Triggering Actin Comets Versus Membrane Ruffles: Distinctive Effects of Phosphoinositides on Actin Reorganization.
Ueno T, Falkenburger BH, Pohlmeyer C, Inoue T.
Sci Signal. 2011;4(203):ra87.
BioModel: 'bfalken: Ueno2011'

System analysis shows distinct mechanisms and common principles of nuclear envelope protein dynamics.
Zuleger, N., Kelly, D.A., Richardson, A.C., Kerr, A.R.W., Goldberg, M.W., Goryachev, A.B., Schirmer, E.C.
The Journal of Cell Biology 193, 109-123, 2011.

The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors.
Craig, E.M., Dey, S., and Mogilner, A.
J Phys Condens Matter 23, 374102, (2011).
MathModel: ‘ecraig: Cytoskeletal bundle_1-motor’
MathModel: ‘ecraig: Cytoskeletal bundle_2-motor’ (for the extended model described in section 6)

Astrocytes as regulators of synaptic function: a quest for the Ca2+ master key.
Rusakov, D.A., Zheng, K., and Henneberger, C.
Neuroscientist 17, 513-523, (2011).

Assessment of cellular mechanisms contributing to cAMP compartmentalization in pulmonary microvascular endothelial cells
Wei P Feinstein, Bing Zhu, Silas J Leavesley, Sarah L. Sayner, and Thomas C Rich
23 November 2011, 10.1152/ajpcell.00361.2011
BioModel: 'wfeinstein: PMVEC cAMP model'
BioModel: 'wfeinstein: PMVEC cAMP model with point source'

Protein Diffusion in Mammalian Cell Cytoplasm.
Kühn, T., T.O. Ihalainen, J. Hyväluoma, N. Dross, S.F. Willman, J. Langowski, M. Vihinen-Ranta, and J. Timonen.
2011, PLoS ONE. 6:e22962.

Quantifying the Waddington landscape and biological paths for development and differentiation.
Wang J, Zhang K, Xu L, Wang E.
Proc Natl Acad Sci U S A. 2011 May 17;108(20):8257-62. Epub 2011 May 2.

The effect of compressive deformations on the rate of build-up of oxygen in isolated skeletal muscle cells.
Leopold E, Sopher R, Gefen A.
Med Eng Phys. 33, 1072-1078, 2011

Coupling of the phosphatase activity of Ci-VSP to its voltage sensor activity over the entire range of voltage sensitivity.
Sakata S, Hossain MI, Okamura Y.
J Physiol. 589:2687-2705, 2011
Public Biomodel: "ssvcell1548: sakata_JP2011-Kir2.1"
Public Biomodel: "ssvcell1548: sakata_JP2011-PHDGFP"

Ca2+ buffering at a drosophila larval synaptic terminal.
He, T., and Lnenicka, G.A.
(2011) Synapse 65, 687-693.

Cooperative Nuclear Localization Sequences Lend a Novel Role to the N-Terminal Region of MSH6.
Gassman, N.R., Clodfelter, J.E., McCauley, A.K., Bonin, K., Salsbury, F.R., Jr., and Scarpinato, K.D.
(2011). PLoS One 6, e17907.

Signaling network triggers and membrane physical properties control the actin cytoskeleton-driven isotropic phase of cell spreading.
Rangamani P, Fardin MA, Xiong Y, Lipshtat A, Rossier O, Sheetz MP, Iyengar R.
Biophys J. 2011 Feb 16;100(4):845-57.
BioModel: 'prangamani: Rangamani et al, BJ Feb 2011'

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.
Brown SA, Moraru II, Schaff JC, Loew LM.
J Comput Neurosci. 31:385-400, 2011
BioModel: 'Brown:GBrown et al 2010 Purkinje MultiCompartmental Combined Biochem and Electrophysiol'

Potassium (K+) gradients serve as a mobile energy source in plant vascular tissues.
Gajdanowicz P, Michard E, Sandmann M, Rocha M, Corrêa LG, Ramírez-Aguilar SJ, Gomez-Porras JL, González W, Thibaud JB, van Dongen JT, Dreyer I.
Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):864-9. Epub 2010 Dec 27.
BioModel: 'IngoDreyer: Gajdanowicz_et_al_20119'

