Soifer I, Robert L, Amir A. Single-Cell Analysis of Growth in Budding Yeast and Bacteria Reveals a Common Size Regulation Strategy. Current Biology [Internet]. 2015. Publisher's Version
Ho P-Y, Amir A. Simultaneous regulation of cell size and chromosome replication in bacteria. Front Microbiol. 2015;6 :662.Abstract
Bacteria are able to maintain a narrow distribution of cell sizes by regulating the timing of cell divisions. In rich nutrient conditions, cells divide much faster than their chromosomes replicate. This implies that cells maintain multiple rounds of chromosome replication per cell division by regulating the timing of chromosome replications. Here, we show that both cell size and chromosome replication may be simultaneously regulated by the long-standing initiator accumulation strategy. The strategy proposes that initiators are produced in proportion to the volume increase and is accumulated at each origin of replication, and chromosome replication is initiated when a critical amount per origin has accumulated. We show that this model maps to the incremental model of size control, which was previously shown to reproduce experimentally observed correlations between various events in the cell cycle and explains the exponential dependence of cell size on the growth rate of the cell. Furthermore, we show that this model also leads to the efficient regulation of the timing of initiation and the number of origins consistent with existing experimental results.
Pugatch R, Bhattacharyya D, Amir A, Sagi Y, Davidson N. Anomalous symmetry breaking in two-dimensional diffusion of coherent atoms. Physical Review A. 2014;80 (033807).Abstract

The electromagnetically induced transparency (EIT) spectrum of atoms diffusing in and out of a narrow beam is measured and shown to manifest the two-dimensional δ-function anomaly in a classical setting. In the limit of small-area beams, the EIT line shape is independent of power, and equal to the renormalized local density of states of a free particle Hamiltonian. The measured spectra for different powers and beam sizes collapses to a single universal curve with a characteristic logarithmic Van Hove singularity close to resonance.

Amir A, Babaeipour F, McIntosh DB, Nelson DR, Jun S. Bending forces plastically deform growing bacterial cell walls. Proc Natl Acad Sci U S A. 2014;111 (16) :5778-83.Abstract
Cell walls define a cell's shape in bacteria. The walls are rigid to resist large internal pressures, but remarkably plastic to adapt to a wide range of external forces and geometric constraints. Currently, it is unknown how bacteria maintain their shape. In this paper, we develop experimental and theoretical approaches and show that mechanical stresses regulate bacterial cell wall growth. By applying a precisely controllable hydrodynamic force to growing rod-shaped Escherichia coli and Bacillus subtilis cells, we demonstrate that the cells can exhibit two fundamentally different modes of deformation. The cells behave like elastic rods when subjected to transient forces, but deform plastically when significant cell wall synthesis occurs while the force is applied. The deformed cells always recover their shape. The experimental results are in quantitative agreement with the predictions of the theory of dislocation-mediated growth. In particular, we find that a single dimensionless parameter, which depends on a combination of independently measured physical properties of the cell, can describe the cell's responses under various experimental conditions. These findings provide insight into how living cells robustly maintain their shape under varying physical environments.
Amir A. Cell size regulation in bacteria. Physical Review Letters. 2014;112 (208102).Abstract

Various bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant, but is typically distributed over a narrow range. Here, we propose an analytically tractable model for cell size control, and calculate the cell size and interdivision time distributions, as well as the correlations between these variables. We suggest ways of extracting the model parameters from experimental data, and show that existing data for E. colisupports partial size control, and a particular explanation: a cell attempts to add a constant volume from the time of initiation of DNA replication to the next initiation event. This hypothesis accounts for the experimentally observed correlations between mother and daughter cells as well as the exponential dependence of size on growth rate.

