Negative friction memory induces persistent motion

Mitterwallner, Bernhard G.; Lavacchi, Laura; Netz, Roland R.

doi:10.1140/epje/i2020-11992-5

Cited by 15 publications

(11 citation statements)

References 50 publications

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“…Fig. 2 C shows that it is accurately reproduced by multiexponential memory and that it disappears when memory effects are eliminated, in line with recent theoretical analysis ( 43 ). The overall good agreement between MD and GLE simulation results shows that the GLE in the form of Eq.…”

Section: Resultssupporting

confidence: 89%

Non-Markovian modeling of protein folding

Ayaz

Tepper

Brünig

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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We extract the folding free energy landscape and the time-dependent friction function, the two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular dynamics (MD) simulations of the α-helix forming polypeptide alanine9 for a one-dimensional reaction coordinate based on the sum of the native H-bond distances. Folding and unfolding times from numerical integration of the GLE agree accurately with MD results, which demonstrate the robustness of our GLE-based non-Markovian model. In contrast, Markovian models do not accurately describe the peptide kinetics and in particular, cannot reproduce the folding and unfolding kinetics simultaneously, even if a spatially dependent friction profile is used. Analysis of the GLE demonstrates that memory effects in the friction significantly speed up peptide folding and unfolding kinetics, as predicted by the Grote–Hynes theory, and are the cause of anomalous diffusion in configuration space. Our methods are applicable to any reaction coordinate and in principle, also to experimental trajectories from single-molecule experiments. Our results demonstrate that a consistent description of protein-folding dynamics must account for memory friction effects.

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Section: Resultssupporting

confidence: 89%

Non-Markovian modeling of protein folding

Ayaz

Tepper

Brünig

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…Our experimental results show that cells, by leaving chemical footprints along their way, are endowed with a spatial memory of their path. Their theoretical analysis, therefore, calls for a framework that goes beyond the classical models invoked in the literature, which are for most of them amenable to markovian, and, therefore, memoryless descriptions [5][6][7]15,17,40 , with the exception of 41,42 . Our observations led us to argue that cell trajectories naturally fall in the class of self interacting random walks, which can be broadly defined as the class of random walks that interact (attractively or repulsively) with the full territory explored until time t [43][44][45][46][47][48][49][50] .…”

Section: Isolated Cells Exhibit Regular Oscillationsmentioning

confidence: 99%

Cell migration guided by long-lived spatial memory

et al. 2021

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Living cells actively migrate in their environment to perform key biological functions—from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion, and has been shown to also integrate various chemical or physical extracellular signals. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodelling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells can retrieve their path: by confining motile cells on 1D and 2D micropatterned surfaces, we demonstrate that they leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.

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“…The oscillatory dynamics in Ref. [19] was reproduced using a generalized Langevin equation with negative memory at long times, which can induce persistent motion [20,21] and stress overshoots [22]. Furthermore, it was noted that the non-linear properties of a bath can already be detected in equilibrium [23].…”

Section: Introductionmentioning

confidence: 98%

Two step micro-rheological behavior in a viscoelastic fluid

Jain,

Ginot,

Berner

et al. 2021

Preprint

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We perform micro-rheological experiments with a colloidal bead driven through a viscoelastic worm-like micellar fluid and observe two distinctive shear thinning regimes, each of them displaying a Newtonian-like plateau. The shear thinning behavior at larger velocities is in qualitative agreement with macroscopic rheological experiments. The second process, observed at Weissenberg numbers as small as a few percent, appears to have no analog in macro rheological findings. A simple model introduced earlier captures the observed behavior, and implies that the two shear thinning processes correspond to two different length scales in the fluid. This model also reproduces oscillations which have been observed in this system previously. While the system under macro-shear seems to be near equilibrium for shear rates in the regime of the intermediate Newtonian-like plateau, the one under micro-shear is thus still far from it. The analysis suggests the existence of a length scale of a few micrometres, the nature of which remains elusive.

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Negative friction memory induces persistent motion

Cited by 15 publications

References 50 publications

Non-Markovian modeling of protein folding

Non-Markovian modeling of protein folding

Cell migration guided by long-lived spatial memory

Two step micro-rheological behavior in a viscoelastic fluid

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