Purification of Actin from Fission Yeast Schizosaccharomyces pombe and Characterization of Functional Differences from Muscle Actin.
Shih-Chieh Ti and Thomas D. Pollard
Journal of Biological Chemistry, 2011, 286(7), 5784-92 Publication Date: Dec 9, 2010
BioModel: 'SCT: PiRelease'

Lysosomal Pathology and Osteopetrosis upon Loss of H+-Driven Lysosomal Cl– Accumulation
Stefanie Weinert, Sabrina Jabs, Chayarop Supanchart, Michaela Schweizer, Niclas Gimber, Martin Richter, Jörg Rademann, Tobias Stauber, Uwe Kornak, and Thomas J. Jentsch
Science 11 June 2010: 1401-1403.Published online 29 April 2010 [DOI:10.1126/science.1188072]

Effect of ATP Binding and Hydrolysis on Dynamics of Canine Parvovirus NS1.
Niskanen, E.A., Ihalainen, T.O., Kalliolinna, O., Hakkinen, M.M., and Vihinen-Ranta, M.
J Virol 84, 5391-5403. (2010).

The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation.
Wang J, Xu L, Wang E, Huang S.
Biophys J. 2010 Jul 7;99(1):29-39.
MathModel: 'xuli: BJ_cellfate_2010'

Purification of actin from fission yeast Schizosaccharomyces pombe and characterization of functional differences from muscle actin.
Ti SC, Pollard TD.
J Biol Chem. 2011 Feb 18;286(7):5784-92. Epub 2010 Dec 9.
PMID: 21148484 [PubMed - in process]
BioModel: 'SCT: PiRelease'

Putting one step before the other: Distinct activation pathways for Cdk1 and Cdk2 bring order to the mammalian cell cycle.
Merrick, K.A., and Fisher, R.P.
Cell Cycle 9, 706-714, (2010).

Cingulin and paracingulin show similar dynamic behaviour, but are recruited independently to junctions.
Paschoud S, Yu D, Pulimeno P, Jond L, Turner JR, Citi S. Mol Membr Biol. 2010 Dec 17. [Epub ahead of print]
BioModel: 'dyu: final cingulin model'

Quantitative Measurement of Ca2+ in the Sarcoplasmic Reticulum Lumen of Mammalian Skeletal Muscle.
Ziman, A.P., C.W. Ward, G.G. Rodney, W.J. Lederer, and R.J. Bloch.
Biophys J, 2010. 99(8): p. 2705-2714.

Quantifying a pathway: kinetic analysis of actin dendritic nucleation.
Kraikivski P, Slepchenko BM.
Biophys J.2010 Aug 4;99(3):708-15.
MathModel: 'pavelkr: Actin_Polymerization and NPF_ARP2/3_Actin'

Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics.
Kapustina M, Vitriol E, Elston TC, Loew LM, Jacobson K.
Cytoskeleton (Hoboken).2010 Aug;67(8):519-34.
BioModel: 'marynka: CALI'

MLCK-dependent exchange and actin binding region-dependent anchoring of ZO-1 regulate tight junction barrier function
Dan Yu, Amanda M. Marchiando, Christopher R. Weber, David R. Raleigh, Yingmin Wang, Le Shen, and Jerrold R. Turner.
PNAS, vol. 107, no. 18, 8237-8241 (2010). Published online, April 19, 2010, doi:10.1072/pnas.0908869107.
BioModel: 'dyu: cacodeltaABR'
BioModel: 'dyu: latrunculin'
BioModel: 'dyu: mouseZO1control&PIK'

A Mitotic Kinesin-6, PavKLP, Mediates Interdependent Cortical Reorganization and Spindle Dynamics in Drosophila Embryos.
P. Sommi, R. Ananthakrishnan, D. K. Cheerambathur, M. Kwon, S. Morales-Mulia, I. Brust-Mascher, A. Mogilner.
J Cell Sci., 123: 1862-1872 (2010).
BioModel: 'ananth: furrowsinglepathwayconstconcabsorbingbcscaling'

Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues.
Lipshtat, A., G. Jayaraman, J.C. He, and R. Iyengar.
Proceedings of the National Academy of Sciences. 107:1247-1252, 2010.
BioModel: 'azilipshtat: PNAS_switch'
BioModel: 'azilipshtat: Rap1_switch'

