Are assumptions about the model type necessary in reaction-diffusion modeling? A FRAP application.


:At present, fluorescence recovery after photobleaching (FRAP) data are interpreted using various types of reaction-diffusion (RD) models: the model type is usually fixed first, and corresponding model parameters are inferred subsequently. In this article, we describe what we believe to be a novel approach for RD modeling without using any assumptions of model type or parameters. To the best of our knowledge, this is the first attempt to address both model-type and parameter uncertainties in inverting FRAP data. We start from the most general RD model, which accounts for a flexible number of molecular fractions, all mobile, with different diffusion coefficients. The maximal number of possible binding partners is identified and optimal parameter sets for these models are determined in a global search of the parameter-space using the Simulated Annealing strategy. The numerical performance of the described techniques was assessed using artificial and experimental FRAP data. Our general RD model outperformed the standard RD models used previously in modeling FRAP measurements and showed that intracellular molecular mobility can only be described adequately by allowing for multiple RD processes. Therefore, it is important to search not only for the optimal parameter set but also for the optimal model type.


Biophys J


Biophysical journal


Mai J,Trump S,Ali R,Schiltz RL,Hager G,Hanke T,Lehmann I,Attinger S




Has Abstract


2011-03-02 00:00:00














  • Stretch-activated cation channels in human fibroblasts.

    abstract::Nonconfluent fibroblasts are relatively depolarized when compared with confluent fibroblasts, and transient hyperpolarizations result from a range of external stimuli as well as internal cellular activities. This electrical activity ceases, along with growth and mitogenic activity, when the cells become confluent. A c...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Stockbridge LL,French AS

    更新日期:1988-07-01 00:00:00

  • Interaction of tea catechin (-)-epigallocatechin gallate with lipid bilayers.

    abstract::A major component of green tea extracts, catechin (-)-Epigallocatechin gallate (EGCg), has been reported to be biologically active and interacting with membranes. A recent study reported drastic effects of EGCg on giant unilamellar vesicles (GUVs). In particular, EGCg above 30 microM caused GUVs to burst. Here we inve...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Sun Y,Hung WC,Chen FY,Lee CC,Huang HW

    更新日期:2009-02-01 00:00:00

  • Events leading to the opening and closing of the exocytotic fusion pore have markedly different temperature dependencies. Kinetic analysis of single fusion events in patch-clamped mouse mast cells.

    abstract::The earliest event in exocytosis is the formation of a fusion pore, an aqueous channel that connects the lumen of a secretory granule with the extracellular space. We can observe the formation of individual fusion pores and their subsequent dilation or closure by measuring the changes in the admittance of patch-clampe...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Oberhauser AF,Monck JR,Fernandez JM

    更新日期:1992-03-01 00:00:00

  • Introducing titratable water to all-atom molecular dynamics at constant pH.

    abstract::Recent development of titratable coions has paved the way for realizing all-atom molecular dynamics at constant pH. To further improve physical realism, here we describe a technique in which proton titration of the solute is directly coupled to the interconversion between water and hydroxide or hydronium. We test the ...

    journal_title:Biophysical journal

    pub_type: 信件


    authors: Chen W,Wallace JA,Yue Z,Shen JK

    更新日期:2013-08-20 00:00:00

  • Photocurrents generated by bacteriorhodopsin adsorbed on nano-black lipid membranes.

    abstract::Purple membranes were adsorbed on freestanding lipid bilayers, termed nano-black lipid membranes (nano-BLMs), suspending the pores of porous alumina substrates with average pore diameters of 280 nm. Nano-BLMs were obtained by first coating the upper surface of the highly ordered porous alumina substrates with a thin g...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Horn C,Steinem C

    更新日期:2005-08-01 00:00:00

  • A simulation of human heart function.

    abstract::A simulation of the function of the human heart and heart muscle has been developed in the form of a digital computer code. For a given set of values for the input variables, realistic values of the cardiac output variables are predicted. A detailed discussion of the simulation and some results obtained from its appli...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Hanna WT

