From: W. Trevor King Date: Tue, 7 May 2013 20:06:00 +0000 (-0400) Subject: root.bib: Add kuhn05, materassi09, aioanei11, and benedetti11 X-Git-Tag: v1.0~242 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=e2bea06ee6915721c95c59a187d3c705b31ef673;p=thesis.git root.bib: Add kuhn05, materassi09, aioanei11, and benedetti11 The first three include alternatives to Hooke, and the last treats my king10 theory with a simulation-avoiding bent. --- diff --git a/src/root.bib b/src/root.bib index 747b582..187121b 100644 --- a/src/root.bib +++ b/src/root.bib @@ -16,6 +16,7 @@ @string{AW = "Addison-Wesley Longman Publishing Co., Inc."} @string{AdvExpMedBiol = "Advances in Experimental Medicine and Biology"} @string{SAinavarapu = "Ainavarapu, Sri Rama Koti"} +@string{DAioanei = "Aioanei, Daniel"} @string{TRAlbrecht = "Albreacht, T.~R."} @string{FAli = "Ali, F."} @string{JFAllemand = "Allemand, Jean-Fran\c{c}ois"} @@ -66,6 +67,7 @@ @string{FWBartels = "Bartels, Frank Wilco"} @string{BBarz = "Barz, Bogdan"} @string{TBasche = "Basche, Th."} +@string{PBaschieri = "Baschieri, Paolo"} @string{ABasu = "Basu, A."} @string{LBaugh = "Baugh, Loren"} @string{BBaumgarth = "Baumgarth, Birgit"} @@ -135,6 +137,7 @@ @string{BBullard = "Bullard, Belinda"} @string{RBunk = "Bunk, Richard"} @string{DBusam = "Busam, D."} +@string{GBussi = "Bussi, Giovanni"} @string{CBustamante = "Bustamante, Carlos"} @string{YBustanji = "Bustanji, Yasser"} @string{HJButt = {Butt, Hans-J\"urgen}} @@ -233,6 +236,7 @@ @string{CDewhurst = "Dewhurst, Charles"} @string{VDiFrancesco = "Di Francesco, V."} @string{KDiemer = "Diemer, K."} +@string{GDietler = "Dietler, Giovanni"} @string{HDietz = "Dietz, Hendrik"} @string{SDietz = "Dietz, S."} @string{EDijkstra = "Dijkstra, Edsger Wybe"} @@ -424,6 +428,7 @@ @string{CKHu = "Hu, Chin-Kun"} @string{BHuang = "Huang, Baiqu"} @string{HHuang = "Huang, Hector Han-Li"} +@string{MHubain = "Hubain, Maurice"} @string{AJHudspeth = "Hudspeth, A.~J."} @string{KHuff = "Huff, Katy"} @string{JHughes = "Hughes, John"} @@ -456,10 +461,12 @@ @string{JBT = "J Biotechnol"} @string{JEChem = "Journal of Electroanalytical Chemistry"} @string{JMathBiol = "J Math Biol"} +@string{JMicro = "Journal of microscopy"} @string{JPhysio = "Journal of physiology"} @string{JStructBiol = "Journal of structural biology"} @string{JTB = "J Theor Biol"} @string{WJang = "Jang, W."} +@string{HJanovjak = "Janovjak, H."} @string{LJanosi = "Janosi, Lorant"} @string{AJanshoff = "Janshoff, Andreas"} @string{JJAP = "Japanese Journal of Applied Physics"} @@ -536,6 +543,7 @@ @string{TAKucaba = "Kucaba, T. A."} @string{Kucherlapati = "Kucherlapati"} @string{JKudoh = "Kudoh, J."} +@string{MKuhn = "Kuhn, Michael"} @string{MKulke = "Kulke, Michael"} @string{CKwok = "Kwok, Carol H."} @string{RLevy = "L\'evy, R"} @@ -629,6 +637,7 @@ @string{MMartin = "Martin, M. J."} @string{YMartin = "Martin, Y."} @string{HMassa = "Massa, H."} +@string{DMaterassi = "Materassi, Donatello"} @string{JMathe = "Math\'e, J\'er\^ome"} @string{AMatouschek = "Matouschek, Andreas"} @string{BMatthews = "Matthews, Brian W."} @@ -656,6 +665,7 @@ @string{NMetropolis = "Metropolis, Nicholas"} @string{GMeyer = "Meyer, Gerhard"} @string{HMi = "Mi, H."} +@string{CMicheletti = "Micheletti, Cristian"} @string{MMickler = "Mickler, Moritz"} @string{AMiller = "Miller, A."} @string{NMilshina = "Milshina, N."} @@ -678,6 +688,7 @@ @string{MMoy = "Moy, M."} @string{VMoy = "Moy, Vincent T."} @string{SMukamel = "Mukamel, Shaul"} +@string{DJMuller = "M{\"u}ller, Daniel J."} @string{PMundel = "Mundel, P."} @string{EMuneyuki = "Muneyuki, Eiro"} @string{RJMural = "Mural, R. J."} @@ -865,6 +876,7 @@ @string{JScott = "Scott, J."} @string{RScott = "Scott, R."} @string{USeifert = "Seifert, Udo"} +@string{SKSekatskii = "Sekatskii, Sergey K."} @string{MSekhon = "Sekhon, M."} @string{TSekiguchi = "Sekiguchi, T."} @string{BSenger = "Senger, B."} @@ -960,6 +972,7 @@ @string{SThornton = "Thornton, S."} @string{RWTillmann = "Tillmann, R.~W."} @string{NNTint = "Tint, N. N."} +@string{BTiribilli = "Tiribilli, Bruno"} @string{TTlusty = "Tlusty, Tsvi"} @string{JTocaHerrera = "Toca-Herrera, Jose L."} @string{AToyoda = "Toyoda, A."} @@ -1101,6 +1114,7 @@ @string{RCZinober = "Zinober, Rebecca C."} @string{JZlatanova = "Zlatanova, Jordanka"} @string{PZou = "Zou, Peng"} +@string{GZuccheri = "Zuccheri, Giampaolo"} @string{RZwanzig = "Zwanzig, R."} @string{arXiv = "arXiv"} @string{PGdeGennes = "de Gennes, P. G."