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  1. Book ; Online: Ion channels in critical membranes

    Suma, Antonio / Sigg, Daniel / Gallagher, Seamus / Gonnella, Giuseppe / Carnevale, Vincenzo

    clustering, cooperativity, and memory effects

    2024  

    Abstract: Much progress has been made in elucidating the inner workings of voltage-gated ion channels, but less understood is the influence of lipid rafts on gating kinetics. Here we propose that state-dependent channel affinity for different lipid species ... ...

    Abstract Much progress has been made in elucidating the inner workings of voltage-gated ion channels, but less understood is the influence of lipid rafts on gating kinetics. Here we propose that state-dependent channel affinity for different lipid species provides a unified explanation for the experimentally observed behaviors of clustering, cooperativity, and hysteresis. We develop models of diffusing lipids and channels engaged in Ising-like interactions to investigate the collective behaviors driven by raft formation in critical membranes close to the demixing transition. The model channels demonstrate lipid-mediated long-range interactions, activation curve steepening, and long-term memory in ionic currents. These behaviors likely play a role in channel-mediated cellular signaling and suggest a universal mechanism for self-organization of biomolecular assemblies.

    Comment: 14 pages, 6 figures
    Keywords Condensed Matter - Soft Condensed Matter ; Physics - Biological Physics ; Quantitative Biology - Biomolecules
    Subject code 612
    Publishing date 2024-01-15
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Modeling ion channels: past, present, and future.

    Sigg, Daniel

    The Journal of general physiology

    2014  Volume 144, Issue 1, Page(s) 7–26

    Abstract: Ion channels are membrane-bound enzymes whose catalytic sites are ion-conducting pores that open and close (gate) in response to specific environmental stimuli. Ion channels are important contributors to cell signaling and homeostasis. Our current ... ...

    Abstract Ion channels are membrane-bound enzymes whose catalytic sites are ion-conducting pores that open and close (gate) in response to specific environmental stimuli. Ion channels are important contributors to cell signaling and homeostasis. Our current understanding of gating is the product of 60 plus years of voltage-clamp recording augmented by intervention in the form of environmental, chemical, and mutational perturbations. The need for good phenomenological models of gating has evolved in parallel with the sophistication of experimental technique. The goal of modeling is to develop realistic schemes that not only describe data, but also accurately reflect mechanisms of action. This review covers three areas that have contributed to the understanding of ion channels: traditional Eyring kinetic theory, molecular dynamics analysis, and statistical thermodynamics. Although the primary emphasis is on voltage-dependent channels, the methods discussed here are easily generalized to other stimuli and could be applied to any ion channel and indeed any macromolecule.
    MeSH term(s) Animals ; Forecasting ; Humans ; Ion Channel Gating/physiology ; Ion Channels/chemistry ; Ion Channels/physiology ; Models, Biological
    Chemical Substances Ion Channels
    Language English
    Publishing date 2014-06-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 3118-5
    ISSN 1540-7748 ; 0022-1295
    ISSN (online) 1540-7748
    ISSN 0022-1295
    DOI 10.1085/jgp.201311130
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A linkage analysis toolkit for studying allosteric networks in ion channels.

    Sigg, Daniel

    The Journal of general physiology

    2012  Volume 141, Issue 1, Page(s) 29–60

    Abstract: A thermodynamic approach to studying allosterically regulated ion channels such as the large-conductance voltage- and Ca(2+)-dependent (BK) channel is presented, drawing from principles originally introduced to describe linkage phenomena in hemoglobin. ... ...

