paper.bib

@article{Hoops:2006gy,
author = {{Hoops, S} and {Sahle, S} and {Gauges, R} and {Lee, C} and {Pahle, J} and {Simus, N} and {Singhal, M} and {Xu, L} and {Mendes, P} and {Kummer, U}},
title = {{COPASI--a COmplex PAthway SImulator}},
journal = {Bioinformatics},
year = {2006},
volume = {22},
number = {24},
pages = {3067--3074},
month = dec
}


@article{Andrews:2004fs,
author = {Andrews, Steven S and Bray, Dennis},
title = {{Stochastic simulation of chemical reactions with spatial resolution and single molecule detail.}},
journal = {Phys Biol},
year = {2004},
volume = {1},
number = {3-4},
pages = {137--151},
month = dec
}

% terminologies such as trapping, autonomous
@article{Kubota:2001ul,
author = {Kubota, Y and Bower, J M},
title = {{Transient versus asymptotic dynamics of CaM kinase II: possible roles of phosphatase.}},
journal = {J Comput Neurosci},
year = {2001},
volume = {11},
number = {3},
pages = {263--279},
month = nov
}


@article{Lisman:2002ki,
author = {Lisman, J and Schulman, H and Cline, H},
title = {{The molecular basis of CaMKII function in synaptic and behavioural memory.}},
journal={Nat Rev Neurosci},
year = {2002},
volume = {3},
number = {3},
pages = {175--190},
month = mar
}

@article{Ma:2014dr,
author = {Ma, Huan and Groth, Rachel D and Cohen, Samuel M and Emery, John F and Li, Boxing and Hoedt, Esthelle and Zhang, Guoan and Neubert, Thomas A and Tsien, Richard W},
title = {{$\gamma$CaMKII shuttles Ca2+/CaM to the nucleus to trigger CREB phosphorylation and gene expression}},
journal = {Cell},
year = {2014},
volume = {159},
number = {2},
pages = {281--294},
month = oct
}

@article{Li:2016cq,
author = {Li, Boxing and Tadross, Michael R and Tsien, Richard W},
title = {{Sequential ionic and conformational signaling by calcium channels drives neuronal gene expression.}},
journal = {Science},
year = {2016},
volume = {351},
number = {6275},
pages = {863--867},
month = feb
}

@article{Stefan:2014gl,
author = {Stefan, Melanie I and Bartol, Thomas M and Sejnowski, Terrence J and Kennedy, Mary B},
title = {{Multi-state modeling of biomolecules}},
journal = {PLoS Comput Biol},
year = {2014},
volume = {10},
number = {9},
pages = {e1003844},
month = sep
}

@article{Hlavacek:2006iq,
author = {Hlavacek, William S and Faeder, James R and Blinov, Michael L and Posner, Richard G and Hucka, Michael and Fontana, Walter},
title = {{Rules for modeling signal-transduction systems.}},
journal = {Sci STKE},
year = {2006},
volume = {2006},
number = {344},
pages = {re6--re6},
month = jul
}

@article{Pepke:2010ju,
author = {Pepke, Shirley and Kinzer-Ursem, Tamara and Mihalas, Stefan and Kennedy, Mary B},
title = {{A dynamic model of interactions of Ca2+, calmodulin, and catalytic subunits of Ca2+/calmodulin-dependent protein kinase II.}},
journal = {PLoS Comput Biol},
year = {2010},
volume = {6},
number = {2},
pages = {e1000675--15},
month = feb
}

@article{Lucic:2008gt,
author = {Luci{\'c}, Vladan and Greif, Gabriela J and Kennedy, Mary B},
title = {{Detailed state model of CaMKII activation and autophosphorylation.}},
journal = {Eur Biophys J},
year = {2008},
volume = {38},
number = {1},
pages = {83--98},
month = nov
}

