1
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Pöverlein MC, Hulm A, Dietschreit JCB, Kussmann J, Ochsenfeld C, Kaila VRI. QM/MM Free Energy Calculations of Long-Range Biological Protonation Dynamics by Adaptive and Focused Sampling. J Chem Theory Comput 2024; 20:5751-5762. [PMID: 38718352 DOI: 10.1021/acs.jctc.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Water-mediated proton transfer reactions are central for catalytic processes in a wide range of biochemical systems, ranging from biological energy conversion to chemical transformations in the metabolism. Yet, the accurate computational treatment of such complex biochemical reactions is highly challenging and requires the application of multiscale methods, in particular hybrid quantum/classical (QM/MM) approaches combined with free energy simulations. Here, we combine the unique exploration power of new advanced sampling methods with density functional theory (DFT)-based QM/MM free energy methods for multiscale simulations of long-range protonation dynamics in biological systems. In this regard, we show that combining multiple walkers/well-tempered metadynamics with an extended system adaptive biasing force method (MWE) provides a powerful approach for exploration of water-mediated proton transfer reactions in complex biochemical systems. We compare and combine the MWE method also with QM/MM umbrella sampling and explore the sampling of the free energy landscape with both geometric (linear combination of proton transfer distances) and physical (center of excess charge) reaction coordinates and show how these affect the convergence of the potential of mean force (PMF) and the activation free energy. We find that the QM/MM-MWE method can efficiently explore both direct and water-mediated proton transfer pathways together with forward and reverse hole transfer mechanisms in the highly complex proton channel of respiratory Complex I, while the QM/MM-US approach shows a systematic convergence of selected long-range proton transfer pathways. In this regard, we show that the PMF along multiple proton transfer pathways is recovered by combining the strengths of both approaches in a QM/MM-MWE/focused US (FUS) scheme and reveals new mechanistic insight into the proton transfer principles of Complex I. Our findings provide a promising basis for the quantitative multiscale simulations of long-range proton transfer reactions in biological systems.
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Affiliation(s)
- Maximilian C Pöverlein
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Andreas Hulm
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
| | - Johannes C B Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
- Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
- Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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2
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Kumar V, Pal A, Shpielberg O. Emerging universality classes in thermally assisted activation of interacting diffusive systems: A perturbative hydrodynamic approach. J Chem Phys 2024; 160:134107. [PMID: 38563303 DOI: 10.1063/5.0195570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Thermal activation of a particle from a deep potential trap follows the Arrhenius law. Recently, this result has been generalized for interacting diffusive particles in the trap, revealing two universality classes-the Arrhenius class and the excluded volume class. The result was demonstrated with the aid of numerical analysis. Here, we present a perturbative hydrodynamic approach to analytically validate the existence and range of validity for the two universality classes.
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Affiliation(s)
- Vishwajeet Kumar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arnab Pal
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Ohad Shpielberg
- Department of Mathematics and Physics, University of Haifa at Oranim, Kiryat Tivon 3600600, Israel
- Haifa Research Center for Theoretical Physics and Astrophysics, University of Haifa, Abba Khoushy Ave. 199, Haifa 3498838, Israel
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3
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Kumar V, Pal A, Shpielberg O. Arrhenius law for interacting diffusive systems. Phys Rev E 2024; 109:L032101. [PMID: 38632768 DOI: 10.1103/physreve.109.l032101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/08/2024] [Indexed: 04/19/2024]
Abstract
Finding the mean time it takes for a particle to escape from a metastable state due to thermal fluctuations is a fundamental problem in physics, chemistry, and biology. Here, we consider the escape rate of interacting diffusive particles, from a deep potential trap within the framework of the macroscopic fluctuation theory-a nonequilibrium hydrodynamic theory. For systems without excluded volume, our investigation reveals adherence to the well-established Arrhenius law. However, in the presence of excluded volume, a universality class emerges, fundamentally altering the escape rate. Remarkably, the modified escape rate within this universality class is independent of the interactions at play. The universality class, demonstrating the importance of excluded volume effects, may bring insights to the interpretation of escape processes in the realm of chemical physics.
