From 33c981de655200b02629edc8496770926027edd3 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Tue, 7 May 2013 21:34:12 -0400 Subject: [PATCH] root.bib: Add livadaru03 and burnham03 and mark typos MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit Typos in equations listed in bechhoefer02, schlierf06, livadaru03, and puchner08. I have contacted the listed author in each case, but so far there are no published errata :(. To be fair, I only emailed Bechhoefer a few hours ago ;). Excerpts from the relevant emails: On Tue, Apr 08, 2008 at 07:16:34PM -0400, W. Trevor King wrote: > ... > > My double integral is exploding, so I was double checking your formulas. > I believe you swapped signs in the exponent in your Kramers' rate equation. > > It should be > k^-1 = 1/D \int_{x_-}^{x_+} e^{ \beta U(x)} [ \int_{0}^{x} e^{- \beta U(x')} dx' ] dx > not > k^-1 = 1/D \int_{x_-}^{x_+} e^{- \beta U(x)} [ \int_{0}^{x} e^{ \beta U(x')} dx' ] dx > > See, for example, H\"anggi et al., Rev. Mod. Phys 1990, > http://prola.aps.org/abstract/RMP/v62/i2/p251_1 > Equation 4.56b, > or Socci et al., J Chem Phy 1996 > http://arxiv.org/pdf/cond-mat/9601091 > Equation 2. On Wed, Apr 09, 2008 at 09:03:02AM +0200, Michael Schlierf wrote: > For your second email: So far I am pretty sure about our published > solution as it worked out. So have you double checked your integral > borders? Try Kramers first in a simple potential, like a cusp-like or > flat one. For those some analytical solutions are known and you could > compare. On Fri, Sep 07, 2012 at 07:09:17AM -0400, W. Trevor King wrote: > On Fri, Sep 07, 2012 at 09:28:41AM +0200, Roland Netz wrote: > > sorry for the confusion: Yes, the formula Eq 46 contains typos, as > > you correctly point out. > > Ah. Some sort of heads-up on the article page would be useful, > because at least Puchner [1] quotes the typo-containing version. On Wed, Sep 12, 2012 at 01:37:23AM +0000, Puchner, Georg Elias Michael wrote: > thanks for pointing this out, I wasn't aware of this typo and also > think they should have published and erratum. > > I dug into my old data and code (I am not doing force spectroscopy > andy more since some years) and implemented your corrected > version. I attached a comparison of my old transformation equation > (black line with the parameters γ=22° and b=0.4 nm as published) and > the fixed equation (dashed red line with γ=41° and b=0.11 nm) > > As you see, the quality is only slightly increased for some peaks > but the parameters now make more sense... On Tue, May 07, 2013 at 07:05:31PM -0400, W. Trevor King wrote: > I'm citing your thermal spring constant calculation [1] in my thesis > [2] to confirm my derivation of the overdamped power spectral density > of a harmonic oscillator. I was just double-checking my PSD (at the > end of section 5.2.1 “Highly damped case”, currently around page 48) > against your equation A12: > > x²(ω) = (2kBTγ) / [k²(1+ω²τ₀²)] (A12) > > It looks like you're missing a factor of 1/π... --- src/root.bib | 158 +++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 142 insertions(+), 16 deletions(-) diff --git a/src/root.bib b/src/root.bib index 187121b..c87d9b0 100644 --- a/src/root.bib +++ b/src/root.bib @@ -136,6 +136,7 @@ @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"} @@ -176,7 +177,8 @@ @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."} @@ -222,6 +224,7 @@ @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."} @@ -408,6 +411,7 @@ @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."} @@ -601,6 +605,7 @@ @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."} @@ -637,6 +642,7 @@ @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"} @@ -715,6 +721,7 @@ @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"} @@ -822,6 +829,7 @@ @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"} @@ -959,6 +967,7 @@ @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"} @@ -969,6 +978,7 @@ @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."} @@ -1345,11 +1355,12 @@ 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" } @@ -3238,6 +3249,35 @@ 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, @@ -6140,7 +6180,13 @@ 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, @@ -6631,14 +6677,24 @@ 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, @@ -8384,7 +8440,7 @@ } @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 @@ -9746,3 +9802,73 @@ 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.}, +} -- 2.26.2