electronic
system for controlling the probe-
sample distance in near-field ultrasonic/shear-force scanning
microscopes (NUSM).
- Integrating a linear scaner z-stage
(Mad City Lab, MCL) with a xy-scanning stage (PiezoJena).
Evaluation of the MCL-stage's time response.
- Modification of the LabView-based
programming feedback circuit design and corresponding
customization
of a FPGA card for automated control of the probe-sample distance.
- Optimization of a 16-bit resolution
ADC for driving a 65-micron travel-range stage at nanometer steps
motion
(Strategy: automated re-calibration, while scanning,
of
the actual z- travel range (1 micron) in order to improve the
ADC's resolution.)
- Implementing in situ automated
adjustment of the proportional and integral gains during the scanning process.
I.1B
Integrating
frequency-modulation feedback control (Nanonis) into the NUSM
- To build custom-made pre-amplifiers
for
proper conditioning of the signals.
- Acquisition of approaching/retraction
curves while updating the z-dependent resonance frequency (where z is the probe-sample
distance.) Monitoring of the amplitude variation should provide information of the damping force
component.
- Acquisition of approaching/retraction
curves with the sample immersed in water environment.
I.1C Development of
an "Acoustic-based
Electronic Feedback System" for probe-sample
distance
control in tuning-fork based scanning probe microscopes.
- To exploit acoustic resonances of the
microscope stage for sensitively monitoring the mechanical vibrations of
the tuning fork. Look
for optimized detection schemes for monitoring the nanometer-size
variations of the TF amplitude upon its interaction with the
interrogated sample.
References
[I.1.1] J. Jersch, T. Maletzky, and H.
Fuchs,
“Interface circuits for quartz crystal sensors in scanning probe
microscopy applications,”
Rev. Sci. Inst 77, 083701 (2006).
Comments: It describes PLL
control feedback of 1Mhz tuning forks.
[I.1.2] U. Rabe and W. Arnold, "
Acoustic microscopy by atomic force microscopy, "Appl. Phys. Lett. 64, 1493 (1994)
Comment: It uses knife edge detection for optical detection of acoustic
waves.
[I.1.3]
R. L. Whitman and A. Korpel, "Probing of Acoustic
Surface Perturbations by Coherent Light," Appl. Opt. 8, 1567 (1969).
Comment: It describes the use of knife edge detection for optical
detection of acoustic waves.
I.2 Developing FAR- and NEAR-field Optical Nanoscopy
I.2A Fabrication of NSOM probes
- Fabrication of tapered glass-fiber
probes by chemical (HF) etching.
I.2B
Far-field optical tracking of individual fluorophores with nanometer
lateral resolution
- Solid-graphic
design
for modifying of the IX-71 Epi-Fluorescence Inverted Microscope.
(Design of a sturdy
sample-stage
for alternatively holding a near-field optics scanning stage.
Design of a lifted
microscope's sample-stage for future laser trapping
experiments.)
I.2C Far-field Nanoscopy:
Stimulated Emission depletion
(STED)
- To reduce
the
effective size of a diffraction-limited light spot (light-beam-1) with
a pico-second doughnut-shape (beam-2).
- Select the proper flurophores for the
techniques testing purposes.
- Undertake test with samples under aqueous conditions
I.2D
Implementation of imaging/spectroscopy capabilities for single molecule
studies
- STED imaging at the interior of cells
- Integrate the EM CCD camera (PhotonMax
512B) of
single-photon sensitivity and
the spectrometer XXX with the IX-71 inverted
microscope.
References:
[I.2.1]
R.
E. Thompson, D. R. Larson, and W. W. Webb, "Precise
Nanometer Localization Analysis for individual Fluorescent
Probes ,"
Biophysical Journal 82, 2775 (2002).
The
image-size of an object is limited by diffraction. However, the
center of the object can be determined arbitrarily precisely,
given a
sufficient number of photons (N) in the
spot. Two important source of noise affect this method: a) the shot
noise of
the
photons
in the
image spot, and b) the background noise created by out-of-focus
fluorescence, charge coupled
device (CCD)
readout noise, dark current, and other
factors.
