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Hu HW, Du L, Fan AL, Deng ZC, Grebogi C. Entropic stochastic resonance of finite-size particles in confined Brownian transport. Phys Rev E 2024; 109:054110. [PMID: 38907477 DOI: 10.1103/physreve.109.054110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/05/2024] [Indexed: 06/24/2024]
Abstract
We demonstrate the existence of entropic stochastic resonance (ESR) of passive Brownian particles with finite size in a double- or triple-circular confined cavity, and compare the similarities and differences of ESR in the double-circular cavity and triple-circular cavity. When the diffusion of Brownian particles is constrained to the double- or triple-circular cavity, the presence of irregular boundaries leads to entropic barriers. The interplay between the entropic barriers, a periodic input signal, the gravity of particles, and intrinsic thermal noise may give rise to a peak in the spectral amplification factor and therefore to the appearance of the ESR phenomenon. It is shown that ESR can occur in both a double-circular cavity and a triple-circular cavity, and by adjusting some parameters of the system, the response of the system can be optimized. The differences are that the spectral amplification factor in a triple-circular cavity is significantly larger than that in a double-circular cavity, and compared with the ESR in a double-circular cavity, the ESR effect in a triple-circular cavity occurs within a wider range of external force parameters. In addition, the strength of ESR also depends on the particle radius, and smaller particles can induce more obvious ESR, indicating that the size effect cannot be safely neglected. The ESR phenomenon usually occurs in small-scale systems where confinement and noise play an important role. Therefore, the mechanism that is found could be used to manipulate and control nanodevices and biomolecules.
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Affiliation(s)
- Hai-Wei Hu
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
- MIIT Key Laboratory of Dynamics and Control of Complex Systems, Northwestern Polytechnical University, Xi'an 710072, China
| | - Lin Du
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
- MIIT Key Laboratory of Dynamics and Control of Complex Systems, Northwestern Polytechnical University, Xi'an 710072, China
| | - Ai-Li Fan
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
- MIIT Key Laboratory of Dynamics and Control of Complex Systems, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zi-Chen Deng
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
- MIIT Key Laboratory of Dynamics and Control of Complex Systems, Northwestern Polytechnical University, Xi'an 710072, China
- School of Aeronautics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Celso Grebogi
- Institute for Complex Systems and Mathematical Biology, Kingdom College, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
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2
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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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3
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Ramirez P, Portillo S, Cervera J, Nasir S, Ali M, Ensinger W, Mafe S. Neuromorphic responses of nanofluidic memristors in symmetric and asymmetric ionic solutions. J Chem Phys 2024; 160:044701. [PMID: 38258920 DOI: 10.1063/5.0188940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
We show that ionic conduction properties of a multipore nanofluidic memristor can be controlled not only by the amplitude and frequency of an external driving signal but also by chemical gating based on the electrolyte concentration, presence of divalent and trivalent cations, and multi-ionic systems in single and mixed electrolytes. In addition, we describe the modulation of current rectification and hysteresis phenomena, together with neuromorphic conductance responses to voltage pulses, in symmetric and asymmetric external solutions. In our case, memristor conical pores act as nanofluidic diodes modulated by ionic solution characteristics due to the surface charge-regulated ionic transport. The above facts suggest potential sensing and actuating applications based on the conversion between ionic and electronic signals in bioelectrochemical hybrid circuits.
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Affiliation(s)
- Patricio Ramirez
- Dept. de Física Aplicada, Universitat Politècnica de València, E-46022 València, Spain
| | - Sergio Portillo
- Dept. de Física de la Terra i Termodinàmica, Universitat de València, E-46100 Burjassot, Spain
| | - Javier Cervera
- Dept. de Física de la Terra i Termodinàmica, Universitat de València, E-46100 Burjassot, Spain
| | - Saima Nasir
- Dept. of Material- and Geo-Sciences, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
- Materials Research Dept., GSI Helmholtzzentrum für Schwerionenforschung, D-64291 Darmstadt, Germany
| | - Mubarak Ali
- Dept. of Material- and Geo-Sciences, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
- Materials Research Dept., GSI Helmholtzzentrum für Schwerionenforschung, D-64291 Darmstadt, Germany
| | - Wolfgang Ensinger
- Materials Research Dept., GSI Helmholtzzentrum für Schwerionenforschung, D-64291 Darmstadt, Germany
| | - Salvador Mafe
- Dept. de Física de la Terra i Termodinàmica, Universitat de València, E-46100 Burjassot, Spain
- Allen Discovery Center at Tufts University, Medford, Massachusetts 02155, USA
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4
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Grebenkov DS. Diffusion-Controlled Reactions: An Overview. Molecules 2023; 28:7570. [PMID: 38005291 PMCID: PMC10674959 DOI: 10.3390/molecules28227570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
We review the milestones in the century-long development of the theory of diffusion-controlled reactions. Starting from the seminal work by von Smoluchowski, who recognized the importance of diffusion in chemical reactions, we discuss perfect and imperfect surface reactions, their microscopic origins, and the underlying mathematical framework. Single-molecule reaction schemes, anomalous bulk diffusions, reversible binding/unbinding kinetics, and many other extensions are presented. An alternative encounter-based approach to diffusion-controlled reactions is introduced, with emphasis on its advantages and potential applications. Some open problems and future perspectives are outlined.
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Affiliation(s)
- Denis S Grebenkov
- Laboratoire de Physique de la Matière Condensée, CNRS-Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
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5
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Antunes GC, Malgaretti P, Harting J. Turning catalytically active pores into active pumps. J Chem Phys 2023; 159:134903. [PMID: 37787144 DOI: 10.1063/5.0160414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023] Open
Abstract
We develop a semi-analytical model of self-diffusioosmotic transport in active pores, which includes advective transport and the inverse chemical reaction that consumes solute. In previous work [Antunes et al., Phys. Rev. Lett. 129, 188003 (2022)], we have demonstrated the existence of a spontaneous symmetry breaking in fore-aft symmetric pores that enables them to function as a micropump. We now show that this pumping transition is controlled by three timescales. Two timescales characterize advective and diffusive transport. The third timescale corresponds to how long a solute molecule resides in the pore before being consumed. Introducing asymmetry to the pore (either via the shape or the catalytic coating) reveals a second type of advection-enabled transition. In asymmetric pores, the flow rate exhibits discontinuous jumps and hysteresis loops upon tuning the parameters that control the asymmetry. This work demonstrates the interconnected roles of shape and catalytic patterning in the dynamics of active pores and shows how to design a pump for optimum performance.
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Affiliation(s)
- G C Antunes
- Helmholtz-Institut Erlangen-Nürnberg für Erneuerbare Energien (IEK-11), Forschungszentrum Jülich, Cauer Str. 1, 91058 Erlangen, Germany
| | - P Malgaretti
- Helmholtz-Institut Erlangen-Nürnberg für Erneuerbare Energien (IEK-11), Forschungszentrum Jülich, Cauer Str. 1, 91058 Erlangen, Germany
| | - J Harting
- Helmholtz-Institut Erlangen-Nürnberg für Erneuerbare Energien (IEK-11), Forschungszentrum Jülich, Cauer Str. 1, 91058 Erlangen, Germany
- Department Chemie- und Bioingenieurwesen und Department Physik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fürther Straße 248, 90429 Nürnberg, Germany
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6
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Gupta A, Burada PS. Separation of interacting active particles in an asymmetric channel. Phys Rev E 2023; 108:034605. [PMID: 37849171 DOI: 10.1103/physreve.108.034605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/25/2023] [Indexed: 10/19/2023]
Abstract
We study the diffusive behavior of interacting active particles (self-propelled) with mass m in an asymmetric channel. The particles are subjected to an external oscillatory force along the length of the channel. In this setup, particles may exhibit rectification. In the absence of interaction, the mean velocity 〈v〉 of the particles shows a maximum at moderate m values. It means that particles of moderate m have higher velocities than the others. However, by incorporating short-range interaction between the particles, 〈v〉 exhibits an additional peak at lower m values, indicating that particles of lower and moderate m can be separated simultaneously from the rest. Furthermore, by tuning the interaction strength, the self-propelled velocity, and the parameters of the oscillatory force, one can selectively separate the particles of lower m, moderate m, or both. Empirical relations for estimating the optimal mass as a function of these parameters are proposed. These findings are beneficial for separating the particles of selective m from the rest of the particles.