Amir A, van Teeffelen S. Getting into shape: How do rod-like bacteria control their geometry?. Syst Synth Biol. 2014;8 (3) :227-35.Abstract
Rod-like bacteria maintain their cylindrical shapes with remarkable precision during growth. However, they are also capable to adapt their shapes to external forces and constraints, for example by growing into narrow or curved confinements. Despite being one of the simplest morphologies, we are still far from a full understanding of how shape is robustly regulated, and how bacteria obtain their near-perfect cylindrical shapes with excellent precision. However, recent experimental and theoretical findings suggest that cell-wall geometry and mechanical stress play important roles in regulating cell shape in rod-like bacteria. We review our current understanding of the cell wall architecture and the growth dynamics, and discuss possible candidates for regulatory cues of shape regulation in the absence or presence of external constraints. Finally, we suggest further future experimental and theoretical directions which may help to shed light on this fundamental problem.
Amir A. Universal frequency-dependent conduction of electron glasses. EPL, [Internet]. 2014;107 (47011). Publisher's VersionAbstract

Characterizing the frequency-dependent response of amorphous systems and glasses can provide important insights into their physics. Here, we study the response of an electron glass, where Coulomb interactions are important and have previously been shown to significantly modify the conductance and lead to memory effects and aging. We propose a model which allows us to take the interactions into account in a self-consistent way, and explore the frequency-dependent conduction at all frequencies. At low frequencies conduction occurs on the percolation backbone, and the model captures the variable-range-hopping behavior. At high frequencies conduction is dominated by localized clusters. Despite the difference in physical mechanisms at low and high frequency, we are able to approximately scale all numerical data onto a single curve, using two parameters: the DC conduction and the DC dielectric constant. The behavior follows the universal scaling that is experimentally observed for a large class of amorphous solids.

Amir A, Vukusic P. Elucidating the stop bands of structurally colored systems through recursion. American Journal of Physics. 2013;81 (253).Abstract

Interference phenomena are the source of some of the spectacular colors of animals and plants in nature. In some of these systems, the physical structure consists of an ordered array of layers with alternating high and low refractive indices. This periodicity leads to an optical band structure that is analogous to the electronic band structure encountered in semiconductor physics; namely, specific bands of wavelengths (the stop bands) are perfectly reflected. Here, we present a minimal model for optical band structure in a periodic multilayer and solve it using recursion relations. We present experimental data for various beetles, whose optical structure resembles the proposed model. The stop bands emerge in the limit of an infinite number of layers by finding the fixed point of the recursive relations. In order for these to converge, an infinitesimal amount of absorption needs to be present, reminiscent of the regularization procedures commonly used in physics calculations. Thus, using only the phenomenon of interference and the idea of recursion, we are able to elucidate the concepts of band structure and regularization in the context of experimentally observed phenomena, such as the high reflectance and the iridescent color appearance of structurally colored beetles.

Amir A, Krich J, Vitelli V, Oreg Y, Imry Y. Emergent percolation length and localization in random elastic networks. Physical Review X. 2013;3 (021017).Abstract

We study, theoretically and numerically, a minimal model for phonons in a disordered system. For sufficient disorder, the vibrational modes of this classical system can become Anderson localized, yet this problem has received significantly less attention than its electronic counterpart. We find rich behavior in the localization properties of the phonons as a function of the density, frequency, and spatial dimension. We use a percolation analysis to argue for a Debye spectrum at low frequencies for dimensions higher than one, and for a localization-delocalization transition (at a critical frequency) above two dimensions. We show that in contrast to the behavior in electronic systems, the transition exists for arbitrarily large disorder, albeit with an exponentially small critical frequency. The structure of the modes reflects a divergent percolation length that arises from the disorder in the springs without being explicitly present in the definition of our model. Within the percolation approach, we calculate the speed of sound of the delocalized modes (phonons), which we corroborate with numerics. We find the critical frequency of the localization transition at a given density and find good agreement of these predictions with numerical results using a recursive Green-function method that was adapted for this problem. The connection of our results to recent experiments on amorphous solids is discussed.