@article{Chin:2000dk,
author = {Chin, David and Means, Anthony R},
title = {{Calmodulin: a prototypical calcium sensor}},
journal = {Trends Cell Biol},
year = {2000},
volume = {10},
number = {8},
pages = {322--328},
month = aug
}

@article{Gaertner:2004jk,
author = {Gaertner, Tara R and Kolodziej, Steven J and Wang, Dan and Kobayashi, Ryuji and Koomen, John M and Stoops, James K and Waxham, M Neal},
title = {{Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II.}},
journal = {J Biol Chem},
year = {2004},
volume = {279},
number = {13},
pages = {12484--12494},
month = mar
}

@article{Dix:2008gy,
author = {Dix, James A and Verkman, A S},
title = {{Crowding Effects on Diffusion in Solutions and Cells}},
journal = {Annu Rev Biophys},
year = {2008},
volume = {37},
number = {1},
pages = {247--263},
month = jun
}


@article{LubyPhelps:2000uj,
author = {Luby-Phelps, K},
title = {{Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area.}},
journal = {Int Rev Cytol},
year = {2000},
volume = {192},
pages = {189--221}
}


@article{LubyPhelps:1995kl,
author = {Luby-Phelps, K and Hori, M and Phelps, J M and Won, D},
title = {{Ca\textsuperscript{2+}-regulated dynamic compartmentalization of calmodulin in living smooth muscle cells.}},
journal = {J Biol Chem},
year = {1995},
volume = {270},
number = {37},
pages = {21532--21538},
month = sep
}

@article{Tran:2003fs,
author = {Tran, Quang-Kim and Black, D J and Persechini, Anthony},
title = {{Intracellular coupling via limiting calmodulin.}},
journal = {J Biol Chem},
year = {2003},
volume = {278},
number = {27},
pages = {24247--24250},
month = jul
}

@article{Mendes:1993ws,
author = {Mendes, P},
title = {{GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems.}},
journal = {Comput Appl Biosci},
year = {1993},
volume = {9},
number = {5},
pages = {563--571},
month = oct
}

@article{Faas:2011fna,
author = {Faas, Guido C and Raghavachari, Sridhar and Lisman, John E and Mody, Istvan},
title = {{Calmodulin as a direct detector of Ca\textsuperscript{2+} signals.}},
journal = {Nat Neurosci},
year = {2011},
volume = {14},
number = {3},
pages = {301--304},
month = mar
}

@inbook{Andrews:2015,
author={Andrews, Steve and Vel Arjunan, Satya Nanda and Balbo, Gianfranco and Liu, Fei},
title={David Gilbert, Monika Heiner, Koichi Takahashi, and Adelinde M. Uhrmacher, eds. Multiscale Spatial Computational Systems Biology},
chapter={Simulating macromolecular crowding with particle and lattice-based methods (Team 3).},    
pages={170--187},
year={2015},
month=jan
}

@book{Carnevale:2006iv,
title = {{The NEURON Book}},
author = {Carnevale, Nicholas T and Hines, Michael L},
publisher={Cambridge University Press},
year = {2006}
}

@article{Keller:2008ez,
author = {Keller, Daniel X and Franks, Kevin M and Bartol, Thomas M and Sejnowski, Terrence J},
title = {{Calmodulin activation by calcium transients in the postsynaptic density of dendritic spines.}},
journal = {PLoS One},
year = {2008},
volume = {3},
number = {4},
pages = {e2045},
month = apr
}

@article{Dupont:2003vq,
author = {Dupont, Genevi{\`e}ve and Houart, G{\'e}rald and De Koninck, Paul},
title = {{Sensitivity of CaM kinase II to the frequency of Ca\textsuperscript{2+} oscillations: a simple model.}},
journal = {Cell Calcium},
year = {2003},
volume = {34},
number = {6},
pages = {485--497},
month = dec
}


@article{DeKoninck:1998wh,
author = {De Koninck, P and Schulman, H},
title = {{Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations.}},
journal = {Science},
year = {1998},
volume = {279},
number = {5348},
pages = {227--230},
month = jan
}

