Nonequilibrium physics

Magnetic actuation of hair cells
David Rowland, Yuttana Roongthumskul, Jae-Hyun Lee, Jinwoo Cheon, Dolores Bozovic

The bullfrog sacculus contains mechanically sensitive hair cells whose stereociliary bundles oscillate spontaneously when decoupled from the overlying membrane. Steady-state offsets on the resting position of a hair bundle can suppress or modulate this native motility. To probe the dynamics of spontaneous oscillation in the proximity of the critical point, we describe here a method for mechanical actuation that avoids loading the bundles or contributing to the viscous drag. Magnetite beads were attached to the tips of the stereocilia, and a magnetic probe was used to impose deflections. This technique allowed us to observe the transition from multi-mode to single-mode state in freely oscillating bundles, as well as the crossover from the oscillatory to the C quiescent state. V 2011 American Institute of Physics. [doi:10.1063/1.3659299]
JPEGs: magnetic.jpg (333.97 KB)
PDFs: Rowland11.pdf (3.36 MB)
Research categories: Biological macromolecules, Nonequilibrium physics


Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism
Timothee Lionnet, Michelle M. Spiering, Stephen J. Benkovic, David Bensimon, Vincent Croquette

Helicases are enzymes that couple ATP hydrolysis to the unwinding of double-stranded (ds) nucleic acids. The bacteriophage T4 helicase (gp41) is a hexameric helicase that promotes DNA replication within a highly coordinated protein complex termed the replisome. Despite recent progress, the gp41 unwinding mechanism and regulatory interactions within the replisome remain unclear. Here we use a single tethered DNA hairpin as a real-time reporter of gp41-mediated dsDNA unwinding and single-stranded (ss) DNA translocation with 3-base pair (bp) resolution. Although gp41 translocates on ssDNA as fast as the in vivo replication fork (400 bp/s), its unwinding rate extrapolated to zero force is much slower (30 bp/s). Together, our results have two implications: first, gp41 unwinds DNA through a passive mechanism; second, this weak helicase cannot efficiently unwind the T4 genome alone. Our results suggest that important regulations occur within the replisome to achieve rapid and processive replication.
JPEGs: Real-time observation of bacteriophage T4 gp41 (390.16 KB)
PDFs: Real-time observation of bacteriophage T4 gp41.pdf (8.38 MB)
Research categories: Biological macromolecules, Cellular mechanics, Nonequilibrium physics


Nonlinear-dynamics theory of up-down transitions in neocortical neural networks

The neurons of the neocortex show ∼1-Hz synchronized transitions between an active up state and a quiescent down state. The up-down state transitions are highly coherent over large sections of the cortex, yet they are accompanied by pronounced, incoherent noise. We propose a simple model for the up-down state oscillations that allows analysis by straightforward dynamical systems theory. An essential feature is a nonuniform network geometry composed of groups of excitatory and inhibitory neurons with strong coupling inside a group and weak coupling between groups. The enhanced deterministic noise of the up state appears as the natural result of the proximity of a partial synchronization transition. The synchronization transition takes place as a function of the long-range synaptic strength linking different groups of neurons.
PDFs: Non-linear dynamics.pdf
JPEGs: levine_nonlineardynamics.jpg (319.59 KB)
Researcn categories: Neuroscience, Nonequilibrium physics


Distribution of Frequencies of Spontaneous Oscillations in Hair Cells of the Bullfrog Sacculus
D. Ramunno-Johnson, C. E. Strimbu, L. Fredrickson, K. Arisaka, and D. Bozovic

Under in vitro conditions, hair bundles of the amphibian inner ear show spontaneous oscillation. We used a high-speed camera to track these active movements, following multiple hair cells in a single field of view. Our techniques enabled us to acquire records on over 100 actively oscillating bundles per epithelium and show the oscillations to be mutually uncorrelated.
JPEGs: spontaneous.jpg (1.17 MB)
PDFs: Ramunno09.pdf (10.57 MB)


 

Bacteria Use Type IV Pili to Walk Upright and Detach from Surfaces
M. L. Gibiansky, J. C. Conrad, F. Jin, V. D. Gordon, D. A. Motto, M. A. Mathewson, W. G. Stopka, D. C. Zelasko, J. Shrout, G. C. L. Wong, “Bacteria use type IV pili to stand, walk upright, and detach from surfaces”, Science, 330, 197 (2010).