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Affiliation(s)
- Ankit Gupta
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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7
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Patitsas SN. Transport theory up to second-order scattering for reaction-diffusion-phonon systems with applications to active transport in catalysis, explosions, and biological membranes. Phys Rev E 2023; 108:024201. [PMID: 37723793 DOI: 10.1103/physreve.108.024201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/02/2023] [Indexed: 09/20/2023]
Abstract
A Boltzmann transport equation approach is developed for reaction-diffusion systems which incorporates phonon transport in addition to the traditional approach. Scattering processes up to second order are taken into account. Two forces emerge from this analysis when a spatial gradient exists, one force on reactants and products, the other force on phonons. The forces are equal and opposite and have the tendency for separation of the phonons away from the reactants and products. These forces are capable of creating the types of instabilities that can lead to the formation of Turing patterns. The existence of these forces allows for exergonic conversion where not all of the released energy from reactions and diffusion becomes heat. When applied to homogeneous catalysis, one finds that reactants and products are pushed toward regions of greater catalytic activity. In the realm of high-energy explosions, calculations show that reactants and products can be accelerated laterally to the direction of a TNT reaction front up to speeds near 1000 m/s. This acceleration is in opposition to diffusion and represents active transport. Calculations also show that active transport observed in biological systems such as bacteria, mitochondria, and chloroplasts may be explained by this second-order transport theory. Using reasonable values for key parameters, calculations show that up to one-third of the available chemical energy can be converted toward pumping protons uphill to a potential of 50 mV.
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Affiliation(s)
- S N Patitsas
- Department of Physics & Astronomy, University of Lethbridge, 4401 University Drive, Lethbridge AB, Canada, T1K 3M4
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8
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Locatelli E, Bianco V, Valeriani C, Malgaretti P. Nonmonotonous Translocation Time of Polymers across Pores. PHYSICAL REVIEW LETTERS 2023; 131:048101. [PMID: 37566871 DOI: 10.1103/physrevlett.131.048101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/06/2023] [Indexed: 08/13/2023]
Abstract
Polymers confined in corrugated channels, i.e., channels of varying amplitude, display multiple local maxima and minima of the diffusion coefficient upon increasing their degree of polymerization N. We propose a theoretical effective free energy for linear polymers based on a Fick-Jacobs approach. We validate the predictions against numerical data, obtaining quantitative agreement for the effective free energy, the diffusion coefficient, and the mean first passage time. Finally, we employ the effective free energy to compute the polymer lengths N_{min} at which the diffusion coefficient presents a minimum: we find a scaling expression that we rationalize with a blob model. Our results could be useful to design porous adsorbers, that separate polymers of different sizes without the action of an external flow.
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Affiliation(s)
- Emanuele Locatelli
- Dipartimento di Fisica e Astronomia, Università di Padova, via Marzolo 8, I-35131 Padova, Italy
- INFN, Sezione di Padova, via Marzolo 8, I-35131 Padova, Italy
| | - Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Chantal Valeriani
- Departamento de Estructura de la Materia, Física Termica y Electronica, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Paolo Malgaretti
- Helmholtz Institut Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Cauer Strasse 1, 91058, Erlangen, Germany
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9
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Slanina F, Kotrla M. Hydrodynamic approximations for driven dense colloidal mixtures in narrow pores. Phys Rev E 2023; 107:064606. [PMID: 37464715 DOI: 10.1103/physreve.107.064606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/09/2023] [Indexed: 07/20/2023]
Abstract
The system of driven dense colloid mixtures is studied in one-, two-, and three-dimensional geometries. We calculate the diffusion coefficients and mobilities for each particle type, including cross-terms, in a hydrodynamic limit, using a mean-field-type approximation. The set of nonlinear diffusion equations are then solved. In one dimension, analytical results are possible. We show that in mixtures, the "Brazil nut" phenomenon, or depletion of larger particles by force of smaller ones, appears quite generically. We calculate the ratchet current and quantify the capability of sorting particles according to their size. We also indicate that the "Brazil nut" effect lies behind the possibility of perfect separation, where large and big particles travel in strictly opposite direction.
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Affiliation(s)
- František Slanina
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Praha, Czech Republic
| | - Miroslav Kotrla
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Praha, Czech Republic
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10
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Rafeek R, Ali SY, Mondal D. Geometric Brownian information engine: Essentials for the best performance. Phys Rev E 2023; 107:044122. [PMID: 37198845 DOI: 10.1103/physreve.107.044122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/03/2023] [Indexed: 05/19/2023]
Abstract
We investigate a geometric Brownian information engine (GBIE) in the presence of an error-free feedback controller that transforms the information gathered on the state of Brownian particles entrapped in monolobal geometric confinement into extractable work. Outcomes of the information engine depend on the reference measurement distance x_{m}, the feedback site x_{f}, and the transverse force G. We determine the benchmarks for utilizing the available information in an output work and the optimum operating requisites for best achievable work. Transverse bias force (G) tunes the entropic contribution in the effective potential and hence the standard deviation (σ) of the equilibrium marginal probability distribution. We recognize that the amount of extractable work reaches a global maximum when x_{f}=2x_{m} with x_{m}∼0.6σ, irrespective of the extent of the entropic limitation. Because of the higher loss of information during the relaxation process, the best achievable work of a GBIE is lower in an entropic system. The feedback regulation also bears the unidirectional passage of particles. The average displacement increases with growing entropic control and is maximum when x_{m}∼0.81σ. Finally, we explore the efficacy of the information engine, a quantity that regulates the efficiency in utilizing the information acquired. With x_{f}=2x_{m}, the maximum efficacy reduces with increasing entropic control and shows a crossover from 2 to 11/9. We discover that the condition for the best efficacy depends only on the confinement lengthscale along the feedback direction. The broader marginal probability distribution accredits the increased average displacement in a cycle and the lower efficacy in an entropy-dominated system.
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Affiliation(s)
- Rafna Rafeek
- Department of Chemistry and Center for Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Syed Yunus Ali
- Department of Chemistry and Center for Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Debasish Mondal
- Department of Chemistry and Center for Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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11
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Modica KJ, Omar AK, Takatori SC. Boundary design regulates the diffusion of active matter in heterogeneous environments. SOFT MATTER 2023; 19:1890-1899. [PMID: 36790413 DOI: 10.1039/d2sm01421a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Physical boundaries play a key role in governing the overall transport properties of nearby self-propelled particles. In this work, we develop dispersion theories and conduct Brownian dynamics simulations to predict the coupling between surface accumulation and effective diffusivity of active particles in boundary-rich media. We focus on three models that are well-understood for passive systems: particle transport in (i) an array of fixed volume-excluding obstacles; (ii) a pore with spatially heterogeneous width; and (iii) a tortuous path with kinks and corners. While the impact of these entropic barriers on passive particle transport is well established, we find that these classical models of porous media flows break down due to the unique interplay between activity and the microstructure of the internal geometry. We study the activity-induced slowdown of effective diffusivity by formulating a Smoluchowski description of long-time self diffusivity which contains contributions from the density and fluctuation fields of the active particles. Particle-based and finite element simulations corroborate this perspective and reveal important nonequilibrium considerations of active transport.
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Affiliation(s)
- Kevin J Modica
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Ahmad K Omar
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sho C Takatori
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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12
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Malgaretti P, Harting J. Closed Formula for Transport across Constrictions. ENTROPY (BASEL, SWITZERLAND) 2023; 25:470. [PMID: 36981357 PMCID: PMC10047801 DOI: 10.3390/e25030470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
In the last decade, the Fick-Jacobs approximation has been exploited to capture transport across constrictions. Here, we review the derivation of the Fick-Jacobs equation with particular emphasis on its linear response regime. We show that, for fore-aft symmetric channels, the flux of noninteracting systems is fully captured by its linear response regime. For this case, we derive a very simple formula that captures the correct trends and can be exploited as a simple tool to design experiments or simulations. Lastly, we show that higher-order corrections in the flux may appear for nonsymmetric channels.