[I.2.2] V. Westphal,
S. O. Rizzoli, M.
A. Lauterbach, D. Kamin, R.
Jahn, Stefan W. Hell, “ Video-Rate Far-Field Optical Nanoscopy
Dissects
Synaptic Vesicle Movement,” Science 320,
246 (2008).
[I.2.3]
S. W. Hell, "Far-field Optical Nanoscopy," Science 316, 1153 (2007).
[I.2.4]
Yildiz et al, "Myosin walks hand-over-hand, Single fluorophore imaging
with 1.5 nm localization" Science
300, 2061 (2003).
[I.2.5]
Yildiz et al, "Kinesin walks hand-over-hand ," Science 303, 676 (2004).
[I.2.6]
D. A. Fletcher, and R. D. Mullins, “Cell mechanics and the
cytoskeleton,” Nature 463, 485 (2010).
Comments: Article displays neurons and
microtubulus and actin filaments.
II. RESEARCH SCOPE
DEVELOPMENT of FAR- and NEAR-FILED OPTO/ACOUSTO
NANOIMAGING TOOLS
for BIO-MATERIALS
CHARACTERIZATION
at the MOLECULAR LEVEL
Morphology, spectroscopy and
single-molecule optical
nano-localization
II.1
TECHNOLOGICAL and SCIENTIFIC BACKGROUND (Why is the thesis topic
important, what type of
problems it aims to
contribute in their solution, etc. )
II.1.A Current
developments of nano-optical techniques (See Section II of Ref [II.1]. )
Conventional
Optical microscopy would be the
preferred tool for characterizing biological dynamic
events
with nanometer
spatial resolution
given its simple use, relatively low cost, and, quite
important, non-invasive character.
Unfortunately,
diffraction effects prevent
conventional optical microscopy from providing spatial lateral
resolution
better than l/2
(where l
~
500 nm
is the wavelength of the radiation used) as enunciated
by Ernst Abbe in 1873. In what follows we highlight how
new technologies are avolving to surpass the DIFFRACTION BARRIER.
PIN-HOLE.
In
1928, Synge conjectured that the
diffraction-limited lateral resolution was
not fundamental, but rather an inherent
constraints resulting from the
(unavoidable
at that time) use of lenses, which have a working distance (WD) greater
than a few
wavelengths (WD > l means“far-field.”).
Synge
argued that IF a metallic pin-hole of sub-wavelength
diameter were i) used as a photon
collector,
ii) brought into the proximity of
the sample (WD < l;
that
is “near-field”), and iii) laterally scanned along the
sample’s surface,
THEN
a lateral resolution
equal to the pin-hole aperture-size
(i.e.
sub-wavelength) could, in principle, be achieved.
NSOM. Based on an evolution of
Synge's ideas, Near-field Scanning Optical Microscopy (NSOM), became
the first optical
technique
to
overcome
the diffraction barrier, as demonstrated
in 1984. NSOM,
however, has its own inherent limitations, one of them
being the
typically low-level
signal available for analysis. The smaller the aperture (aiming for a
finer
resolution), the more stringent the
requirements on the NSOM’s detection
system. NSOM beats the diffraction limited
resolution by imposing the requirement to place
the excitation source
very close to the sample. In many cases that is not possible to do
(imaging inside living cells, for
example.) Optical
imaging with subwavelength resolution
remained a
challenge.
STED.
In 1994 J. Wichmann and Hell
outlined a concept to eliminate the resolution-limiting effect of
diffraction without eliminating
diffraction
itself. It
requires i) coating the
sample with fluorophores, ii)
excite the region of interest with a diffraction-limited light beam
(l1) iii)
simultaneously applying a doughnut shape beam (l2), concentric with
the excitation beam, to quench the fluorophores located on
the
periphery. The net
effect is an excitation region of smaller dimension than l1.
FAR-FIELD FLUORESCENCE NANOSCOPY. A plethora of far field-based
alternative
solutions for attaining sub-wavelength
optical resolution
have appeared lately (FIONA, RESOLFT, PALM), altogether referred to as
Far-field Fluorescence
Nanoscopy [II.2].