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Affiliation(s)
- Vishwajeet Kumar
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arnab Pal
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Ohad Shpielberg
- Department of Mathematics and Physics, University of Haifa at Oranim, Kiryat Tivon 3600600, Israel
- Haifa Research Center for Theoretical Physics and Astrophysics, University of Haifa, Abba Khoushy Avenue 199, Haifa 3498838, Israel
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4
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Bebon R, Godec A. Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime. PHYSICAL REVIEW LETTERS 2023; 131:237101. [PMID: 38134782 DOI: 10.1103/physrevlett.131.237101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 12/24/2023]
Abstract
We derive general bounds on the probability that the empirical first-passage time τ[over ¯]_{n}≡∑_{i=1}^{n}τ_{i}/n of a reversible ergodic Markov process inferred from a sample of n independent realizations deviates from the true mean first-passage time by more than any given amount in either direction. We construct nonasymptotic confidence intervals that hold in the elusive small-sample regime and thus fill the gap between asymptotic methods and the Bayesian approach that is known to be sensitive to prior belief and tends to underestimate uncertainty in the small-sample setting. We prove sharp bounds on extreme first-passage times that control uncertainty even in cases where the mean alone does not sufficiently characterize the statistics. Our concentration-of-measure-based results allow for model-free error control and reliable error estimation in kinetic inference, and are thus important for the analysis of experimental and simulation data in the presence of limited sampling.
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Affiliation(s)
- Rick Bebon
- Mathematical bioPhysics Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Aljaž Godec
- Mathematical bioPhysics Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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5
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Zhu Y, You M, Shi Y, Huang H, Wei Z, He T, Xiong S, Wang Z, Cheng X. Optofluidic Tweezers: Efficient and Versatile Micro/Nano-Manipulation Tools. MICROMACHINES 2023; 14:1326. [PMID: 37512637 PMCID: PMC10384111 DOI: 10.3390/mi14071326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Optical tweezers (OTs) can transfer light momentum to particles, achieving the precise manipulation of particles through optical forces. Due to the properties of non-contact and precise control, OTs have provided a gateway for exploring the mysteries behind nonlinear optics, soft-condensed-matter physics, molecular biology, and analytical chemistry. In recent years, OTs have been combined with microfluidic chips to overcome their limitations in, for instance, speed and efficiency, creating a technology known as "optofluidic tweezers." This paper describes static OTs briefly first. Next, we overview recent developments in optofluidic tweezers, summarizing advancements in capture, manipulation, sorting, and measurement based on different technologies. The focus is on various kinds of optofluidic tweezers, such as holographic optical tweezers, photonic-crystal optical tweezers, and waveguide optical tweezers. Moreover, there is a continuing trend of combining optofluidic tweezers with other techniques to achieve greater functionality, such as antigen-antibody interactions and Raman tweezers. We conclude by summarizing the main challenges and future directions in this research field.
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Affiliation(s)
- Yuchen Zhu
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Minmin You
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuzhi Shi
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Haiyang Huang
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Zeyong Wei
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Tao He
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Sha Xiong
- School of Automation, Central South University, Changsha 410083, China
| | - Zhanshan Wang
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Xinbin Cheng
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
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6
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Guéry-Odelin D, Jarzynski C, Plata CA, Prados A, Trizac E. Driving rapidly while remaining in control: classical shortcuts from Hamiltonian to stochastic dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023; 86:035902. [PMID: 36535018 DOI: 10.1088/1361-6633/acacad] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Stochastic thermodynamics lays down a broad framework to revisit the venerable concepts of heat, work and entropy production for individual stochastic trajectories of mesoscopic systems. Remarkably, this approach, relying on stochastic equations of motion, introduces time into the description of thermodynamic processes-which opens the way to fine control them. As a result, the field of finite-time thermodynamics of mesoscopic systems has blossomed. In this article, after introducing a few concepts of control for isolated mechanical systems evolving according to deterministic equations of motion, we review the different strategies that have been developed to realize finite-time state-to-state transformations in both over and underdamped regimes, by the proper design of time-dependent control parameters/driving. The systems under study are stochastic, epitomized by a Brownian object immersed in a fluid; they are thus strongly coupled to their environment playing the role of a reservoir. Interestingly, a few of those methods (inverse engineering, counterdiabatic driving, fast-forward) are directly inspired by their counterpart in quantum control. The review also analyzes the control through reservoir engineering. Besides the reachability of a given target state from a known initial state, the question of the optimal path is discussed. Optimality is here defined with respect to a cost function, a subject intimately related to the field of information thermodynamics and the question of speed limit. Another natural extension discussed deals with the connection between arbitrary states or non-equilibrium steady states. This field of control in stochastic thermodynamics enjoys a wealth of applications, ranging from optimal mesoscopic heat engines to population control in biological systems.
