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  1. Article ; Online: Optimal control with a strong harmonic trap.

    Blaber, Steven / Sivak, David A

    Physical review. E

    2022  Volume 106, Issue 2, Page(s) L022103

    Abstract: Quadratic trapping potentials are widely used to experimentally probe biopolymers and molecular machines and drive transitions in steered molecular-dynamics simulations. Approximating energy landscapes as locally quadratic, we design multidimensional ... ...

    Abstract Quadratic trapping potentials are widely used to experimentally probe biopolymers and molecular machines and drive transitions in steered molecular-dynamics simulations. Approximating energy landscapes as locally quadratic, we design multidimensional trapping protocols that minimize dissipation. The designed protocols are easily solvable and applicable to a wide range of systems. The approximation does not rely on either fast or slow limits and is valid for any duration provided the trapping potential is sufficiently strong. We demonstrate the utility of the designed protocols with a simple model of a periodically driven rotary motor. Our results elucidate principles of effective single-molecule manipulation and efficient nonequilibrium free-energy estimation.
    Language English
    Publishing date 2022-09-15
    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.106.L022103
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Skewed thermodynamic geometry and optimal free energy estimation.

    Blaber, Steven / Sivak, David A

    The Journal of chemical physics

    2020  Volume 153, Issue 24, Page(s) 244119

    Abstract: Free energy differences are a central quantity of interest in physics, chemistry, and biology. We develop design principles that improve the precision and accuracy of free energy estimators, which have potential applications to screening for targeted ... ...

    Abstract Free energy differences are a central quantity of interest in physics, chemistry, and biology. We develop design principles that improve the precision and accuracy of free energy estimators, which have potential applications to screening for targeted drug discovery. Specifically, by exploiting the connection between the work statistics of time-reversed protocol pairs, we develop near-equilibrium approximations for moments of the excess work and analyze the dominant contributions to the precision and accuracy of standard nonequilibrium free-energy estimators. Within linear response, minimum-dissipation protocols follow the geodesics of the Riemannian metric induced by the Stokes friction tensor. We find that the next-order contribution arises from the rank-3 supra-Stokes tensor that skews the geometric structure such that minimum-dissipation protocols follow the geodesics of a generalized cubic Finsler metric. Thus, near equilibrium, the supra-Stokes tensor determines the leading-order contribution to the bias of bidirectional free-energy estimators.
    Language English
    Publishing date 2020-12-28
    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 10.1063/5.0033405
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Optimal control of protein copy number.

    Blaber, Steven / Sivak, David A

    Physical review. E

    2020  Volume 101, Issue 2-1, Page(s) 22118

    Abstract: Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane affinity near the ... ...

    Abstract Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane affinity near the receptor for certain cytosolic proteins, effectively altering their chemical potential. We analyze the minimum-dissipation schedules for dynamically changing chemical potential to induce steady-state changes in protein copy-number distributions, and illustrate with analytic solutions for linear chemical reaction networks. Protocols that change chemical potential on biologically relevant timescales are experimentally accessible using optogenetic manipulations, and our framework provides nontrivial predictions about functional dynamical cell-cell interactions.
    MeSH term(s) Markov Chains ; Models, Biological ; Proteins/metabolism ; Signal Transduction ; Thermodynamics
    Chemical Substances Proteins
    Language English
    Publishing date 2020-03-13
    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.101.022118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Steps minimize dissipation in rapidly driven stochastic systems.

    Blaber, Steven / Louwerse, Miranda D / Sivak, David A

    Physical review. E

    2021  Volume 104, Issue 2, Page(s) L022101

    Abstract: Micro- and nanoscale systems driven by rapid changes in control parameters (control protocols) dissipate significant energy. In the fast-protocol limit, we find that protocols that minimize dissipation at fixed duration are universally given by a two- ... ...

    Abstract Micro- and nanoscale systems driven by rapid changes in control parameters (control protocols) dissipate significant energy. In the fast-protocol limit, we find that protocols that minimize dissipation at fixed duration are universally given by a two-step process, jumping to and from a point that balances jump size with fast relaxation. Jump protocols could be exploited by molecular machines or thermodynamic computing to improve energetic efficiency, and implemented in nonequilibrium free-energy estimation to improve accuracy.
    Language English
    Publishing date 2021-09-16
    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.104.L022101
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Optimal control of protein copy number

    Blaber, Steven / Sivak, David A.

    2018  

    Abstract: Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane affinity near the ... ...

    Abstract Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane affinity near the receptor for certain cytosolic proteins, effectively altering their chemical potential. We analyze the minimum-dissipation schedules for dynamically changing chemical potential to induce steady-state changes in protein copy-number distributions, and illustrate with analytic solutions for linear chemical reaction networks. Protocols that change chemical potential on biologically relevant timescales are experimentally accessible using optogenetic manipulations, and our framework provides non-trivial predictions about functional dynamical cell-cell interactions.

    Comment: 10 pages, 4 figures
    Keywords Quantitative Biology - Subcellular Processes ; Condensed Matter - Statistical Mechanics
    Publishing date 2018-10-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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