} @@ -8419,6 +8433,58 @@ language = "eng", } +@article{ kuhn05, + author = MKuhn #" and "# HJanovjak #" and "# MHubain #" and "# DJMuller, + title = {Automated alignment and pattern recognition of + single-molecule force spectroscopy data.}, + year = 2005, + month = may, + address = {Division of Computer Science, California Institute of + Technology, Pasadena, California 91125, USA.}, + journal = JMicro, + volume = 218, + number = 2, + pages = {125--132}, + ISSN = {0022-2720}, + doi = {10.1111/j.1365-2818.2005.01478.x}, + URL = {http://www.ncbi.nlm.nih.gov/pubmed/15857374}, + language = {eng}, + keywords = {Algorithms}, + keywords = {Bacteriorhodopsins}, + keywords = {Data Interpretation, Statistical}, + keywords = {Escherichia coli Proteins}, + keywords = {Microscopy, Atomic Force}, + keywords = {Protein Folding}, + keywords = {Sodium-Hydrogen Antiporter}, + keywords = {Software}, + abstract = {Recently, direct measurements of forces stabilizing + single proteins or individual receptor-ligand bonds became + possible with ultra-sensitive force probe methods like the atomic + force microscope (AFM). In force spectroscopy experiments using + AFM, a single molecule or receptor-ligand pair is tethered between + the tip of a micromachined cantilever and a supporting + surface. While the molecule is stretched, forces are measured by + the deflection of the cantilever and plotted against extension, + yielding a force spectrum characteristic for each biomolecular + system. In order to obtain statistically relevant results, several + hundred to thousand single-molecule experiments have to be + performed, each resulting in a unique force spectrum. We developed + software and algorithms to analyse large numbers of force + spectra. Our algorithms include the fitting polymer extension + models to force peaks as well as the automatic alignment of + spectra. The aligned spectra allowed recognition of patterns of + peaks across different spectra. We demonstrate the capabilities of + our software by analysing force spectra that were recorded by + unfolding single transmembrane proteins such as bacteriorhodopsin + and NhaA. Different unfolding pathways were detected by + classifying peak patterns. Deviant spectra, e.g. those with no + attachment or erratic peaks, can be easily identified. The + software is based on the programming language C++, the GNU + Scientific Library (GSL), the software WaveMetrics IGOR Pro and + available open-source at http://bioinformatics.org/fskit/.}, + note = {Development stalled in 2005 after Michael graduated.}, +} + @article{ sandal09, author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "# AGomezCasado #" and "# BSamori, @@ -8458,6 +8524,146 @@ language = "eng", } +@article{ materassi09, + author = DMaterassi #" and "# PBaschieri #" and "# BTiribilli #" and "# + GZuccheri #" and "# BSamori, + title = {An open source/real-time atomic force microscope + architecture to perform customizable force spectroscopy + experiments}, + year = 2009, + month = aug, + address = {Department of Electrical and Computer Engineering, + University of Minnesota, 200 Union St. SE, Minneapolis, + Minnesota 55455, USA. mater013@umn.edu}, + journal = RSI, + volume = 80, + number = 8, + pages = 084301, + issn = "1089-7623", + doi = "10.1063/1.3194046", + url = "http://www.ncbi.nlm.nih.gov/pubmed/19725671", + language = "eng", + keywords = {Algorithms}, + keywords = {Animals}, + keywords = {Calibration}, + keywords = {Gold}, + keywords = {Microscopy, Atomic Force}, + keywords = {Muscle Proteins}, + keywords = {Myocardium}, + keywords = {Optics and Photonics}, + keywords = {Ownership}, + keywords = {Protein Kinases}, + keywords = {Software}, + keywords = {Spectrum Analysis}, + keywords = {Time Factors}, + abstract = {We describe the realization of an atomic force + microscope architecture designed to perform customizable + experiments in a flexible and automatic way. Novel technological + contributions are given by the software implementation platform + (RTAI-LINUX), which is free and open source, and from a functional + point of view, by the implementation of hard real-time control + algorithms. Some other technical solutions such as a new way to + estimate the optical lever constant are described as well. The + adoption of this architecture provides many degrees of freedom in + the device behavior and, furthermore, allows one to obtain a + flexible experimental instrument at a relatively low cost. In + particular, we show how such a system has been employed to obtain + measures in sophisticated single-molecule force spectroscopy + experiments\citep{fernandez04}. Experimental results on proteins + already studied using the same methodologies are provided in order + to show the reliability of the measure system.