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Affiliation(s)
- David Guéry-Odelin
- Laboratoire Collisions, Agrégats, Réactivité, IRSAMC, Université de Toulouse, CNRS, Toulouse, France
| | - Christopher Jarzynski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States of America
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, United States of America
- Department of Physics, University of Maryland, College Park, MD, United States of America
| | - Carlos A Plata
- Física Teórica, Universidad de Sevilla, Apartado de Correos 1065, E-41080 Sevilla, Spain
| | - Antonio Prados
- Física Teórica, Universidad de Sevilla, Apartado de Correos 1065, E-41080 Sevilla, Spain
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7
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Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap. iScience 2022; 25:104731. [PMID: 36034218 PMCID: PMC9400092 DOI: 10.1016/j.isci.2022.104731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 11/22/2022] Open
Abstract
While particle trajectories encode information on their governing potentials, potentials can be challenging to robustly extract from trajectories. Measurement errors may corrupt a particle’s position, and sparse sampling of the potential limits data in higher energy regions such as barriers. We develop a Bayesian method to infer potentials from trajectories corrupted by Markovian measurement noise without assuming prior functional form on the potentials. As an alternative to Gaussian process priors over potentials, we introduce structured kernel interpolation to the Natural Sciences which allows us to extend our analysis to large datasets. Structured-Kernel-Interpolation Priors for Potential Energy Reconstruction (SKIPPER) is validated on 1D and 2D experimental trajectories for particles in a feedback trap. A feedback trap was used to generate noisy Langevin microbead trajectories The potential energy surface is recovered using a Bayesian formulation The formulation uses a structured-kernel-interpolation Gaussian process (SKI-GP) to tractably approximate Gaussian process regression for larger datasets Thanks to our adaptation of SKI-GP, we have broadened the use of Gaussian processes for natural science applications
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8
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Yang X, Lu ZY. Nanoparticle cluster formation mechanisms elucidated via Markov state modeling: Attraction range effects, aggregation pathways, and counterintuitive transition rates. J Chem Phys 2022; 156:214902. [DOI: 10.1063/5.0086110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nanoparticle clusters are promising candidates for developing functional materials. However, it is still a challenging task to fabricate them in a predictable and controllable way, which requires investigation of the possible mechanisms underlying cluster formation at the nanoscale. By constructing Markov state models (MSMs) at the microstate level, we find that for highly dispersed particles to form a highly aggregated cluster, there are multiple coexisting pathways, which correspond to direct aggregation, or pathways that need to pass through partially aggregated, intermediate states. Varying the range of attraction between nanoparticles is found to significantly affect pathways. As the attraction range becomes narrower, compared to direct aggregation, some pathways that need to pass through partially aggregated intermediate states become more competitive. In addition, from MSMs constructed at the macrostate level, the aggregation rate is found to be counterintuitively lower with a lower free-energy barrier, which is also discussed.
