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Ali SY, Bauri P, Mondal D. Optimizing Work Extraction in the Presence of an Entropic Potential: An Entropic Stochastic Resonance. J Phys Chem B 2024; 128:3824-3832. [PMID: 38616737 DOI: 10.1021/acs.jpcb.3c08066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
We study the nontrivial thermodynamic responses of an overdamped Brownian system driven by an unbiased driving force when the particle is confined inside a bilobal irregular structure. The spatial irregularity of the confinement results in an effective entropic bistable potential along the direction of transport. We calculate the thermodynamic response functions in terms of the averaged work done and the absorbed heat over a cycle of driving. We find that the thermodynamic responses are influenced by the nonlinearity of the effective entropic potential, the frequency of the external periodic driving force, and the random thermal fluctuations in a nontrivial way. In the presence of an optimal amount of thermal noise and a favoring driving frequency, the process exhibits a resonance-like precedent in terms of both output work and absorbed heat. We explore the conditions to get best synchronized work extraction (or absorbed heat), which can be utilized as a potential quantifier of an entropic stochastic resonance phenomenon. Finally, we identify a hallmark of entropy dominance over an analogous energy-driven scenario in terms of output work.
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Affiliation(s)
- Syed Yunus Ali
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Prashanta Bauri
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Debasish Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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2
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Kalinay P, Slanina F. Dimensional reduction of a general advection-diffusion equation in 2D channels. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:244002. [PMID: 29708500 DOI: 10.1088/1361-648x/aac146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Diffusion of point-like particles in a two-dimensional channel of varying width is studied. The particles are driven by an arbitrary space dependent force. We construct a general recurrence procedure mapping the corresponding two-dimensional advection-diffusion equation onto the longitudinal coordinate x. Unlike the previous specific cases, the presented procedure enables us to find the one-dimensional description of the confined diffusion even for non-conservative (vortex) forces, e.g. caused by flowing solvent dragging the particles. We show that the result is again the generalized Fick-Jacobs equation. Despite of non existing scalar potential in the case of vortex forces, the effective one-dimensional scalar potential, as well as the corresponding quasi-equilibrium and the effective diffusion coefficient [Formula: see text] can be always found.
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Affiliation(s)
- Pavol Kalinay
- Institute of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 11 Bratislava, Slovakia
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3
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Chávez Y, Chacón-Acosta G, Dagdug L. Effects of curved midline and varying width on the description of the effective diffusivity of Brownian particles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:194001. [PMID: 29583127 DOI: 10.1088/1361-648x/aaba0d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Axial diffusion in channels and tubes of smoothly-varying geometry can be approximately described as one-dimensional diffusion in the entropy potential with a position-dependent effective diffusion coefficient, by means of the modified Fick-Jacobs equation. In this work, we derive analytical expressions for the position-dependent effective diffusivity for two-dimensional asymmetric varying-width channels, and for three-dimensional curved midline tubes, formed by straight walls. To this end, we use a recently developed theoretical framework using the Frenet-Serret moving frame as the coordinate system (2016 J. Chem. Phys. 145 074105). For narrow tubes and channels, an effective one-dimensional description reducing the diffusion equation to a Fick-Jacobs-like equation in general coordinates is used. From this last equation, one can calculate the effective diffusion coefficient applying Neumann boundary conditions.
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Affiliation(s)
- Yoshua Chávez
- Physics Department, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Mexico City, 09340, Mexico
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4
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Abstract
We derive a general closed expression for the local pressure exerted onto the corrugated walls of a channel confining a fluid medium. When the fluid medium is at equilibrium, the local pressure is a functional of the shape of the walls. It is shown that, due to the intrinsic nonlocal character of the interactions among the particles forming the fluid, the applicability of approximate schemes such as the concept of a surface of tension or morphometric thermodynamics is limited to wall curvatures that are small compared to the range of particle-particle interactions.