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Affiliation(s)
- Paolo Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy, Forschungszentrum Jülich, 90429 Erlangen, Germany
| | - Jens Harting
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy, Forschungszentrum Jülich, 90429 Erlangen, Germany
- Department of Chemical and Biological Engineering and Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 90429 Erlangen, Germany
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13
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M P A, Joseph T. Driven particle in a two-dimensional periodic substrate: Nonmonotonic dependence of drift velocity on temperature. Phys Rev E 2023; 107:034116. [PMID: 37073011 DOI: 10.1103/physreve.107.034116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 02/17/2023] [Indexed: 04/20/2023]
Abstract
Motion of a driven particle in a two-dimensional (2D) periodic potential of square symmetry is studied by means of Brownian dynamics simulations. The average drift velocity and long time diffusion coefficients are obtained as a function of driving force and temperature. For driving forces above the critical depinning force, a reduction of drift velocity is observed as temperature is increased. The drift velocity reaches a minimum for temperatures at which k_{B}T is of the order of the barrier height of the substrate potential and then increases and saturates to the value of drift velocity for the substrate free case. Depending on the driving force, the drop in drift velocity can be as large as 36% of its value at low temperatures. While this phenomenon is observed in 2D for different types of substrate potentials studied and for various drive directions, studies using the exact result show no such dip in drift velocity in one dimension (1D). As in the case of 1D, a peak is observed in the longitudinal diffusion coefficient as the driving force is varied at a fixed temperature. But unlike in 1D, the location of the peak is temperature dependent. Approximate analytical expressions for the average drift velocity and the longitudinal diffusion coefficient are formulated using the exact results in 1D by finding a temperature dependent effective 1D potential to model the motion in the presence of a 2D substrate. This approximate analysis is successful in qualitatively predicting the observations.
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Affiliation(s)
- Akhilesh M P
- Department of Physics, BITS-Pilani, K K Birla Goa Campus, Zuarinagar, Goa-403726, India
| | - Toby Joseph
- Department of Physics, BITS-Pilani, K K Birla Goa Campus, Zuarinagar, Goa-403726, India
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14
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Ledesma-Durán A, León-Velasco DA, Chacón-Acosta G, Juárez-Valencia LH. Surface diffusion in narrow channels on curved domains. Phys Rev E 2023; 107:034801. [PMID: 37072965 DOI: 10.1103/physreve.107.034801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/15/2023] [Indexed: 04/20/2023]
Abstract
We study the transport properties of diffusing particles restricted to confined regions on curved surfaces. We relate particle mobility to the curvature of the surface where they diffuse and the constraint due to confinement. Applying the Fick-Jacobs procedure to diffusion in curved manifolds shows that the local diffusion coefficient is related to average geometric quantities such as constriction and tortuosity. Macroscopic experiments can record such quantities through an average surface diffusion coefficient. We test the accuracy of our theoretical predictions of the effective diffusion coefficient through finite-element numerical solutions of the Laplace-Beltrami diffusion equation. We discuss how this work contributes to understanding the link between particle trajectories and the mean-square displacement.
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Affiliation(s)
- Aldo Ledesma-Durán
- Departamento de Matemáticas, Universidad Autónoma Metropolitana Iztapalapa, Iztapalapa, Vicentina, 09340 Ciudad de México, Mexico
| | - D Assaely León-Velasco
- Departamento de Matemáticas Aplicadas y Sistemas, Universidad Autónoma Metropolitana Cuajimalpa, 05348 Ciudad de México, Mexico
| | - Guillermo Chacón-Acosta
- Departamento de Matemáticas Aplicadas y Sistemas, Universidad Autónoma Metropolitana Cuajimalpa, 05348 Ciudad de México, Mexico
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - L Héctor Juárez-Valencia
- Departamento de Matemáticas, Universidad Autónoma Metropolitana Iztapalapa, Iztapalapa, Vicentina, 09340 Ciudad de México, Mexico
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15
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Magill M, Nagel AM, de Haan HW. Parallel computing for mobilities in periodic geometries. Phys Rev E 2022; 106:045304. [PMID: 36397582 DOI: 10.1103/physreve.106.045304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.
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Affiliation(s)
- Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Andrew M Nagel
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
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16
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Zhu Q, Zhou Y, Marchesoni F, Zhang HP. Colloidal Stochastic Resonance in Confined Geometries. PHYSICAL REVIEW LETTERS 2022; 129:098001. [PMID: 36083679 DOI: 10.1103/physrevlett.129.098001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/01/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
We investigate the dynamical properties of a colloidal particle in a double cavity. Without external driving, the particle hops between two free-energy minima with transition mean time depending on the system's entropic and energetic barriers. We then drive the particle with a periodic force. When the forcing period is set at twice the transition mean time, a statistical synchronization between particle motion and forcing phase marks the onset of a stochastic resonance mechanism. Comparisons between experimental results and predictions from the Fick-Jacobs theory and Brownian dynamics simulation reveal significant hydrodynamic effects, which change both resonant amplification and noise level. We further show that hydrodynamic effects can be incorporated into existing theory and simulation by using an experimentally measured particle diffusivity.
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Affiliation(s)
- Qian Zhu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Zhou
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fabio Marchesoni
- Center for Phononics and Thermal Energy Science, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- Dipartimento di Fisica, Universitá di Camerino, I-62032 Camerino, Italy
| | - H P Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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17
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Alexandre A, Mangeat M, Guérin T, Dean DS. How Stickiness Can Speed Up Diffusion in Confined Systems. PHYSICAL REVIEW LETTERS 2022; 128:210601. [PMID: 35687439 DOI: 10.1103/physrevlett.128.210601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
The paradigmatic model for heterogeneous media used in diffusion studies is built from reflecting obstacles and surfaces. It is well known that the crowding effect produced by these reflecting surfaces slows the dispersion of Brownian tracers. Here, using a general adsorption desorption model with surface diffusion, we show analytically that making surfaces or obstacles attractive can accelerate dispersion. In particular, we show that this enhancement of diffusion can exist even when the surface diffusion constant is smaller than that in the bulk. Even more remarkably, this enhancement effect occurs when the effective diffusion constant, when restricted to surfaces only, is lower than the effective diffusivity with purely reflecting boundaries. We give analytical formulas for this intriguing effect in periodic arrays of spheres as well as undulating microchannels. Our results are confirmed by numerical calculations and Monte Carlo simulations.
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Affiliation(s)
- A Alexandre
- Laboratoire Ondes et matière d'Aquitaine, CNRS/University of Bordeaux, F-33400 Talence, France
| | - M Mangeat
- Center for Biophysics and Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
| | - T Guérin
- Laboratoire Ondes et matière d'Aquitaine, CNRS/University of Bordeaux, F-33400 Talence, France
| | - D S Dean
- Laboratoire Ondes et matière d'Aquitaine, CNRS/University of Bordeaux, F-33400 Talence, France
- Team MONC, INRIA Bordeaux Sud Ouest, CNRS UMR 5251, Bordeaux INP, University Bordeaux, F-33400 Talence, France
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18
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Gray TH, Castelnovo C, Yong EH. Enhanced diffusion in soft-walled channels with a periodically varying curvature. Phys Rev E 2022; 105:054141. [PMID: 35706207 DOI: 10.1103/physreve.105.054141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
The motion of particles along channels of finite width is known to be hindered by either the presence of energy barriers along the channel direction or by variations in the width of the channel in the transverse direction (rugged channel). Remarkably, when both features are present, they can interact to produce a counterintuitive result: adding energy barriers to a rugged channel can enhance the rate of diffusion along it. This is the result of competing energetic and entropic effects. Under the approximation of particles instantaneously in equilibrium in the transverse direction, one can tailor the energy barriers to the ruggedness to recover free diffusion. However, such fine-tuning and potentially restrictive approximations are not necessary to observe an enhanced rate of diffusion as we demonstrate by adding a range of (non-fine-tuned) energy barriers to a channel of sinusoidally varying curvature. Furthermore, this was observed to hold for systems with a finite characteristic timescale for motion in the transverse direction, thus, suggesting that the phenomenon lends itself to be exploited for practical applications.