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Affiliation(s)
- Xi Yang
- Institute of Theoretical Chemistry, State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130021, China
| | - Zhong-Yuan Lu
- Institute of Theoretical Chemistry, State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130021, China
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9
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Mondal M, Ochoa MA, Sukharev M, Nitzan A. Coupling, lifetimes, and "strong coupling" maps for single molecules at plasmonic interfaces. J Chem Phys 2022; 156:154303. [PMID: 35459293 DOI: 10.1063/5.0077739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The interaction between excited states of a molecule and excited states of a metal nanostructure (e.g., plasmons) leads to hybrid states with modified optical properties. When plasmon resonance is swept through molecular transition frequency, an avoided crossing may be observed, which is often regarded as a signature of strong coupling between plasmons and molecules. Such strong coupling is expected to be realized when 2|⟨U⟩|/ℏΓ > 1, where ⟨U⟩ and Γ are the molecule-plasmon coupling and the spectral width of the optical transition, respectively. Because both ⟨U⟩ and Γ strongly increase with decreasing distance between a molecule and a plasmonic structure, it is not obvious that this condition can be satisfied for any molecule-metal surface distance. In this work, we investigate the behavior of ⟨U⟩ and Γ for several geometries. Surprisingly, we find that if the only contributions to Γ are lifetime broadenings associated with the radiative and nonradiative relaxation of a single molecular vibronic transition, including effects on molecular radiative and nonradiative lifetimes induced by the metal, the criterion 2|⟨U⟩|/ℏΓ > 1 is easily satisfied by many configurations irrespective of the metal-molecule distance. This implies that the Rabi splitting can be observed in such structures if other sources of broadening are suppressed. Additionally, when the molecule-metal surface distance is varied keeping all other molecular and metal parameters constant, this behavior is mitigated due to the spectral shift associated with the same molecule-plasmon interaction, making the observation of Rabi splitting more challenging.
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Affiliation(s)
- Monosij Mondal
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Maicol A Ochoa
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Maxim Sukharev
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, USA
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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10
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Meibohm J, Forastiere D, Adeleke-Larodo T, Proesmans K. Relaxation-speed crossover in anharmonic potentials. Phys Rev E 2021; 104:L032105. [PMID: 34654171 DOI: 10.1103/physreve.104.l032105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/08/2021] [Indexed: 11/07/2022]
Abstract
In a recent Letter [A. Lapolla and A. Godec, Phys. Rev. Lett. 125, 110602 (2020)PRLTAO0031-900710.1103/PhysRevLett.125.110602], thermal relaxation was observed to occur faster from cold to hot (heating) than from hot to cold (cooling). Here we show that overdamped diffusion in anharmonic potentials generically exhibits both faster heating and faster cooling, depending on the initial temperatures and on the potential's degree of anharmonicity. We draw a relaxation-speed phase diagram that localizes the different behaviors in parameter space. In addition to faster-heating and faster-cooling regions, we identify a crossover region in the phase diagram, where heating is initially slower but asymptotically faster than cooling. The structure of the phase diagram is robust against the inclusion of a confining, harmonic term in the potential as well as moderate changes of the measure used to define initially equidistant temperatures.
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Affiliation(s)
- Jan Meibohm
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Danilo Forastiere
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Tunrayo Adeleke-Larodo
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Karel Proesmans
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg.,Hasselt University, B-3590 Diepenbeek, Belgium
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11
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Dybiec B, Capała K, Barbasz J. Physics of free climbing. Phys Rev E 2021; 103:062135. [PMID: 34271740 DOI: 10.1103/physreve.103.062135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/02/2021] [Indexed: 11/07/2022]
Abstract
The theory of stochastic processes provides theoretical tools which can be efficiently used to explore the properties of noise-induced escape kinetics. Since noise-facilitated escape over the potential barrier resembles free climbing, one can use the first-passage time theory in an analysis of rock climbing. We perform the analysis of the mean first-passage time in order to answer the question regarding the optimal, i.e., resulting in the fastest climbing, rope length. It is demonstrated that there is a discrete set of favorable rope lengths assuring the shortest climbing times, as they correspond to local minima of mean first-passage time. Within the set of favorable rope lengths there is the optimal rope giving rise to the shortest climbing time. In particular, more experienced climbers can decrease their climbing time by using longer ropes.