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Affiliation(s)
- Paolo Malgaretti
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany and Institute for Theoretical Physics IV, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Markus Bier
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany and Institute for Theoretical Physics IV, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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5
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Hydrodynamic and entropic effects on colloidal diffusion in corrugated channels. Proc Natl Acad Sci U S A 2017; 114:9564-9569. [PMID: 28831004 DOI: 10.1073/pnas.1707815114] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the absence of advection, confined diffusion characterizes transport in many natural and artificial devices, such as ionic channels, zeolites, and nanopores. While extensive theoretical and numerical studies on this subject have produced many important predictions, experimental verifications of the predictions are rare. Here, we experimentally measure colloidal diffusion times in microchannels with periodically varying width and contrast results with predictions from the Fick-Jacobs theory and Brownian dynamics simulation. While the theory and simulation correctly predict the entropic effect of the varying channel width, they fail to account for hydrodynamic effects, which include both an overall decrease and a spatial variation of diffusivity in channels. Neglecting such hydrodynamic effects, the theory and simulation underestimate the mean and standard deviation of first passage times by 40% in channels with a neck width twice the particle diameter. We further show that the validity of the Fick-Jacobs theory can be restored by reformulating it in terms of the experimentally measured diffusivity. Our work thus shows that hydrodynamic effects play a key role in diffusive transport through narrow channels and should be included in theoretical and numerical models.
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Kalinay P. Nonscaling calculation of the effective diffusion coefficient in periodic channels. J Chem Phys 2017; 146:034109. [DOI: 10.1063/1.4974090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pavol Kalinay
- Institute of Physics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84511 Bratislava, Slovakia
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7
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8
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Martens S. Note: From reaction-diffusion systems to confined Brownian motion. J Chem Phys 2016; 145:016101. [PMID: 27394126 DOI: 10.1063/1.4955492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S Martens
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
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9
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Kalinay P. Integral formula for the effective diffusion coefficient in two-dimensional channels. Phys Rev E 2016; 94:012102. [PMID: 27575072 DOI: 10.1103/physreve.94.012102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 06/06/2023]
Abstract
The effective one-dimensional description of diffusion in two-dimensional channels of varying cross section is revisited. The effective diffusion coefficient D(x), extending Fick-Jacobs equation, depending on the longitudinal coordinate x, is derived here without use of scaling of the transverse coordinates. The result of the presented method is an integral formula for D(x), calculating its value at x as an integral of contributions from the neighboring positions x^{'} depending on h(x^{'}), a function shaping the channel. Unlike the standard formulas based on the scaling, the new proposed formula also describes D(x) correctly near the cusps, or in wider channels.
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Affiliation(s)
- Pavol Kalinay
- Institute of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 84511, Bratislava, Slovakia
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10
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Wang X. Biased transport of Brownian particles in a weakly corrugated serpentine channel. J Chem Phys 2016; 144:044101. [DOI: 10.1063/1.4940314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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11
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Malgaretti P, Pagonabarraga I, Miguel Rubi J. Entropically induced asymmetric passage times of charged tracers across corrugated channels. J Chem Phys 2016; 144:034901. [DOI: 10.1063/1.4939799] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paolo Malgaretti
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany
- IV Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
- Department de Fisica Fonamental, Universitat de Barcelona, Barcelona, Spain
| | | | - J. Miguel Rubi
- Department de Fisica Fonamental, Universitat de Barcelona, Barcelona, Spain
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Marini Bettolo Marconi U, Malgaretti P, Pagonabarraga I. Tracer diffusion of hard-sphere binary mixtures under nano-confinement. J Chem Phys 2015; 143:184501. [DOI: 10.1063/1.4934994] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Umberto Marini Bettolo Marconi
- Scuola di Scienze e Tecnologie, Università di Camerino, Via Madonna delle Carceri, 62032 Camerino,Italy and INFN Perugia, Perugia, Italy
| | - Paolo Malgaretti
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
- Departament de Fisica Fonamental, Universitat de Barcelona, Av. Martí i Franques 1, Barcelona, Spain
| | - Ignacio Pagonabarraga
- Departament de Fisica Fonamental, Universitat de Barcelona, Av. Martí i Franques 1, Barcelona, Spain
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13
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Wang X, Drazer G. Transport of Brownian particles in a narrow, slowly varying serpentine channel. J Chem Phys 2015; 142:154114. [DOI: 10.1063/1.4917020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xinli Wang
- Division of Mathematics and Computer Science, University of South Carolina Upstate, Spartanburg, South Carolina 29303, USA
| | - German Drazer
- Department of Mechanical and Aerospace Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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14
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Martens S, Löber J, Engel H. Front propagation in channels with spatially modulated cross section. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022902. [PMID: 25768565 DOI: 10.1103/physreve.91.022902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 06/04/2023]
Abstract
Propagation of traveling fronts in a three-dimensional channel with spatially varying cross section is reduced to an equivalent one-dimensional reaction-diffusion-advection equation with boundary-induced advection term. Treating the advection term as a weak perturbation, an equation of motion for the front position is derived. We analyze channels whose cross sections vary periodically with L along the propagation direction of the front. Taking the Schlögl model as a representative example, we calculate analytically the nonlinear dependence of the front velocity on the ratio L/l where l denotes the intrinsic front width. In agreement with finite-element simulations of the three-dimensional reaction-diffusion dynamics, our theoretical results predicts boundary-induced propagation failure for a finite range of L/l values. In particular, the existence of the upper bound of L/l can be completely understood based on the linear eikonal equation. Last, we demonstrate that the front velocity is determined by the suppressed diffusivity of the reactants for L≪l.