}, + note = {Although this paper claims to present an open source + experiment control framework (on Linux!), it doesn't actually link + to any source code. This is puzzling and frusterating.}, +} + +@article{ aioanei11, + author = DAioanei #" and "# MBrucale #" and "# BSamori, + title = {Open source platform for the execution and analysis of + mechanical refolding experiments.}, + year = 2011, + month = feb, + day = 1, + address = {Department of Biochemistry G.~Moruzzi, + University of Bologna, Via Irnerio 48, 40126 Bologna, Italy. + aioaneid@gmail.com}, + journal = BIOINFO, + volume = 27, + number = 3, + pages = {423--425}, + issn = {1367-4811}, + doi = {10.1093/bioinformatics/btq663}, + url = {http://www.ncbi.nlm.nih.gov/pubmed/21123222}, + language = {eng}, + keywords = {Computational Biology}, + keywords = {Kinetics}, + keywords = {Protein Denaturation}, + keywords = {Protein Refolding}, + keywords = {Software}, + abstract = {Single-molecule force spectroscopy has facilitated the + experimental investigation of biomolecular force-coupled kinetics, + from which the kinetics at zero force can be extrapolated via + explicit theoretical models. The atomic force microscope (AFM) in + particular is routinely used to study protein unfolding kinetics, + but only rarely protein folding kinetics. The discrepancy arises + because mechanical protein refolding studies are more technically + challenging.}, + note = {\href{http://code.google.com/p/refolding/}{Refolding} is a + suite for performing and analyzing double-pulse refolding + experiments. The experiment-driver is mostly written in Java with + the analysis code in Python. The driver is curious; it uses the + NanoScope scripting interface to drive the experiment through the + NanoScope software by impersonating a mouse-wielding user (like + Selenium does for web browsers). See the + \imint{sh}|RobotNanoDriver.java| code for details. There is also + support for automatic velocity clamp analysis.}, +} + +@article{ benedetti11, + author = FBenedetti #" and "# CMicheletti #" and "# GBussi #" and "# + SKSekatskii #" and "# GDietler, + title = {Nonkinetic modeling of the mechanical unfolding of + multimodular proteins: theory and experiments.}, + year = 2011, + month = sep, + day = 21, + address = {Laboratory of Physics of Living Matter, + Ecole Polytechnique F{\'e}d{\'e}rale de Lausanne, + Lausanne, Switzerland.}, + journal = BPJ, + volume = 101, + number = 6, + pages = {1504--1512}, + issn = {1542-0086}, + doi = {10.1016/j.bpj.2011.07.047}, + url = {http://www.ncbi.nlm.nih.gov/pubmed/21943432}, + language = {eng}, + keywords = {Kinetics}, + keywords = {Microscopy, Atomic Force}, + keywords = {Models, Molecular}, + keywords = {Monte Carlo Method}, + keywords = {Protein Unfolding}, + keywords = {Stochastic Processes}, + abstract = {We introduce and discuss a novel approach called + back-calculation for analyzing force spectroscopy experiments on + multimodular proteins. The relationship between the histograms of + the unfolding forces for different peaks, corresponding to a + different number of not-yet-unfolded protein modules, is exploited + in such a manner that the sole distribution of the forces for one + unfolding peak can be used to predict the unfolding forces for + other peaks. The scheme is based on a bootstrap prediction method + and does not rely on any specific kinetic model for multimodular + unfolding. It is tested and validated in both + theoretical/computational contexts (based on stochastic + simulations) and atomic force microscopy experiments on (GB1)(8) + multimodular protein constructs. The prediction accuracy is so + high that the predicted average unfolding forces corresponding to + each peak for the GB1 construct are within only 5 pN of the + averaged directly-measured values. Experimental data are also used + to illustrate how the limitations of standard kinetic models can + be aptly circumvented by the proposed approach.}, +} + @article{ kempe85, author = TKempe #" and "# SBHKent #" and "# FChow #" and "# SMPeterson #" and "# WSundquist #" and "# JLItalien #" and "# DHarbrecht