Diffusive lensing as a mechanism of intracellular transport and compartmentalization

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    The authors discuss an effect, "diffusive lensing", by which particles would accumulate in high-viscosity regions, for instance in the intracellular medium. To obtain these results, the authors rely on agent-based simulations using custom rules performed with the Ito stochastic calculus convention. The "lensing effect" discussed is a direct consequence of the choice of the Ito convention without spurious drift which has been discussed before and is likely to be inadequate for the intracellular medium, causing the presented results to likely have little relevance for biology.

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Abstract

While inhomogeneous viscosity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales remain largely unexplored. In this work, we use agent-based simulations of diffusion to investigate how heterogenous viscosity affects movement and concentration of diffusing particles. We propose that a nonequilibrium mode of membraneless compartmentalization arising from the convergence of diffusive trajectories into viscous sinks, which we call “diffusive lensing,” can occur in a wide parameter space and is thus likely to be ubiquitous in living systems. Our work highlights the phenomenon of diffusive lensing as a potentially key driver of mesoscale dynamics in the cytoplasm, with possible far-reaching implications for biochemical processes.

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  1. eLife assessment

    The authors discuss an effect, "diffusive lensing", by which particles would accumulate in high-viscosity regions, for instance in the intracellular medium. To obtain these results, the authors rely on agent-based simulations using custom rules performed with the Ito stochastic calculus convention. The "lensing effect" discussed is a direct consequence of the choice of the Ito convention without spurious drift which has been discussed before and is likely to be inadequate for the intracellular medium, causing the presented results to likely have little relevance for biology.

  2. Reviewer #1 (Public Review):

    The manuscript "Diffusive lensing as a mechanism of intracellular transport and compartmentalization", explores the implications of heterogeneous viscosity on the diffusive dynamics of particles. The authors analyze three different scenarios:

    (i) diffusion under a gradient of viscosity,

    (ii) clustering of interacting particles in a viscosity gradient, and

    (iii) diffusive dynamics of non-interacting particles with circular patches of heterogeneous viscous medium.

    The implications of a heterogeneous environment on phase separation and reaction kinetics in cells are under-explored. This makes the general theme of this manuscript very relevant and interesting. However, the analysis in the manuscript is not rigorous, and the claims in the abstract are not supported by the analysis in the main text.

    Following are my main comments on the work presented in this manuscript:

    (a) The central theme of this work is that spatially varying viscosity leads to position-dependent diffusion constant. This, for an overdamped Langevin dynamics with Gaussian white noise, leads to the well-known issue of the interpretation of the noise term. The authors use the Ito interpretation of the noise term because their system is non-equilibrium.

    One of the main criticisms I have is on this central point. The issue of interpretation arises only when there are ill-posed stochastic dynamics that do not have the relevant timescales required to analyze the noise term properly. Hence, if the authors want to start with an ill-posed equation it should be mentioned at the start. At least the Langevin dynamics considered should be explicitly mentioned in the main text. Since this work claims to be relevant to biological systems, it is also of significance to highlight the motivation for using the ill-posed equation rather than a well-posed equation. The authors refer to the non-equilibrium nature of the dynamics but it is not mentioned what non-equilibrium dynamics to authors have in mind. To properly analyze an overdamped Langevin dynamics a clear source of integrated timescales must be provided. As an example, one can write the dynamics as
    Eq. (1) \dot x = f(x) + g(x) \eta , which is ill-defined if the noise \eta is delta correlated in time but well-defined when \eta is exponentially correlated in time. One can of course look at the limit in which the exponential correlation goes to a delta correlation which leads to Eq. (1) interpreted in Stratonovich convention. The choice to use the Ito convention for Eq. (1) in this case is not justified.

    (b) Generally, the manuscript talks of viscosity gradient but the equations deal with diffusion which is a combination of viscosity, temperature, particle size, and particle-medium interaction. There is no clear motivation provided for focus on viscosity (cytoplasm as such is a complex fluid) instead of just saying position-dependent diffusion constant. Maybe authors should use viscosity only when talking of a context where the existence of a viscosity gradient is established either in a real experiment or in a thought experiment.

    (c) The section "Viscophoresis drives particle accumulation" seems to not have new results. Fig. 1 verifies the numerical code used to obtain the results in the later sections. If that is the case maybe this section can be moved to supplementary or at least it should be clearly stated that this is to establish the correctness of the simulation method. It would also be nice to comment a bit more on the choice of simulation methods with changing hopping sizes instead of, for example, numerically solving stochastic ODE.

    A minor comment, the statement "the physically appropriate convention to use depends upon microscopic parameters and timescale hierarchies not captured in a coarse-grained model of diffusion." is not true as is noted in the references that authors mention, a correct coarse-grained model provides a suitable convention (see also Phys. Rev. E, 70(3), 036120., Phys. Rev. E, 100(6), 062602.).

    (d) The section "Interaction-mediated clustering is affected by viscophoresis" makes an interesting statement about the positioning of clusters by a viscous gradient. As a theoretical calculation, the interplay between position-dependent diffusivity and phase separation is indeed interesting, but the problem needs more analysis than that offered in this manuscript. Just a plot showing clustering with and without a gradient of diffusion does not give enough insight into the interplay between density-dependent diffusion and position-dependent diffusion. A phase plot that somehow shows the relative contribution of the two effects would have been nice. Also, it should be emphasized in the main text that the inter-particle interaction is through a density-dependent diffusion constant and not a conservative coupling by an interaction potential.