Amir A, Paulose J, Nelson DR. Theory of interacting dislocations on cylinders. Phys Rev E Stat Nonlin Soft Matter Phys. 2013;87 (4) :042314.Abstract
We study the mechanics and statistical physics of dislocations interacting on cylinders, motivated by the elongation of rod-shaped bacterial cell walls and cylindrical assemblies of colloidal particles subject to external stresses. The interaction energy and forces between dislocations are solved analytically, and analyzed asymptotically. The results of continuum elastic theory agree well with numerical simulations on finite lattices even for relatively small systems. Isolated dislocations on a cylinder act like grain boundaries. With colloidal crystals in mind, we show that saddle points are created by a Peach-Koehler force on the dislocations in the circumferential direction, causing dislocation pairs to unbind. The thermal nucleation rate of dislocation unbinding is calculated, for an arbitrary mobility tensor and external stress, including the case of a twist-induced Peach-Koehler force along the cylinder axis. Surprisingly rich phenomena arise for dislocations on cylinders, despite their vanishing Gaussian curvature.
Nelson DR, Amir A. Defects on cylinders: superfluid helium films and bacterial cell walls. Lectures given by D. R. Nelson at the Les Houches School on ”Soft Interfaces,” July 2-27. 2012;arxiv:1303.5896.
Amir A, Oreg Y, Imry Y. On relaxations and aging of various glasses. Proc Natl Acad Sci U S A. 2012;109 (6) :1850-5.Abstract
Slow relaxation occurs in many physical and biological systems. "Creep" is an example from everyday life. When stretching a rubber band, for example, the recovery to its equilibrium length is not, as one might think, exponential: The relaxation is slow, in many cases logarithmic, and can still be observed after many hours. The form of the relaxation also depends on the duration of the stretching, the "waiting time." This ubiquitous phenomenon is called aging, and is abundant both in natural and technological applications. Here, we suggest a general mechanism for slow relaxations and aging, which predicts logarithmic relaxations, and a particular aging dependence on the waiting time. We demonstrate the generality of the approach by comparing our predictions to experimental data on a diverse range of physical phenomena, from conductance in granular metals to disordered insulators and dirty semiconductors, to the low temperature dielectric properties of glasses.
Amir A, Nelson DR. Dislocation-mediated growth of bacterial cell walls. Proc Natl Acad Sci U S A. 2012;109 (25) :9833-8.Abstract
Recent experiments have illuminated a remarkable growth mechanism of rod-shaped bacteria: proteins associated with cell wall extension move at constant velocity in circles oriented approximately along the cell circumference [Garner EC, et al., (2011) Science 333:222-225], [Domínguez-Escobar J, et al. (2011) Science 333:225-228], [van Teeffelen S, et al. (2011) PNAS 108:15822-15827]. We view these as dislocations in the partially ordered peptidoglycan structure, activated by glycan strand extension machinery, and study theoretically the dynamics of these interacting defects on the surface of a cylinder. Generation and motion of these interacting defects lead to surprising effects arising from the cylindrical geometry, with important implications for growth. We also discuss how long range elastic interactions and turgor pressure affect the dynamics of the fraction of actively moving dislocations in the bacterial cell wall.
Amir A, Oreg Y, Imry Y. Electron glass dynamics. Annu. Rev. Condens. Matter Phys. 2011;2 (235-62).Abstract

Examples of glasses are abundant, yet it remains one of the phases of matter whose understanding is very elusive. In recent years, remarkable experiments have been performed on the dynamical aspects of glasses. Electron glasses offer a particularly good example of the trademarks of glassy behavior, such as aging and slow relaxations. In this work we review the experimental literature on electron glasses, as well as the local mean-field theoretical framework put forward in recent years to understand some of these results. We also present novel theoretical results explaining the periodic aging experiment.