    更新日期:1973-07-01 00:00:00

  • Kinetics of intracellular ice formation in one-dimensional arrays of interacting biological cells.

    abstract::Although cell-cell interactions are known to significantly affect the kinetics of intracellular ice formation (IIF) during tissue freezing, this effect is not well understood. Progress in elucidating the mechanism and role of intercellular ice propagation in tissue freezing has been hampered in part by limitations in ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Irimia D,Karlsson JO

    更新日期:2005-01-01 00:00:00

  • The effect of thin filament activation on the attachment of weak binding cross-bridges: A two-dimensional x-ray diffraction study on single muscle fibers.

    abstract::To study possible structural changes in weak cross-bridge attachment to actin upon activation of the thin filament, two-dimensional (2D) x-ray diffraction patterns of skinned fibers from rabbit psoas muscle were recorded at low and high calcium concentration in the presence of saturating concentrations of MgATPgammaS,...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kraft T,Xu S,Brenner B,Yu LC

    更新日期:1999-03-01 00:00:00

  • Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding.

    abstract::Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b λx isotype was raised against a 12-residue conserved peptide from the...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Hardouin P,Velours C,Bou-Nader C,Assrir N,Laalami S,Putzer H,Durand D,Golinelli-Pimpaneau B

    更新日期:2018-12-04 00:00:00

  • Organelle transport along microtubules in Xenopus melanophores: evidence for cooperation between multiple motors.

    abstract::Xenopus melanophores have pigment organelles or melanosomes which, in response to hormones, disperse in the cytoplasm or aggregate in the perinuclear region. Melanosomes are transported by microtubule motors, kinesin-2 and cytoplasmic dynein, and an actin motor, myosin-V. We explored the regulation of melanosome trans...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Levi V,Serpinskaya AS,Gratton E,Gelfand V

    更新日期:2006-01-01 00:00:00

  • Octopus photoreceptor membranes. Surface charge density and pK of the Schiff base of the pigments.

    abstract::The chromophore of octopus rhodopsin is 11-cis retinal, linked via a protonated Schiff base to the protein backbone. Its stable photoproduct, metarhodopsin, has all-trans retinal as its chromphore. The Schiff base of acid metarhodopsin (lambda max = 510 nm) is protonated, whereas that of alkaline metarhodopsin (lambda...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Koutalos Y,Ebrey TG,Gilson HR,Honig B

    更新日期:1990-08-01 00:00:00

  • Effect of structural transition of the host assembly on dynamics of an ion channel peptide: a fluorescence approach.

    abstract::Structural transition can be induced in charged micelles by increasing the ionic strength of the medium. We have monitored the organization and dynamics of the functionally important tryptophan residues of gramicidin in spherical and rod-shaped sodium dodecyl sulfate micelles utilizing a combination of wavelength-sele...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Rawat SS,Kelkar DA,Chattopadhyay A

    更新日期:2005-11-01 00:00:00

  • Specific ion effects: why the properties of lysozyme in salt solutions follow a Hofmeister series.

    abstract::Protein solubility in aqueous solutions depends in a complicated and not well understood way on pH, salt type, and salt concentration. Why for instance does the use of two different monovalent salts, potassium thiocyanate and potassium chloride, produce such different results? One important and previously neglected so...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Boström M,Williams DR,Ninham BW

    更新日期:2003-08-01 00:00:00

  • The monovalent cation "leak" transport in human erythrocytes: an electroneutral exchange process.

    abstract::The mechanism of the "ground permeability" of the human erythrocyte membrane for K+ and Na+ was investigated with respect to a possible involvement of a previously unidentified specific transport pathway, because earlier studies showed that it cannot be explained on the basis of simple electrodiffusion. In particular,...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Richter S,Hamann J,Kummerow D,Bernhardt I

    更新日期:1997-08-01 00:00:00

  • Tropomyosins Regulate the Severing Activity of Gelsolin in Isoform-Dependent and Independent Manners.