They exploit basically the
following principles
to
bypass Abbe’s
barrier:
(1)
Diffraction does not prevent
finding out the coordinates of a point-source with arbitrary
precision if
there is no other
similar point-source within a l/2 distance.
or
(2)
Localization of
individual fluorophores positioned within a distance much smaller than l/2
can be achieved by
sequentially imaging them based on either different
spectral response
or selectively activating their “ON” and “OFF”
states).
Principle
(1
)
exploits the fact that when particles are widely spaced from each
other (separation distance greater than the wavelength),
their
diffraction-limited
images may superimpose but the position of their
corresponding centroids (spot of maximun intensity) can be
estimated
with nanometer precision by
fitting the experimental
data (light intensity) to Gaussian functions. Hence, a direct
correlation can
be
made between the
light point source and the
center of its diffraction limitted image. Nanometer-sized step motion
of the centroid have
been
obtained with a CCD camera of
sufficient dynamic range (i.e able to dictiguish fine difference in
intensity levels.) The fitting method
has
successfully been used to
track the motion of cargo-carrying
myosin with 2 nm precision, helping to
figure out that they undergo
hand-over-hand
motion.
This
thesis aims at the development of a new Integrated
Near- and Far- Field Optics
(INFO) method for overcoming the
diffraction-limited lateral-resolution that
hampers conventional microscopy is proposed. It envisions the use of a) a metal-coated
near-field probe, to optically isolate, one at a time,
sparse fluorophore
markers within a region of sub-wavelength dimension; and
b) a far-field
localization method for locating the selected fluorophore marker’s
position with
nanometer precision. For its implementation,
INFO turns into an advantage the
non-radiative energy transfer that fluorophores experience when placed
in the
vicinity of a metal wall.
Thus, fluorophores closer to the near-field probe’s
rim (see figure below) become dimmer, which, by contrast, helps to
localize more
clearly the fluorophore underneath the probe’s aperture that is less
affected
by the metal. A sequential repetition
of the process a) and
b), in synchronization with the lateral scanning
of the near-field probe,
allows the localization of sparse fluorophores within a region of
sub-wavelength size hence overcoming the diffraction barrier. We will
investigate the flexibility of implementing INFO with low and high
power laser
system, as well as standard fluorophores (rhodamine), quantum dots, and
photo-switchable fluorophores.
References:
[II.1] A. La
Rosa et al, "Integrated
Near- and Far-Field Optics (INFO)"
Alternative
method for overcoming
the diffraction-limited lateral-resolution that hampers
conventional microscopy.
[II.2]
S. W. Hell, "Far-field Optical Nanoscopy," Science 316, 1153 (2007).
[II.3]
NALMS microscopy. Nanometer accuracy is
demonstrated for two
to five single molecules within a diffraction-limited area.
X. Qu,
D. Wu, L. Mets, and N. F. Scherer,"Nanometer-localized
multiple single-molecule fluorescence microscopy," PNAS
101,
11298 (2004).
[II.4]
PALMS MICROSCOPY Samuel T. Hess,
Thanu P.K. Girirajan, Michael D. Mason, "Ultra-High Resolution
Imaging
by Fluorescence
Photoactivation Localization Microscopy," Biophysical Journal
91, 4258 (2006).
Authors
make an estimation of
the the requirements for imaging with
either 80-nm or 20-nm localization precision
JOHN
LEDESMA
DEVELOPMENT
of PROGRAMABLE OPTO/ELECTRONIC DEVICES
for BIOSENSING APPLICATIONS
I.
TASKS:
I.1 Fabrication of probes for Near-Field
Scanning Optical Microscopy
(Apertures of sub-wavelengths
dimensions, for optical imaging with high lateral resolution.
I.1A
Metal coating tapered-fiber probes using a vacuum
thermal evaporator. (Rodolfo will train John in the use of the thermal
evaporator.)
I.1B
Modification of probe morphology (to create a metalic aperture
at the
probe's apex) using a focused ion
beam system. (Rodolfo will
train John in the use of the FIB.)