@article{Hanson:1994te,
author = {Hanson, P I and Meyer, T and Stryer, L and Schulman, H},
title = {{Dual role of calmodulin in autophosphorylation of multifunctional CaM kinase may underlie decoding of calcium signals.}},
journal = {Neuron},
year = {1994},
volume = {12},
number = {5},
pages = {943--956},
month = may
}

@article{Andrews:2009dr,
author = {Andrews, Steven S},
title = {{Accurate particle-based simulation of adsorption, desorption and partial transmission.}},
journal = {Phys Biol},
year = {2009},
volume = {6},
number = {4},
pages = {046015},
month = nov
}

@article{Mori:2004fb,
author = {Mori, Masayuki X and Erickson, Michael G and Yue, David T},
title = {{Functional stoichiometry and local enrichment of calmodulin interacting with Ca\textsuperscript{2+} channels.}},
journal = {Science},
year = {2004},
volume = {304},
number = {5669},
pages = {432--435},
month = apr
}
@article{Shifman:2006hw,
author = {Shifman, Julia M and Choi, Mee H and Mihalas, Stefan and Mayo, Stephen L and Kennedy, Mary B},
title = {{Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums.}},
journal = {Proceedings of the National Academy of Sciences},
year = {2006},
volume = {103},
number = {38},
pages = {13968--13973},
month = sep
}


@article{2013PNAS..11015794T,
author = {Tadross, Michael R and Tsien, Richard W and Yue, David T},
title = {{Ca\textsuperscript{2+} channel nanodomains boost local Ca\textsuperscript{2+} amplitude.}},
journal = {Proc Natl Acad Sci USA},
year = {2013},
volume = {110},
number = {39},
pages = {15794--15799},
month = sep
}

@article{Wheeler:2008ja,
author = {Wheeler, D G and Barrett, C F and Groth, R D and Safa, P and Tsien, R W},
title = {{CaMKII locally encodes L-type channel activity to signal to nuclear CREB in excitation-transcription coupling.}},
journal = {J Cell Biol},
year = {2008},
volume = {183},
number = {5},
pages = {849--863},
month = nov
}

@article{Ma:2015bg,
author = {Ma, Huan and Li, Boxing and Tsien, Richard W},
title = {{Distinct roles of multiple isoforms of CaMKII in signaling to the nucleus.}},
journal = {Biochim Biophys Acta},
year = {2015},
volume = {1853},
number = {9},
pages = {1953--1957},
month = sep
}

@article{Wayman:2008gla,
author = {Wayman, Gary A and Lee, Yong-Seok and Tokumitsu, Hiroshi and Silva, Alcino J and Silva, Alcino and Soderling, Thomas R},
title = {{Calmodulin-kinases: modulators of neuronal development and plasticity.}},
journal = {Neuron},
year = {2008},
volume = {59},
number = {6},
pages = {914--931},
month = sep
}

@article{Zeng:2010bq,
author = {Zeng, Shangyou and Holmes, William R},
title = {{The effect of noise on CaMKII activation in a dendritic spine during LTP induction.}},
journal = {J Neurophysiol},
year = {2010},
volume = {103},
number = {4},
pages = {1798--1808},
month = apr
}

@article{Holmes:2000uk,
author = {Holmes, W R},
title = {{Models of calmodulin trapping and CaM kinase II activation in a dendritic spine.}},
journal = {J Comput Neurosci},
year = {2000},
volume = {8},
number = {1},
pages = {65--85},
month = jan
}

@BOOK{Rice:198505, 
title={Comprehensive Chemical Kinetics: Diffusion-Limited Reactions},
author={Rice, S A},
publisher={Elsevier Science Ltd},
year={1985},
month={5},
volume={25},
isbn={9780444423542},
totalpages={420},
}

