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Researcher profile

Ariel Amir

Ariel Amir contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Biological Physicscond-mat.stat-mechcond-mat.dis-nnPopulations and Evolutioncond-mat.softCell Behaviorcond-mat.mes-hallphysics.flu-dynSubcellular Processes

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Published work

11 published item(s)

preprint2026arXiv

Essential Role of Extrinsic Noise in Models of E. coli Division Control

Our understanding of cell division control in bacteria still relies largely on interpreting correlations between phenomenological variables, with limited connection to the underlying molecular mechanisms. Here, we analytically solve a stochastic threshold-accumulation model in which a size-dependent divisor protein triggers division upon reaching a noisy, autocorrelated threshold, quantifying within a unified framework the combined effects of intrinsic and extrinsic noise and key mechanistic parameters such as protein reset and threshold memory. We show that incorporating these elements yields behavior far richer than the commonly assumed adder, spanning a continuum of division strategies from timer to sizer while modulating size fluctuations in a nontrivial fashion. Comparison with single-cell E. coli data shows that extrinsic noise and additional mechanistic ingredients are required to account for the observed size fluctuations. The adder emerges when threshold correlations balance protein reset, generalizing the hypothesis that full reset is necessary to maintain adder control. Our results establish a unified analytical framework linking stochastic molecular processes to emergent division laws, to be used in more complex bacterial cell-cycle models.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Conditional Probability as Found in Nature: Facilitated Diffusion

Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a vanishingly small part of the entire DNA, where at the same time the search must end in a matter of tens of seconds at most for its biological purpose to be fulfilled - this makes the search a problem of high interest. Facilitated Diffusion is a mechanism used in nature for a robust and efficient search process. This mechanism combines 1D diffusion along the DNA and "excursions" of diffusion in 3D that help the TF to quickly arrive at distant parts of the DNA. In this paper we provide a derivation concerning this mechanism that links this search process to fundamental concepts in probability theory (conditional probability).

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Universal catastrophe time distributions of dynamically unstable polymers

Dynamic instability -- the growth, catastrophe, and shrinkage of quasi-one-dimensional filaments -- has been observed in multiple biopolymers. Scientists have long understood the catastrophic cessation of growth and subsequent depolymerization as arising from the interplay of hydrolysis and polymerization at the tip of the polymer. Here, we show that for a broad class of catastrophe models, the expected catastrophe time distribution is exponential. We show that the distribution shape is insensitive to noise, but that depletion of monomers from a finite pool can dramatically change the distribution shape by reducing the polymerization rate. We derive a form for this finite-pool catastrophe time distribution and show that finite-pool effects can be important even when the depletion of monomers does not greatly alter the polymerization rate.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Bending Instability of Rod-shaped Bacteria

A thin-walled tube, e.g., a drinking straw, manifests an instability when bent by localizing the curvature change in a small region. This instability has been extensively studied since the seminal work of Brazier nearly a century ago. However, the scenario of pressurized tubes has received much less attention. Motivated by rod-shaped bacteria such as E. coli, whose cell walls are much thinner than their radius and are subject to a substantial internal pressure, we study, theoretically, how this instability is affected by this internal pressure. In the parameter range relevant to the bacteria, we find that the internal pressure significantly postpones the onset of the instability, while the bending stiffness of the cell wall has almost no influence. This study suggests a new method to infer turgor pressure in rod-shaped bacteria from bending experiments.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Temporal Evolution of Flow in Pore-Networks: From Homogenization to Instability

We study the dynamics of flow-networks in porous media using a pore-network model. First, we consider a class of erosion dynamics assuming a constitutive law depending on flow rate, local velocities, or shear stress at the walls. We show that depending on the erosion law, the flow may become uniform and homogenized or become unstable and develop channels. By defining an order parameter capturing these different behaviors we show that a phase transition occurs depending on the erosion dynamics. Using a simple model, we identify quantitative criteria to distinguish these regimes and correctly predict the fate of the network, and discuss the experimental relevance of our result.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

A large deviation principle linking lineage statistics to fitness in microbial populations