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Affiliation(s)
- Bartłomiej Dybiec
- Institute of Theoretical Physics, Department of Statistical Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Karol Capała
- Institute of Theoretical Physics, Department of Statistical Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Jakub Barbasz
- J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland
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12
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Abstract
Information-driven engines that rectify thermal fluctuations are a modern realization of the Maxwell-demon thought experiment. We introduce a simple design based on a heavy colloidal particle, held by an optical trap and immersed in water. Using a carefully designed feedback loop, our experimental realization of an "information ratchet" takes advantage of favorable "up" fluctuations to lift a weight against gravity, storing potential energy without doing external work. By optimizing the ratchet design for performance via a simple theory, we find that the rate of work storage and velocity of directed motion are limited only by the physical parameters of the engine: the size of the particle, stiffness of the ratchet spring, friction produced by the motion, and temperature of the surrounding medium. Notably, because performance saturates with increasing frequency of observations, the measurement process is not a limiting factor. The extracted power and velocity are at least an order of magnitude higher than in previously reported engines.
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13
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Berezhkovskii AM, Bezrukov SM, Makarov DE. Localized potential well vs binding site: Mapping solute dynamics in a membrane channel onto one-dimensional description. J Chem Phys 2021; 154:111101. [PMID: 33752368 DOI: 10.1063/5.0044044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In the one-dimensional description, the interaction of a solute molecule with the channel wall is characterized by the potential of mean force U(x), where the x-coordinate is measured along the channel axis. When the molecule can reversibly bind to certain amino acid(s) of the protein forming the channel, this results in a localized well in the potential U(x). Alternatively, this binding can be modeled by introducing a discrete localized site, in addition to the continuum of states along x. Although both models may predict identical equilibrium distributions of the coordinate x, there is a fundamental difference between the two: in the first model, the molecule passing through the channel unavoidably visits the potential well, while in the latter, it may traverse the channel without being trapped at the discrete site. Here, we show that when the two models are parameterized to have the same thermodynamic properties, they automatically yield identical translocation probabilities and mean translocation times, yet they predict qualitatively different shapes of the translocation time distribution. Specifically, the potential well model yields a narrower distribution than the model with a discrete site, a difference that can be quantified by the distribution's coefficient of variation. This coefficient turns out to be always smaller than unity in the potential well model, whereas it may exceed unity when a discrete trapping site is present. Analysis of the translocation time distribution beyond its mean thus offers a way to differentiate between distinct translocation mechanisms.
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Affiliation(s)
- Alexander M Berezhkovskii
- Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dmitrii E Makarov
- Department of Chemistry and Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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14
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Ferrer BR, Gomez-Solano JR, Arzola AV. Fluid Viscoelasticity Triggers Fast Transitions of a Brownian Particle in a Double Well Optical Potential. PHYSICAL REVIEW LETTERS 2021; 126:108001. [PMID: 33784172 DOI: 10.1103/physrevlett.126.108001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Thermally activated transitions are ubiquitous in nature, occurring in complex environments which are typically conceived as ideal viscous fluids. We report the first direct observations of a Brownian bead transiting between the wells of a bistable optical potential in a viscoelastic fluid with a single long relaxation time. We precisely characterize both the potential and the fluid, thus enabling a neat comparison between our experimental results and a theoretical model based on the generalized Langevin equation. Our findings reveal a drastic amplification of the transition rates compared to those in a Newtonian fluid, stemming from the relaxation of the fluid during the particle crossing events.
