@string{HErickson = "Erickson, Harold P."}
@string{MEsaki = "Esaki, Masatoshi"}
@string{SEsparham = "Esparham, S."}
+@string{EBJ = "European biophysics journal: EBJ"}
@string{EJP = "European Journal of Physics"}
@string{EPL = "Europhysics Letters"}
@string{CEvangelista = "Evangelista, C."}
@string{VMoy = "Moy, Vincent T."}
@string{SMukamel = "Mukamel, Shaul"}
@string{DJMuller = "M{\"u}ller, Daniel J."}
-@string{PMundel = "Mundel, P."}
+@string{PMundel = "Mundeol, P."}
@string{EMuneyuki = "Muneyuki, Eiro"}
@string{RJMural = "Mural, R. J."}
@string{BMurphy = "Murphy, B."}
of the oscillator's amplitude fluctuations. We evaluate this
method in comparison to the three others and recommend it for its
ease of use and broad applicability.},
- note = {Contains both the overdamped (Eq.~6) and general (Eq.~8)
- power spectral densities used in thermal cantilever calibration,
- but punts to textbooks for the derivation.},
+ note = {Contains both the overdamped (\fref{equation}{6}) and
+ general (\fref{equation}{8}) power spectral densities used in
+ thermal cantilever calibration, but punts to textbooks for the
+ derivation.},
}
@article { forde02,
season = "Fall",
numpages = 12,
eprint = "http://chirality.swarthmore.edu/PHYS81/OpticalTweezers.pdf",
- note = "Fairly complete overdamped PSD derivation in section 4.3., cites
- \citet{tlusty98} and \citet{bechhoefer02} for further details. However,
- Tlusty (listed as reference 8) doesn't contain the thermal response
- fn.\ derivation it was cited for. Also, the single sided PSD definition
- credited to reference 9 (listed as Bechhoefer) looks more like Press
- (listed as reference 10). I imagine Grossman and Stout mixed up their
- references, and meant to refer to \citet{bechhoefer02} and
- \citet{press92} respectively instead.",
+ note = {Fairly complete overdamped PSD derivation in
+ \fref{section}{4.3}. Cites \citet{tlusty98} and
+ \citet{bechhoefer02} for further details. However, Tlusty
+ (listed as reference 8) doesn't contain the thermal response
+ fn.\ derivation it was cited for. Also, the single sided PSD
+ definition credited to reference 9 (listed as Bechhoefer)
+ looks more like Press (listed as reference 10). I imagine
+ Grossman and Stout mixed up their references, and meant to
+ refer to \citet{bechhoefer02} and \citet{press92} respectively
+ instead.},
project = "Cantilever Calibration"
}
mechanical unfolding experiments of proteins and RNA, the ruggedness
energy scale epsilon, can be directly measured.",
note = "Derives the major theory behind my thesis. The Kramers rate
- equation is \citet{hanggi90} Eq.~4.56c (page 275).",
+ equation is \xref{hanggi90}{equation}{4.56c} (page 275).",
project = "Energy Landscape Roughness"
}
allowed us to map the features of the complex energy landscape of GFP
including a characterization of the structures, albeit at a coarse-
grained level, of the three metastable intermediates.",
- note = "Hiccup in unfolding leg corresponds to unfolding intermediate (See
- Figure 2). The unfolding timescale in GFP is about 6 ms."
+ note = {Hiccup in unfolding leg corresponds to unfolding
+ intermediate (\fref{figure}{2}). The unfolding timescale in GFP
+ is about $6\U{ms}.}
}
@article { nevo03,
publisher = CUP,
address = "New York",
eprint = "http://www.nrbook.com/a/bookcpdf.php",
- note = "See sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to
+ note = "See Sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to
Fourier transforms and power spectrum estimation.",
project = "Cantilever Calibration"
}
shown with bacteriorhodopsin and with protein constructs containing GFP
and titin kinase.",
note = {Contour length space and barrier position fingerprinting.
- There are errors in Eq.~(3), propagated from \citet{livadaru03}.