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Affiliation(s)
- Thomas H Gray
- T.C.M. Group, Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Claudio Castelnovo
- T.C.M. Group, Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ee Hou Yong
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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19
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Chen H, Huang F. First passage of a diffusing particle under stochastic resetting in bounded domains with spherical symmetry. Phys Rev E 2022; 105:034109. [PMID: 35428076 DOI: 10.1103/physreve.105.034109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
We investigate the first passage properties of a Brownian particle diffusing freely inside a d-dimensional sphere with absorbing spherical surface subject to stochastic resetting. We derive the mean time to absorption (MTA) as functions of resetting rate γ and initial distance r of the particle to the center of the sphere. We find that when r>r_{c} there exists a nonzero optimal resetting rate γ_{opt} at which the MTA is a minimum, where r_{c}=sqrt[d/(d+4)]R and R is the radius of the sphere. As r increases, γ_{opt} exhibits a continuous transition from zero to nonzero at r=r_{c}. Furthermore, we consider that the particle lies between two two-dimensional or three-dimensional concentric spheres with absorbing boundaries, and obtain the domain in which resetting expedites the MTA, which is (R_{1},r_{c_{1}})∪(r_{c_{2}},R_{2}), with R_{1} and R_{2} being the radii of inner and outer spheres, respectively. Interestingly, when R_{1}/R_{2} is less than a critical value, γ_{opt} exhibits a discontinuous transition at r=r_{c_{1}}; otherwise, such a transition is continuous. However, at r=r_{c_{2}} the transition is always continuous.
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Affiliation(s)
- Hanshuang Chen
- School of Physics and Optoelectronics Engineering, Anhui University, Hefei 230601, China
| | - Feng Huang
- Key Laboratory of Advanced Electronic Materials and Devices & School of Mathematics and Physics, Anhui Jianzhu University, Hefei 230601, China
- Key Laboratory of Architectural Acoustic Environment of Anhui Higher Education Institutes, Hefei 230601, China
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20
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Ali SY, Rafeek R, Mondal D. Geometric Brownian information engine: Upper bound of the achievable work under feedback control. J Chem Phys 2022; 156:014902. [PMID: 34998347 DOI: 10.1063/5.0069582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We design a geometric Brownian information engine by considering overdamped Brownian particles inside a two-dimensional monolobal confinement with irregular width along the transport direction. Under such detention, particles experience an effective entropic potential which has a logarithmic form. We employ a feedback control protocol as an outcome of error-free position measurement. The protocol comprises three stages: measurement, feedback, and relaxation. We reposition the center of the confinement to the measurement distance (xp) instantaneously when the position of the trapped particle crosses xp for the first time. Then, the particle is allowed for thermal relaxation. We calculate the extractable work, total information, and unavailable information associated with the feedback control using this equilibrium probability distribution function. We find the exact analytical value of the upper bound of extractable work as (53-2ln2)kBT. We introduce a constant force G downward to the transverse coordinate (y). A change in G alters the effective potential of the system and tunes the relative dominance of entropic and energetic contributions in it. The upper bound of the achievable work shows a crossover from (53-2ln2)kBT to 12kBT when the system changes from an entropy-dominated regime to an energy-dominated one. Compared to an energetic analog, the loss of information during the relaxation process is higher in the entropy-dominated region, which accredits the less value in achievable work. Theoretical predictions are in good agreement with the Langevin dynamics simulation studies.
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Affiliation(s)
- Syed Yunus Ali
- Department of Chemistry and Center for Molecular and Optical Sciences and Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Rafna Rafeek
- Department of Chemistry and Center for Molecular and Optical Sciences and Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Debasish Mondal
- Department of Chemistry and Center for Molecular and Optical Sciences and Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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21
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Arango-Restrepo A, Rubi JM, Kjelstrup S, Angelsen BAJ, Davies CDL. Enhancing carrier flux for efficient drug delivery in cancer tissues. Biophys J 2021; 120:5255-5266. [PMID: 34757075 DOI: 10.1016/j.bpj.2021.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/27/2021] [Accepted: 10/26/2021] [Indexed: 01/24/2023] Open
Abstract
Ultrasound focused toward tumors in the presence of circulating microbubbles improves the delivery of drug-loaded nanoparticles and therapeutic outcomes; however, the efficacy varies among the different properties and conditions of the tumors. Therefore, there is a need to optimize the ultrasound parameters and determine the properties of the tumor tissue important for the successful delivery of nanoparticles. Here, we propose a mesoscopic model considering the presence of entropic forces to explain the ultrasound-enhanced transport of nanoparticles across the capillary wall and through the interstitium of tumors. The nanoparticles move through channels of variable shape whose irregularities can be assimilated to barriers of entropic nature that the nanoparticles must overcome to reach their targets. The model assumes that focused ultrasound and circulating microbubbles cause the capillary wall to oscillate, thereby changing the width of transcapillary and interstitial channels. Our analysis provides values for the penetration distances of nanoparticles into the interstitium that are in agreement with experimental results. We found that the penetration increased significantly with increasing acoustic intensity as well as tissue elasticity, which means softer and more deformable tissue (Young modulus lower than 50 kPa), whereas porosity of the tissue and pulse repetition frequency of the ultrasound had less impact on the penetration length. We also considered that nanoparticles can be absorbed into cells and to extracellular matrix constituents, finding that the penetration length is increased when there is a low absorbance coefficient of the nanoparticles compared with their diffusion coefficient (close to 0.2). The model can be used to predict which tumor types, in terms of elasticity, will successfully deliver nanoparticles into the interstitium. It can also be used to predict the penetration distance into the interstitium of nanoparticles with various sizes and the ultrasound intensity needed for the efficient distribution of the nanoparticles.
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Affiliation(s)
- Andrés Arango-Restrepo
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain; Institut de Nanociencia i Nanotecnologia, Universitat de Barcelona, Barcelona, Spain.
| | - J Miguel Rubi
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain; Institut de Nanociencia i Nanotecnologia, Universitat de Barcelona, Barcelona, Spain; PoreLab, Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Signe Kjelstrup
- PoreLab, Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bjørn Atle J Angelsen
- PoreLab, Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
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22
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Khatri N, Burada PS. Mass separation in an asymmetric channel. Phys Rev E 2021; 104:044109. [PMID: 34781428 DOI: 10.1103/physreve.104.044109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/23/2021] [Indexed: 11/07/2022]
Abstract
We present a mechanism to sort out particles of different masses in an asymmetric channel, where the entropic barriers arise naturally and control the diffusion of these particles. When particles are subjected to an oscillatory force, with the scaled amplitude a and frequency ω, the mean particle velocity exhibits a bell-shaped behavior as a function of the particle mass, indicating that particles with an optimal mass m_{op} drift faster than other particles. By tuning a and ω, we get an empirical relation to estimate m_{op}∼(aω^{2})^{-0.4}. An additional static bias, applied in the opposite direction of the rectified velocity, would push the particles of lighter mass to move in its direction while the others drift opposite to it. This study is useful to design lab-on-a-chip devices for separating particles of different masses.