    Abstract A thermodynamic approach to studying allosterically regulated ion channels such as the large-conductance voltage- and Ca(2+)-dependent (BK) channel is presented, drawing from principles originally introduced to describe linkage phenomena in hemoglobin. In this paper, linkage between a principal channel component and secondary elements is derived from a four-state thermodynamic cycle. One set of parallel legs in the cycle describes the "work function," or the free energy required to activate the principal component. The second are "lever operations" activating linked elements. The experimental embodiment of this linkage cycle is a plot of work function versus secondary force, whose asymptotes are a function of the parameters (displacements and interaction energies) of an allosteric network. Two essential work functions play a role in evaluating data from voltage-clamp experiments. The first is the conductance Hill energy W(H)([g]), which is a "local" work function for pore activation, and is defined as kT times the Hill transform of the conductance (G-V) curve. The second is the electrical capacitance energy W(C)([q]), representing "global" gating charge displacement, and is equal to the product of total gating charge per channel times the first moment (V(M)) of normalized capacitance (slope of Q-V curve). Plots of W(H)([g]) and W(C)([q]) versus voltage and Ca(2+) potential can be used to measure thermodynamic parameters in a model-independent fashion of the core gating constituents (pore, voltage-sensor, and Ca(2+)-binding domain) of BK channel. The method is easily generalized for use in studying other allosterically regulated ion channels. The feasibility of performing linkage analysis from patch-clamp data were explored by simulating gating and ionic currents of a 17-particle model BK channel in response to a slow voltage ramp, which yielded interaction energies deviating from their given values in the range of 1.3 to 7.2%.
    MeSH term(s) Allosteric Regulation/physiology ; Animals ; Hemoglobins/physiology ; Humans ; Ion Channel Gating/physiology ; Ion Channels/physiology ; Large-Conductance Calcium-Activated Potassium Channels/physiology ; Models, Biological ; Patch-Clamp Techniques ; Thermodynamics
    Chemical Substances Hemoglobins ; Ion Channels ; Large-Conductance Calcium-Activated Potassium Channels
    Language English
    Publishing date 2012-12-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3118-5
    ISSN 1540-7748 ; 0022-1295
    ISSN (online) 1540-7748
    ISSN 0022-1295
    DOI 10.1085/jgp.201210859
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.150: Show issues Location:
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  4. Article ; Online: Microcanonical coarse-graining of the kinetic Ising model.

    Sigg, Daniel / Voelz, Vincent A / Carnevale, Vincenzo

    The Journal of chemical physics

    2020  Volume 152, Issue 8, Page(s) 84104

    Abstract: We propose a scheme for coarse-graining the dynamics of the 2-D kinetic Ising model onto the microcanonical ensemble. At subcritical temperatures, 2-D and higher-dimensional Ising lattices possess two basins of attraction separated by a free energy ... ...

    Abstract We propose a scheme for coarse-graining the dynamics of the 2-D kinetic Ising model onto the microcanonical ensemble. At subcritical temperatures, 2-D and higher-dimensional Ising lattices possess two basins of attraction separated by a free energy barrier. Projecting onto the microcanonical ensemble has the advantage that the dependence of the crossing rate constant on environmental conditions can be obtained from a single Monte Carlo trajectory. Using various numerical methods, we computed the forward rate constants of coarse-grained representations of the Ising model and compared them with the true value obtained from brute force simulation. While coarse-graining preserves detailed balance, the computed rate constants for barrier heights between 5 kT and 9 kT were consistently 50% larger than the true value. Markovianity testing revealed loss of dynamical memory, which we propose accounts for coarse-graining error. Committor analysis did not support the alternative hypothesis that microcanonical projection is incompatible with an optimal reaction coordinate. The correct crossing rate constant was obtained by spectrally decomposing the diffusion coefficient near the free energy barrier and selecting the slowest (reactive) component. The spectral method also yielded the correct rate constant in the 3-D Ising lattice, where coarse-graining error was 6% and memory effects were diminished. We conclude that microcanonical coarse-graining supplemented by spectral analysis of short-term barrier fluctuations provides a comprehensive kinetic description of barrier crossing in a non-inertial continuous-time jump process.
    Language English
    Publishing date 2020-02-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/1.5139228
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    In stock of ZB MED Bonn / Germany

    Z 4' 49/16: Show issues

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  5. Article ; Online: Particle-based Ising model.

    Novinger, Quentin / Suma, Antonio / Sigg, Daniel / Gonnella, Giuseppe / Carnevale, Vincenzo

    Physical review. E

    2021  Volume 103, Issue 1-1, Page(s) 12125

    Abstract: We characterize equilibrium properties and relaxation dynamics of a two-dimensional lattice containing, at each site, two particles connected by a double-well potential (dumbbell). Dumbbells are oriented in the orthogonal direction with respect to the ... ...

    Abstract We characterize equilibrium properties and relaxation dynamics of a two-dimensional lattice containing, at each site, two particles connected by a double-well potential (dumbbell). Dumbbells are oriented in the orthogonal direction with respect to the lattice plane and interact with each other through a Lennard-Jones potential truncated at the nearest neighbor distance. We show that the system's equilibrium properties are accurately described by a two-dimensional Ising model with an appropriate coupling constant. Moreover, we characterize the coarsening kinetics by calculating the cluster size as a function of time and compare the results with Monte Carlo simulations based on Glauber or reactive dynamics rate constants.
    Language English
    Publishing date 2021-02-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.103.012125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book: Trendsport, ein Sport für die Schule?