Kinetics of M1 muscarinic receptor and G protein signaling to phospholipase C in iving cells.
Bjorn H. Falkenburger, Jill B. Jensen, and Bertil Hille
J. Gen. Physiol. 2010; 135 81-97, Published online Jan 25 2010, 10.1085/jgp.200910344.
BioModel: 'hillelab: FalkenburgerJGP2010'

Kinetics of PIP2 metabolism and KCNQ2/3 channel regulation studied with a voltage-sensitive phosphatase in iving cells.
Bjorn H. Falkenburger, Jill B. Jensen, and Bertil Hille
J. Gen. Physiol. 2010; 135 99-114, Published online Jan 25 2010, 10.1085/jgp.200910345.
BioModel: 'hillelab: FalkenburgerJGP2010'

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives
Wang J, Xu L, Wang E.
Biophys J. 2009 Dec 2;97(11):3038-46.
MathModel: 'xuli: BJ_Circadian_2009'

Phosphodiesterase 1C is dispensable for rapid response termination of olfactory sensory neurons.
Cygnar, K.D., and H. Zhao.
Nat Neurosci. 12:454-62, 2009. PMID 19305400 2712288. 
BioModel: 'cygnar: NatureNeuroscience2009'

A genetically encoded reporter of synaptic activity in vivo.
Dreosti E, Odermatt B, Dorostkar MM, Lagnado L.
Nat Methods. 2009 Dec;6(12):883-9. Epub 2009 Nov 8.
PubMed PMID: 19898484.
BioModel: 'Leon: Fig.1v7'
BioModel: 'Leon: GECI_Synapse'

Effects of excluded volume due to internal membranes and cytoskeletal structures.
Novak, I.L., Kraikivski, P., Slepchenko, B.M.
Biophysical Journal 97(3): 758-767(2009).
This paper employed a customized VCell-based application. The code is available upon request from Igor Novak.

Modeling Spatial and Temporal Dynamics of Chemotactic Networks
Liu Yang and Pablo A. Iglesias
Chemotaxis: Methods and Protocols, Methods in Molecular Biology, vol. 571, pp. 489-505, 2009.
BioModel: 'LiuYang: LEGI'.

Subcellular dynamics of type II PKA in neurons.
Zhong, H., G.M. Sia, T.R. Sato, N.W. Gray, T. Mao, Z. Khuchua, R.L. Huganir, and K. Svoboda.
Neuron. 62:363-374, 2009.
In the BioModel Database dialog, scroll down and open Shared Models. The models can be found under user 'globus' and are entitled 'CAT diffusion', 'PKA2D' and 'PKA2D with AKAP'.

Intracellular fluid flow in rapidly moving cells
Kinneret Keren, Patricia T. Yam, Anika Kinkhabwala, Alex Mogilner & Julie A. Theriot
Nature Cell Biology 11, 1219 - 1224 (2009) Published online: 20 September 2009
MathModel: 'mogilner: JulyConc'
MathModel: 'mogilner: JulyPressure'

Affinity for phosphatidylinositol 4,5-bisphosphate determines muscarinic agonist sensitivity of Kv7 K+ channels
Ciria C. Hernandez, Bjorn Falkenburger, and Mark S. Shapiro
J. Gen. Physiol. 2009;134 437-448, Published online Oct 26 2009, 10.1085/jgp.200910313.
BioModel: 'bfalken :HernandexFalkenburgerShapiro2009'.

A Tridimensional Model of Proangiogenic Calcium Signals in Endothelial Cells
Luca Munaron
The Open Biology Journal, 2009, 2, 114-129 Publication Date: October 2009
BioModel: 'Annalisa03: Imunaron'.

