Research

 

Areas of interest:

  • Physics of Microbial Growth
    • Mechanics of bacterial cell wall growth;  Developing stochastic models for cell cycle regulation in microbes; Coupling of transcription and translation to cell cycle progression; Effects of variability at the single-cell level on population growth.
  • 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

cells

Image credit: Lars Renner, Dresden Institute of Polymer Research

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 shown, 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. 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, highlighted in Harvard SEAS News, Nature Microbiology community, and the cover of Nature Microbiology.
  2. Amir A, Babaeipour F, McIntosh DB, Nelson DR, Jun S. Bending forces plastically deform growing bacterial cell walls. Proc Natl Acad Sci USA. 2014;111 (16) :5778-83, highlighted in Nat. Phys. 10, 332 (2014).
  3. Amir A, van Teeffelen S. Getting into shape: How do rod-like bacteria control their geometry?. Syst Synth Biol. 2014;8 (3) :227-35, invited article for special issue of Systems and Synthetic Biology on cell division.
  4. Amir A, Paulose J, Nelson DR. Theory of interacting dislocations on cylinders. Phys Rev E Stat Nonlin Soft Matter Phys. 2013;87 (4) :042314.
  5. 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.
  6. Amir A, Nelson DR. Dislocation-mediated growth of bacterial cell walls. Proc Natl Acad Sci U S A. 2012;109 (25) :9833-8,  highlighted in Journal Club for Condensed Matter Physics.

 

Regulation and stochasticity within the cell cycle 

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 [1,2,3,4,5].  Results on budding yeast [6] and archaea [7] show similar behavior, suggesting that the principles involved may be prevalent in nature across different domains of life - for reasons yet to be elucidated. Recently we have also began to explore how such variability at the single-cell level affects the growth of the population as a whole [8].

Relevant publications:

  1. Amir A. Cell size regulation in bacteria. Physical Review Letters. 2014;112 (208102), highlighted in Physics 7, 55 (2014).
  2. Amir A. Point of view: Is cell size a spandrel?. eLife [Internet]. 2017;6 :e22186.
  3. 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.
  4. Ho P-Y, Amir A. Simultaneous regulation of cell size and chromosome replication in bacteria. Front Microbiol. 2015;6 :662.
  5. Marantan A, Amir A. Stochastic modeling of cell growth with symmetric or asymmetric division. 2016.
  6. 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, highlighted in Harvard SEAS News
  7. Eun Y. et al., Archaeal cells share common size control with bacteria despite noisier growth and divisionNature microbiology (2017).
  8. Lin J, Amir A. How does cell size regulation affect population growth?. [Internet]. 2016. arXiv

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. 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.
  2. 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, highlighted in Physics Viewpoint.
  3. 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.
  4. Amir A. Universal frequency-dependent conduction of electron glasses. EPL, [Internet]. 2014;107 (47011).
  5. 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.
  6. Amir A, Oreg Y, Imry Y. Electron glass dynamics. Annu. Rev. Condens. Matter Phys. 2011;2 (235-62).
  7. 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.
  8. Amir A, Oreg Y, Imry Y. 1/f noise and slow relaxations in glasses. TIDS conference. 2009;18 (12) :836.
  9. Amir A, Oreg Y, Imry Y. Slow relaxations and aging in the electron glass. Phys Rev Lett. 2009;103 (12) :126403.
  10. Amir A, Oreg Y, Imry Y. Variable range hopping in the Coulomb glass. Physical Review B. 2009;80 (245214).
  11. Amir A, Oreg Y, Imry Y. Mean-field model for electron-glass dynamics. Physical Review B. 2008;77 (165207).

 

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:

  1. Cook CQ, Amir A. Chirped photonic crystals: a natural strategy for broadband reflectance. Optica [Internet]. 2016;3 :1436-1439, highlighted on the cover of Optica.
  2. Amir A, Vukusic P. Elucidating the stop bands of structurally colored systems through recursion. American Journal of Physics. 2013;81 (253).


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. Amir A, Oreg Y, Imry Y. Localization, anomalous diffusion, and slow relaxations: a random distance matrix approach. Phys Rev Lett. 2010;105 (7) :070601.
  2. 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).
            

Miscellaneous      

 

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.