Lin J, Amir A. Homeostasis of protein and mRNA concentrations in growing cells. [Internet]. 2018. bioRxivAbstract

Many experiments show that the numbers of mRNA and protein are proportional to the cell volume in growing cells. However, models of stochastic gene expression often assume constant transcription rate per gene and constant translation rate per mRNA, which are incompatible with these experiments. Here, we construct a minimal gene expression model to fill this gap. Assuming ribosomes and RNA polymerases are limiting in gene expression, we find that (1) because the ribosomes translate all proteins, the concentrations of proteins and mRNAs are regulated in an exponentially growing cell volume; (2) the competition between genes for the RNA polymerases makes the transcription rate independent of the genome number. Furthermore, by extending the model to situations in which DNA (mRNA) can be saturated by RNA polymerases (ribosomes) and becomes limiting, we predict a transition from exponential to linear growth of cell volume as the protein-to-DNA ratio increases.

Wong F, Amir A. Bacterial cell lysis: geometry, elasticity, and implications. [Internet]. 2018. bioRxivAbstract
Membrane lysis, or rupture, is a cell death pathway in bacteria frequently caused by cell wall-targeting antibiotics. Although several studies have clarified biochemical mechanisms of antibiotic action, a physical understanding of the processes leading to lysis remains lacking. Here, we analyze the dynamics of membrane bulging and lysis in Escherichia coli, where, strikingly, the formation of an initial bulge ("bulging") after cell wall digestion occurs on a characteristic timescale as fast as 100 ms and the growth of the bulge ("swelling") occurs on a slower characteristic timescale of 10-100 s. We show that bulging can be energetically favorable due to the relaxation of the entropic and stretching energies of the inner membrane, cell wall, and outer membrane and that experimentally observed bulge shapes are consistent with model predictions. We then show that swelling can involve both the continued flow of water into the cytoplasm and the enlargement of wall defects, after which cell lysis is consistent with both the inner and outer membranes exceeding characteristic estimates of the yield areal strains of biological membranes. Our results contrast biological membrane physics and the physics of thin shells, reveal principles of how all bacteria likely function in their native states, and may have implications for cellular morphogenesis and antibiotic discovery across different species of bacteria.
Lin J, Amir A. Population growth with correlated generation times at the single-cell level. [Internet]. 2018. arXivAbstract
Single-cell experiments have revealed significant cell-to-cell variability in generation times for genetically identical cells. Theoretical models relating the fluctuating generation times of single cells to the growth rate of the entire population are usually based on the assumption that the generation times of mother and daughter cells are uncorrelated. However, it was recently realized that this assumption is inconsistent with exponentially growing cell volume at the single-cell level. Here we propose an analytically solvable model in which the generation times of mother and daughter cells are explicitly correlated. Surprisingly, we find that the population growth rate only depends on the distribution of single-cell growth rates for cells growing exponentially at the single-cell level. We find that for weakly correlated single-cell growth rates, the variability of the single-cell growth rates is detrimental for the population. When the correlation coefficient of mother-daughter cells' growth rates is above a certain threshold, the variability becomes beneficial.
Lin J, Min J, Amir A. Optimal segregation of proteins: phase transitions and symmetry breaking. [Internet]. 2018. arXivAbstract
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.
Amir A, Balaban NQ. Learning from Noise: How Observing Stochasticity May Aid Microbiology. Trends in Microbiology [Internet]. 2018;26 :374-385. Publisher's VersionAbstract
For many decades, the wedding of quantitative data with mathematical modeling has been fruitful, leading to important biological insights. Here, we review some of the ongoing efforts to gain insights into problems in microbiology – and, in particular, cell-cycle progression and its regulation – through observation and quantitative analysis of the natural fluctuations in the system. We first illustrate this idea by reviewing a classic example in microbiology – the Luria–Delbrück experiment – and discussing how, in that case, useful information was obtained by looking beyond the mean outcome of the experiment, but instead paying attention to the variability between replicates of the experiment. We then switch gears to the contemporary problem of cell cycle progression and discuss in more detail how insights into cell size regulation and, when relevant, coupling between the cell cycle and the circadian clock, can be gained by studying the natural fluctuations in the system and their statistical properties. We end with a more general discussion of how (in this context) the correct level of phenomenological model should be chosen, as well as some of the pitfalls associated with this type of analysis. Throughout this review the emphasis is not on providing details of the experimental setups or technical details of the models used, but rather, in fleshing out the conceptual structure of this particular approach to the problem. For this reason, we choose to illustrate the framework on a rather broad range of problems, and on organisms from all domains of life, to emphasize the commonality of the ideas and analysis used (as well as their differences).
Amir A, Oreg Y, Imry Y. Thermal conductivity in 1d: disorder-induced transition from anomalous to normal scaling. [Internet]. 2018. arXivAbstract
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 √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.
Upadhyaya N, Amir A. Disorder engineering: From structural coloration to acoustic filters. [Internet]. 2018. arXivAbstract
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.
Ho P-Y, Lin J, Amir A. Modeling cell size regulation: From single-cell level statistics to molecular mechanisms and population level effects. Annual Review of Biophysics [Internet]. 2018;47. Publisher's VersionAbstract
Most microorganisms regulate their cell size. In this article, we review some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics that they generate. We review the biologically relevant insights obtained from these models. We then describe cell cycle regulation and its 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.