Bacterial biofilms are structured multicellular communities involved in a broad range of infections. Knowing how free-swimming bacteria adapt their motility mechanisms near surfaces is crucial for understanding the
transition between planktonic and biofilm phenotypes. By translating microscopy movies into searchable databases of bacterial behavior, we identified fundamental type IV pili–driven mechanisms for Pseudomonas aeruginosa surface motility involved in distinct foraging strategies. Bacteria stood upright and “walked” with trajectories optimized for two-dimensional surface exploration. Vertical orientation facilitated surface detachment and could influence biofilm morphology.
JPEGs: walking_bacteria.jpg (397.02 KB)
PDFs: Science Gibiansky Conrad Wong 2010.pdf (21.73 MB)
Research categories: Cellular mechanics, Tissues and organisms, Nonequilibrium physics


Depiction of a localized retinal delamination
Chou and Siegel, The mechanics of retinal detachment, Submitted to: Physical Biology, (2012).

We present a model of the mechanical and fluid forces associated with retinal detachments where the retinal photoreceptor cells separate from the underlying retinal pigment epithelium (RPE). We determine the conditions under which the subretinal fluid pressure exceeds the maximum yield stress holding the retina and RPE together, giving rise to an irreversible, extended retinal delamination. For detachments induced by traction forces, we find a critical radius beyond which the blister is unstable to growth. Growth of a detached blister can also be driven by inflamed tissue within which, for example, the hydraulic conductivities of the retina or choroid increase, the RPE pumps fail, or the adhesion properties change. We determine the parameter regimes in which the blister either becomes unstable to growth, remains stable and finite-sized, or shrinks, allowing possible healing. The corresponding stable blister radius and shape are calculated. Our analysis provides a quantitative description of the physical mechanisms involved in exudative retinal detachments and can help guide the development of retinal reattachment protocols or preventative procedures.
PNGs: Depiction of a localized retinal delamination.png (153.42 KB)
Research categories: Cellular mechanics, Tissues and Organisms, Nonequilibrium physics


Bacteria use type IV pili to slingshot on surfaces
F. Jin, J. C. Conrad, M. L. Gibiansky, G. C. L. Wong, “Bacteria use type IV pili to slingshot on surfaces”, Proc. Nat. Acad. Sci. USA, 108 12617-12622 (2011).
Fan Jina, Jacinta C. Conrad, Maxsim L. Gibianskya, and Gerard C. L. Wong
Bacteria optimize the use of their motility appendages to move efficiently on a wide range of surfaces prior to forming multicellu- lar bacterial biofilms. The “twitching” motility mode employed by many bacterial species for surface exploration uses type-IV pili (TFP) as linear actuators to enable directional crawling. In addition to linear motion, however, motility requires turns and changes of direction. Moreover, the motility mechanism must be adaptable to the continually changing surface conditions encountered during biofilm formation. Here, we develop a novel two-point tracking algorithm to dissect twitching motility in this context. We show that TFP-mediated crawling in Pseudomonas aeruginosa consistently alternates between two distinct actions: a translation of constant velocity and a combined translation-rotation that is approximately 20× faster in instantaneous velocity. Orientational distributions of these actions suggest that the former is due to pulling by multiple TFP, whereas the latter is due to release by single TFP. The release action leads to a fast “slingshot” motion that can turn the cell body efficiently by oversteering. Furthermore, the large velocity of the slingshot motion enables bacteria to move efficiently through environments that contain shear-thinning vis- coelastic fluids, such as the extracellular polymeric substances (EPS) that bacteria secrete on surfaces during biofilm formation.
JPEGs: slingshot.jpg (363.20 KB)
PDFs: PNAS Jin Wong 2011.pdf (7.95 MB)
Cellular mechanics, Tissues and Organisms, Nonequilibrium physics


