arXiv subjects

Ariel Amir

Publications and source records attributed to Ariel Amir.

At least 37 records · Page 2Linked to original sources

arXiv2020

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.

q-bio.PE↗

arXiv2020

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.

q-bio.PE↗

arXiv2019

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.

cond-mat.dis-nn↗

arXiv2019

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.

cond-mat.stat-mech↗

arXiv2018

Quantum Diffusion in the Strong Tunneling Regime

We study the spread of a quantum-mechanical wavepacket in a noisy environment, modeled using a tight-binding Hamiltonian. Despite the coherent dynamics, the fluctuating environment may give rise to diffusive behavior. When correlations between different level-crossing events can be neglected, we use the solution of the Landau-Zener problem to find how the diffusion constant depends on the noise. We also show that when an electric field or external disordered potential is applied to the system, the diffusion constant is suppressed with no drift term arising. The results are relevant to various quantum systems, including exciton diffusion in photosynthesis and electronic transport in solid-state physics.

cond-mat.stat-mech↗

arXiv2018

Optimal segregation of proteins: phase transitions and symmetry breaking

Asymmetric segregation of key proteins at cell division -- be it a beneficial or deleterious protein -- is ubiquitous in unicellular organisms and often considered as an evolved trait to increase fitness in a stressed environment. Here, we provide a general framework to describe the evolutionary origin of this asymmetric segregation. We compute the population fitness as a function of the protein segregation asymmetry $a$, and show that the value of $a$ which optimizes the population growth manifests a phase transition between symmetric and asymmetric partitioning phases. Surprisingly, the nature of phase transition is different for the case of beneficial proteins as opposed to proteins which decrease the single-cell growth rate. Our study elucidates the optimization problem faced by evolution in the context of protein segregation, and motivates further investigation of asymmetric protein segregation in biological systems.

q-bio.PE↗

arXiv2018

Thermal conductivity in 1d: disorder-induced transition from anomalous to normal scaling

It is well known that the contribution of harmonic phonons to the thermal conductivity of 1D systems diverges with the harmonic chain length $L$ (explicitly, increases with $L$ as a power-law with a positive power). Furthermore, within various one-dimensional models containing disorder it was shown that this divergence persists, with the thermal conductivity scaling as $\sqrt{L}$ under certain boundary conditions, where $L$ is the length of the harmonic chain. Here we show that when the chain is weakly coupled to the heat reservoirs and there is strong disorder this scaling can be violated. We find a weaker power-law dependence on $L$, and show that for sufficiently strong disorder the thermal conductivity stops being anomalous -- despite both density-of-states and the diverging localization length scaling anomalously. Surprisingly, in this strong disorder regime two anomalously scaling quantities cancel each other to recover Fourier's law of heat transport.

cond-mat.dis-nn↗

arXiv2018

Disorder engineering: From structural coloration to acoustic filters

We study Anderson localization of waves in a one dimensional disordered meta-material of bilayers comprising of thin fixed length scatterers placed randomly along a homogenous medium. As an interplay between order and disorder, we identify a new regime of strong disorder where the localization length becomes independent of the amount of disorder but depends on the frequency of the wave excitation and on the properties of the fixed length scatterer. As an example of a naturally occurring nearly one dimensional disordered bilayer, we calculate the wavelength dependent reflection spectrum for Koi fish using the experimentally measured parameters, and find that the main mechanisms for the emergence of their silver structural coloration can be explained through the phenomenon of Anderson localization of light in the regime of strong disorder discussed above. Finally, we show that by tuning the thickness of the fixed length scatterer, the above design principles could be used to engineer disordered meta-materials which selectively allows harmonics of a fundamental frequency to be transmitted in an effect which is similar to the insertion of a half wave cavity in a quarter wavelength stack. However, in contrast to the Lorentzian resonant peak of a half-wave cavity, we find that our disordered layer has a Gaussian lineshape whose width becomes narrower as the number of disordered layers is increased.

cond-mat.dis-nn↗

arXiv2018

Modeling cell size regulation: From single-cell level statistics to molecular mechanisms and population level effects

Most microorganisms regulate their cell size. We review here some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics they generate. We review the biologically relevant insights obtained from these models. We then describe cell cycle regulation and their molecular implementations, protein number regulation, and population growth, all in relation to size regulation. Finally, we discuss several future directions for developing understanding beyond phenomenological models of cell size regulation.