I.1C Coupling laser light
into the NSOM probes
Note1:
Be patient with these steps as the thermal evaporator and the FIB
are sometimes temperamental, and coupling light into a fiber
sometimes takes 10 minutes and sometime one
hour..
Note2:
The tapered
glass-fiber
probes will initially be provided by another graduate student who
is already well-trained in handling HF acid)
Note3: This task is urgently needed at
the lab. If we can have those probes yesterday it will be great !!!
References:
- Application of NSOM: A. La
Rosa, Near-field
characterization of semicondustor nanostructures and devices
-
[Ref]
Fabrication of probes by chemical etching R. Stockle, C.
Fokas,V. Deckert, and R. Zenobi, " High-quality
near-field
optical probes by
tube etching," Appl.Phys.
Lett. 75, 160
(1999).
"A method called tube etching for the
fabrication of near-field
optical probes is presented. Tip formation occurs inside
a cylindrical cavity formed by the polymer coating of an
optical fiber which is not stripped away prior to etching in
hydrofluoric acid.
... In the case of fiber
with permeable jacket, the tip forms by the same mechanism as in the case
of the impermeable
polymer
coating."
- Introduction: Focused Ion
Beam Systems
- Focused
Ion Beam Principle
- A. La Rosa, "Near-field
Scanning Optical Microscopy."
I.2 Opto/acousto characterization of
(antibody/antigen, protein-carbohydrate) molecular interactions
1.2A Identify the proper
molecules/samples that can optimize their molecular
interactions
(We are pursuing the development of acousto detection methods developed
by our group.)
Ref: Questions:
on how to optimize the experimental set up for acousto sensing
molecular interactions
Find in this file some preliminary questions addressing the potential
samples to be used in this project.
I.2B
Optical Tracking of Individual Particles with Nanometer Resolution
(LABELED MOLECULES)
"The
image-size of an object is limited by diffraction. However, the
center of the object can be determined arbitrarily precisely,
given a
sufficient number of photons (N) in the
spot. Two important source of noise affect this method: a) the shot
noise of
the
photons
in the
image spot, and b) the background noise created by out-of-focus
fluorescence, charge coupled
device (CCD)
readout
noise, dark current, and other factors."
Task iscludes
- Hands-on work integrating the PhotonMax EMCCD camera
(of single photon sensitivity) into the IX-71 Epi-
fluorescence inverted optical microscope.
- Identify proper sample for facilitating the application of the
tracking techniques Again, sample preparation is key for the success
of tracking single fluorophores in in-vitro samples.
- Data acquisition tracking the position of single molecules.
References:
[I.2B1]
R.
E. Thompson, D. R. Larson, and W. W. Webb, "Precise
Nanometer Localization Analysis for individual Fluorescent
Probes ,"
Biophysical Journal 82, 2775 (2002).
[I.2B2]
Yildiz et al, "Myosin walks hand-over-hand, Single fluorophore imaging
with 1.5 nm localization" Science
300, 2061 (2003).
[I.2.B3]
Yildiz et al, "Kinesin walks hand-over-hand ," Science 303, 676 (2004).
[II.2B4]
A. La
Rosa et al, "Integrated
Near- and Far-Field Optics (INFO)"
I.2C
Spectral analysis of single molecules (UNLABELED MOLECULES)
Ultimately, our objective is to
spectrally identify single molecules using Raman spectroscopy.
This responds to the current interest for
characterizing unlabeled molecules, as typical
fluorophores could affect the natural dynamics of the
interrogated molecule.
I.3 Build
programanble BIO/MEMS devices
MICHAEL
HOPKINS
NEAR-FIELD
PROBES FABRICATION
I.
TASKS:
I.1 Fabrication of FIBER-GLASS PROBES for
Near-Field
Scanning Optical Microscopy
(Apertures of sub-wavelengths
dimensions, for optical imaging with high lateral resolution.
I.1A
Rodolfo will provide the tapered glass-fiber probes
I.1B
Metal coating tapered-fiber probes using a vacuum
thermal evaporator. (Rodolfo will
train Mike in the use of the thermal
evaporator.)
I.1C
Modification of probe morphology (to create a metalic aperture
at the
probe's apex) using a focused ion
beam system. (Rodolfo
will
train Mike in the use of the FIB. Subsequently, Mike will train Joshua in the use
of the FIB.)