The physics of retinal detachments

Tom Chou, Michael Siegel
We develop mathematical model describing the mechanical and fluid forces associated with ex- udative retinal detachments. We assume that the retina adheres to the underlying retinal pigment epitelium (RPE) cells layer via an attractive interaction potential that can be irreversibly destroyed. By computing the total water flow arising from transretinal, vascular, and retinal pigment epithe- lium (RPE) pump currents, we determine the conditions under which the subretinal fluid pressure exceeds the maximum yield stress holding the retina and RPE together, giving rise to an extended retinal delamination. We also investigate localized, blister-like retinal detachments by balancing mechanical tension in the retina with both the chorioretinal adhesion energy and the pressure jump across the retina. For detachments formed by traction, we find a critical radius beyond which the blister is unstable to unbounded growth. On the other hand, if growth of the detached blister is further driven by inflamed choroidal tissue (in which e.g., the RPE pumps do not function), we find in certain cases the blister size depends simply on two parameters, the normal-tissue, dimensionless RPE pump flux, and a dimensionless combination comprising the retinal stretching elasticity, the retina-RPE adhesion energy, and the area of the inflamed lesion. We find parameter regimes which lead to either a finite or infinite blister radii, and to the corresponding blister shape. Our model provides a mathematical description of the physical mechanisms involved in exudative retinal de- tachments and macular edema and can guide further development of retinal reattachment protocols or preventative procedures.
JPEGs: csr-oct.jpg (3.01 MB)
PDFs: blister16.pdf (2.72 MB), Fig1_blister.pdf (89.75 KB)
Research categories: Cellular mechanics, Tissues and Organisms, Nonequilibrium physics, Soft and fragile matter


Propulsion of African trypanosomes is driven by bihelical waves with alternating chirality separated by kinks
Jose A. Rodrígueza, Miguel A. Lopez, Michelle C. Thayer, Yunzhe Zhao, Michael Oberholzer, Donald D. Chang, Neville K. Kisalu, Manuel L. Penichet, Gustavo Helguera, Robijn Bruinsma, Kent L. Hill, and Jianwei Miao
Trypanosoma brucei, a parasitic protist with a single flagellum, is the causative agent of African sleeping sickness. Propulsion of T. brucei was long believed to be by a drill-like, helical motion. Using millisecond differential interference-contrast microscopy and analyzing image sequences of cultured procyclic-form and bloodstream-form parasites, as well as bloodstream-form cells in infected mouse blood, we find that, instead, motility of T. brucei is by the propagation of kinks, separating left-handed and right-handed helical waves. Kink-driven motility, previously encountered in prokaryotes, permits T. brucei a helical propagation mechanism while avoiding the large viscous drag associated with a net rotation of the broad end of its tapering body. Our study demonstrates that millisecond differential interference-contrast microscopy can be a useful tool for uncovering important short-time features of microorganism locomotion.
PDFs: zpq19322.pdf (15.10 MB)
PNGs: Propulsion of African trypanosomes is drivenby bihelical waves with alternating chiralityseparated by kinks.png (903.81 KB)
Reseaerch categories: Tissues and Organisms, Nonequilibrium physics


 

One-dimensional deterministic transport in neurons measured by dispersion-relation phase spectroscopy
Ru Wang , Zhuo Wang, Joe Leigh, Nahil Sobh, Larry Millet, Martha U Gillette, Alex J Levine and Gabriel Popescu
Professor Levine, working with experimental colleagues at the University of Illinois at Urbana-Champaign, explores the “traffic jams” in transport of vesicles down the narrow neural filaments, axons and and dendrites.
JPEGs: One-dimensional deterministic transport.jpg (1.04 MB)
PDFs: One-dimensional-deterministic-transport.pdf (7.20 MB)
Research categories: Tissues and Organisms, Nonequilibrium physics, Experimental probes