q-bio.CB↗

arXiv2017

Details Matter: noise and model structure set the relationship between cell size and cell cycle timing

Organisms across all domains of life regulate the size of their cells. However, the means by which this is done is poorly understood. We study two abstracted "molecular" models for size regulation: inhibitor dilution and initiator accumulation. We apply the models to two settings: bacteria like Escherichia coli, that grow fully before they set a division plane and divide into two equally sized cells, and cells that form a bud early in the cell division cycle, confine new growth to that bud, and divide at the connection between that bud and the mother cell, like the budding yeast Saccharomyces cerevisiae. In budding cells, delaying cell division until buds reach the same size as their mother leads to very weak size control, with average cell size and standard deviation of cell size increasing over time and saturating up to 100-fold higher than those values for cells that divide when the bud is still substantially smaller than its mother. In budding yeast, both inhibitor dilution or initiator accumulation models are consistent with the observation that the daughters of diploid cells add a constant volume before they divide. This adder behavior has also been observed in bacteria. We find that in bacteria an inhibitor dilution model produces adder correlations that are not robust to noise in the timing of DNA replication initiation or in the timing from initiation of DNA replication to cell division (the C + D period). In contrast, in bacteria an initiator accumulation model yields robust adder correlations in the regime where noise in the timing of DNA replication initiation is much greater than noise in the C + D period, as reported previously [1]. In bacteria, division into two equally sized cells does not broaden the size distribution.

q-bio.MN↗

arXiv2017

An energy-speed-accuracy relation in complex networks for biological discrimination

Discriminating between correct and incorrect substrates is a core process in biology but how is energy apportioned between the conflicting demands of accuracy ($μ$), speed ($σ$) and total entropy production rate ($P$)? Previous studies have focussed on biochemical networks with simple structure or relied on simplifying kinetic assumptions. Here, we use the linear framework for timescale separation to analytically examine steady-state probabilities away from thermodynamic equilibrium for networks of arbitrary complexity. We also introduce a method of scaling parameters that is inspired by Hopfield's treatment of kinetic proofreading. Scaling allows asymptotic exploration of high-dimensional parameter spaces. We identify in this way a broad class of complex networks and scalings for which the quantity $σ\ln(μ)/P$ remains asymptotically finite whenever accuracy improves from equilibrium, so that $μ_{eq}/μ\to 0$. Scalings exist, however, even for Hopfield's original network, for which $σ\ln(μ)/P$ is asymptotically infinite, illustrating the parametric complexity. Outside the asymptotic regime, numerical calculations suggest that, under more restrictive parametric assumptions, networks satisfy the bound, $σ\ln(μ/μ_{eq})/P < 1$, and we discuss the biological implications for discrimination by ribosomes and DNA polymerase. The methods introduced here may be more broadly useful for analysing complex networks that implement other forms of cellular information processing.

q-bio.MN↗

arXiv2017

The effects of stochasticity at the single-cell level and cell size control on the population growth

Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally observed correlations between mother-daughter generation times that are unavoidable when cell size is controlled for - which is essentially always the case. Here, we study population-level growth in the presence of cell size control and corroborate our theory using experimental measurements of single-cell growth rates. We derive a closed formula for the population growth rate and demonstrate that it only depends on the single-cell growth rate variability, not other sources of stochasticity. Our work provides an evolutionary rationale for the narrow growth rate distributions often observed in nature: when single-cell growth rates are less variable but have a fixed mean, the population will exhibit an enhanced population growth rate, as long as the correlations between the mother and daughter cells' growth rates are not too strong.

q-bio.PE↗

arXiv2017

Theory of chirped photonic crystals in biological broadband reflectors

One-dimensional photonic crystals with slowly varying, i.e. "chirped", lattice period are responsible for broadband light reflectance in many diverse biological contexts, ranging from the shiny coatings of various beetles to the eyes of certain butterflies. We present a quantum scattering analogy for light reflection from these adiabatically chirped photonic crystals (ACPCs) and apply a WKB-type approximation to obtain a closed-form expression for the reflectance. From this expression we infer several design principles, including a differential equation for the chirp pattern required to elicit a given reflectance spectrum and the minimal number of bilayers required to exceed a desired reflectance threshold. Comparison of the number of bilayers found in ACPCs throughout nature and our predicted minimal required number also gives a quantitative measure of the optimality of chirped biological reflectors. Together these results elucidate the design principles of chirped reflectors in nature and their possible application to future optical technologies.

