Counterintuitive Short Uphill Transitions in Single-File Diffusion

Ryabov, Artem; Lips, Dominik; Maass, Philipp

doi:10.1021/acs.jpcc.8b12081

Cited by 17 publications

(20 citation statements)

References 60 publications

(71 reference statements)

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“…In contrast to expectations, it takes longer to go along the bias than against the bias. For example, such phenomena have been reported in the single-file diffusion [16], in the biased random walk with exclusion interactions [17], in the single-molecule motion with two different dynamic modes [18] and in the particle dynamics on cycle processes with strong coupling to the environment [19]. It was proposed that the asymmetry in the transition times is the sign that the system is out of equilibrium [18], as well as the consequence of the multi-particle interactions in the system [16,19].…”

Section: Introductionmentioning

confidence: 84%

“…For example, such phenomena have been reported in the single-file diffusion [16], in the biased random walk with exclusion interactions [17], in the single-molecule motion with two different dynamic modes [18] and in the particle dynamics on cycle processes with strong coupling to the environment [19]. It was proposed that the asymmetry in the transition times is the sign that the system is out of equilibrium [18], as well as the consequence of the multi-particle interactions in the system [16,19]. These theoretical studies, however, involved mostly numerical simulations or considered special simplified systems, raising the question if the observed phenomena are valid for more general cases.…”

Section: Introductionmentioning

confidence: 84%

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Crowding breaks the forward/backward symmetry of transition times in biased random walks

Shin

Berezhkovskii

Kolomeisky

2021

The Journal of Chemical Physics

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Microscopic mechanisms of natural processes are frequently understood in terms of random walk models by analyzing local particle transitions. This is because these models properly account for dynamic processes at the molecular level and provide a clear physical picture. Recent theoretical studies made a surprising discovery that in complex systems the symmetry of molecular forward/backward transition times with respect to local bias in the dynamics may be broken and it may take longer to go downhill than uphill. The physical origins of these phenomena remain not fully understood. Here we explore in more detail the microscopic features of the symmetry breaking in the forward/backward transition times by analyzing exactly solvable discrete-state stochastic models. In particular, we consider a specific case of two random walkers on four-sites periodic lattice as the way to represent the general systems with multiple pathways. It is found that the asymmetry in transition times depends on several factors that include the degree of deviation from equilibrium, the particle crowding and methods of measurements of dynamic properties. Our theoretical analysis suggests that the asymmetry in transition times can be explored experimentally for determining the important microscopic features of natural processes by quantitative measuring the local deviations from equilibrium and the degrees of crowding.

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Section: Introductionmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 84%

Crowding breaks the forward/backward symmetry of transition times in biased random walks

Shin

Berezhkovskii

Kolomeisky

2021

The Journal of Chemical Physics

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“…The case f e = f corresponds to particle flow in the environment as in the system and for g → +∞ resembles the situations in the single file models studied in previous work, i.e. in the BASEP 21 and ASEP. 22 The case f e = 0 corresponds to an equilibrium environment, where the flow has no preferred direction.…”

mentioning

confidence: 84%

“…In the extreme case g → ∞, the particles would mutually block each other, corresponding to a single-file diffusion, where similar effects have been reported recently for times of single transitions in crowded environments. 21,22 For attractive interactions, the particles form a low-energy bound state when encountering each other. To escape from such a bound state requires a longer time on average.…”

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confidence: 99%

Cycle completion times probe interactions with environment

Voráč,

Maass,

Ryabov

2020

Preprint

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Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems only.Little is known for interacting systems in non-equilibrium environments. Here, we introduce and study a basic model for cycle processes interacting with an environment that can exhibit a net particle flow. We find a surprising richness of cycle time variations with environmental conditions. This manifests itself in unequal cycle times τ + and τ − in forward and backward cycle direction with both asymmetries τ − < τ + and τ − > τ + , speeding up of backward cycles by interactions, and dynamical phase transitions, where cycle times become multimodal functions of the bias. The model allows us to relate these effects to specific microscopic mechanisms, which can be helpful for interpreting experiments.

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“…ψ ± (t) = ψ(t). In the presence of hidden dissipative mechanisms the symmetry may be lifted counterintuitively [64,65]. Denoting the mean waiting time by t = ∞ 0 tψ(t)dt, the steady state current becomes J M = φ + / t −φ − / t = J.…”

mentioning

confidence: 99%

Violation of Local Detailed Balance Despite a Clear Time-Scale Separation

Hartich¹,

Godec²

2021

Preprint

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Integrating out fast degrees of freedom is known to yield, to a good approximation, memory-less, i.e. Markovian, dynamics. In the presence of such a time-scale separation local detailed balance is believed to emerge and to guarantee thermodynamic consistency arbitrarily far from equilibrium.Here we present a transparent example of a Markov model of a molecular motor where local detailed balance can be violated despite a clear time-scale separation and hence Markovian dynamics. Driving the system far from equilibrium can lead to a violation of local detailed balance against the driving force. We further show that local detailed balance can be restored, even in the presence of memory, if the coarse-graining is carried out as Milestoning. Our work establishes Milestoning not only as a kinetically but for the first time also as a thermodynamically consistent coarse-graining method. Our results are relevant as soon as individual transition paths are appreciable or can be resolved.

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Counterintuitive Short Uphill Transitions in Single-File Diffusion

Cited by 17 publications

References 60 publications

Crowding breaks the forward/backward symmetry of transition times in biased random walks

Crowding breaks the forward/backward symmetry of transition times in biased random walks

Cycle completion times probe interactions with environment

Violation of Local Detailed Balance Despite a Clear Time-Scale Separation

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