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Affiliation(s)
- S Martens
- Institut für Theoretische Physik, Hardenbergstraße 36, EW 7-1, Technische Universität Berlin, 10623 Berlin, Germany
| | - J Löber
- Institut für Theoretische Physik, Hardenbergstraße 36, EW 7-1, Technische Universität Berlin, 10623 Berlin, Germany
| | - H Engel
- Institut für Theoretische Physik, Hardenbergstraße 36, EW 7-1, Technische Universität Berlin, 10623 Berlin, Germany
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15
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Kalinay P. Generalized method calculating the effective diffusion coefficient in periodic channels. J Chem Phys 2015; 142:014106. [DOI: 10.1063/1.4905079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Das M, Ray DS. Control of logic gates by dichotomous noise in energetic and entropic systems. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032122. [PMID: 24125228 DOI: 10.1103/physreve.88.032122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/07/2013] [Indexed: 06/02/2023]
Abstract
We consider the stochastic response of a nonlinear dynamical system towards a combination of input signals. The response can assume binary values if the state of the system is considered to be the output and the system can make transitions between two states separated by an energetic or entropic barrier. We show how the input-output correspondence can be controlled by an external exponentially correlated dichotomous noise optimizing the logical response which exhibits a maximum at an intermediate value of correlation time. This resonance manifests itself as a "logical" resonance correlation effect and sets the condition for performance of the stochastic system as a logic gate. The role of asymmetry of the dichotomous noise is examined and the results on numerical simulations are correlated with a two-state model using a master equation approach.
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Affiliation(s)
- Moupriya Das
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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17
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18
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Dagdug L, Berezhkovskii AM, Makhnovskii YA, Zitserman VY, Bezrukov SM. Force-dependent mobility and entropic rectification in tubes of periodically varying geometry. J Chem Phys 2012; 136:214110. [PMID: 22697533 DOI: 10.1063/1.4726193] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate transport of point Brownian particles in a tube formed by identical periodic compartments of varying diameter, focusing on the effects due to the compartment asymmetry. The paper contains two parts. First, we study the force-dependent mobility of the particle. The mobility is a symmetric non-monotonic function of the driving force, F, when the compartment is symmetric. Compartment asymmetry gives rise to an asymmetric force-dependent mobility, which remains non-monotonic when the compartment asymmetry is not too high. The F-dependence of the mobility becomes monotonic in tubes formed by highly asymmetric compartments. The transition of the F-dependence of the mobility from non-monotonic to monotonic behavior results in important consequences for the particle motion under the action of a time-periodic force with zero mean, which are discussed in the second part of the paper: In a tube formed by moderately asymmetric compartments, the particle under the action of such a force moves with an effective drift velocity that vanishes at small and large values of the force amplitude having a maximum in between. In a tube formed by highly asymmetric compartments, the effective drift velocity monotonically increases with the amplitude of the driving force and becomes unboundedly large as the amplitude tends to infinity.
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Affiliation(s)
- Leonardo Dagdug
- Departamento de Fisica, Universidad Autonoma Metropolitana-Iztapalapa, Mexico, 09340 Distrito Federal, Mexico
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Das M, Mondal D, Ray DS. Logic gates for entropic transport. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:041112. [PMID: 23214534 DOI: 10.1103/physreve.86.041112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Indexed: 06/01/2023]
Abstract
We consider a Brownian particle that is confined in a two-dimensional enclosure and driven by a combination of input signals. It has been shown that the logic gates can be formed by considering the state of the particle experiencing an entropic barrier as the output signal. For a consistent logical output, it is necessary to optimize the strength of the noise driving the particle for a given system size. The variation of the logical output behavior exhibits a turnover at an optimal value of system size parameter, implying a size resonance condition in entropic transport. The role of a transverse bias field used to tune the transport between the entropy dominated regime and the energy dominated regime is elucidated.