    (e) The section "In silico microrheology shows that viscophoresis manifests as anomalous diffusion" the authors show that the MSD with and without spatial heterogeneity is different. This is not a surprise - as the underlying equations are different the MSD should be different. There are various analogies drawn in this section without any justification:
    (i) "the saturation MSD was higher than what was seen in the homogeneous diffusion scenario possibly due to particles robustly populating the bulk milieu followed by directed motion into the viscous zone (similar to that of a Brownian ratchet, (Peskin et al., 1993))."
    (ii) "Note that lensing may cause particle displacements to deviate from a Gaussian distribution, which could explain anomalous behaviors observed both in our simulations and in experiments in cells (Parry et al., 2014)."
    Since the full trajectory of the particles is available, it can be analyzed to check if this is indeed the case.

    (f) The final section "In silico FRAP in a heterogeneously viscous environment ... " studies the MSD of the particles in a medium with heterogeneous viscous patches which I find the most novel section of the work. As with the section on inter-particle interaction, this needs further analysis.

    To summarise, as this is a theory paper, just showing MSD or in silico FRAP data is not sufficient. Unlike experiments where one is trying to understand the systems, here one has full access to the dynamics either analytically or in simulation. So just stating that the MSD in heterogeneous and homogeneous environments are not the same is not sufficient. With further analysis, this work can be of theoretical interest. Finally, just as a matter of personal taste, I am not in favor of the analogy with optical lensing. I don't see the connection.

  3. Reviewer #2 (Public Review):

    Summary:
    The authors study through theory and simulations the diffusion of microscopic particles and aim to account for the effects of inhomogeneous viscosity and diffusion - in particular regarding the intracellular environment. They propose a mechanism, termed "Diffusive lensing", by which particles are attracted towards high-viscosity regions where they remain trapped. To obtain these results, the authors rely on agent-based simulations using custom rules performed with the Ito stochastic calculus convention, without spurious drift. They acknowledge the fact that this convention does not describe equilibrium systems, and that their results would not hold at equilibrium - and discard these facts by invoking the fact that cells are out-of-equilibrium. Finally, they show some applications of their findings, in particular enhanced clustering in the high-viscosity regions. The authors conclude that as inhomogeneous diffusion is ubiquitous in life, so must their mechanism be, and hence it must be important.

    Strengths:
    The article is well-written, and clearly intelligible, its hypotheses are stated relatively clearly and the models and mathematical derivations are compatible with these hypotheses.

    Weaknesses:
    The main problem of the paper is these hypotheses. Indeed, it all relies on the Ito interpretation of the stochastic integrals. Stochastic conventions are a notoriously tricky business, but they are both mathematically and physically well-understood and do not result in any "dilemma" [some citations in the article, such as (Lau and Lubensky) and (Volpe and Wehr), make an unambiguous resolution of these]. Conventions are not an intrinsic, fixed property of a system, but a choice of writing; however, whenever going from one to another, one must include a "spurious drift" that compensates for the effect of this change - a mathematical subtlety that is entirely omitted in the article: if the drift is zero in one convention, it will thus be non-zero in another in the presence of diffusive gradients. It is well established that for equilibrium systems obeying fluctuation-dissipation, the spurious drift vanishes in the anti-Ito stochastic convention (which is not "anticipatory", contrarily to claims in the article, are the "steps" are local and infinitesimal). This ensures that the diffusion gradients do not induce currents and probability gradients, and thus that the steady-state PDF is the Gibbs measure. This equilibrium case should be seen as the default: a thermal system NOT obeying this law should warrant a strong justification (for instance in the Volpe and Wehr review this can occur through memory effects in robotic dynamics, or through strong fluctuation-dissipation breakdown). In near-equilibrium thermal systems such as the intracellular medium (where, although out-of-equilibrium, temperature remains a relevant and mostly homogeneous quantity), deviations from this behavior must be physically justified and go to zero when going towards equilibrium.

    Here, drifts are arbitrarily set to zero in the Ito convention (the exact opposite of the equilibrium anti-Ito), which is the equilibrium equivalent to adding a force (with drift $- grad D$) exactly compensating the spurious drift. If we were to interpret this as a breakdown of detailed balance with inhomogeneous temperature, the "hot" region would be effectively at 4x higher temperature than the cold region (i.e. 1200K) in Fig 1A.

    It is the effects of this arbitrary force (exactly compensating the Ito spurious drift) that are studied in the article. The fact that it results in probability gradients is trivial once formulated this way (and in no way is this new - many of the references, for instance, Volpe and Wehr, mention this). Enhanced clustering is also a trivial effect of this probability gradient (the local concentration is increased by this force field, so phase separation can occur). As a side note the "neighbor sensing" scheme to describe interactions is very peculiar and not physically motivated - it violates stochastic thermodynamics laws too, as the detailed balance is apparently not respected. Finally, the "anomalous diffusion" discussion is at odds with what the literature on this subject considers anomalous (the exponent does not appear anomalous).

    The authors make no further justification of their choice of convention than the fact that cells are out-of-equilibrium, leaving the feeling that this is a detail. They make mentions of systems (eg glycogen, prebiotic environment) for which (near-)equilibrium physics should mostly prevail, and of fluctuation-dissipation ("Diffusivity varies inversely with viscosity", in the introduction). Yet the "phenomenon" they discuss is entirely reliant on an undiscussed mechanism by which these assumptions would be completely violated (the citations they make for this - Gnesotto '18 and Phillips '12 - are simply discussions of the fact that cells are out-of-equilibrium, not on any consequences on the convention).

    Finally, while inhomogeneous diffusion is ubiquitous, the strength of this effect in realistic conditions is not discussed (this would be a significant problem if the effect were real, which it isn't). Gravitational attraction is also an ubiquitous effect, but it is not important for intracellular compartmentalization.

    To conclude, the "diffusive lensing" effect presented here is not a deep physical discovery, but a well-known effect of sticking to the wrong stochastic convention.