    abstract::The actin cytoskeleton fulfills numerous key cellular functions, which are tightly regulated in activity, localization, and temporal patterning by actin binding proteins. Tropomyosins and gelsolin are two such filament-regulating proteins. Here, we investigate how the effects of tropomyosins are coupled to the binding...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kis-Bicskei N,Bécsi B,Erdődi F,Robinson RC,Bugyi B,Huber T,Nyitrai M,Talián GC

    更新日期:2018-02-27 00:00:00

  • Termination of cardiac Ca(2+) sparks: an investigative mathematical model of calcium-induced calcium release.

    abstract::A Ca(2+) spark arises when a cluster of sarcoplasmic reticulum (SR) channels (ryanodine receptors or RyRs) opens to release calcium in a locally regenerative manner. Normally triggered by Ca(2+) influx across the sarcolemmal or transverse tubule membrane neighboring the cluster, the Ca(2+) spark has been shown to be t...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Sobie EA,Dilly KW,dos Santos Cruz J,Lederer WJ,Jafri MS

    更新日期:2002-07-01 00:00:00

  • Order in phospholipid Langmuir-Blodgett monolayers determined by total internal reflection fluorescence.

    abstract::Orientational order parameters of two diphenylhexatriene (DPH)-based fluorescent probes, 2-(3-(diphenylhexatrienyl)propanoyl)-1-hexadecanoyl-sn-glycero-3-p hosphocholine (DPHpPC) and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH), in dipalmitoylphosphatidylcholine (DPPC) Langmuir-Blodgett monolayers...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Zhai X,Kleijn JM

    更新日期:1997-06-01 00:00:00

  • Reconstruction of a kinetic model of the chromatophore vesicles from Rhodobacter sphaeroides.

    abstract::We present a molecular model of a chromatophore vesicle from Rhodobacter sphaeroides. These vesicles are ideal benchmark systems for molecular and systemic simulations, because they have been well studied, they are small, and they are naturally separated from their cellular environment. To set up a photosynthetic chai...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Geyer T,Helms V

    更新日期:2006-08-01 00:00:00

  • In situ analysis of spatial relationships between proteins of the nuclear pore complex.

    abstract::Macromolecular transport between the nucleus and cytoplasm occurs through the nuclear pore complexes (NPCs). The NPC in the budding yeast Saccharomyces cerevisiae is a 60-MDa structure embedded in the nuclear envelope and composed of ~30 proteins, termed nucleoporins or nups. Here we present a large-scale analysis of ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Damelin M,Silver PA

    更新日期:2002-12-01 00:00:00

  • Properties of palmitoyl phosphatidylcholine, sphingomyelin, and dihydrosphingomyelin bilayer membranes as reported by different fluorescent reporter molecules.

    abstract::The properties of vesicle membranes prepared from 16:0-SM, 16:0-DHSM, or DPPC were characterized using steady-state and time-resolved fluorescence spectroscopy and different fluorescent reporter molecules. The acyl-chain region was probed using free and phospholipid-bound 1,6-diphenyl-1,3,5-hexatriene. 16:0-DHSM was f...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Nyholm T,Nylund M,Söderholm A,Slotte JP

    更新日期:2003-02-01 00:00:00

  • The structure of tip links and kinocilial links in avian sensory hair bundles.

    abstract::Recent studies have indicated that the tip links and kinocilial links of sensory hair bundles in the inner ear have similar properties and share a common epitope, and that cadherin 23 may also be a component of each link type. Transmission electron microscopy was therefore used to study and compare the fine structure ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Tsuprun V,Goodyear RJ,Richardson GP

    更新日期:2004-12-01 00:00:00

  • Dynamic compression augments interstitial transport of a glucose-like solute in articular cartilage.

    abstract::Solute transport through the extracellular matrix is essential for cellular activities in articular cartilage. Increased solute transport via fluid convection may be a mechanism by which dynamic compression stimulates chondrocyte metabolism. However, loading conditions that optimally augment transport likely vary for ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Evans RC,Quinn TM