- I contacted Elias Puchner and pointed out the typos, and he
- revised his FRC fit parameters from $\gamma=22\dg$ and
- $b=0.4\U{nm}$ to $\gamma=41\dg$ and $b=0.11\U{nm}$. The combined
- effect on Fig.~(3) of fixing the equation typos and adjusting the
- fit parameters was small, so their conclusions are still sound.},
+ There are errors in \fref{equation}{3}, propagated from
+ \citet{livadaru03}. I contacted Elias Puchner and pointed out the
+ typos, and he revised his FRC fit parameters from $\gamma=22\dg$
+ and $b=0.4\U{nm}$ to $\gamma=41\dg$ and $b=0.11\U{nm}$. The
+ combined effect on \fref{figure}{3} of fixing the equation typos
+ and adjusting the fit parameters was small, so their conclusions
+ are still sound.},
}
@article { raible04,
beyond the Bell model.",
note = {The inspiration behind my sawtooth simulation. Bell model
fit to $f_{unfold}(v)$, but Kramers model fit to unfolding
- distribution for a given $v$. Eqn.~3 in the supplement is
- \citet{evans99} 1999's Eqn.~2, but it is just
+ distribution for a given $v$. \fref{equation}{3} in the
+ supplement is \xref{evans99}{equation}{2}, but it is just
$[\text{dying percent}] \cdot [\text{surviving population}]
= [\text{deaths}]$.
$\nu \equiv k$ is the force/time-dependent off rate. The Kramers'
rate equation (on page L34, the second equation in the paper) is
- \citet{hanggi90} Eq.~4.56b (page 275) and \citet{socci96} Eq.~2,
- but \citet{schlierf06} gets the minus sign wrong in the exponent.
- $U_F(x=0)\gg 0$ and $U_F(x_\text{max})\ll 0$ (\cf~Schlierf's
- Fig.~1). Schlierf's integral (as written) contains
+ \xref{hanggi90}{equation}{4.56b} (page 275) and
+ \xref{socci96}{equation}{2} but \citet{schlierf06} gets the minus
+ sign wrong in the exponent. $U_F(x=0)\gg 0$ and
+ $U_F(x_\text{max})\ll 0$ (\cf~\xref{schlierf06}{figure}{1}).
+ Schlierf's integral (as written) contains
$\exp{-U_F(x_\text{max})}\cdot\exp{U_F(0)}$, which is huge, when
it should contain $\exp{U_F(x_\text{max})}\cdot\exp{-U_F(0)}$,
which is tiny. For more details and a picture of the peak that
note = {Development stalled in 2005 after Michael graduated.},
}
+@article{ janovjak05,
+ author = HJanovjak #" and "# JStruckmeier #" and "# DJMuller,
+ title = {Hydrodynamic effects in fast {AFM} single-molecule
+ force measurements.},
+ year = 2005,
+ month = feb,
+ day = 15,
+ address = {BioTechnological Center, University of Technology
+ Dresden, 01307 Dresden, Germany.},
+ journal = EBJ,
+ volume = 34,
+ number = 1,
+ pages = {91--96},
+ issn = {0175-7571},
+ doi = {10.1007/s00249-004-0430-3},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/15257425},
+ language = {eng},
+ keywords = {Algorithms},
+ keywords = {Computer Simulation},
+ keywords = {Elasticity},
+ keywords = {Microfluidics},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Models, Chemical},
+ keywords = {Models, Molecular},
+ keywords = {Physical Stimulation},
+ keywords = {Protein Binding},
+ keywords = {Proteins},
+ keywords = {Stress, Mechanical},
+ keywords = {Viscosity},
+ abstract = {Atomic force microscopy (AFM) allows the critical forces
+ that unfold single proteins and rupture individual receptor-ligand
+ bonds to be measured. To derive the shape of the energy landscape,
+ the dynamic strength of the system is probed at different force
+ loading rates. This is usually achieved by varying the pulling
+ speed between a few nm/s and a few $\mu$m/s, although for a more
+ complete investigation of the kinetic properties higher speeds are
+ desirable. Above 10 $\mu$m/s, the hydrodynamic drag force acting
+ on the AFM cantilever reaches the same order of magnitude as the
+ molecular forces. This has limited the maximum pulling speed in
+ AFM single-molecule force spectroscopy experiments. Here, we
+ present an approach for considering these hydrodynamic effects,
+ thereby allowing a correct evaluation of AFM force measurements
+ recorded over an extended range of pulling speeds (and thus
+ loading rates). To support and illustrate our theoretical
+ considerations, we experimentally evaluated the mechanical
+ unfolding of a multi-domain protein recorded at $30\U{$mu$m/s}
+ pulling speed.},
+}
+
@article{ sandal09,
author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "#
AGomezCasado #" and "# BSamori,
might help to resolve the discrepancies encountered when trying to
fit experimental data for the stretching response of polymers in a
broad force range with a single effective persistence length.},
- note = {There are two typos in Eq.~(46). \citet{livadaru03} have
+ note = {There are two typos in \fref{equation}{46}.