Persistent cAMP-Signals Triggered by Internalized G-Protein-Coupled Receptors.
Calebiro D, Nikolaev VO, Gagliani MC, de Filippis T, Dees C, Tacchetti C, Persani L, Lohse MJ.
PLoS Biol. 2009 Aug;7(8):e1000172 Publication Date: Epub 2009 Aug 18
BioModel: 'davide.calebiro: Calebiro_Plos-Biol_2009'

An open model of actin dendritic nucleation.
Ditlev, J.A., N.M. Vacanti, I.L. Novak, and L.M. Loew.
Biophys J. 2009 96:3529-3542.
BioModel: 'les: Actin Dendritic Nucleation_Detailed Branching'
BioModel: 'les: Actin Dendritic Nucleation'
MathModel: 'les: Actin Advection and Diffusion'
MathModel: 'les: Actin Advection and Diffusion 2D Cylindrical Transform'

A model of action potentials and fast Ca2+ dynamics in pancreatic beta-cells.
Fridlyand LE, Jacobson DA, Kuznetsov A, Philipson LH.
Biophys J. 2009 Apr 22;96(8):3126-39.
MathModel: 'Fridlyand: MouseSpike'

Energetic requirements for processive elongation of actin filaments by FH1FH2-formins
Aditya S. Paul and Thomas D. Pollard
J. Biol. Chem. 284:12533-40, 2009
BioModel: 'abiggiep: Formin FH1FH2-Profilin-Actin Elongation'

Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives
Wang J, Xu L, Wang E.
PMC Biophys. 2008 Dec 30;1(1):7.
MathModel: 'xuli: PMCBiophysics2008'

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations
Wang J, Xu L, Wang E.
Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12271-6. Epub 2008 Aug 21.
MathModel:'xuli: PNAS2008'.

Quantitative analysis of G-actin transport in motile cells
I.L. Novak, B.M. Slepchenko, A. Mogilner
Biophysical Journal, 95(4):1627-38, 2008
MathModel: 'ignovak: Analysis of G_actin transport in 2D fragment'
MathModel: 'ignovak: Analysis of G_actin transport in keratocyte'

Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity
A.B. Goryachev, and A.V. Pokhilkos
FEBS Letters, v. 582, p.1437, (2008)
BioModel: 'alex1: full01'.

Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines.
Brown, S., F. Morgan, J. Watras, and L.M. Loew.
Biophys J. 95:1795-1812,2008.
BioModel: 'brown: Purkinje Compartmental-adapted from Hernjak et al.'
BioModel: 'brown: Purkinje 1D'
BioModel: 'brown: Purkinje 3D-12 PF Stimuli'
BioModel: 'brown: Purkinje 3D-4 PF Stimuli'
BioModel: 'brown: Purkinje 3D Several Spines-12 PF Stimuli'
BioModel: 'brown: PIP2 Diffusion 1D and 3D'

Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.
Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R.
Cell. 2008 May 16;133(4):666-80.
BioModel: 'susana: neves_cell_2008'.

The tight junction protein complex undergoes rapid and continuous molecular remodeling at steady state.
Shen L, Weber CR, Turner JR.
J Cell Biol. 2008 May 19;181(4):683-95. Epub 2008 May 12.
BioModel: 'leshen: intracellular bleach FLIP'
BioModel: 'leshen: large area membrane bleach FRAP
BioModel: 'leshen: membrane bleach FLIP'
BioModel: 'leshen: small area membrane bleach FRAP'

Calcium Transport Mechanisms of PC12 Cells.
Duman, J.G., L. Chen, and B. Hille.
J. Gen. Physiol. 131:307-323, 2008.
BioModel: 'hillelab: DumanJGP2008Fig1A-4block'
BioModel: 'hillelab: DumanJGP2008Fig1A-control'
BioModel: 'hillelab: DumanJGP2008Fig9diff'
BioModel: 'hillelab: DumanJGP2008Fig9undiff'

Calcium signal transmission in chick sensory neurones is diffusion based.
Coatesworth W, Bolsover S.
Cell Calcium. 2008 Mar;43(3):236-49. Epub 2007 Jul 12
BioModel: 'coatesworth: 120504_SCAB100B'
BioModel: 'coatesworth: 140105_SCAB100B'
BioModel: 'coatesworth: 190105_SCAB100B'
BioModel: 'coatesworth: 190105_SCAB100P'
BioModel: 'coatesworth: 221204_SCAB100B'
BioModel: 'coatesworth: 240604_SCAB100B'

The role of the FH1 domain and profilin in formin-mediated actin-filament elongation and nucleation.
Paul, A., Pollard, T.
Current Biology, 2008 Jan 8;18(1):9-19.
BioModel: 'abiggiep: Formin-Profilin-Actin Polymerization'

Pathway of actin filament branch formation by Arp2/3 complex.
Beltzner CC, Pollard TD.
J Biol Chem 283: 7135-7144.2008.
Contact author regarding access to model.