Frequency-dependent Chemotactic Target Selection
Sarah A. Nowak, Buddhapriya Chakrabarti, Tom Chou, and Ajay Gopinathan, Frequency-dependent Chemotactic Target Selection, Physic
Chemotaxis is often modeled in the context of cellular motion towards a static, exogenous source of chemoattractant. Here, we propose a time-dependent mechanism of chemotaxis in which a motile particle (the cell) releases a chemical that diffuses to fixed particles (targets) and signals the production of a second chemical by these targets. The motile cell moves up concentration gradients of this second chemical. When one target is present, we describe probe release strategies that optimize travel of the cell to the target. In the presence of multiple targets, the one selected by the cell depends on the strength and, interestingly, on the frequency of probe chemical release. Although involving an additional chemical signaling step, our chemical "pinging" hypothesis allows for greater flexibility in regulating target selection, as seen in a number of physical or biological realizations.
PDFs: 1478-3975_7_2_026003.pdf (3.01 MB)
PNGs: Chemotactic signals emanating from two communicating organisms.png (907.28 KB)
Research categories: Tissues and Organisms, Nonequilibrium physics


A mathematical model for intercellular signaling during epithelial wound healing
Posta and Chou, A mathematical model for intercellular signaling during epithelial wound healing, Journal of Theoretical Biology
Filippo Posta, Tom Chou
Recent experiments monitoring the healing process of wounded epithelial monolayers have demonstrated the necessity of MAPK activation for coordinated cell movement after damage. This MAPK activity is characterized by two wave-like phenomena. One MAPK ``wave'' that originates immediately after injury, propagates deep into the cell sheet, away from the edge, and then rebounds back to the wound interface. After this initial MAPK activity has largely disappeared, a second MAPK front propagates slowly from the wound interface and also continues into the cell sheet, maintaining a sustained level of MAPK activity throughout the cell sheet. It has been suggested that the first wave is initiated by Reactive Oxygen Species (ROS) generated at the time of injury. Here, we develop a minimal mathematical model that reproduces the observed behavior. The main ingredients of our model are a competition between ligands and ROS for the activation of Epithelial Growth Factor Receptor, and a feedback loop between receptor occupancy and MAPK activation. We explore the mathematical properties of the model and look for traveling wave solutions consistent with the experimentally observed MAPK activity patterns.
PDFs: jtb_final.pdf (3.55 MB)
PNGs: A mathematical model for intercellular signaling during epithelial wound healing.png (2.71 MB)
Research categories: Tissues and Organisms, Nonequilibrium physics


Hydrodynamics in curved membranes: The effect of geometry on particulate mobility
Mark L. Henle and Alex J. Levine
We determine the particulate transport properties of fluid membranes with nontrivial geometries that are surrounded by viscous Newtonian solvents. Previously, this problem in membrane hydrodynamics was discussed for the case of flat membranes by Saffman and Delbrück ͓P. G. Saffman and M. Delbrück, Proc. Natl. Acad. Sci. U.S.A. 72, 3111 ͑1975͔͒. We review and develop the formalism necessary to consider the hydrodynamics of membranes with arbitrary curvature and show that the effect of local geometry is twofold. First, local Gaussian curvature introduces in-plane viscous stresses even for situations in which the velocity field is coordinate-independent. Secondly, even in the absence of Gaussian curvature, the geometry of the membrane modifies the momentum transport between the bulk fluids and the membrane. We illustrate these effects by examining in detail the mobilities of particles bound to spherical and cylindrical membranes. These two examples provide experimentally testable predictions for particulate mobilities and membrane velocity fields on giant unilamellar vesicles and membrane tethers. Finally, we use the examples of spherical and cylindrical membranes to demonstrate how the global geometry and topology of the membrane influences the membrane velocities and the particle mobilities.
JPEGs: Hydrodynamics in curved membranes: The effect of geometry on particulate mobility.jpg (1.75 MB)
PDFs: Phys. Rev. E 2010 Henle.pdf (5.48 MB)
Research categories: Nonequilibrium physics, Soft and fragile matter