Eun Y-J, Ho P-Y, Kim M, LaRussa S, Robert L, Renner LD, Schmid A, Garner E, Amir A. Archaeal cells share common size control with bacteria despite noisier growth and division. Nature Microbiology [Internet]. 2018;3 :148-154. Publisher's VersionAbstract
In nature, microorganisms exhibit different volumes spanning six orders of magnitude 1 . Despite their capability to create different sizes, a clonal population in a given environment maintains a uniform size across individual cells. Recent studies in eukaryotic and bacterial organisms showed that this homogeneity in cell size can be accomplished by growing a constant size between two cell cycle events (that is, the adder model 2-6 ). Demonstration of the adder model led to the hypothesis that this phenomenon is a consequence of convergent evolution. Given that archaeal cells share characteristics with both bacteria and eukaryotes, we investigated whether and how archaeal cells exhibit control over cell size. To this end, we developed a soft-lithography method of growing the archaeal cells to enable quantitative time-lapse imaging and single-cell analysis, which would be useful for other microorganisms. Using this method, we demonstrated that Halobacterium salinarum, a hypersaline-adapted archaeal organism, grows exponentially at the single-cell level and maintains a narrow-size distribution by adding a constant length between cell division events. Interestingly, the archaeal cells exhibited greater variability in cell division placement and exponential growth rate across individual cells in a population relative to those observed in Escherichia coli 6-9 . Here, we present a theoretical framework that explains how these larger fluctuations in archaeal cell cycle events contribute to cell size variability and control.
Hussain S, Wivagg CN, Szwedziak P, Wong F, Schaefer K, Izoré T, Renner LD, Holmes MJ, Sun Y, Bisson-Filho AW, et al. MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis. eLife [Internet]. 2018;7 :e32471. Publisher's VersionAbstract
MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape of Bacillus subtilis. MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomes in vitro, orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape.
Logsdon MM, Ho P-Y, Papavinasasundaram K, Richardson K, Cokol M, Sassetti CM, Amir A, Aldridge BB. A Parallel Adder Coordinates Mycobacterial Cell-Cycle Progression and Cell-Size Homeostasis in the Context of Asymmetric Growth and Organization. Current Biology [Internet]. 2017. Publisher's VersionAbstract
In model bacteria, such as Ecoli and Bsubtilis, regulation of cell-cycle progression and cellular organization achieves consistency in cell size, replication dynamics, and chromosome positioning [ 1–3 ]. Mycobacteria elongate and divide asymmetrically, giving rise to significant variation in cell size and elongation rate among closely related cells [ 4, 5 ]. Given the physical asymmetry of mycobacteria, the models that describe coordination of cellular organization and cell-cycle progression in model bacteria are not directly translatable [ 1, 2, 6–8 ]. Here, we used time-lapse microscopy and fluorescent reporters of DNA replication and chromosome positioning to examine the coordination of growth, division, and chromosome dynamics at a single-cell level in Mycobacterium smegmatis (M. smegmatis) and Mycobacterium bovis Bacillus Calmette-Guérin (BCG). By analyzing chromosome and replisome localization, we demonstrated that chromosome positioning is asymmetric and proportional to cell size. Furthermore, we found that cellular asymmetry is maintained throughout the cell cycle and is not established at division. Using measurements and stochastic modeling of mycobacterial cell size and cell-cycle timing in both slow and fast growth conditions, we found that well-studied models of cell-size control are insufficient to explain the mycobacterial cell cycle. Instead, we showed that mycobacterial cell-cycle progression is regulated by an unprecedented mechanism involving parallel adders (i.e., constant growth increments) that start at replication initiation. Together, these adders enable mycobacterial populations to regulate cell size, growth, and heterogeneity in the face of varying environments.
Barber F, Ho P-Y, Murray AW, Amir A. Details Matter: noise and model structure set the relationship between cell size and cell cycle timing. [Internet]. 2017. Publisher's VersionAbstract
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.
Wong F, Amir A, Gunawardena J. An energy-speed-accuracy relation in complex networks for biological discrimination. [Internet]. 2017. arXivAbstract
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→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.
Lin J, Amir A. The Effects of Stochasticity at the Single-Cell Level and Cell Size Control on the Population Growth. Cell Systems [Internet]. 2017. Publisher's VersionAbstract
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.
Wong F, Renner LD, Özbaykal G, Paulose J, Weibel DB, van Teeffelen S, Amir A. Mechanical strain sensing implicated in cell shape recovery in Escherichia coli. Nature Microbiology [Internet]. 2017;2 :17115. Publisher's VersionAbstract
The shapes of most bacteria are imparted by the structures of their peptidoglycan cell walls, which are determined by many dynamic processes that can be described on various length scales ranging from short-range glycan insertions to cellular-scale elasticity. Understanding the mechanisms that maintain stable, rod-like morphologies in certain bacteria has proved to be challenging due to an incomplete understanding of the feedback between growth and the elastic and geometric properties of the cell wall. Here, we probe the effects of mechanical strain on cell shape by modelling the mechanical strains caused by bending and differential growth of the cell wall. We show that the spatial coupling of growth to regions of high mechanical strain can explain the plastic response of cells to bending and quantitatively predict the rate at which bent cells straighten. By growing filamentous Escherichia coli cells in doughnut-shaped microchambers, we find that the cells recovered their straight, native rod-shaped morphologies when released from captivity at a rate consistent with the theoretical prediction. We then measure the localization of MreB, an actin homologue crucial to cell wall synthesis, inside confinement and during the straightening process, and find that it cannot explain the plastic response to bending or the observed straightening rate. Our results implicate mechanical strain sensing, implemented by components of the elongasome yet to be fully characterized, as an important component of robust shape regulation in E. coli.
Asban O, Amir A, Imry Y, Schechter M. Effect of interactions and disorder on the relaxation of two-level systems in amorphous solids. Physical Review B [Internet]. 2017;95 :144207. Publisher's VersionAbstract