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Affiliation(s)
- Narender Khatri
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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23
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Mei R, Xu Y, Li Y, Kurths J. Characterizing stochastic resonance in a triple cavity. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200230. [PMID: 33840209 DOI: 10.1098/rsta.2020.0230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 05/22/2023]
Abstract
Many biological systems possess confined structures, which produce novel influences on the dynamics. Here, stochastic resonance (SR) in a triple cavity that consists of three units and is subjected to noise, periodic force and vertical constance force is studied, by calculating the spectral amplification η numerically. Meanwhile, SR in the given triple cavity and differences from other structures are explored. First, it is found that the cavity parameters can eliminate or regulate the maximum of η and the noise intensity that induces this maximum. Second, compared to a double cavity with similar maximum/minimum widths and distances between two maximum widths as the triple cavity, η in the triple one shows a larger maximum. Next, the conversion of the natural boundary in the pure potential to the reflection boundary in the triple cavity will create the necessity of a vertical force to induce SR and lead to a decrease in the maximum of η. In addition, η monotonically decreases with the increase of the vertical force and frequency of the periodic force, while it presents several trends when increasing the periodic force's amplitude for different noise intensities. Finally, our studies are extended to the impact of fractional Gaussian noise excitations. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 2)'.
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Affiliation(s)
- Ruoxing Mei
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, People's Republic of China
- Potsdam Institute for Climate Impact Research, Potsdam 14412, Germany
| | - Yong Xu
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, People's Republic of China
- MIIT Key Laboratory of Dynamics and Control of Complex Systems, Northwestern Polytechnical University, Xi'an 710072, People's Republic of China
| | - Yongge Li
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, People's Republic of China
| | - Jürgen Kurths
- Potsdam Institute for Climate Impact Research, Potsdam 14412, Germany
- Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow 119146, Russia
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24
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Du LC, Yue WH, Jiang JH, Yang LL, Ge MM. Entropic stochastic resonance induced by a transverse driving force. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200228. [PMID: 33840218 DOI: 10.1098/rsta.2020.0228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 05/22/2023]
Abstract
The phenomenon of entropic stochastic resonance (ESR) is investigated with the presence of a time-periodic force in the transverse direction. Simulation results manifest that the ESR can survive even if there is no static bias force in any direction, just if a transverse driving field is applied. In the weak noise region, the transverse driving force leads to a giant-suppression of the escape rate from one well to another, i.e. the entropic trapping. The increase in noise intensity will eliminate this suppression and induce the ESR phenomenon. An alternative quantity, called the mean free flying time, is also proposed to characterize the ESR as well as the conventional spectral power amplification. The ESR can be modulated conveniently by the transverse periodic force, which implies an alternative method for controlling the dynamics of small-scale systems. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 2)'.
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Affiliation(s)
- L C Du
- Department of Physics, Yunnan University, Kunming, 650091, People's Republic of China
| | - W H Yue
- Department of Physics, Yunnan University, Kunming, 650091, People's Republic of China
| | - J H Jiang
- Department of Physics, Yunnan University, Kunming, 650091, People's Republic of China
| | - L L Yang
- Department of Physics, Yunnan University, Kunming, 650091, People's Republic of China
| | - M M Ge
- Department of Physics, Yunnan University, Kunming, 650091, People's Republic of China
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25
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Singh AK, Burada PS, Roy A. Biomolecular response to hour-long ultralow field microwave radiation: An effective coarse-grained model simulation. Phys Rev E 2021; 103:042416. [PMID: 34005990 DOI: 10.1103/physreve.103.042416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/16/2021] [Indexed: 11/07/2022]
Abstract
Various electronic devices, which we commonly use, radiate microwaves. Such external perturbation influences the functionality of biomolecules. In an ultralow field, the cumulative response of a molecule is expected only over a time scale of hours. To study the structural dynamics of biomolecules over hours, we adopt a simple methodology for constructing the coarse-grained structure of the protein molecule and solve the Langevin equation under different working potentials. In this approach, each amino acid residue of a biomolecule is mapped onto a number of beads, a few for the backbone, and few for the side chain, depending on the complexity of its chemical structure. We choose the force field in such a way that the dynamics of the protein molecule in the presence of ultralow radiation field of microvolt/nm could be followed over the time frame of 2 h. We apply the model to describe a biomolecule, hen egg white lysozyme, and simulate its structural evolution under ultralow strength electromagnetic radiation. The simulation revealed the finer structural details, like the extent of exposure of bioactive residues and the state of the secondary structures of the molecule, further confirmed from spectroscopic measurements [details are available in Phys. Rev. E 97, 052416 (2018)10.1103/PhysRevE.97.052416 and briefly described here]. Though tested for a specific system, the model is quite general. We believe that it harnesses the potential in studying the structural dynamics of any biopolymer under external perturbation over an extended time scale.
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Affiliation(s)
- Anang Kumar Singh
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Anushree Roy
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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26
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Lin C, Ashwin P, Steinberg G. Modelling the motion of organelles in an elongated cell via the coordination of heterogeneous drift-diffusion and long-range transport. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:10. [PMID: 33683507 DOI: 10.1140/epje/s10189-020-00007-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Cellular distribution of organelles in living cells is achieved via a variety of transport mechanisms, including directed motion, mediated by molecular motors along microtubules (MTs), and diffusion which is predominantly heterogeneous in space. In this paper, we introduce a model for particle transport in elongated cells that couples poleward drift, long-range bidirectional transport and diffusion with spatial heterogeneity in a three-dimensional space. Using stochastic simulations and analysis of a related population model, we find parameter regions where the three-dimensional model can be reduced to a coupled one-dimensional model or even a one-dimensional scalar model. We explore the efficiency with which individual model components can overcome drift towards one of the cell poles to reach an approximately even distribution. In particular, we find that if lateral movement is well mixed, then increasing the binding ability of particles to MTs is an efficient way to overcome a poleward drift, whereas if lateral motion is not well mixed, then increasing the axial diffusivity away from MTs becomes an efficient way to overcome the poleward drift. Our three-dimensional model provides a new tool that will help to understand the mechanisms by which eukaryotic cells organize their organelles in an elongated cell, and in particular when the one-dimensional models are applicable.
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Affiliation(s)
- Congping Lin
- School of Mathematics and Statistics, Huazhong University of Science and Technology, Wuhan, China.
- Center for Mathematical Sciences, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Key Lab of Engineering Modeling and Scientific Computing, Huazhong University of Science and Technology, Wuhan, China.
| | - Peter Ashwin
- Department of Mathematics, University of Exeter, Exeter, UK
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27
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Malgaretti P, Harting J. Transport of neutral and charged nanorods across varying-section channels. SOFT MATTER 2021; 17:2062-2070. [PMID: 33475112 DOI: 10.1039/d0sm02045a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We study the dynamics of neutral and charged rods embedded in varying-section channels. By means of systematic approximations, we derive the dependence of the local diffusion coefficient on both the geometry and charge of the rods. This microscopic insight allows us to provide predictions for the permeability of varying-section channels to rods with diverse lengths, aspect ratios and charge. Our analysis shows that the dynamics of charged rods is sensitive to the geometry of the channel and that their transport can be controlled by tuning both the shape of the confining walls and the charge of the rod. Interestingly, we find that the channel permeability does not depend monotonically on the charge of the rod. This opens the possibility of a novel mechanism to separate charged rods.
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Affiliation(s)
- Paolo Malgaretti
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany and IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany and Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Fürther Straße 248, 90429 Nürnberg, Germany.
| | - Jens Harting
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Fürther Straße 248, 90429 Nürnberg, Germany. and Department of Chemical and Biological Engineering and Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fürther Straße 248, 90429 Nürnberg, Germany
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28
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Ray S. Space-dependent diffusion with stochastic resetting: A first-passage study. J Chem Phys 2020; 153:234904. [DOI: 10.1063/5.0034432] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Somrita Ray
- School of Chemistry, The Raymond and Beverly Sackler Center for Computational Molecular and Materials Science, The Center for Physics and Chemistry of Living Systems, and The Ratner Center for Single Molecule Science, Tel Aviv University, Tel Aviv 69978, Israel
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29
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Slanina F. Colloid particles in microfluidic inertial hydrodynamic ratchet at moderate Reynolds number. Phys Rev E 2020; 102:052601. [PMID: 33327115 DOI: 10.1103/physreve.102.052601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/08/2020] [Indexed: 11/07/2022]
Abstract
The movement of spherical Brownian particle carried by an alternating fluid flow in a tube of periodically variable diameter is investigated. On the basis of our previous results [Phys. Rev. E 99, 012604 (2019)10.1103/PhysRevE.99.012604] on the hydrodynamics of the problem, we look at the competition of hydrodynamics and diffusion. We use the method of Fick-Jacobs mapping on an effective one-dimensional problem. We calculate the ratchet current and show that is is strictly related to finite size of the particles. The ratchet current grows quadratically with particle radius. We also show that the dominant contribution to the ratchet current is due to inertial hydrodynamic effects. This means that Reynolds number must be at least of order one. We discuss the possible use for separation of particles by size and perspectives of optimization of the tube shape.