I.1D Coupling laser light
into the NSOM probes (Gangandeep).
I.1D Implementation of
acousto-optic modulation setup for amplitude modulation of laser
systems (Gandeep).
Note1:
Be patient with these steps as the thermal evaporator and the FIB
are sometimes temperamental, and coupling light into a fiber
sometimes takes 10 minutes and sometime one
hour..
Note2:
The tapered
glass-fiber
probes will initially be provided by another graduate student who
is already well-trained in handling HF acid)
References:
- Application of NSOM: A. La
Rosa, Near-field
characterization of semicondustor nanostructures and devices
-
[Ref]
Fabrication of probes by chemical etching R. Stockle, C.
Fokas,V. Deckert, and R. Zenobi, " High-quality
near-field
optical probes by
tube tching," Appl.Phys.
Lett. 75, 160
(1999).
"A method called tube etching for the
fabrication of near-field
optical probes is presented. Tip formation occurs inside
a cylindrical cavity formed by the polymer coating of an
optical fiber which is not stripped away prior to etching in
hydrofluoric acid.
... In the case of fiber
with permeable jacket, the tip formes by the same mechanism as in the case
of the impermeable
polymer
coating."
- Introduction: Focused Ion
Beam Systems
- Focused
Ion Beam Principle
- A. La Rosa, "Near-field
Scanning Optical Microscopy."
I.2 Desingn and fabrication of COAXIAL PROBES for Near-Field
Scanning Optical Microscopy
I.1A Fabication
of tapered metallic probes (tungsten, gold) by etching processes (Joshua)
I.1A
Fabication of tapered probes out of commercially available glass pipettes using a commercially
available pipette puller.
I.1C
Fabrication of coaxial probes (Mike,
Joshua).
I.1D
Teraherta characterization of biomolecules (Gagandeep).
References:
- A. La Rosa, "Combined
Terahertz/visible Near-field Optical Microscopy."
It includes different type of probes being pursued at Dr. La Rosa's Lab.
I.3 Molecular layering in confined mesoscpic
films
[Ref-1]
M. Antognozzi, A. D. Humphris, and M. J. Miles, "Observatin of
mlecular layering in a confined water film and study of the l
ayers viscoelastic properties. Appl.
Phys. Lett. 78, 300
(2001).
KEITH
PARKER
1) Design and
construction of high-sensitivity (108 gain), dual-stage (for
increase
bandwidth) pre-amplifier.
Focused effort on
building a replica of existent design that includes a dual FETs (a
design already proven
to
work well.)
Reference: R. D.Grober,
J. Acimovic, J. Schuck, D. Hessman, P. J. Kindlemann,
J. Hespanha, A. S. Morse, K. Karrai,
I.Tiemann, and S. Manus,
“Fundamental
limits to force detection using quartz tuning forks ,” Rev.
Scientific.
Instrum.
71, 2776 (2000).
Comments: Our objective is to achieve their sensitivity detection levels
2) Design and construction of a frequency modulation electronics
circuit, for monitoring approaching-
retraction curves along the z-direction. (No lateral xy scanning involved here.)
Focused effort in building a replica
of existent designs based on Edwards's
and/or Kobayashi's
papers.
Reference: H. Edwards,
L. Taylor, and W. Duncan, "Fast,
high-resolution atomic force microscopy using a quartz tuning fork
as actuator and sensor," J.
Appl. Phys. 82, 980
(1997).
Reference: K. Kobayashi,
H. Yamada, H. Itoh, T. Horiuchi, and K. Matsushige, "Analog
frequency modulation detector for
dynamic force microscopy," Rev.
Scientific.
Instrum. 72, 4383 (2001).
3) Use the previous designs as a basis for a design based on more
updated electronic components.
PROTEINS FOLDING/UNFOLDING
References:
- Chritoph
Kowitz, The Entropic Force (April-2008)
- J. S. Graham, "Mechanical
Properties of Complex Biological Systems using AFM-Based Force
Spectroscopy,"
Ph.D. Thesis (2005)