Coordination of Chromosome Alignment and Mitotic Progression Chromosome-Based Ran Signal
Hoi Y. Li, Win Pin Ng, Wong Chi Hang, Pablo A. Iglesias and Yixian Zheng
Cell Cycle. 6(15):1886-1895, 2007.
BioModel: 'piglesias: Gorlich6'

Membrane-binding/modification model of signaling protein activation and analysis of its control by cell morphology.
Haugh, J.M.
Biophys J 92, L93-95, 2007.
BioModel: 'jmhaugh: Cell shape control'.

Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport.
Slepchenko, B.M., Semenova, I., Zaliapin, I., and Rodionov, V.
J. Cell Biol., jcb.200705146, 2007.
MathModel: 'boris: fish_melanophore_pigment_aggregation'
MathModel: 'boris: 'fish_melanophore_pigment_dispersion'

Regulation of cAMP dynamics by Ca2+ and G-protein coupled receptors in the pancreatic beta-cell: A computational approach.
Fridlyand, L.E., M.C. Harbeck, M.W. Roe, and L.H. Philipson
Am J Physiol Cell Physiol:293:C1924-C1933, 2007.
MathModel: 'Fridlyand: cAMP'.

Compartment-Specific Feedback Loop and Regulated Trafficking Can Result in Sustained Activation of Ras at the Golgi.
Narat J. Eungdamrong and Ravi Iyengar
Biophys. J. 2007; 92(3): p. 808-815
BioModel: 'eungdamr: eungdamrong and iyengar BiophysJ'

Rapid redistribution of synaptic PSD-95 in the neocortex in vivo.
Gray, N, Weimer R.M., Bureau, I. Svoboda, K
PLoS, v4, Iss 11, e370, 2006.
BioModel: 'rweimer: 10 spines'

Does diacylglycerol regulate KCNQ channels?
Suh, B.-C., and B. Hille.
Pflügers Archiv European Journal of Physiology. 453:293-301,2006.
BioModel: 'hillelab: SuhHilleEJP2006Fig1b'

Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations.
Kowalewski, J.M., P. Uhlen, H. Kitano, and H. Brismar.
Mathematical Biosciences. 204:232-249, 2006.

In vivo dynamics of Rac-membrane interactions.
Moissoqlu K, Slepchenko BM, Meller N, Horwitz AF, Schwartz, MAA
Mol Biol Cell. 2006 Jun; 17(6):2770-9. Epub 2006 Apr.5
MathModel: 'boris: Schwartz_2D_membrane_diffusion'
MathModel: 'boris: Schwartz_3D_FLIP'

Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes.
J.J. Saucerman, J. Zhang, J.C. Martin, L.X. Peng, A.E. Stenbit, R.Y. Tsien, and A.D. McCulloch..
Proceedings of the National Academy of Sciences. 103:12923-12928.
BioModel: 'jsaucer: AKARmyocyte'
BioModel: 'jsaucer: AKARmyocyte_2compart’
BioModel: 'jsaucer: AKARmyocyte_no_cAMP_buffering’

Analysis of a RanGTP-regulated gradient in mitotic somatic cells.
Kalab, P., A. Pralle, E.Y. Isacoff, R. Heald, and K. Weis.
Nature 2006. 440:(7084)697-701.
BioModel: 'Pralle: MitoticExtract_added_ImportinB'
BioModel: 'Pralle: MitoticExtract_added_RanQ69L'

Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts.
Schneider, I.C. and Haugh, J.M.
J.Cell B 171:883-892 (2005)
BioModel: 'jmhaugh: pdgf gradient sensing'

Modeling and Analysis of Calcium Signaling Events Leading to Long-Term Depression in Cerebellar Purkinje Cells.
N. Hernjak, B. M. Slepchenko, K. Fernald, C.C. Fink, D. Fortin, I.I. Moraru, J. Watras, and L.M. Loew.
Biophysical Journal Volume 89, Dec. 2005, pp. 3790-3806
BioModel: 'hernjak: purkinje_compartmental'
BioModel: 'hernjak: purkinje_2d'
Mathmodel: 'hernjak: purkinje_1d'