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Affiliation(s)
- František Slanina
- Institute of Physics, Czech Academy of Sciences, CZ-18221 Praha, Czech Republic
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30
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López-Alamilla NJ, Jack MW, Challis KJ. Enhanced diffusion and the eigenvalue band structure of Brownian motion in tilted periodic potentials. Phys Rev E 2020; 102:042405. [PMID: 33212597 DOI: 10.1103/physreve.102.042405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/22/2020] [Indexed: 11/07/2022]
Abstract
We consider enhanced diffusion for Brownian motion on a tilted periodic potential. Expressing the effective diffusion in terms of the eigenvalue band structure, we establish a connection between band gaps in the eigenspectrum and enhanced diffusion. We explain this connection for a simple cosine potential with a linear force and then generalize to more complicated potentials including one-dimensional potentials with multiple frequency components and nonseparable multidimensional potentials. We find that potentials with multiple band gaps in the eigenspectrum can lead to multiple maxima or broadening of the force-diffusion curve. These features are likely to be observable in experiments.
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Affiliation(s)
- N J López-Alamilla
- Department of Physics, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | | | - K J Challis
- Scion, Private Bag 3020, Rotorua 3046, New Zealand
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31
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Kalinay P. Taylor dispersion in Poiseuille flow in three-dimensional tubes of varying diameter. Phys Rev E 2020; 102:042606. [PMID: 33212693 DOI: 10.1103/physreve.102.042606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/15/2020] [Indexed: 11/07/2022]
Abstract
Diffusion of particles carried by Poiseuille flow of the surrounding solvent in a three-dimensional (3D) tube of varying diameter is considered. We revisit our mapping technique [F. Slanina and P. Kalinay, Phys. Rev. E 100, 032606 (2019)2470-004510.1103/PhysRevE.100.032606], projecting the corresponding 3D advection-diffusion equation onto the longitudinal coordinate and generating an effective one-dimensional modified Fick-Jacobs (or Smoluchowski) equation. A different scaling of the transverse forces by a small auxiliary parameter ε is used here. It results in a recurrence scheme enabling us to derive the corrections of the effective diffusion coefficient and the averaged driving force up to higher orders in ε. The new scaling also preserves symmetries of the stationary solution in any order of ε. Finally we show that Reguera-Rubí's formula, widely applied for description of diffusion in corrugated tubes, can be systematically corrected by the strength of the flow Q; we give here the first two terms in the form of closed analytic formulas.
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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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32
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Khatri N, Burada PS. Confined diffusion in a random Lorentz gas environment. Phys Rev E 2020; 102:012137. [PMID: 32794985 DOI: 10.1103/physreve.102.012137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/30/2020] [Indexed: 11/07/2022]
Abstract
We study the diffusive behavior of biased Brownian particles in a two dimensional confined geometry filled with the freezing obstacles. The transport properties of these particles are investigated for various values of the obstacle density η and the scaling parameter f, which is the ratio of work done to the particles to available thermal energy. We show that, when the thermal fluctuations dominate over the external force, i.e., small f regime, particles get trapped in the given environment when the system percolates at the critical obstacle density η_{c}≈1.2. However, as f increases, we observe that particle trapping occurs prior to η_{c}. In particular, we find a relation between η and f which provides an estimate of the minimum η up to a critical scaling parameter f_{c} beyond which the Fick-Jacobs description is invalid. Prominent transport features like nonmonotonic behavior of the nonlinear mobility, anomalous diffusion, and greatly enhanced effective diffusion coefficient are explained for various strengths of f and η. Also, it is interesting to observe that particles exhibit different kinds of diffusive behaviors, i.e., subdiffusion, normal diffusion, and superdiffusion. These findings, which are genuine to the confined and random Lorentz gas environment, can be useful to understand the transport of small particles or molecules in systems such as molecular sieves and porous media, which have a complex heterogeneous environment of the freezing obstacles.
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Affiliation(s)
- Narender Khatri
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.,Center for Theoretical Studies, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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33
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Abstract
To know how liquid matter moves through a crowded medium due to the action of a force constitutes currently a problem of great practical importance, present in cases as diverse as the transport of particles through a cell membrane and through a particulate porous medium. To calculate the mass flow through the system, we present an approach that emulates the texture of the medium by using entropic barriers that the particles must overcome in order to move. The model reproduces the scaling behavior of the velocity with the force found in many systems in order to show how the scaling exponent depends on the micro-structure of the medium. Our model offers a new perspective that is able to characterize the flow of matter through the medium and may be useful in studies of nano-fluids, oil recovery, soil drainage, tissue engineering, and drug delivery.
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Affiliation(s)
- A Arango-Restrepo
- Departament de Física de la Matéria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - J M Rubi
- Departament de Física de la Matéria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
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34
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Nagarajan K, Chen SB. Polyelectrolyte Translocation through a Corrugated Nanopore. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Karthik Nagarajan
- Department of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
| | - Shing Bor Chen
- Department of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
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35
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Karimi H, Setare MR, Moradian A. Rod separation by sawtooth channel. Phys Rev E 2020; 102:012610. [PMID: 32794973 DOI: 10.1103/physreve.102.012610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
By applying entropic barriers, we present a rod separation mechanism that induces the movement of rods of different sizes in the opposite directions. This mechanism is based on the combination of the saw-tooth channel, a static force, and an oscillating driving force. The asymmetric shape of the channel and the elongated shape of the rod causesa complicated interaction effect between the rods and the channel walls which reduces the accessible configuration space for the rods and leads to entropic free-energy effects.
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Affiliation(s)
- H Karimi
- Department of Science, University of Kurdistan, Sanandaj, Iran
| | - M R Setare
- Department of Science, University of Kurdistan, Sanandaj, Iran
| | - A Moradian
- Department of Science, Campus of Bijar, University of Kurdistan, Bijar, Iran
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36
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Mangeat M, Guérin T, Dean DS. Effective diffusivity of Brownian particles in a two dimensional square lattice of hard disks. J Chem Phys 2020; 152:234109. [PMID: 32571035 DOI: 10.1063/5.0009095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We revisit the classic problem of the effective diffusion constant of a Brownian particle in a square lattice of reflecting impenetrable hard disks. This diffusion constant is also related to the effective conductivity of non-conducting and infinitely conductive disks in the same geometry. We show how a recently derived Green's function for the periodic lattice can be exploited to derive a series expansion of the diffusion constant in terms of the disk's volume fraction φ. Second, we propose a variant of the Fick-Jacobs approximation to study the large volume fraction limit. This combination of analytical results is shown to describe the behavior of the diffusion constant for all volume fractions.
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Affiliation(s)
- M Mangeat
- Univ. Bordeaux, CNRS, Laboratoire Ondes et Matière d'Aquitaine (LOMA), UMR 5798, F-33405 Talence, France
| | - T Guérin
- Univ. Bordeaux, CNRS, Laboratoire Ondes et Matière d'Aquitaine (LOMA), UMR 5798, F-33405 Talence, France
| | - D S Dean
- Univ. Bordeaux, CNRS, Laboratoire Ondes et Matière d'Aquitaine (LOMA), UMR 5798, F-33405 Talence, France
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37
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Slanina F, Kalinay P. Hydrodynamic separation of colloidal particles in tubes: Effective one-dimensional approach. Phys Rev E 2019; 100:032606. [PMID: 31639959 DOI: 10.1103/physreve.100.032606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Indexed: 11/07/2022]
Abstract
We investigate diffusion of colloidal particles carried by flow in tubes of variable diameter and under the influence of an external field. We generalize the method mapping the three-dimensional confined diffusion onto an effective one-dimensional problem to the case of nonconservative forces and use this mapping for the problem in question. We show that in the presence of hydrodynamic drag, the lowest approximation (the Fick-Jacobs approximation) may be insufficient, and inclusion of at least the first-order correction is desirable to obtain more reliable results. As a practical application, we use the method for investigation of separation of colloidal particles carried by a fluid flow according to their size, using flotation and centrifugation.
