@string{ABulhassan = "Bulhassan, Ahmed"}
@string{BBullard = "Bullard, Belinda"}
@string{RBunk = "Bunk, Richard"}
+@string{NABurnham = "Burnham, N.~A."}
@string{DBusam = "Busam, D."}
@string{GBussi = "Bussi, Giovanni"}
@string{CBustamante = "Bustamante, Carlos"}
@string{HCChen = "Chen, H. C."}
@string{LChen = "Chen, L."}
@string{XNChen = "Chen, X. N."}
-@string{XChen = "Chen, Xuming"}
+@string{XiChen = "Chen, Xinyong"}
+@string{XuChen = "Chen, Xuming"}
@string{JFCheng = "Cheng, J. F."}
@string{MLCheng = "Cheng, M. L."}
@string{VGCheung = "Cheung, V. G."}
@string{FDahlquist = "Dahlquist, Frederick W."}
@string{SDanaher = "Danaher, S."}
@string{LDavenport = "Davenport, L."}
+@string{MCDavies = "Davies, M.~C."}
@string{MDavis = "Davis, Matt"}
@string{SDecatur = "Decatur, Sean M."}
@string{WDeGrado = "DeGrado, William F."}
@string{SHladun = "Hladun, S."}
@string{WKHo = "Ho, W.~K."}
@string{RHochstrasser = "Hochstrasser, Robin M."}
+@string{CSHodges = "Hodges, C.~S."}
@string{CHoff = "Hoff, C."}
@string{WHoff = "Hoff, Wouter D."}
@string{JLHolden = "Holden, J. L."}
@string{WLiu = "Liu, W."}
@string{XLiu = "Liu, X."}
@string{YLiu = "Liu, Yichun"}
+@string{LLivadaru = "Livadaru, L."}
@string{YSLo = "Lo, Yu-Shiu"}
@string{GLois = "Lois, Gregg"}
@string{JLopez = "Lopez, J."}
@string{MMartin = "Martin, M. J."}
@string{YMartin = "Martin, Y."}
@string{HMassa = "Massa, H."}
+@string{GAMatei = "Matei, G.~A."}
@string{DMaterassi = "Materassi, Donatello"}
@string{JMathe = "Math\'e, J\'er\^ome"}
@string{AMatouschek = "Matouschek, Andreas"}
@string{MNeitzert = "Neitzert, Marcus"}
@string{CNelson = "Nelson, C."}
@string{KNelson = "Nelson, K."}
+@string{RRNetz = "Netz, R.~R."}
@string{NEURON = "Neuron"}
@string{RNevo = "Nevo, Reinat"}
@string{NJP = "New Journal of Physics"}
@string{MRief = "Rief, Matthias"}
@string{KRitchie = "Ritchie, K."}
@string{MRobbins = "Robbins, Mark O."}
+@string{CJRoberts = "Roberts, C.~J."}
@string{RJRoberts = "Roberts, R. J."}
@string{RRobertson = "Robertson, Ragan B."}
@string{HRoder = "Roder, Heinrich"}
@string{BNTaylor = "Taylor, Barry N."}
@string{THEMath = "Technische Hogeschool Eindhoven, Nederland,
Onderafdeling der Wiskunde"}
+@string{SJBTendler = "Tendler, S.~J.~B."}
@string{STeukolsky = "Teukolsky, S."}
@string{CJ = "The Computer Journal"}
@string{JCP = "The Journal of Chemical Physics"}
@string{PDThomas = "Thomas, P. D."}
@string{RThomas = "Thomas, R."}
@string{JThompson = "Thompson, J. B."}
+@string{EJThoreson = "Thoreson, E.~J."}
@string{SThornton = "Thornton, S."}
@string{RWTillmann = "Tillmann, R.~W."}
@string{NNTint = "Tint, N. N."}
url = "http://link.aip.org/link/?AJP/70/393/1",
keywords = "student experiments; safety; radiation pressure; laser beam
applications",
- note = "Good discussion of the effect of correlation time on calibration.
- Excellent detail on power spectrum derivation and thermal noise for
- extremely overdamped oscillators in Appendix A (references
- \citet{rief65}). References work on deconvolving thermal noise from
- other noise\citep{cowan98}",
+ note = {Good discussion of the effect of correlation time on
+ calibration. Excellent detail on power spectrum derivation and
+ thermal noise for extremely overdamped oscillators in Appendix A
+ (references \citet{rief65}), except that their equation A12 is
+ missing a factor of $1/\pi$. References work on deconvolving
+ thermal noise from other noise\citep{cowan98}.},
project = "Cantilever Calibration"
}
project = "Cantilever Calibration"
}
+@article{ burnham03,
+ author = NABurnham #" and "# XiChen #" and "# CSHodges #" and "#
+ GAMatei #" and "# EJThoreson #" and "# CJRoberts #" and "#
+ MCDavies #" and "# SJBTendler,
+ title = {Comparison of calibration methods for atomic-force
+ microscopy cantilevers},
+ year = 2003,
+ month = jan,
+ journal = NT,
+ volume= 14,
+ number = 1,
+ pages = {1--6},
+ url = {http://stacks.iop.org/0957-4484/14/i=1/a=301},
+ abstract = {The scientific community needs a rapid and reliable way
+ of accurately determining the stiffness of atomic-force microscopy
+ cantilevers. We have compared the experimentally determined values
+ of stiffness for ten cantilever probes using four different
+ methods. For rectangular silicon cantilever beams of well defined
+ geometry, the approaches all yield values within 17\% of the
+ manufacturer's nominal stiffness. One of the methods is new, based
+ on the acquisition and analysis of thermal distribution functions
+ 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.},
+}
+
@article { forde02,
author = NRForde #" and "# DIzhaky #" and "# GRWoodcock #" and "# GJLWuite
#" and "# CBustamante,
force spectroscopy data and for novel automated screening techniques is
shown with bacteriorhodopsin and with protein constructs containing GFP
and titin kinase.",
- note = "Contour length space and barrier position fingerprinting.",
+ 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.},
}
@article { raible04,
resolved details of the unfolding energy landscape from mechanical
single-molecule protein unfolding experiments requires models that go
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 ``[dying percent] * [surviving population] = [deaths]''
- (TODO, check). $\nu \equiv k$ is the force/time-dependent off rate...
