Research

Areas of interest:

  • Biophysics of Bacterial Growth
    • Mechanics of bacterial cell walls; regulation of bacterial growth; cell cycle control in microorganisms, focusing on bacteria and budding yeast.
  • Structural Coloration
    • Disorder effects and multilayer interference phenomena in nature.
  • Theory of Glasses
    • Aging and slow relaxations; out-of-equilibrium systems; dynamics and noise

Mechanics of bacterial growth

 
Cell straightening

Image credit: Lars Renner

How do microorganisms maintain their shapes? We are applying ideas from statistical mechanics and materials science to this interdisciplinary problem, in collaboration with our experimental colleagues. Previously we have showed, experimentally and theoretically, that mechanical stresses can strongly affect cell wall growth in bacteria [1,2,3,4,5]. We are currently working on elucidating how such mechanical cues may aid bacteria in restoring their native forms when their shape is perturbed, and how the binding of proteins to membranes may act as a curvature sensor.

Relevant publications:

  1. Dislocation-mediated growth of bacterial cell walls, Ariel Amir and David R. Nelson, PNAS, 109, 9833 (2012), highlighted in Journal Club for Condensed Matter Physics.
  2. Theory of interacting dislocations on cylinders, Ariel Amir, Jayson Paulose and David R. Nelson, Phys. Rev. E 87, 042314 (2013).
  3. Defects on cylinders: superfluid helium films and bacterial cell walls , Ariel Amir and David R. Nelson, Lectures given by D. R. Nelson at the Les Houches School on "Soft Interfaces", July 2-27, 2012.
  4. Getting into shape: how do rod-like bacteria control their geometry?, Ariel Amir and Sven van Teeelen, invited article for special issue of Systems and Synthetic Biology on cell division, 10.1007/s11693-014-9143-9 (2014).

  5. Bending forces plastically deform growing bacterial cell walls, Ariel Amir, Farinaz Babaeipour, Dustin B. McIntosh, David R. Nelson and Suckjoon Jun, PNAS 111, 16, 5778 (2014), highlighted in Nat. Phys. 10, 332 (2014).

Regulation and stochasticity within the cell cycle of bacterial growth

Microorganisms such as bacteria and yeast are able to maintain a narrow distribution of cell sizes by regulating the timing of cell divisions. In rich nutrient conditions, bacteria such as E. coli divide faster than their chromosomes replicate, implying that cells maintain multiple ongoing rounds of chromosome replication. How these processes are coupled and controlled is a fundamental question in cellular biology. We have shown that ideas from statistical mechanics are helpful is deciphering this problem, and lead to a simple model where cell size and chromosome replication may be simultaneously regulated [1,2]. The model elucidates the experimentally observed correlations between various events in the cell cycle, and explains the known exponential dependence of cell size on the growth rate. Results on budding yeast show similar behavior, suggesting that the principles involved may be prevalent in nature across different domains of life [3].

Relevant publications:

  1. Cell size regulation in microorganismsAriel AmirPhys. Rev. Lett. 112, 208102 (2014), highlighted in Physics 7, 55 (2014).
  2. Simultaneous regulation of cell size and chromosome replication in bacteriaPo-Yi Ho and Ariel Amir,  Front. Microbiol. 6, 662 (2015).
  3. Single-Cell Analysis of Growth in Budding Yeast and Bacteria Reveals a Common Size Regulation Strategy, Ilya Soifer, Lydia Robert, and Ariel Amir, Current Biology 26, 3 (2016), highlighted in Harvard SEAS News

The physics of glasses

 

 

The interplay of disorder and interactions can lead to remarkable effects, such as a glassy phase - many systems in nature exhibit slow dynamics, aging and memory effects, on time scales ranging from seconds to days. Previously, we studied electron glasses, which are systems in which electrons exhibit these phenomena. Recently, we are also trying to extend our approach to other, "non-conventional" glasses, such as crumpled thin sheets and other mechanical systems, in collaboration with the Rubinstein lab at Harvard.