    更新日期:2006-08-15 00:00:00

  • Dynamics of the HIV Gag Lattice Detected by Localization Correlation Analysis and Time-Lapse iPALM.

    abstract::Immature human immunodeficiency virus (HIV) virions have a lattice of Gag and Gag-Pol proteins anchored to the lumen of their envelope. Using electron microscopy, we demonstrate that HIV virus-like particles (VLPs) assembled by the viral protein Gag and tagged at its C-terminus with the fluorescent protein Dendra2 hav...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Saha I,Saffarian S

    更新日期:2020-08-04 00:00:00

  • Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: principles of ion pumping.

    abstract::We report the crystal structure of a bromide-bound form of the D85S mutant of bacteriorhodopsin, bR(D85S), a protein that uses light energy rather than ATP to pump halide ions across the cell membrane. Comparison of the structure of the halide-bound and halide-free states reveals that both displacements of individual ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Facciotti MT,Cheung VS,Nguyen D,Rouhani S,Glaeser RM

    更新日期:2003-07-01 00:00:00

  • Enantiomeric effects on excitation-contraction coupling in frog skeletal muscle by a chiral phenoxy carboxylic acid.

    abstract::Aromatic monocarboxylic acids are known to significantly potentiate the mechanical response of skeletal muscle fibers. In this study we investigated the effects of enantiomers of 2-(4-chlorophenoxy)propionic acid, chemically one of the simplest aromatic monocarboxylic acids with chiral properties, on mechanical thresh...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Heiny JA,Jong D,Bryant SH,Conte-Camerino D,Tortorella V

    更新日期:1990-01-01 00:00:00

  • Model of red blood cell rotation in the flow toward a cell sizing orifice. Application to volume distribution.

    abstract::The rotation of human red blood cells (RBC) as they flow in the shear field established by a Coulter type orifice is modeled. This model, based on hydrodynamics of ellipsoid rotation in laminar creeping flow, is used to calculate the probability of the cells entering the orifice with a specific orientation. The electr...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Breitmeyer MO,Lightfoot EN,Dennis WH

    更新日期:1971-02-01 00:00:00

  • Cell volume and plasma membrane osmotic water permeability in epithelial cell layers measured by interferometry.

    abstract::The development of strategies to measure plasma membrane osmotic water permeability (Pf) in epithelial cells has been motivated by the identification of a family of molecular water channels. A general approach utilizing interferometry to measure cell shape and volume was developed and applied to measure Pf in cell lay...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Farinas J,Verkman AS

    更新日期:1996-12-01 00:00:00

  • The location of photopigment molecules in the cross-section of frog retinal receptor disk membranes.

    abstract::The location of the photopigment molecules relative to the lipid hydrocarbon core of retinal receptor disk membranes was unknown. The photopigment molecules could occur entirely on the surface of the membrane, completely embedded in its hydrocarbon core, or at some intermediate location protruding into both the aqueou...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Blasie JK

    更新日期:1972-02-01 00:00:00

  • PIP2 Reshapes Membranes through Asymmetric Desorption.

    abstract::Phosphatidylinositol-4,5-bisphosphate (PIP2) is an important signaling lipid in eukaryotic cell plasma membranes, playing an essential role in diverse cellular processes. The headgroup of PIP2 is highly negatively charged, and this lipid displays a high critical micellar concentration compared to housekeeping phosphol...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Shukla S,Jin R,Robustelli J,Zimmerman ZE,Baumgart T

    更新日期:2019-09-03 00:00:00

  • A dynamical model of kinesin-microtubule motility assays.

    abstract::A two-dimensional stochastic model for the dynamics of microtubules in gliding-assay experiments is presented here, which includes the viscous drag acting on the moving fiber and the interaction with the kinesins. For this purpose, we model kinesin as a spring, and explicitly use parameter values to characterize the m...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Gibbons F,Chauwin JF,Despósito M,José JV

    更新日期:2001-06-01 00:00:00