- (TODO) The Kramers' rate equation (second equation in the paper) is
- \citet{hanggi90} Eq.~4.56b (page 275). It is important to extract $k_0$
- and $\Delta x$ using every available method."
+ 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
+ $[\text{dying percent}] \cdot [\text{surviving population}]
+ = [\text{deaths}]$.
+ $\nu \equiv k$ 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
+ $\exp{-U_F(x_\text{max})}\cdot\exp{U_F(0)}$, 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
+ forms the bulk of the integrand, see
+ \cref{eq:kramers,fig:kramers:integrand}. I pointed out this
+ problem to Michael Schlierf, but he was unconvinced.},
}
@article { schwaiger04,
}
@article { lli06,
- author = LiLi #" and "# YYang #" and "# GYang #" and "# XChen
+ author = LiLi #" and "# YYang #" and "# GYang #" and "# XuChen
#" and "# BHsiao #" and "# BChu #" and "#
JSpanier #" and "# CYLi,
title = "Patterning polyethylene oligomers on carbon nanotubes
are given. The reporting of the uncertainties of final results is
discussed.},
}
+
+@article{ livadaru03,
+ author = LLivadaru #" and "# RRNetz #" and "# HJKreuzer,
+ title = {Stretching Response of Discrete Semiflexible Polymers},
+ year = 2003,
+ month = apr,
+ day = 25,
+ journal = Macromol,
+ volume = 36,
+ number = 10,
+ pages = {3732--3744},
+ doi = {10.1021/ma020751g},
+ URL = {http://pubs.acs.org/doi/abs/10.1021/ma020751g},
+ eprint = {http://pubs.acs.org/doi/pdf/10.1021/ma020751g},
+ abstract = {We demonstrate that semiflexible polymer chains
+ (characterized by a persistence length $l$) made up of discrete
+ segments or bonds of length $b$ show at large stretching forces a
+ crossover from the standard wormlike chain (WLC) behavior to a
+ discrete-chain (DC) behavior. In the DC regime, the stretching
+ response is independent of the persistence length and shows a
+ different force dependence than in the WLC regime. We perform
+ extensive transfer-matrix calculations for the force-response of a
+ freely rotating chain (FRC) model as a function of varying bond
+ angle $\gamma$ (and thus varying persistence length) and chain
+ length. The FRC model is a first step toward the understanding of
+ the stretching behavior of synthetic polymers, denatured proteins,
+ and single-stranded DNA under large tensile forces. We also
+ present scaling results for the force response of the elastically
+ jointed chain (EJC) model, that is, a chain made up of freely
+ jointed bonds that are connected by joints with some bending
+ stiffness; this is the discretized version of the continuum WLC
+ model. The EJC model might be applicable to stiff biopolymers such
+ as double-stranded DNA or Actin. Both models show a similar
+ crossover from the WLC to the DC behavior, which occurs at a force
+ $f/k_BT\sim l/b^2$ and is thus (for polymers with a moderately
+ large persistence length) in the piconewton range probed in many
+ AFM experiments. We also give a heuristic simple function for the
+ force--distance relation of a FRC, valid in the global force
+ range, which can be used to fit experimental data. Our findings
+ 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
+ \begin{equation}
+ \frac{R_z}{L} = \begin{cases}
+ \frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\
+ 1 - \p({\frac{fl}{4k_BT}})^{-0.5}
+ & \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
+ 1 - \p({\frac{fb}{ck_BT}})^{-1} & \frac{1}{b} < \frac{fb}{k_BT} \;,
+ \end{cases}
+ \end{equation}
+ but the correct formula is
+ \begin{equation}
+ \frac{R_z}{L} = \begin{cases}
+ \frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\
+ 1 - \p({\frac{4fl}{k_BT}})^{-0.5}
+ & \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
+ 1 - \p({\frac{cfb}{k_BT}})^{-1} & \frac{1}{b} < \frac{fb}{k_BT} \;,
+ \end{cases}
+ \end{equation}
+ with both the $4$ and the $c$ moved into their respective
+ numerators. I pointed these errors out to Roland Netz in 2012,
+ 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
+ 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.},
+}
projects / thesis.git / commitdiff