@article{Kubota:2007kq,
author = {Kubota, Yoshihisa and Putkey, John A and Waxham, M Neal},
title = {{Neurogranin controls the spatiotemporal pattern of postsynaptic Ca\textsuperscript{2+}/CaM signaling}},
journal = {Biophys J},
year = {2007},
volume = {93},
number = {11},
pages = {3848--3859},
month = dec
}

@article{Michalski:2012ds,
author = {Michalski, P J and Loew, L M},
title = {{CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation.}},
journal = {Phys Biol},
year = {2012},
volume = {9},
number = {3},
pages = {036010},
month = jun
}

@article{Zhabotinsky:2000fp,
author = {Zhabotinsky, Anatol M},
title = {{Bistability in the Ca\textsuperscript{2+}/Calmodulin-Dependent Protein Kinase-Phosphatase system.}},
journal = {Biophys J},
year = {2000},
volume = {79},
number = {5},
pages = {2211--2221},
month = nov
}


@article{2008BpJ....95.6002S,
author = {Sanabria, Hugo and Digman, Michelle A and Gratton, Enrico and Waxham, M Neal},
title = {{Spatial diffusivity and availability of intracellular calmodulin.}},
journal = {Biophys J},
year = {2008},
volume = {95},
number = {12},
pages = {6002--6015},
month = dec
}

@book{citeulike:306134,
    abstract = {{Ion channels underlie a broad range of the most basic biological processes, from excitation and signaling to secretion and absorption. Like enzymes, they are diverse and ubiquitous macromolecular catalysts with high substrate specificity and subject to strong regulation. This fully revised and expanded Third Edition of Ion Channels of Excitable Membranes describes the known channels and their physiological functions, then develops the conceptual background needed to understand their architecture and molecular mechanisms of operation. It includes new chapters on calcium signaling, structural biology, and molecular biology and genomics. Ion Channels of Excitable Membranes begins with the classical biophysical work of Hodgkin and Huxley, continues with the roles of channels in cellular signaling, then develops the physical and molecular principles needed for explaining permeation, gating, pharmacological modification, and molecular diversity, and ends with a discussion of channel evolution. Ion Channels of Excitable Membranes is written to be accessible and interesting to life scientists and physical scientists of all kinds. It introduces all the concepts that a graduate student should be aware of but is also effective in advanced undergraduate courses. It has long been the recognized authoritative overview of this field used by all neuroscientists.}},
    author = {Hille, Bertil},
    citeulike-article-id = {306134},
    citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0878933212},
    citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0878933212},
    citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0878933212},
    citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0878933212},
    citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0878933212/citeulike00-21},
    citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0878933212},
    citeulike-linkout-6 = {http://www.worldcat.org/isbn/0878933212},
    citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0878933212},
    citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0878933212\&index=books\&linkCode=qs},
    citeulike-linkout-9 = {http://www.librarything.com/isbn/0878933212},
    day = {01},
    edition = {3},
    howpublished = {Hardcover},
    isbn = {0878933212},
    keywords = {book, channel, ion},
    month = jul,
    posted-at = {2008-05-01 04:27:09},
    priority = {2},
    publisher = {Sinauer Associates},
    title = {{Ion Channels of Excitable Membranes}},
    year = {2001}
}


@conference{Li:2014fv,
author = {Li, Ximing and Holmes, William R},
title = {{Comparing calcium influx with high-frequency stimulation and burst stimulation LTP protocols.}},
booktitle = {BMC Neurosci},
year = {2014},
volume = {15},
number = {Suppl 1},
pages = {P140--2}
}

@article{Grover:2009hb,
author = {{Grover, L M} and {Kim, E} and {Cooke, J D} and {Holmes, W R}},
title = {{LTP in hippocampal area CA1 is induced by burst stimulation over a broad frequency range centered around delta.}},
journal={Learn Mem},
year = {2009},
volume = {16},
number = {1},
pages = {69--81},
month = jan
}

