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Ma TC, Gicking AM, Feng Q, Hancock WO. Simulations suggest robust microtubule attachment of kinesin and dynein in antagonistic pairs. Biophys J 2023; 122:3299-3313. [PMID: 37464742 PMCID: PMC10465704 DOI: 10.1016/j.bpj.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 05/04/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Intracellular transport is propelled by kinesin and cytoplasmic dynein motors that carry membrane-bound vesicles and organelles bidirectionally along microtubule tracks. Much is known about these motors at the molecular scale, but many questions remain regarding how kinesin and dynein cooperate and compete during bidirectional cargo transport at the cellular level. The goal of the present study was to use a stochastic stepping model constructed by using published load-dependent properties of kinesin-1 and dynein-dynactin-BicD2 (DDB) to identify specific motor properties that determine the speed, directionality, and transport dynamics of a cargo carried by one kinesin and one dynein motor. Model performance was evaluated by comparing simulations to recently published experiments of kinesin-DDB pairs connected by complementary oligonucleotide linkers. Plotting the instantaneous velocity distributions from kinesin-DDB experiments revealed a single peak centered around zero velocity. In contrast, velocity distributions from simulations displayed a central peak around 100 nm/s, along with two side peaks corresponding to the unloaded kinesin and DDB velocities. We hypothesized that frequent motor detachment events and relatively slow motor reattachment rates resulted in periods in which only one motor is attached. To investigate this hypothesis, we varied specific model parameters and compared the resulting instantaneous velocity distributions, and we confirmed this systematic investigation using a machine-learning approach that minimized the residual sum of squares between the experimental and simulation velocity distributions. The experimental data were best recapitulated by a model in which the kinesin and dynein stall forces are matched, the motor detachment rates are independent of load, and the kinesin-1 reattachment rate is 50 s-1. These results provide new insights into motor dynamics during bidirectional transport and put forth hypotheses that can be tested by future experiments.
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Affiliation(s)
- Tzu-Chen Ma
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Allison M Gicking
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania; Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania.
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Albaugh A, Gingrich TR. Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics. Nat Commun 2022; 13:2204. [PMID: 35459863 PMCID: PMC9033874 DOI: 10.1038/s41467-022-29393-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 02/23/2022] [Indexed: 01/26/2023] Open
Abstract
Most computer simulations of molecular dynamics take place under equilibrium conditions-in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.
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Affiliation(s)
- Alex Albaugh
- grid.16753.360000 0001 2299 3507Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Todd R. Gingrich
- grid.16753.360000 0001 2299 3507Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
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3
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Rao R, Esposito M. Conservation laws and work fluctuation relations in chemical reaction networks. J Chem Phys 2018; 149:245101. [DOI: 10.1063/1.5042253] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Riccardo Rao
- Complex Systems and Statistical Mechanics, Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, G.D. Luxembourg
| | - Massimiliano Esposito
- Complex Systems and Statistical Mechanics, Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, G.D. Luxembourg
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4
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Chiuchiù D, Pigolotti S. Mapping of uncertainty relations between continuous and discrete time. Phys Rev E 2018; 97:032109. [PMID: 29776092 DOI: 10.1103/physreve.97.032109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 11/07/2022]
Abstract
Lower bounds on fluctuations of thermodynamic currents depend on the nature of time, discrete or continuous. To understand the physical reason, we compare current fluctuations in discrete-time Markov chains and continuous-time master equations. We prove that current fluctuations in the master equations are always more likely, due to random timings of transitions. This comparison leads to a mapping of the moments of a current between discrete and continuous time. We exploit this mapping to obtain uncertainty bounds. Our results reduce the quests for uncertainty bounds in discrete and continuous time to a single problem.
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Affiliation(s)
- Davide Chiuchiù
- Biological Complexity Unit, Okinawa Institute of Science and Technology and Graduate University, Onna, Okinawa 904-0495, Japan
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology and Graduate University, Onna, Okinawa 904-0495, Japan
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5
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Altaner B, Polettini M, Esposito M. Fluctuation-Dissipation Relations Far from Equilibrium. PHYSICAL REVIEW LETTERS 2016; 117:180601. [PMID: 27835007 DOI: 10.1103/physrevlett.117.180601] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Indexed: 06/06/2023]
Abstract
Near equilibrium, where all currents of a system vanish on average, the fluctuation-dissipation relation (FDR) connects a current's spontaneous fluctuations with its response to perturbations of the conjugate thermodynamic force. Out of equilibrium, fluctuation-response relations generally involve additional nondissipative contributions. Here, in the framework of stochastic thermodynamics, we show that an equilibriumlike FDR holds for internally equilibrated currents, if the perturbing conjugate force only affects the microscopic transitions that contribute to the current. We discuss the physical requirements for the validity of our result and apply it to nanosized electronic devices.