STAT module can function as a biphasic amplitude filter.
V. Mayya and L.M. Loew.
IEE Proceedings Systems Biology, March 2005, Volume 2, Issue 1, p. 43-52
BioModel: 'mayya: STATmodulePaper'

Phospholipase C in living cells: activation, inhibition, Ca2+ requirement, and regulation of M current.
Horowitz LF, Hirdes W, Suh B-C, Hilgemann DW, Mackie K, Hille B.
J. Gen. Physiol. 2005. 126(3):243-262.
BioModel: 'hillelab: Horowitz2005JGPprobes'

Rearrangement of the endoplasmic reticulum and calcium transient formation: The computational approach.
Pomorski P, Targos B, Baranska J.
Biochem Biophys Res Commun. 2005 Mar 25;328(4):1126-32.

Adenine nucleotide regulation in pancreatic beta cells: Modelling of ATP/ADP - Ca2+ interaction
Fridlyand L., Li Ma, Philipson LH.
Am J Physiol Endocrinol Metab. 289, E839-E848, 2005.
MathModel: 'Fridlyand: Chicago2'

Bio-switches: what makes them robust?
Slepchenko, B. M. and Terasaki, M.
Opin. Genet. Dev. 2004; 14/4: 428-434.
MathModel: 'boris: MPF_2D Tyson's Model, all speices mobile, slightly different inits in nucleus and outside' MathModel: 'boris: MPF_ODEs_simplified, no aggregates or buffers'
MathModel: 'boris: MPF_ODEs_simplified1, with aggregates'
MathModel: 'boris: MPF_ODEs_simplified2, with buffers'
BioModel: 'boris: Terasaki_MPF1'

A multi-enzyme model for pyrosequencing.
Ali Agah, Mariam Aghajan, Foad Mashayekhi, Sasan Amini, Ronald W. Davis, James D. Plummer, Mostafa Ronaghi, and Peter B. Griffin.
Nucleic Acids Research 2004 32(21):e166
BioModel:'Foad:pyro_fin'.

Two Complementary, Local Excitation, Global Inhibition Mechanisms Acting in Parallel Can Explain the Chemoattractant-Induced Regulation of PI(3,4,5)P₃ Response in Dictyostelium Cells.
Lan Ma, Chris Janetopoulos, Liu Yang, Peter N. Devreotes and Pablo A. Iglesias.
Biophys. J. 2004; 87(6): p. 3764-3774
BioModel: 'LiuYang: uniform_public'
BioModel: 'LiuYang: needle_public'

A Signal Transduction Pathway Model Prototype I: Application to Ca2+-Calmodulin Signaling and Myosin Light Chain Phosphorylation.
Lukas, TJ
Biophys. J. 2004;87 1417-1425
BioModel: 'tjlukas: Ca_Release_Coupled_MLC'

A Signal Transduction Pathway Model Prototype I: From Agonist to Cellular Endpoint.
Lukas, TJ
Biophys. J. 2004; 87 1406-1416
BioModel: 'tjlukas: Ca_Release_Coupled_MLC'

High Mobility of Vesicles Supports Continuous Exocytosis at a Ribbon Synapse.
Matthew Holt, Anne Cooke, Andreas Neef, and Leon Lagnado.
Current Biology, Vol. 14, 173-183, February 3, 2004
BioModel: 'Lagnado Lab: TIR_FRAP'

Regulation of KCNQ2/KCNQ3 Current by G Protein Cycling: the kinetics of receptor-mediated signaling by Gq.
Byung-Chang Suh, Lisa R. Horowitz, Wiebke Hirdes, Ken Mackie and Bertil Hille.
Journal of General Physiology, Volume 123, Number 6, June 2004 663-683
BioModel: 'hillelab: SuhJGP2004Fig11A
BioModel: 'hillelab: SuhJGP2004Fig12
BioModel: 'hillelab: SuhJGP2004Fig13B'
BioModel: 'hillelab: SuhJGP2004Fig15'

Cyclin aggregation and robustness of bio-switching.
Slepchenko, B. M. and Terasaki, M.
Mol. Biol. Cell 2003;14: 4695 - 4706.
MathModel: 'boris: MPF_2D Tyson's Model, all speices mobile, slightly different inits in nucleus and outside'
MathModel: 'boris: MPF_ODEs_simplified, no aggregates or buffers
MathModel: 'boris: MPF_ODEs_simplified1, with aggregates
MathModel: 'boris: MPF_ODEs_simplified2, with buffers
BioModel: 'boris: Terasaki_MPF1'