physics.optics↗

arXiv2017

Nonmonotonic Aging and Memory Retention in Disordered Mechanical Systems

We observe non-monotonic aging and memory effects, two hallmarks of glassy dynamics, in two disordered mechanical systems: crumpled thin sheets and elastic foams. Under fixed compression, both systems exhibit monotonic non-exponential relaxation. However, when after a certain waiting time the compression is partially reduced, both systems exhibit a non-monotonic response: the normal force first increases over many minutes or even hours until reaching a peak value, and only then relaxation is resumed. The peak-time scales linearly with the waiting time, indicating that these systems retain long-lasting memory of previous conditions. Our results and the measured scaling relations are in good agreement with a theoretical model recently used to describe observations of monotonic aging in several glassy systems, suggesting that the non-monotonic behavior may be generic and that a-thermal systems can show genuine glassy behavior.

cond-mat.soft↗

arXiv2017

Interrogating the Escherichia coli cell cycle by cell dimension perturbations

Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter 's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed adder-per-origin model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.

q-bio.CB↗

arXiv2016

Surprises in numerical expressions of physical constants

In science, as in life, `surprises' can be adequately appreciated only in the presence of a null model, what we expect a priori. In physics, theories sometimes express the values of dimensionless physical constants as combinations of mathematical constants like pi or e. The inverse problem also arises, whereby the measured value of a physical constant admits a `surprisingly' simple approximation in terms of well-known mathematical constants. Can we estimate the probability for this to be a mere coincidence, rather than an inkling of some theory? We answer the question in the most naive form.

physics.pop-ph↗

arXiv2016

Single-cell analysis of growth in budding yeast and bacteria reveals a common size regulation strategy

To maintain a constant cell size, dividing cells have to coordinate cell cycle events with cell growth. This coordination has for long been supposed to rely on the existence of size thresholds determining cell cycle progression [1]. In budding yeast, size is controlled at the G1/S transition [11]. In agreement with this hypothesis, the size at birth influences the time spent in G1: smaller cells have a longer G1 period [3]. Nevertheless, even though cells born smaller have a longer G1, the compensation is imperfect and they still bud at smaller cell sizes. In bacteria, several recent studies have shown that the incremental model of size control, in which size is controlled by addition of a constant volume (in contrast to a size threshold), is able to quantitatively explain the experimental data on 4 different bacterial species [6, 5, 6, 7]. Here, we report on experimental results for the budding yeast Saccharomyces cerevisiae, finding, surprisingly, that cell size control in this organism is very well described by the incremental model, suggesting a common strategy for cell size control with bacteria. Additionally, we argue that for S. cerevisiae the volume increment is not added from birth to division, but rather between two budding events.

q-bio.CB↗

arXiv2016

Stochastic modeling of cell growth with symmetric or asymmetric division

We consider a class of biologically-motivated stochastic processes in which a unicellular organism divides its resources (volume or damaged proteins, in particular) symmetrically or asymmetrically between its progeny. Assuming the final amount of the resource is controlled by a growth policy and subject to additive and multiplicative noise, we derive the "master equation" describing how the resource distribution evolves over subsequent generations and use it to study the properties of stable resource distributions. We find conditions under which a unique stable resource distribution exists and calculate its moments for the class of affine linear growth policies. Moreover, we apply an asymptotic analysis to elucidate the conditions under which the stable distribution (when it exists) has a power-law tail. Finally, we use the results of this asymptotic analysis along with the moment equations to draw a stability phase diagram for the system that reveals the counterintuitive result that asymmetry serves to increase stability while at the same time widening the stable distribution. We also briefly discuss how cells can divide damaged proteins asymmetrically between their progeny as a form of damage control. In the appendix, motivated by the asymmetric division of cell volume in Saccharomyces cerevisiae, we extend our results to the case wherein mother and daughter cells follow different growth policies.

q-bio.QM↗