Universität Stuttgart

Permanent URI for this communityhttps://elib.uni-stuttgart.de/handle/11682/1

Browse

Institute: search.filters.UBSInstitut.Institut für Theoretische Physik IIInstitute: search.filters.UBSInstitut.Fakultätsübergreifend / Sonstige EinrichtungPublication Type: search.filters.UBSTyp.ZeitschriftenartikelAuthor: search.filters.author.Seifert, Udo

Search Results

Now showing 1 - 4 of 4
  • Thumbnail Image
    ItemOpen Access
    Focus on stochastic thermodynamics
    (2016) Broeck, Christian Van den; Sasa, Shin-ichi; Seifert, Udo
    We introduce the thirty papers collected in this ‘focus on’ issue. The contributions explore conceptual issues within and around stochastic thermodynamics, use this framework for the theoretical modeling and experimental investigation of specific systems, and provide further perspectives on and for this active field.
  • Thumbnail Image
    ItemOpen Access
    Multiscale approaches to protein-mediated interactions between membranes : relating microscopic and macroscopic dynamics in radially growing adhesions
    (2015) Bihr, Timo; Seifert, Udo; Smith, Ana-Sunčana
    Macromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of deformable membranes, the diffusion of proteins and the molecular binding and unbinding. Because these stochastic processes couple over a multitude of time and length scales, theoretical modeling of membrane adhesion has been a major challenge. Here we present an effective Monte Carlo scheme within which the effects of the membrane are integrated into local rates for molecular recognition. The latter step in the Monte Carlo approach enables us to simulate the nucleation and growth of adhesion domains within a system of the size of a cell for tens of seconds without loss of accuracy, as shown by comparison to 106 times more expensive Langevin simulations. To perform this validation, the Langevin approach was augmented to simulate diffusion of proteins explicitly, together with reaction kinetics and membrane dynamics. We use the Monte Carlo scheme to gain deeper insight to the experimentally observed radial growth of micron sized adhesion domains, and connect the effective rate with which the domain is growing to the underlying microscopic events. We thus demonstrate that our technique yields detailed information about protein transport and complexation in membranes, which is a fundamental step toward understanding even more complex membrane interactions in the cellular context.
  • Thumbnail Image
    ItemOpen Access
    Thermodynamic cost of external control
    (2017) Barato, Andre C.; Seifert, Udo
    Artificial molecular machines are often driven by the periodic variation of an external parameter. This external control exerts work on the system of which a part can be extracted as output if the system runs against an applied load. Usually, the thermodynamic cost of the process that generates the external control is ignored. Here, we derive a refined second law for such small machines that include this cost, which is, for example, generated by free energy consumption of a chemical reaction that modifies the energy landscape for such a machine. In the limit of irreversible control, this refined second law becomes the standard one. Beyond this ideal limiting case, our analysis shows that due to a new entropic term unexpected regimes can occur: the control work can be smaller than the extracted work and the work required to generate the control can be smaller than this control work. Our general inequalities are illustrated by a paradigmatic three-state system.
  • Thumbnail Image
    ItemOpen Access
    Thermodynamics of micro- and nano-systems driven by periodic temperature variations
    (2015) Brandner, Kay; Saito, Keiji; Seifert, Udo