At low temperatures the dynamical degrees of freedom in amorphous solids are tunneling 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 et al.Phys. Rev. B 77, 165207 (2008)]. Similarly to the electron glass, we find a 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.

Amir A. Point of view: Is cell size a spandrel?. eLife [Internet]. 2017;6 :e22186. Publisher's VersionAbstract

All organisms control the size of their cells. We focus here on the question of size regulation in bacteria, and suggest that the quantitative laws governing cell size and its dependence on growth rate may arise as byproducts of a regulatory mechanism which evolved to support multiple DNA replication forks. In particular, we show that the increase of bacterial cell size during Lenski’s long-term evolution experiments is a natural outcome of this proposal. This suggests that, in the context of evolution, cell size may be a 'spandrel'

Lahini Y, Gottesman O, Amir A, Rubinstein S. Non-Monotonic Aging and Memory Retention in Disordered Mechanical Systems. Physical Review Letters [Internet]. 2017;118 :085501. Physics ViewpointAbstract

We observe nonmonotonic 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 nonexponential relaxation. However, when after a certain waiting time the compression is partially reduced, both systems exhibit a nonmonotonic response: the normal force first increases over many minutes or even hours until reaching a peak value, and only then is relaxation 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 nonmonotonic behavior may be generic and that athermal systems can show genuine glassy behavior.

Zheng H, Ho P-Y, Jiang M, Tang B, Liu W, Li D, Yu X, Kleckner NE, Amir A, Liu C. Interrogating the Escherichia coli cell cycle by cell dimension perturbations. Proc. Natl. Acad. Sci. USA [Internet]. 2016. Publisher's VersionAbstract

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.

Eisenbach A, Havdala T, Delahaye J, Grenet T, Amir A, Frydman A. Glassy Dynamics in Disordered Electronic Systems Reveal Striking Thermal Memory Effects. Physical Review Letters. 2016;117 :116601.Abstract

Memory is one of the unique qualities of a glassy system. The relaxation of a glass to equilibrium contains information on the sample’s excitation history, an effect often refer to as “aging.” We demonstrate that under the right conditions a glass can also possess a different type of memory. We study the conductance relaxation of electron glasses that are fabricated at low temperatures. Remarkably, the dynamics are found to depend not only on the ambient measurement temperature but also on the maximum temperature to which the system was exposed. Hence the system “remembers” its highest temperature. This effect may be qualitatively understood in terms of energy barriers and local minima in configuration space and therefore may be a general property of the glass state.