@article{Tuckwell:2012tt,
author = {Tuckwell, H C},
title = {{Quantitative aspects of L-type Ca\textsuperscript{2+} currents.}},
journal = {Prog Neurobiol},
year = {2012},
volume = {96},
number = {1},
pages = {1--31}
}

@article{Bading:2013cb,
author = {Bading, Hilmar},
title = {{Nuclear calcium signalling in the regulation of brain function.}},
journal = {Nature},
year = {2013},
volume = {14},
number = {9},
pages = {593--608},
month = aug
}

@article{vanZon:2005jd,
author = {van Zon, Jeroen S and ten Wolde, Pieter Rein},
title = {{Simulating biochemical networks at the particle level and in time and space: Green{\textquoteright}s function reaction dynamics.}},
journal = {Phys Rev Lett},
year = {2005},
volume = {94},
number = {12},
pages = {128103},
month = apr
}

@article{Chao:2010fn,
author = {Chao, Luke H and Pellicena, Patricia and Deindl, Sebastian and Barclay, Lauren A and Schulman, Howard and Kuriyan, John},
title = {{Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation.}},
journal = {Nat Struct Mol Biol},
year = {2010},
volume = {17},
number = {3},
pages = {264--272},
month = mar
}

@article{Hudmon:2005kf,
author = {Hudmon, Andy and LeBel, Eric and Roy, Hugo and Sik, Attila and Schulman, Howard and Waxham, M Neal and De Koninck, Paul},
title = {{A mechanism for Ca\textsuperscript{2+}/Calmodulin-Dependent Protein Kinase II clustering at synaptic and nonsynaptic sites based on self-association.}},
journal = {J Neurosci},
year = {2005},
volume = {25},
number = {30},
pages = {6971--6983},
month = jul
}

@article{Persechini:2002tb,
author = {Persechini, Anthony and Stemmer, Paul M},
title = {{Calmodulin is a limiting factor in the cell.}},
journal = {Trends Cardiovasc Med},
year = {2002},
volume = {12},
number = {1},
pages = {32--37},
month = jan
}

%CamKII phosphorylation of AMPAR on Ser831 and increasing conductance, and facilitate AMPAR trafficking
@article{Herring:2016bh,
author = {Herring, Bruce E and Nicoll, Roger A},
title = {{Long-term potentiation: from CaMKII to AMPA receptor trafficking.}},
journal = {Annu Rev Physiol},
year = {2016},
volume = {78},
number = {1},
pages = {351--365},
month = feb
}


@article{Silva:1992uh,
author = {Silva, A J and Stevens, C F and Tonegawa, S and Wang, Y},
title = {{Deficient hippocampal long-term potentiation in alpha-calcium-calmodulin kinase II mutant mice.}},
journal = {Science},
year = {1992},
volume = {257},
number = {5067},
pages = {201--206},
month = jul
}

@article{Hell:2014bd,
author = {Hell, Johannes W},
title = {{CaMKII: claiming center stage in postsynaptic function and organization.}},
journal = {Neuron},
year = {2014},
volume = {81},
number = {2},
pages = {249--265},
month = jan
}

@article{Bhalla:2004cu,
author = {Bhalla, Upinder S},
title = {{Signaling in small subcellular volumes. I. stochastic and diffusion effects on individual pathways.}},
journal = {Biophys J},
year = {2004},
volume = {87},
number = {2},
pages = {733--744},
month = aug
}

@article{Byrne:2010ci,
author = {Byrne, Michael J and Waxham, M Neal and Kubota, Yoshihisa},
title = {{The impacts of geometry and binding on CaMKII diffusion and retention in dendritic spines.}},
journal = {J Comput Neurosci},
year = {2010},
volume = {31},
number = {1},
pages = {1--12},
month = nov
}


@article{Coultrap:2012ip,
author = {Coultrap, Steven J and Bayer, K Ulrich},
title = {{CaMKII regulation in information processing and storage.}},
journal = {Trends Neurosci},
year = {2012},
volume = {35},
number = {10},
pages = {607--618},
month = oct
}