In exponentially proliferating populations of microbes, the population typically doubles at a rate less than the average doubling time of a single-cell due to variability at the single-cell level. It is known that the distribution of generation times obtained from a single lineage is, in general, insufficient to determine a population's growth rate. Is there an explicit relationship between observables obtained from a single lineage and the population growth rate? We show that a population's growth rate can be represented in terms of averages over isolated lineages. This lineage representation is related to a large deviation principle that is a generic feature of exponentially proliferating populations. Due to the large deviation structure of growing populations, the number of lineages needed to obtain an accurate estimate of the growth rate depends exponentially on the duration of the lineages, leading to a non-monotonic convergence of the estimate, which we verify in both synthetic and experimental data sets.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

From single-cell variability to population growth

Single-cell experiments have revealed cell-to-cell variability in generation times and growth rates for genetically identical cells. Theoretical models relating the fluctuating generation times of single cells to the population growth rate are usually based on the assumption that the generation times of mother and daughter cells are uncorrelated. This assumption, however, is inconsistent with the exponential growth of cell volume in time observed for many cell types. Here we develop a more general and biologically relevant model in which cells grow exponentially and generation times are correlated in a manner which controls cell size. In addition to the fluctuating generation times, we also allow the single-cell growth rates to fluctuate and account for their correlations across the lineage tree. Surprisingly, we find that the population growth rate only depends on the distribution of single-cell growth rates and their correlations.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Non-genetic variability: survival strategy or nuisance?

The observation that phenotypic variability is ubiquitous in isogenic populations has led to a multitude of experimental and theoretical studies seeking to probe the causes and consequences of this variability. Whether it be in the context of antibiotic treatments or exponential growth in constant environments, non-genetic variability has shown to have significant effects on population dynamics. Here, we review research that elucidates the relationship between cell-to-cell variability and population dynamics. After summarizing the relevant experimental observations, we discuss models of bet-hedging and phenotypic switching. In the context of these models, we discuss how switching between phenotypes at the single-cell level can help populations survive in uncertain environments. Next, we review more fine-grained models of phenotypic variability where the relationship between single-cell growth rates, generation times and cell sizes is explicitly considered. Variability in these traits can have significant effects on the population dynamics, even in a constant environment. We show how these effects can be highly sensitive to the underlying model assumptions. We close by discussing a number of open questions, such as how environmental and intrinsic variability interact and what the role of non-genetic variability in evolutionary dynamics is.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

The effect of interactions and disorder on the relaxation of two-level systems in amorphous solids

At low temperatures the dynamical degrees of freedom in amorphous solids are tunnelling two-level systems (TLSs). Concentrating on these degrees of freedom, and taking into account disorder and TLS-TLS interactions, we obtain a "TLS-glass", described by the random field Ising model with random $1/r^3$ interactions. In this paper we perform a self consistent mean field calculation, previously used to study the electron-glass (EG) model [A.~Amir {\it et al.}, Phys. Rev. B {\bf 77}, 165207, (2008)]. Similar to the electron-glass, we find $\frac{1}λ$ distribution of relaxation rates $λ$, leading to logarithmic slow relaxation. However, with increased interactions the EG model shows slower dynamics whereas the TLS glass model shows faster dynamics. This suggests that given system specific properties, glass dynamics can be slowed down or sped up by the interactions.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

An elementary renormalization-group approach to the Generalized Central Limit Theorem and Extreme Value Distributions

The Generalized Central Limit Theorem is a remarkable generalization of the Central Limit Theorem, showing that the sum of a large number of independent, identically-distributed (i.i.d) random variables with infinite variance may converge under appropriate scaling to a distribution belonging to a special family known as Levy stable distributions. Similarly, the maximum of i.i.d. variables may converge to a distribution belonging to one of three universality classes (Gumbel, Weibull and Frechet). Here, we rederive these known results following a mathematically non-rigorous yet highly transparent renormalization-group-like approach that captures both of these universal results following a nearly identical procedure.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Thermal conductance of one dimensional disordered harmonic chains

We study heat conduction mediated by longitudinal phonons in one dimensional disordered harmonic chains. Using scaling properties of the phonon density of states and localization in disordered systems, we find non-trivial scaling of the thermal conductance with the system size. Our findings are corroborated by extensive numerical analysis. We show that a system with strong disorder, characterized by a `heavy-tailed' probability distribution, and with large impedance mismatch between the bath and the system satisfies Fourier's law. We identify a dimensionless scaling parameter, related to the temperature scale and the localization length of the phonons, through which the thermal conductance for different models of disorder and different temperatures follows a universal behavior.

0 citations0 reviewsNo code linkedOpen access