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Affiliation(s)
- František Slanina
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Praha, Czech Republic
| | - Pavol Kalinay
- Institute of Physics, Slovak Academy of Sciences, Dúbravska cesta 9, 84511, Bratislava, Slovakia
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38
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Wu JC, An M, Ma WG. Spontaneous rectification and absolute negative mobility of inertial Brownian particles induced by Gaussian potentials in steady laminar flows. SOFT MATTER 2019; 15:7187-7194. [PMID: 31464332 DOI: 10.1039/c9sm00853e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We study the transport of inertial Brownian particles in steady laminar flows in the presence of two-dimensional Gaussian potentials. Through extensive numerical simulations, it is found that the transport is sensitively dependent on the external constant force and the Gaussian potential. Within tailored parameter regimes, the system exhibits a rich variety of transport behaviors. There exists the phenomenon of spontaneous rectification (SR), where the directed transport of particles can occur in the absence of any external driving forces. It is found that SR of the particles can be manipulated by the spatial position of the Gaussian potential. Moreover, when the potential lies at the center of the cellular flow, the system exhibits absolute negative mobility (ANM), i.e., the particles can move in a direction opposite to the constant force. More importantly, the phenomenon of ANM induced by Gaussian potentials is robust in a wide range of system parameters and can be further strengthened with the optimized parameters, which may pave the way to the implementation of related experiments.
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Affiliation(s)
- Jian-Chun Wu
- School of Physics and Electronic Information, Shangrao Normal University, Shangrao 334001, China.
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39
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Khatri N, Burada PS. Diffusion of interacting particles in a channel with reflection boundary conditions. J Chem Phys 2019; 151:094103. [DOI: 10.1063/1.5116330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Narender Khatri
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
| | - P. S. Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
- Center for Theoretical Studies, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
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40
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Mei R, Xu Y, Kurths J. Transport and escape in a deformable channel driven by fractional Gaussian noise. Phys Rev E 2019; 100:022114. [PMID: 31574709 DOI: 10.1103/physreve.100.022114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Indexed: 06/10/2023]
Abstract
Fractional Gaussian noise (FGN) with the Hurst exponent H is an important tool to model various phenomena in biophysical systems, like subdiffusion in a single protein molecule. Considering that there also exists a confined structure which can be modeled as a channel in these systems, transport and escape driven by FGN in a deformable channel are investigated in this paper. By calculating the mean velocity, and the mean first passage time (MFPT) for crossing the nearest bottleneck and the probability distribution of the final position, effects of FGN and channel structure on the system dynamics are illustrated. Our results indicate that FGN has a complex influence mechanism under different combinations of H and the noise intensity. For a persistence case (H>0.5), the mean velocity decreases but MFPT increases with the increase of the noise intensity and H. While for an antipersistence case (H<0.5), when H is small, the relationships among the mean velocity, MFPT and the noise intensity are exactly the opposite to persistence cases. When H has a large value, the mean velocity tends to first decrease and then increase. Moreover, effects of the bottleneck and channel asymmetry are investigated. It is shown that a small H and a large channel width can lead to a large mean velocity and fast crossing. Besides, a channel asymmetry can affect the system dynamics by inducing asymmetric structure and adjusting the width of bottleneck. However, the effect of the bottleneck is the main factor. Therefore, a combination of channel with wide bottleneck and FGN in an antipersistence regime is the optimal choice to promote the transport and escape. These results provide a basis for the explanation of molecular activity in living organisms and the design of particle mixture separators.
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Affiliation(s)
- Ruoxing Mei
- Department of Applied Mathematics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yong Xu
- Department of Applied Mathematics, Northwestern Polytechnical University, Xi'an 710072, China and MIIT Key Laboratory of Dynamics and Control of Complex Systems, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jürgen Kurths
- Potsdam Institute for Climate Impact Research, Potsdam 14412, Germany
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41
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Dal Cengio S, Pagonabarraga I. Confinement-controlled rectification in a geometric nanofluidic diode. J Chem Phys 2019; 151:044707. [PMID: 31370530 DOI: 10.1063/1.5108723] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent experiments with electrolytes driven through conical nanopores give evidence of strong rectified current response. In such devices, the asymmetry in the confinement is responsible for the non-Ohmic response, suggesting that the interplay of entropic and enthalpic forces plays a major role. Here, we propose a theoretical model to shed light on the physical mechanism underlying ionic current rectification. By use of an effective description of the ionic dynamics, we explore the system's response in different electrostatic regimes. We show that the rectification efficiency, as well as the channel selectivity, is driven by the surface-to-bulk conductivity ratio Dukhin length rather than the electrical double layer overlap.
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Affiliation(s)
- S Dal Cengio
- Department of Condensed Matter, Universitat de Barcelona, Martí i Franqués 1, 08028 Barcelona, Spain
| | - I Pagonabarraga
- Department of Condensed Matter, Universitat de Barcelona, Martí i Franqués 1, 08028 Barcelona, Spain
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42
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Xu Y, Mei R, Li Y, Kurths J. Particle Transport in a Confined Ratchet Driven by the Colored Noise. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-15096-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
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43
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Makhnovskii YA. Effect of particle size oscillations on drift and diffusion along a periodically corrugated channel. Phys Rev E 2019; 99:032102. [PMID: 30999518 DOI: 10.1103/physreve.99.032102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 06/09/2023]
Abstract
We study diffusive transport of a particle in a channel with periodically varying cross-section, occurring when the size of the particle periodically switches between two values. In such a situation, the entropy potential, which accounts for the area accessible for diffusion particle, varies both spatially (along the channel axis) and temporally. This underlies the complex interplay between different timescales of the system and leads to novel dynamic regimes. The most notable observations are: emergence of directed motion (in case of asymmetric channel) and resonant diffusion, both controlled by the switching frequency. Resonantlike behaviors of the drift velocity and the effective diffusion coefficient are shown and discussed. Based on heuristic arguments, an approximate analytical treatment of the transport process is proposed. As a comparison with the results obtained from Brownian dynamics simulations indicates, this approach provides a satisfactory way to handle the problem analytically.
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Affiliation(s)
- Yu A Makhnovskii
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky Prospect 29, Moscow 119991, Russia
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44
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Xiao Z, Wei M, Wang W. A Review of Micromotors in Confinements: Pores, Channels, Grooves, Steps, Interfaces, Chains, and Swimming in the Bulk. ACS APPLIED MATERIALS & INTERFACES 2019; 11:6667-6684. [PMID: 30562451 DOI: 10.1021/acsami.8b13103] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
One of the recent frontiers of nanotechnology research involves machines that operate at nano- and microscales, also known as nano/micromotors. Their potential applications in biomedicine, environmental sciences and engineering, military and defense industries, self-assembly, and many other areas have fueled an intense interest in this topic over the last 15 years. Despite deepened understanding of their propulsion mechanisms, we are still in the early days of exploring the dynamics of micromotors in complex and more realistic environments. Confinements, as a typical example of complex environments, are extremely relevant to the applications of micromotors, which are expected to travel in mucus gels, blood vessels, reproductive and digestive tracts, microfluidic chips, and capillary tubes. In this review, we summarize and critically examine recent studies (mostly experimental ones) of micromotor dynamics in confinements in 3D (spheres and porous network, channels, grooves, steps, and obstacles), 2D (liquid-liquid, liquid-solid, and liquid-air interfaces), and 1D (chains). In addition, studies of micromotors moving in the bulk solution and the usefulness of acoustic levitation is discussed. At the end of this article, we summarize how confinements can affect micromotors and offer our insights on future research directions. This review article is relevant to readers who are interested in the interactions of materials with interfaces and structures at the microscale and helpful for the design of smart and multifunctional materials for various applications.