@article{Erickson:2014fs,
author = {Erickson, Jeffrey R},
title = {{Mechanisms of CaMKII activation in the heart}},
journal = {Front Pharmacol},
year = {2014},
volume = {5},
number = {e1000583},
pages = {289}
}

@article{Bartol:2015de,
author = {Bartol, Thomas M and Keller, Daniel X and Kinney, Justin P and Bajaj, Chandrajit L and Harris, Kristen M and Sejnowski, Terrence J and Kennedy, Mary B},
title = {{Computational reconstitution of spine calcium transients from individual proteins.}},
journal = {Front Synaptic Neurosci},
year = {2015},
volume = {7},
pages = {1812--24},
month = oct
}

@article{Skene:1990kf,
author = {Skene, JHP},
title = {{GAP-43 as a 'calmodulin sponge' and some implications for calcium signalling in axon terminals.}},
journal = {Neurosci Res Suppl},
year = {1990},
volume = {13},
pages = {S112--S125}
}

@article{Stratton:2014ct,
author = {Stratton, Margaret and Lee, Il-Hyung and Bhattacharyya, Moitrayee and Christensen, Sune M and Chao, Luke H and Schulman, Howard and Groves, Jay T and Kuriyan, John},
title = {{Activation-triggered subunit exchange between CaMKII holoenzymes facilitates the spread of kinase activity.}},
journal = {eLife},
year = {2014},
volume = {3},
pages = {2342--28},
month = jan
}

@article{Bliss:1973jg,
author = {Bliss, T V P and L{\o}mo, T},
title = {{Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path.}},
journal = {J Physiol},
year = {1973},
volume = {232},
number = {2},
pages = {331--356},
month = jul
}

@article{Meyer:1992dp,
author = {Meyer, T and Hanson, P I and Stryer, L and Schulman, H},
title = {{Calmodulin trapping by calcium-calmodulin-dependent protein kinase.}},
journal = {Science},
year = {1992},
volume = {256},
number = {5060},
pages = {1199--1202},
month = may
}

@article{Fujii:2013bg,
author = {Fujii, Hajime and Inoue, Masatoshi and Okuno, Hiroyuki and Sano, Yoshikazu and Takemoto-Kimura, Sayaka and Kitamura, Kazuo and Kano, Masanobu and Bito, Haruhiko},
title = {{Nonlinear decoding and asymmetric representation of neuronal input information by CaMKII$\alpha$ and calcineurin.}},
journal = {Cell Rep},
year = {2013},
volume = {3},
number = {4},
pages = {978--987},
month = apr
}

@article{Chao:2011iw,
author = {Chao, Luke H and Stratton, Margaret M and Lee, Il-Hyung and Rosenberg, Oren S and Levitz, Joshua and Mandell, Daniel J and Kortemme, Tanja and Groves, Jay T and Schulman, Howard and Kuriyan, John},
title = {{A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme}},
journal = {Cell},
year = {2011},
volume = {146},
number = {5},
pages = {732--745},
month = sep
}

@article{Bayer:2002er,
author = {Bayer, K Ulrich and De Koninck, Paul and Schulman, Howard},
title = {{Alternative splicing modulates the frequency- 
dependent response of CaMKII to Ca$^{2+ }$oscillations 
}},
journal = {The EMBO journal},
year = {2002},
volume = {21},
number = {14},
pages = {3590--3597},
month = jul
}


@article{Stratton:2013el,
author = {Stratton, Margaret M and Chao, Luke H and Schulman, Howard and Kuriyan, John},
title = {{Structural studies on the regulation of Ca2+/calmodulin dependent protein kinase II}},
journal = {Current Opinion in Structural Biology},
year = {2013},
volume = {23},
number = {2},
pages = {292--301},
month = apr
}

@article{Mironov:2013,
author={Mironov,SL},
title={Maxwell's demon for calcium binding to calmodulin?},
journal={eprint arXiv:1305.3553},
year={2013},    
month= may
}