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Affiliation(s)
- Brandon R Ferrer
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Codigo Postal 04510, México
| | - Juan Ruben Gomez-Solano
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Codigo Postal 04510, México
| | - Alejandro V Arzola
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México, Codigo Postal 04510, México
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15
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Piscitelli A, Ciamarra MP. Liquid to supercooled-liquid crossover from a Boltzmann transport approach to escape and diffusion. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:104007. [PMID: 33264762 DOI: 10.1088/1361-648x/abcff7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We develop a model describing the motion of a non-Brownian particle in a periodic potential, which we then use to predict the temperature dependence of the diffusivity of a glass-former. In the model, the velocity of the particle is drawn for the equilibrium distribution at rate 1/t c, where t c is the intercollision time in the relaxation time approximation. Solutions within a Boltzmann transport approach show that the diffusivity crossovers from a low-t c regime in which the particle at most crosses a single barrier in between two successive collisions, to a high-t c regime in which the particle may cross several barriers. We then use our model to predict the temperature dependence of the diffusion coefficient of a system of harmonic-spheres, whose energy landscape has features resembling those of the potential considered in our model. We successfully recover a crossover in the temperature dependence of the diffusion coefficient observed through numerical dynamics simulations, as well as the relationship of the diffusivity on the temperature in the high-temperature limit.
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Affiliation(s)
- A Piscitelli
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore
| | - M Pica Ciamarra
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore
- CRN-SPIN, Dipartimento di Scienze Fisiche, University of Naples Federico II, Italy
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Zimmermann U, Löwen H, Kreuter C, Erbe A, Leiderer P, Smallenburg F. Negative resistance for colloids driven over two barriers in a microchannel. SOFT MATTER 2021; 17:516-522. [PMID: 33226041 DOI: 10.1039/d0sm01700k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
When considering the flow of currents through obstacles, one core expectation is that the total resistance of sequential single resistors is additive. While this rule is most commonly applied to electronic circuits, it also applies to other transport phenomena such as the flow of colloids or nanoparticles through channels containing multiple obstacles, as long as these obstacles are sufficiently far apart. Here we explore the breakdown of this additivity for fluids of repulsive colloids driven over two energetic barriers in a microchannel, using real-space microscopy experiments, particle-resolved simulations, and dynamical density functional theory. If the barrier separation is comparable to the particle correlation length, the resistance is highly non-additive, such that the resistance added by the second barrier can be significantly higher or lower than that of the first. Surprisingly, in some cases the second barrier can even add a negative resistance, such that two identical barriers are easier to cross than a single one. We explain this counterintuitive observation in terms of the structuring of particles trapped between the barriers.
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Affiliation(s)
- Urs Zimmermann
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | | | - Artur Erbe
- Institut für Ionenstrahlphysik und Materialforschung, Helmholtz-Zentrum Dresden-Rossendorf, D-01328 Dresden, Germany
| | - Paul Leiderer
- Fachbereich Physik, Universität Konstanz, D-78457 Konstanz, Germany
| | - Frank Smallenburg
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany and Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France.
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Sabhapandit S, Majumdar SN. Freezing Transition in the Barrier Crossing Rate of a Diffusing Particle. PHYSICAL REVIEW LETTERS 2020; 125:200601. [PMID: 33258622 DOI: 10.1103/physrevlett.125.200601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/21/2020] [Accepted: 10/08/2020] [Indexed: 06/12/2023]
Abstract
We study the decay rate θ(a) that characterizes the late time exponential decay of the first-passage probability density F_{a}(t|0)∼e^{-θ(a)t} of a diffusing particle in a one dimensional confining potential U(x), starting from the origin, to a position located at a>0. For general confining potential U(x) we show that θ(a), a measure of the barrier (located at a) crossing rate, has three distinct behaviors as a function of a, depending on the tail of U(x) as x→-∞. In particular, for potentials behaving as U(x)∼|x| when x→-∞, we show that a novel freezing transition occurs at a critical value a=a_{c}, i.e., θ(a) increases monotonically as a decreases till a_{c}, and for a≤a_{c} it freezes to θ(a)=θ(a_{c}). Our results are established using a general mapping to a quantum problem and by exact solution in three representative cases, supported by numerical simulations. We show that the freezing transition occurs when in the associated quantum problem, the gap between the ground state (bound) and the continuum of scattering states vanishes.
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Affiliation(s)
| | - Satya N Majumdar
- LPTMS, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
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Exponentially faster cooling in a colloidal system. Nature 2020; 584:64-68. [DOI: 10.1038/s41586-020-2560-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/15/2020] [Indexed: 11/08/2022]
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