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Affiliation(s)
- Zuyao Xiao
- School of Materials Science and Engineering , Harbin Institute of Technology (Shenzhen) , Shenzhen , Guangdong 518055 , China
| | - Mengshi Wei
- School of Materials Science and Engineering , Harbin Institute of Technology (Shenzhen) , Shenzhen , Guangdong 518055 , China
| | - Wei Wang
- School of Materials Science and Engineering , Harbin Institute of Technology (Shenzhen) , Shenzhen , Guangdong 518055 , China
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45
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Yang X, Zhu Q, Liu C, Wang W, Li Y, Marchesoni F, Hänggi P, Zhang HP. Diffusion of colloidal rods in corrugated channels. Phys Rev E 2019; 99:020601. [PMID: 30934353 DOI: 10.1103/physreve.99.020601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 06/09/2023]
Abstract
In many natural and artificial devices diffusive transport takes place in confined geometries with corrugated boundaries. Such boundaries cause both entropic and hydrodynamic effects, which have been studied only for the case of spherical particles. Here we experimentally investigate the diffusion of particles of elongated shape confined in a corrugated quasi-two-dimensional channel. The elongated shape causes complex excluded-volume interactions between particles and channel walls which reduce the accessible configuration space and lead to novel entropic free-energy effects. The extra rotational degree of freedom also gives rise to a complex diffusivity matrix that depends on both the particle location and its orientation. We further show how to extend the standard Fick-Jacobs theory to incorporate combined hydrodynamic and entropic effects, so as, for instance, to accurately predict experimentally measured mean first passage times along the channel. Our approach can be used as a generic method to describe translational diffusion of anisotropic particles in corrugated channels.
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Affiliation(s)
- Xiang Yang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Chang Liu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Yunyun Li
- Center for Phononics and Thermal Energy Science, School of Physics Science and Engineering, Tongji University, Shanghai, China
| | - Fabio Marchesoni
- Center for Phononics and Thermal Energy Science, School of Physics Science and Engineering, Tongji University, Shanghai, China
- Dipartimento di Fisica, Università di Camerino, I-62032 Camerino, Italy
| | - Peter Hänggi
- Institut für Physik, Universität Augsburg, D-86135 Augsburg, Germany
- Nanosystems Initiative Munich, Schellingstrasse 4, D-80799 München, Germany
| | - H P Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing, China
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46
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Slanina F. Movement of spherical colloid particles carried by flow in tubes of periodically varying diameter. Phys Rev E 2019; 99:012604. [PMID: 30780301 DOI: 10.1103/physreve.99.012604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 06/09/2023]
Abstract
We provide analytical formulas for the movement of spherical particles in a corrugated tube, in the approximation of small amplitude of the tube diameter variation. We calculate how the particle is pushed toward the wall at some places and pulled off the wall at others. We show that this effect causes rectification of the particle movement, when the direction of the fluid flow is alternated, thus leading to the hydrodynamic ratchet effect. We propose such scheme as a particle-separation device.
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Affiliation(s)
- František Slanina
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Praha, Czech Republic
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47
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Wu JC, Lv K, Zhao WW, Ai BQ. Transport of active particles induced by wedge-shaped barriers in straight channels with hard and soft walls. CHAOS (WOODBURY, N.Y.) 2018; 28:123102. [PMID: 30599529 DOI: 10.1063/1.5050614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
The transport of active particles in straight channels is numerically investigated. The periodic wedge-shaped barriers can produce the asymmetry of the system and induce the directed transport of the active particles. The direction of the transport is determined by the apex angle of the wedge-shaped barriers. By confining the particles in channels with hard and soft walls, the transport exhibits similar behaviors. The average velocity is a peaked function of the translational diffusion, while it decreases monotonously with the increase of the rotational diffusion. Moreover, the simulation results show that the transport is sensitive to the parameters of the confined structures, such as the pore width, the intensity of potential, and the channel period.
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Affiliation(s)
- Jian-Chun Wu
- School of Physics and Electronic Information, Shangrao Normal University, Shangrao 334001, China
| | - Kui Lv
- School of Physics and Electronic Information, Shangrao Normal University, Shangrao 334001, China
| | - Wen-Wen Zhao
- School of Physics and Electronic Information, Shangrao Normal University, Shangrao 334001, China
| | - Bao-Quan Ai
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
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48
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Puertas AM, Malgaretti P, Pagonabarraga I. Active microrheology in corrugated channels. J Chem Phys 2018; 149:174908. [DOI: 10.1063/1.5048343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Antonio M. Puertas
- Department of Applied Physics, Universidad de Almería, 04120 Almería, Spain
| | - Paolo Malgaretti
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany and IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Ignacio Pagonabarraga
- CECAM, Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lasuanne, Batochime, Avenue Forel 2, 1015 Lausanne, Switzerland
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49
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Singh AK, Burada PS, Bhattacharya S, Bag S, Bhattacharya A, Dasgupta S, Roy A. Microwave-radiation-induced molecular structural rearrangement of hen egg-white lysozyme. Phys Rev E 2018; 97:052416. [PMID: 29906821 DOI: 10.1103/physreve.97.052416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Indexed: 11/07/2022]
Abstract
We have investigated the nonthermal effect of 10 GHz/22 dBm microwave radiation on hen egg-white lysozyme (HEWL) over different irradiation times, ranging from 2 min to 1 h. To ensure a control over the radiation parameters, a pair of microwave rectangular waveguides is used to irradiate the samples. Optical spectroscopic measurements, which include UV-visible absorption spectroscopy, Raman spectroscopy, and far UV CD spectroscopy, reveal the exposure of the buried tryptophan (Trp) residues of the native molecule between 15 and 30 min of radiation. The higher duration of the perturbation leads to a compact structure of the protein and Trp residues are buried again. Interestingly, we do not find any change in the secondary structure of the protein even for 1 h duration of radiation. The relaxation dynamics of the irradiated molecules also has been discussed. We have shown that the molecules relax to their native configuration in 7-8 h after the radiation field is turned off. The structural rearrangement over the above timescale has further been probed by a model calculation, based on a modified Langevin equation. Our coarse-grained simulation approach utilizes the mean of atomic positions and net atomic charge of each amino acid of native HEWL to mimic the initial conformation of the molecule. The modified positions of the residues are then calculated for the given force fields. The simulation results reveal the nonmonotonous change in overall size of the molecule, as observed experimentally. The radiation parameters used in our experiments are very similar to those of some of the electronic devices we often come across. Thus, we believe that the results of our studies on a simple protein structure may help us in understanding the effect of radiation on complex biological systems as well.
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Affiliation(s)
- Anang K Singh
- Department of Physics, Indian Institute of Technology, Kharagpur 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology, Kharagpur 721302, India
| | | | - Sudipta Bag
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Amitabha Bhattacharya
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Anushree Roy
- Department of Physics, Indian Institute of Technology, Kharagpur 721302, India
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50
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Mangeat M, Guérin T, Dean DS. Dispersion in two-dimensional periodic channels with discontinuous profiles. J Chem Phys 2018; 149:124105. [DOI: 10.1063/1.5045183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Mangeat
- Laboratoire Ondes et Matière d’Aquitaine (LOMA), CNRS, UMR 5798, Université de Bordeaux, F-33400 Talence, France
| | - T. Guérin
- Laboratoire Ondes et Matière d’Aquitaine (LOMA), CNRS, UMR 5798, Université de Bordeaux, F-33400 Talence, France
| | - D. S. Dean
- Laboratoire Ondes et Matière d’Aquitaine (LOMA), CNRS, UMR 5798, Université de Bordeaux, F-33400 Talence, France
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