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Affiliation(s)
- Moupriya Das
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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20
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Das M, Mondal D, Ray DS. Shape fluctuation-induced dynamic hysteresis. J Chem Phys 2012; 136:114104. [DOI: 10.1063/1.3693333] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Martens S, Sokolov IM, Schimansky-Geier L. Communication: Impact of inertia on biased Brownian transport in confined geometries. J Chem Phys 2012; 136:111102. [DOI: 10.1063/1.3696002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Malgaretti P, Pagonabarraga I, Rubí JM. Cooperative rectification in confined Brownian ratchets. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:010105. [PMID: 22400501 DOI: 10.1103/physreve.85.010105] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 12/27/2011] [Indexed: 05/31/2023]
Abstract
We analyze the rectified motion of a Brownian particle in a confined environment. We show the emergence of strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by spatial confinement. Net particle transport may develop even in situations where separately the ratchet and the geometric restrictions do not give rise to particle motion. The combined rectification effects can lead to bidirectional transport depending on particle size, resulting in a different route for segregation. The reported mechanism can be used to control transport in mesostructures and nanodevices in which particles move in a reduced space.
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Affiliation(s)
- Paolo Malgaretti
- Department de Fisica Fonamental, Universitat de Barcelona, Barcelona, Spain.
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Martens S, Schmid G, Schimansky-Geier L, Hänggi P. Biased Brownian motion in extremely corrugated tubes. CHAOS (WOODBURY, N.Y.) 2011; 21:047518. [PMID: 22225392 DOI: 10.1063/1.3658621] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biased Brownian motion of point-size particles in a three-dimensional tube with varying cross-section is investigated. In the fashion of our recent work, Martens et al. [Phys. Rev. E 83, 051135 (2011)] we employ an asymptotic analysis to the stationary probability density in a geometric parameter of the tube geometry. We demonstrate that the leading order term is equivalent to the Fick-Jacobs approximation. Expression for the higher order corrections to the probability density is derived. Using this expansion orders, we obtain that in the diffusion dominated regime the average particle current equals the zeroth order Fick-Jacobs result corrected by a factor including the corrugation of the tube geometry. In particular, we demonstrate that this estimate is more accurate for extremely corrugated geometries compared with the common applied method using a spatially-dependent diffusion coefficient D(x, f) which substitutes the constant diffusion coefficient in the common Fick-Jacobs equation. The analytic findings are corroborated with the finite element calculation of a sinusoidal-shaped tube.
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Affiliation(s)
- S Martens
- Department of Physics, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany.
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24
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Mondal D, Ray DS. Asymmetric stochastic localization in geometry controlled kinetics. J Chem Phys 2011; 135:194111. [DOI: 10.1063/1.3658486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Debasish Mondal
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
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Zitserman VY, Berezhkovskii AM, Antipov AE, Makhnovskii YA. Communication: drift velocity of Brownian particle in a periodically tapered tube induced by a time-periodic force with zero mean: dependence on the force period. J Chem Phys 2011; 135:121102. [PMID: 21974505 PMCID: PMC3203121 DOI: 10.1063/1.3647873] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 09/16/2011] [Indexed: 11/14/2022] Open
Abstract
We study the drift of a Brownian particle in a periodically tapered tube, induced by a longitudinal time-periodic force of amplitude ∣F∣ that alternates in sign every half-period. The focus is on the velocity dependence on the force period, which is usually considered not tractable analytically. For large ∣F∣ we derive an analytical solution that gives the velocity as a function of the amplitude and the period of the force as well as the geometric parameters of the tube. The solution shows how the velocity decreases from its maximum value to zero as the force period decreases from infinity (adiabatic regime) to zero. Our analytical results are in excellent agreement with those obtained from 3D Brownian dynamics simulations.
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Affiliation(s)
- V Yu Zitserman
- Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya 13, Bldg. 2, Moscow 125412, Russia
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26
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Berezhkovskii AM, Dagdug L. Analytical treatment of biased diffusion in tubes with periodic dead ends. J Chem Phys 2011; 134:124109. [PMID: 21456647 PMCID: PMC3078163 DOI: 10.1063/1.3567187] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 02/25/2011] [Indexed: 11/14/2022] Open
Abstract
Effective mobility and diffusion coefficient of a particle in a tube with identical periodic dead ends characterize the motion on large time scale, when the particle displacement significantly exceeds the tube period. We derive formulas that show how these transport coefficients depend on the driving force and the geometric parameters of the system. Numerical tests show that values of the transport coefficients obtained from Brownian dynamics simulations are in excellent agreement with our theoretical predictions.
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Affiliation(s)
- Alexander M Berezhkovskii
- Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
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