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Affiliation(s)
- Bernhard Altaner
- Complex Systems and Statistical Mechanics, Physics and Materials Science Research Unit, University of Luxembourg, Luxembourg 1511, Luxembourg
| | - Matteo Polettini
- Complex Systems and Statistical Mechanics, Physics and Materials Science Research Unit, University of Luxembourg, Luxembourg 1511, Luxembourg
| | - Massimiliano Esposito
- Complex Systems and Statistical Mechanics, Physics and Materials Science Research Unit, University of Luxembourg, Luxembourg 1511, Luxembourg
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6
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Gingrich TR, Horowitz JM, Perunov N, England JL. Dissipation Bounds All Steady-State Current Fluctuations. PHYSICAL REVIEW LETTERS 2016; 116:120601. [PMID: 27058064 DOI: 10.1103/physrevlett.116.120601] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 06/05/2023]
Abstract
Near equilibrium, small current fluctuations are described by a Gaussian distribution with a linear-response variance regulated by the dissipation. Here, we demonstrate that dissipation still plays a dominant role in structuring large fluctuations arbitrarily far from equilibrium. In particular, we prove a linear-response-like bound on the large deviation function for currents in Markov jump processes. We find that nonequilibrium current fluctuations are always more likely than what is expected from a linear-response analysis. As a small-fluctuations corollary, we derive a recently conjectured uncertainty bound on the variance of current fluctuations.
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Affiliation(s)
- Todd R Gingrich
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jordan M Horowitz
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Nikolay Perunov
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jeremy L England
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Technology Square, Cambridge, Massachusetts 02139, USA
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Bénichou O, Illien P, Oshanin G, Sarracino A, Voituriez R. Nonlinear response and emerging nonequilibrium microstructures for biased diffusion in confined crowded environments. Phys Rev E 2016; 93:032128. [PMID: 27078313 DOI: 10.1103/physreve.93.032128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 06/05/2023]
Abstract
We study analytically the dynamics and the microstructural changes of a host medium caused by a driven tracer particle moving in a confined, quiescent molecular crowding environment. Imitating typical settings of active microrheology experiments, we consider here a minimal model comprising a geometrically confined lattice system (a two-dimensional striplike or a three-dimensional capillary-like system) populated by two types of hard-core particles with stochastic dynamics (a tracer particle driven by a constant external force and bath particles moving completely at random). Resorting to a decoupling scheme, which permits us to go beyond the linear-response approximation (Stokes regime) for arbitrary densities of the lattice gas particles, we determine the force-velocity relation for the tracer particle and the stationary density profiles of the host medium particles around it. These results are validated a posteriori by extensive numerical simulations for a wide range of parameters. Our theoretical analysis reveals two striking features: (a) We show that, under certain conditions, the terminal velocity of the driven tracer particle is a nonmonotonic function of the force, so in some parameter range the differential mobility becomes negative, and (b) the biased particle drives the whole system into a nonequilibrium steady state with a stationary particle density profile past the tracer, which decays exponentially, in sharp contrast with the behavior observed for unbounded lattices, where an algebraic decay is known to take place.
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Affiliation(s)
- O Bénichou
- Laboratoire de Physique Théorique de la Matière Condensée, UPMC, CNRS UMR 7600, Sorbonne Universités, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - P Illien
- Laboratoire de Physique Théorique de la Matière Condensée, UPMC, CNRS UMR 7600, Sorbonne Universités, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, United Kingdom
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - G Oshanin
- Laboratoire de Physique Théorique de la Matière Condensée, UPMC, CNRS UMR 7600, Sorbonne Universités, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - A Sarracino
- Laboratoire de Physique Théorique de la Matière Condensée, UPMC, CNRS UMR 7600, Sorbonne Universités, 4 Place Jussieu, 75252 Paris Cedex 05, France
- CNR-ISC and Dipartimento di Fisica, Sapienza Università di Roma, p.le A. Moro 2, 00185 Roma, Italy
| | - R Voituriez
- Laboratoire de Physique Théorique de la Matière Condensée, UPMC, CNRS UMR 7600, Sorbonne Universités, 4 Place Jussieu, 75252 Paris Cedex 05, France
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Wachtel A, Vollmer J, Altaner B. Fluctuating currents in stochastic thermodynamics. I. Gauge invariance of asymptotic statistics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042132. [PMID: 26565193 DOI: 10.1103/physreve.92.042132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 06/05/2023]
Abstract
Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the edges of the graph representing the network of states. The asymptotic statistics of such currents are characterized by scaled cumulants. In the present work, we use the algebraic and topological structure of Markovian models to prove a gauge invariance of the scaled cumulant-generating function. Exploiting this invariance yields an efficient algorithm for practical calculations of asymptotic averages and correlation integrals. We discuss how our approach generalizes the Schnakenberg decomposition of the average entropy-production rate, and how it unifies previous work. The application of our results to concrete models is presented in an accompanying publication.
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Affiliation(s)
- Artur Wachtel
- Department of Dynamics of Complex Fluids (DCF), Max Planck Institute for Dynamics and Self-Organization (MPI DS), Am Fassberg 17, 37077 Göttingen, Germany and Institute for Nonlinear Dynamics, Faculty of Physics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Jürgen Vollmer
- Department of Dynamics of Complex Fluids (DCF), Max Planck Institute for Dynamics and Self-Organization (MPI DS), Am Fassberg 17, 37077 Göttingen, Germany and Institute for Nonlinear Dynamics, Faculty of Physics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Bernhard Altaner
- Department of Dynamics of Complex Fluids (DCF), Max Planck Institute for Dynamics and Self-Organization (MPI DS), Am Fassberg 17, 37077 Göttingen, Germany and Institute for Nonlinear Dynamics, Faculty of Physics, Georg-August University Göttingen, 37077 Göttingen, Germany
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