    Sigg, Daniel

    Eine empirische Untersuchung mit didaktischen Überlegungen für eine Integration in den Schulsport

    2014  

    Author's details Daniel Sigg
    Size 75 Seiten: Illustrationen
    Edition [Nachdr.]
    Publisher Diplomica Verl.; Hamburg
    Document type Book
    HBZ-ID HT018209379
    ISBN 978-3-8428-9331-3 ; 3-8428-9331-0
    Database Central Library of Sport Science of the German Sport University Cologne

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  7. Book ; Thesis: Le Parkour - Kompetenzorientierter Sportunterricht mit der Möglichkeiten zur Förderung der Kreativität und Kooperation in der Schule

    Sigg, Daniel

    Theorie und Praxis

    (Staatsexamensarbeit)

    2013  

    Author's details Daniel Sigg
    Series title Staatsexamensarbeit
    Size 58 Seiten: Illustrationen
    Publisher Bachelor + Master Publishing; Hamburg
    Document type Book ; Thesis
    Thesis / German Habilitation thesis zugleich: Heidelberg, Staatliches Seminar für Didaktik und Lehrerbildung (Gymnasien und Sonderschulen), Staatsexamensarbeit, 2012
    HBZ-ID HT017657642
    ISBN 978-3-95549-304-2 ; 3-95549-304-0
    Database Central Library of Sport Science of the German Sport University Cologne

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  8. Article ; Online: Squeezed light for advanced gravitational wave detectors and beyond.

    Oelker, E / Barsotti, L / Dwyer, S / Sigg, D / Mavalvala, N

    Optics express

    2014  Volume 22, Issue 17, Page(s) 21106–21121

    Abstract: Recent experiments have demonstrated that squeezed vacuum states can be injected into gravitational wave detectors to improve their sensitivity at detection frequencies where they are quantum noise limited. Squeezed states could be employed in the next ... ...

    Abstract Recent experiments have demonstrated that squeezed vacuum states can be injected into gravitational wave detectors to improve their sensitivity at detection frequencies where they are quantum noise limited. Squeezed states could be employed in the next generation of more sensitive advanced detectors currently under construction, such as Advanced LIGO, to further push the limits of the observable gravitational wave Universe. To maximize the benefit from squeezing, environmentally induced disturbances such as back scattering and angular jitter need to be mitigated. We discuss the limitations of current squeezed vacuum sources in relation to the requirements imposed by future gravitational wave detectors, and show a design for squeezed light injection which overcomes these limitations.
    Language English
    Publishing date 2014-08-25
    Publishing country United States
    Document type Journal Article ; Research Support, American Recovery and Reinvestment Act ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1491859-6
    ISSN 1094-4087 ; 1094-4087
    ISSN (online) 1094-4087
    ISSN 1094-4087
    DOI 10.1364/OE.22.021106
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Thesis: Trendsport, ein Sport für die Schule?

    Sigg, Daniel

    Eine empirische Untersuchung

    2009  

    Author's details Daniel Sigg
    Size 78 Seiten: graphische Darstellungen
    Edition 1. Aufl.
    Publisher Grin-Verl.; München
    Document type Book ; Thesis
    Thesis / German Habilitation thesis zugleich: Tübingen, Universität, Examensarbeit, 2009
    HBZ-ID HT016210042
    ISBN 978-3-640-30232-1 ; 3-640-30232-X
    Database Central Library of Sport Science of the German Sport University Cologne

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  10. Article ; Online: Self-amplified lock of an ultra-narrow linewidth optical cavity.

    Izumi, Kiwamu / Sigg, Daniel / Barsotti, Lisa

    Optics letters

    2014  Volume 39, Issue 18, Page(s) 5285–5288

    Abstract: High finesse optical cavities are an essential tool in modern precision laser interferometry. The incident laser field is often controlled and stabilized with an active feedback system such that the field resonates in the cavity. The Pound-Drever-Hall ... ...

    Abstract High finesse optical cavities are an essential tool in modern precision laser interferometry. The incident laser field is often controlled and stabilized with an active feedback system such that the field resonates in the cavity. The Pound-Drever-Hall reflection locking technique is a convenient way to derive a suitable error signal. However, it only gives a strong signal within the cavity linewidth. This poses a problem for locking an ultra-narrow linewidth cavity. We present a novel technique for acquiring lock by utilizing an additional weak control signal, but with a much larger capture range. We numerically show that this technique can be applied to the laser frequency stabilization system used in the Laser Interferometric Gravitational-wave Observatory (LIGO), which has a linewidth of 0.8 Hz. This new technique will allow us to robustly and repeatedly lock the LIGO laser frequency to the common mode of the interferometer.
    Language English
    Publishing date 2014-09-15
    Publishing country United States
    Document type Journal Article
    ISSN 1539-4794
    ISSN (online) 1539-4794
    DOI 10.1364/OL.39.005285
    Database MEDical Literature Analysis and Retrieval System OnLINE

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