Amir A, Borini S, Oreg Y, Imry Y. Huge (but finite) time scales in slow relaxations: beyond simple aging. Phys Rev Lett. 2011;107 (18) :186407.Abstract
Experiments performed in the last years demonstrated slow relaxations and aging in the conductance of a large variety of materials. Here, we present experimental and theoretical results for conductance relaxation and aging for the case-study example of porous silicon. The relaxations are experimentally observed even at room temperature over time scales of hours, and when a strong electric field is applied for a time tw, the ensuing relaxation depends on tw. We derive a theoretical curve and show that all experimental data collapse onto it with a single time scale as a fitting parameter. This time scale is found to be of the order of thousands of seconds at room temperature. The generic theory suggested is not fine-tuned to porous silicon, and thus we believe the results should be universal, and the presented method should be applicable for many other systems manifesting memory and other glassy effects.
Amir A, Oreg Y, Imry Y. Localization, anomalous diffusion, and slow relaxations: a random distance matrix approach. Phys Rev Lett. 2010;105 (7) :070601.Abstract
We study the spectral properties of a class of random matrices where the matrix elements depend exponentially on the distance between uniformly and randomly distributed points. This model arises naturally in various physical contexts, such as the diffusion of particles, slow relaxations in glasses, and scalar phonon localization. Using a combination of a renormalization group procedure and a direct moment calculation, we find the eigenvalue distribution density (i.e., the spectrum), for low densities, and the localization properties of the eigenmodes, for arbitrary dimension. Finally, we discuss the physical implications of the results.
Imry Y, Amir A. The localization transition at finite temperatures: electric and thermal transport. In: Abrahams E 50 Years of Anderson Localization. Singapore: World Scientific ; 2010. Publisher's VersionAbstract

The Anderson localization transition is considered at finite temperatures. This includes the electrical conductivity as well as the electronic thermal conductivity and the thermoelectric coefficients. An interesting critical behavior of the latter is found. A method for characterizing the conductivity critical exponent, an important signature of the transition, using the conductivity and thermopower measurements, is outlined.

Amir A, Oreg Y, Imry Y. 1/f noise and slow relaxations in glasses. TIDS conference. 2009;18 (12) :836.Abstract

Recently we have shown that slow relaxations in the electron glass system can be understood in terms of the spectrum of a matrix describing the relaxation of the system close to a metastable state. The model focused on the electron glass system, but its generality was demonstrated on various other examples. Here, we study the noise spectrum in the same framework. We obtain a remarkable relation between the spectrum of relaxation rates λ described by the distribution function P(λ)1/λ and the 1/f noise in the fluctuating occupancies of the localized electronic sites. This noise can be observed using local capacitance measurements. We confirm our analytic results using numerics, and also show how the Onsager symmetry is fulfilled in the system.

Amir A, Lahini Y, Perets HB. Classical diffusion of a quantum particle in a noisy environment. Phys Rev E Stat Nonlin Soft Matter Phys. 2009;79 (5 Pt 1) :050105.Abstract
We study the spreading of a quantum-mechanical wave packet in a tight-binding model with a noisy potential and analyze the emergence of classical diffusion from the quantum dynamics due to decoherence. We consider a finite correlation time of the noisy environment and treat the system by utilizing the separation of fast (dephasing) and slow (diffusion) processes. We show that classical diffusive behavior emerges at long times and we calculate analytically the dependence of the classical diffusion coefficient on the noise magnitude and correlation time. This method provides a general solution to this problem for arbitrary conditions of the noisy environment. The calculation can be done in any dimension, but we demonstrate it in one dimension for clarity of representation. The results are relevant to a large variety of physical systems, from electronic transport in solid-state physics to light transmission in optical devices, diffusion of excitons, and quantum computation.
Amir A, Oreg Y, Imry Y. Slow relaxations and aging in the electron glass. Phys Rev Lett. 2009;103 (12) :126403.Abstract
Glassy systems are ubiquitous in nature. They are characterized by slow relaxations to equilibrium without a typical time scale, aging, and memory effects. Understanding this has been a long-standing problem in physics. We study the aging of the electron glass, a system showing remarkable slow relaxations of the conductance. We find that the appropriate broad distribution of relaxation rates leads to a universal relaxation of the form log(1 + t_{w}/t) for the common aging protocol, where t_{w} is the length of time the perturbation driving the system out of equilibrium was on, and t the time of measurement. These results agree well with several experiments performed on different glassy systems, and examining different physical observables, for times ranging from seconds to several hours. The suggested theoretical framework appears to offer a paradigm for aging in a broad class of glassy materials.