Kinetic analysis of receptor-activated phosphoinositide turnover
Chang Xu, James Watras and Leslie M. Loew
Journal of Cell Biology, vol. 161, no. 4, May 26, 2003
BioModel:'les: PIP2 Hydrolysis JCB Submission'.
Alternatively, the model is available here in an XML-compliant format that can be imported directly into you own workspace within the Virtual Cell. Download the XML file (Do not open this link, use your right mouse button and Save Target As.). Alternatively you may use the html version,(open the link and select all within the browser, copy and paste into a text editor and save as an xml file). Using either version, access the 'Import' dialog box under the 'File' menu item within the Virtual Cell.

Centrosome positioning in interphase cells.
Anton Burakov, Elena Nadezhdina, Boris Slepchenko, and Vladimir Rodionov
Journal of Cell Biology, 2003 Sep 15;162(6):963-9..
MathModel: 'boris: NocodazoleTubulin_3D'
Alternatively, the model is available here in an XML-compliant format that can be imported directly into you own workspace within the Virtual Cell. Download the XML file (Do not open this link, use your right mouse button and Save Target As.). Alternatively you may use the html version,(open the link and select all within the browser, copy and paste into a text editor and save as an xml file) Using either version, access the 'Import' dialog box under the 'File' menu item within the Virtual Cell.

Modeling Ca2+ flux in pancreaticB-cells: role of the plasma membrane and intracellular stores.
Leonid E. Fridlyand, Natalia Tamarina, and Louis H. Philipson
Am J Physiol Endocrinol Metab, Jul 2003;285: E138-154
MathModel: 'Fridlyand: Chicago'

Systems Analysis of Ran Transport
Alicia E. Smith, Boris M. Slepchenko, James C. Schaff, Leslie M. Loew, Ian G. Macara.
Science. 2002 Jan 18;295(5554):488-91
MathModel: 'boris: AliciaProblem1_5; basic nonspatial model used to obtain results published in the Science paper'
MathModel: 'boris: AliciaProblem1_5Fast; as in AliciaProblem1_5 but the reactions with mass action kinetics are treated as fast; this model was used to obtain initial conditions for spatial simulations'
MathModel: 'boris: AliciaSpatial_NewFast; the basic spatial model used in the Science paper'
Biomodel: 'les: Smith et al System Analysis of Ran Transport'. This is a later version and is corrected for the competiton between RanGDP and NTF2:RanGDP for the same site on RCC1.

Targeting of rough endoplasmic reticulum membrane proteins and ribosomes in invertebrate neurons.
Rolls MM, Hall DH, Victor M, Stelzer EH, Rapoport TA.
Mol Biol Cell. 2002 May;13(5):1778-91.PMID: 12006669 [PubMed - indexed for MEDLINE]
Please contact author for access to this model.

Distinct intracellular calcium transients in neurites and somata integrate neuronal signals.
Johenning FW, Zochowski M, Conway SJ, Holmes AB, Koulen P, Ehrlich BE.
J Neurosci 22: 5344-5353.2002.
Please contact author for access to this model.

Computational Cell Biology
Christopher P. Fall, Eric S. Marland, John M. Wagner, John J. Tyson.
The models from the text were implemented into the Virtual Cell by Johann Frederick Cutiongco.

The following BioModels are available from user: 'CompCell'

Chay-Keizer ER - Models pancreatic beta-cell bursting. Described in 5.4 and illustrated in Figure 5.21.

Hodgkin-Huxley - Models electrical behavior of the squid giant axon. Used to demonstrate interacting ion channels. Described in 2.5.

Keizer-Levine Open-Cell - Models calcium oscillations in bullfrog sympathetic ganglion neurons via RyR channel kinetics. Described in 5.2.3 and illustrated in Figure 5.8.

L-Type Calcium Channels - Models L-type calcium channel kinetics in the Aplysia neuron. Used to demonstrate the rapid equilibrium approximation. Described in 4.1 and illustrated in Figure 4.3.