Relevant publications:

  1. Mean-field model for electron-glass dynamics,
    Ariel Amir, Yuval Oreg, and Yoseph Imry, Phys. Rev. B 77, 165207 (2008) .
  2. Slow Relaxations and Aging in the Electron Glass,
    Ariel Amir, Yuval Oreg, and Yoseph Imry, Phys. Rev. Lett. 103, 126403 (2009) .
  3. Variable range hopping in the Coulomb glass,
    Ariel Amir, Yuval Oreg, and Yoseph Imry, Phys. Rev. B 80, 245214 (2009) .
  4. 1/f noise and slow relaxations in glasses,
    Ariel Amir, Yuval Oreg, and Yoseph Imry,
    Ann. Phys. (Berlin) 18, 12, 836 (2009),
    proceedings of the TIDS conference
    .
  5. Huge (but Finite) Time Scales in Slow Relaxations: Beyond Simple Aging,
    Ariel Amir, Stefano Borini, Yuval Oreg, and Yoseph Imry, Phys. Rev. Lett. 107, 186407 (2011) .
  6. Dynamics of electron glasses, Ariel Amir, Yuval Oreg, and Yoseph Imry, invited review for Annual Review of Condensed Matter Physics, Vol. 2, p. 235-262 .
  7. On relaxations and memories of certain materials Ariel Amir, Yuval Oreg, and Yoseph Imry, PNAS, 109, 1850 (2012).
  8. Universal frequency-dependent conduction of electron glasses Ariel Amir, EPL, 107, 4 (2014).

Structural Coloration

 

 

Various insects, fish, birds and flowers use interference phenomena to achieve color, rather than use pigments (the above photo shows the multilayer-Fabry-Perot-type structure used by this beetle to get its green color). Thus, with only two transparent materials arranged in a periodic or in some cases amorphous arrangment, a wide range of coloration can be achieved. Yet little is known regarding the effects of disorder on this structural coloration. How can these systems be robust to it, and can they actually use the disorder?

Relevant publications:

Elucidating the stop bands of structurally colored systems through recursion, Ariel Amir, Peter Vukusic , American Journal of Physics, 81, 253 (2013).


Phonons in disordered media

  

 

Anderson localization was mostly studied for electronic systems, but in fact it is a wave phenomena not restricted only to quantum mechanics. We found that the vibration eigenmodes ("phonons") of a disordered network of massses and springs can exhibit a localization/delocalization transition, which is similar to the electronic systems yet with various distinct differences.

Relevant publications:

  1. Localization, Anomalous Diffusion, and Slow Relaxations: A Random Distance Matrix Approach,
    Ariel Amir, Yuval Oreg, and Yoseph Imry, Phys. Rev. Lett. 105, 070601 (2010) .
  2. Emergent percolation length and localization in random elastic networks,Ariel Amir, Jacob Krich, Vincenzo Vitelli, Yuval Oreg, and Yoseph Imry Phys. Rev. X 3, 021017 (2013).

            

Miscellaneous 

       
  • Quantum Zeno and Dicke effect

Decays in quantum hierarchical modelsAriel Amir, Yuval Oreg, and Yoseph Imry, Phys. Rev. A 77, 050101(R) (2008).

  • Classical vs. Quantum diffusion

Classical diffusion of a quantum particle in a noisy environmentAriel Amir, Yoav Lahini and Hagai B. Perets, Phys. Rev. E 79, 050105(R) (2009).

  • Anomalies in two-dimensional diffusing, measured using Electromagnetically-Induced-Transparency:

Anomalous symmetry breaking in two-dimensional diffusion of coherent atoms, Rami Pugatch, Dipankar Bhattacharyya, Ariel Amir, Yoav Sagi and Nir Davidson, Phys. Rev. A 80, 033807 (2014).

  • Thermopower and electric conductance near the Anderson localization transition:

The localization transition at finite temperatures: electric and thermal transport,
Yoseph Imry and Ariel Amir, Chapter in book "50 years of Anderson localization", edited by E. Abrahams (World Scientific, Singapore, 2010).

  • On the geometry of hives and optimization problems (in Hebrew):

On the Mathematical and Biological Complexity of Honeybee Hives, Ariel Amir, PhysicaPlus 4 (2005).

We anticipate openings at the intersection of physics, applied mathematics, and biology. The candidate should have a strong quantitative background. The position can start at any time. Qualified persons are advised to send their CV and names of references.

Harvard is an equal opportunity employer and encourages applications from under-represented groups such as women and minorities.