+ \citet{livadaru03} have
\begin{equation}
\frac{R_z}{L} = \begin{cases}
\frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\
along with the fact that even with the corrected formula there is
a discontinuity between the low- and moderate-force regimes. Netz
confirmed the errors, and pointed out that the discontinuity is
- because Eq.~(46) only accounts for the scaling (without
+ because \fref{equation}{46} only accounts for the scaling (without
prefactors). Unfortunately, there does not seem to be a published
erratum pointing out the error and at least \citet{puchner08} have
quoted the incorrect form.},
{\Large M\"uller notes} \\
\end{center}
-We had some trouble with their notation, so I'll try and clear some things up...
+We had some trouble with the notation in \citet{janovjak05}, so I'll
+try and clear some things up\ldots
\begin{center}
\begin{tabular}{r|l|l}
\end{align}
Trevor derivations: \\
-For Eqn. \ref{mul_delF}, we assume that all the fluid in the cell moves with the surface
+For \cref{mul_delF}, we assume that all the fluid in the cell moves with the surface
(i.e., fluid flow does not depend on height above the surface).
So the drag force is proportional to the speed of the tip relative to the surface.
\begin{equation}
F_d = D(h) v_{tip,surface}
\end{equation}
Where $D(h)$ is some constant that can depend on $h$ (like $6 \pi \eta a_{eff}^2 / (h + d_{eff})$).
-This is M\"uller Eqn \ref{mul_Fd}.
+This is \xref{janovjak05}{equation}{mul\_Fd??}.
Substituting in $v_{tip,surface} = v_{eq,surface} - v_{tip,eq}$ we have
\begin{align}
F_d &= D(h) v_{eq,surface} - D(h)v_{tip,eq} = F_{d:eq,surface} - F_{d:tip,eq} \\
F_{d:tip, eq} &= F_{d:eq,surface} - F_d
\end{align}
-This is M\"uller Eqn \ref{mul_delF}.
+This is \xref{janovjak05}{equation}{mul\_delF??}.
The measured force deflecting the cantilever is then
\begin{align}
F_{measured} &= F_{protein} + F_d \\
F_{protein} &= F_{measured} - F_d = F_{measured} - (F_{d:eq,surface} - F_{d:tip,eq}) \\
&= F_{meas,zeroed}' + F_{d:tip,eq} = F_{meas,zeroed}' + D(h)v_{tip,eq}
\end{align}
-This is M\"uller Eqn \ref{mul_Fnet}.
+This is \xref{janovjak05}{equation}{mul\_Fnet??}.
-The treatment assumes the drag force on a detached cantilever doesn't depend on distance (see dashed line in Figure 4b,c), which doesn't make sense because
+The treatment assumes the drag force on a detached cantilever doesn't depend on distance (see dashed line in \xref{janovjak05}{figure}{4b,c}), which doesn't make sense because
\begin{equation}
F_{d:eq,surface} = D(h)v_{eq,surface}
\end{equation}
\end{equation}
What can we do about this?
-The correction from $F_{meas,zeroed}'$ (solid line in Figure 3a) to $F_{protein}$ (dashed line) comes from adding $F_{d:tip,eq}$, which is why $F_{protein} = F_{meas,zeroed}'$ when
+The correction from $F_{meas,zeroed}'$ (solid line in \xref{janovjak05}{figure}{3a}) to $F_{protein}$ (dashed line) comes from adding $F_{d:tip,eq}$, which is why $F_{protein} = F_{meas,zeroed}'$ when
\begin{align}
0 = F_{d:tip,eq} \propto v_{tip,eq} = \frac{dz_{cantilever}}{dt} \propto \frac{dF_{meas,zeroed}}{dt}, \\
\end{align}
projects / thesis.git / commitdiff