Morris-Lecar Coincidence Detection - Demonstrates coincidence detection for excitatory inputs. Described in 6.4 and illustrated in Figure 6.9.

Morris-Lecar Gap Junction Coupled - Demonstrates electrical coupling and gap junctions. Described in 6.1.

Morris-Lecar Mutual Excitation - Demonstrates how fast excitatory synapses lead to synchrony and slow excitatory synapses lead to asynchrony in two identically electrically coupled cells. The only parameter modified is beta (=1000/s in Figure 6.6A and =100/s in Figure 6.6C). Described in 6.3.

Morris-Lecar Mutual Inhibition - Demonstrates how fast inhibition leads to antiphase behavior (for t<0.8, beta=1000/s) and slow inhibition leads to in-phase behavior (for t>0.8s, beta=100/s). SurfToVol_PlasmaMembrane 1 and SurfToVol_PlasmaMembrane 2 were changed to 1806 to cancel out KMOLE in the equations for s1 and s2 kinetics. Described in 6.3 and illustrated in Figure 6.7.

Morris-Lecar Mutual Type II - Models electrical behavior of barnacle muscle fiber. Used to demonstrate interacting ion channels. Described in 2.4.

Local Photorelease of Caged Thymosin beta4 in Locomoting Keratocytes Causes Cell Turning.
Roy P, Rajfur Z, Jones D, Marriott G, Loew L, Jacobson K.
J Cell Biol. 2001 May 28;153(5):1035-48
BioModel: 'partharoy: 7_12_00_model1'.

An image-based model of calcium waves in differentiated neuroblastoma cells.
Fink, C. C., B. Slepchenko, I. I. Moraru, J. Watras, J. Schaff, and L. M. Loew.
Biophys. J. 2000 79:163-183.2000.
There are five mathematical descriptions from the following two publications that were generated using the Virtual Cell software. Refer to the detailed model description that describes the following mathematical descriptions. NE_Full is best described in the model description while the other models have slight variations to the description. See Virtual Cell Calcium Dynamics for an introduction to the experiment and to view the experimental and simulation data.

MathModels: 'Boris'

'NE_DifferentGeom1' Basic model for simulations presented in Biophys. J., July 2000. It uses experimental ER and BkR distributions. Geometry from the image cellmnucnew2.tif

'NE_DifferentGeom2_1' Simulation presented in Biophys. J. July 2000 with bipolar geometry from the image bpolargeo2.tif

'NE_DifferentGeom3' Simulation presented in Biophys. J., July 2000 with geometry from the image 525am.tif

'NE_Full' Simulation provides the best fit to experimental data presented in J. Cell Biol., November 1999 and on WWW (Calcium Dynamics). It uses ER and BkR distributions that are slightly different from experimental. Geometry from the image mask2_smallnucl.tif

'NE_Full_best' Best fit to experimental data presented in Biophys. J., July 2000. Geometry from the image cellmnucnew2.tif

Morphological control of inositol-1,4,5-triphosphate-dependent signals.
Fink, C. C., B. Slepchenko, I. I. Moraru, J. Schaff, J. Watras, and L. M. Loew.
J. Cell Biol. 147:929-936, 1999.
There are five mathematical descriptions from the following two publications that were generated using the Virtual Cell software. Refer to the detailed model description that describes the following mathematical descriptions. NE_Full is best described in the model description while the other models have slight variations to the description.
See Virtual Cell Calcium Dynamics for an introduction to the experiment and to view the experimental and simulation data.

MathModels: 'Boris'

'NE_DifferentGeom1' Basic model for simulations presented in Biophys. J., July 2000. It uses experimental ER and BkR distributions. Geometry from the image cellmnucnew2.tif

'NE_DifferentGeom2_1' Simulation presented in Biophys. J. July 2000 with bipolar geometry from the image bpolargeo2.tif

'NE_DifferentGeom3' Simulation presented in Biophys. J., July 2000 with geometry from the image 525am.tif

'NE_Full' Simulation provides the best fit to experimental data presented in J. Cell Biol., November 1999 and on WWW (Calcium Dynamics). It uses ER and BkR distributions that are slightly different from experimental. Geometry from the image mask2_smallnucl.tif

'NE_Full_best' Best fit to experimental data presented in Biophys. J., July 2000. Geometry from the image cellmnucnew2.tif