Stochastic self-assembly of incommensurate clusters
D'Orsogna, Lakatos, Chou, Stochastic self-assembly of incommensurate clusters, Journal of Chemical Physics, 136, 084110, (2012).
M. R. D’Orsogna, G. Lakatos, T. Chou
Nucleation and molecular aggregation are important processes in numerous physical and biological systems. In many applications, these processes often take place in confined spaces, involving a finite number of particles. We examine the classic problem of homogeneous nucleation and self-assembly by deriving and analyzing a fully discrete stochastic master equation, enumerating the highest probability steady-states, and deriving exact analytical formulae for quenched and equilibrium mean cluster size distributions. We find striking differences between the our results and those derived from mass-action equations that depend primarily on the divisibility of the total available mass by the maximum allowed cluster size, and the remainder. When such mass ``incommensurability'' arises, a single remainder particle can ``emulsify'' the system by significantly broadening the equilibrium mean cluster size distribution. This discreteness-induced broadening effect is periodic in the total mass of the system but arises even when the system size is asymptotically large, provided the ratio of the total mass to the maximum cluster size is finite. Our findings define a new scaling regime in which results from classic mass-action theories are qualitatively inaccurate, even in the limit of large total system size.
PDFs: JCP_final.pdf (8.73 MB)
PNGs: Stochastic self-assembly.png (725.98 KB)
Research categories: Nonequilibrium physics, Soft and fragile matter


Magnetocaloritronic Nanomachines
A. A. Kovalev and Y. Tserkovnyak, Solid State Commun. (Special Issue on Caloritronics), 150, 50
A. A. Kovalev, Y. Tserkovnyak
We introduce and study a magnetocaloritronic circuit element based on a domain wall that can move under applied voltage, magnetic field and temperature gradient. We draw analogies between Carnot machines and possible devices employing such a circuit element. We propose a realization of magnetocaloritronic cooling and point out the parallels between the operational principles of magnetocaloritronic and thermoelectric cooling and power generation. Following this analogy, we introduce a magnetocaloritronic figure of merit that encodes information about the maximum efficiency of such devices. Even though the magnetocaloritronic figure of merit turns out to be very small for transition-metal based magnets, we speculate that larger numbers may be expected in ferromagnetic insulators.
JPEGs: PastedGraphic-3.jpg (206.22 KB)
PDFs: kovalevSSC10.pdf (10.34 MB)
Research categories: Nonequilibrium physics

Dissipative dynamics of magnetic solitons in metals
Dissipative Dynamics of Magnetic Solitons in Metals C. H. Wong and Y. Tserkovnyak, Phys. Rev. B (Rap. Comm.) 81, 060404(R) (2010)
Clement H. Wong, Yaroslav Tserkovnyak
Soliton dynamics in spin-textured metals generate electrical currents, which produce backaction through spin torques. We modify the Landau-Lifshitz-Gilbert equation and the corresponding solitonic equations of motion to include such higher-order texture effects. We also find a quasistatic equation for the induced electrochemical potential, which needs to be solved for self-consistently, in the incompressible limit. As an example, we consider the gyration of a vortex in a point-contact spin valve and discuss modifications of orbit radius, frequency, and dissipation power.
JPEGs: PastedGraphic-2.jpg (319.67 KB)
PDFs: wongPRB10.pdf (959.07 KB)
Research categories: Nonequilibrium physics


Non-equilibrium statistical mechanics: Fundamental issues, a paradigmatic model, and applications to biological transport
Chou, Mallick, Zia, Non-equilibrium statistical mechanics: Fundamental issues, a paradigmatic model, and applications to biological transport, Reports on Progess in Physics, 74, 116601, (2011).
T Chou, K Mallick, R K P Zia
Unlike equilibrium statistical mechanics, with its well-established foundations, a similar widely-accepted framework for non-equilibrium statistical mechanics (NESM) remains elusive. Here, we review some of the many recent activities on NESM and emphasize general properties of the evolution of configurational probabilities, as described by master equations. Of particular interest are systems in which the dynamics violate detailed balance. We next review two distinct approaches for investigating such problems. One approach focuses on models sufficiently simple to allow us to find exact, analytic, non-trivial results. We provide detailed mathematical analyses of a one-dimensional continuous-time lattice gas, the totally asymmetric exclusion process (TASEP). It is regarded as a paradigmatic model for NESM, much like the role the Ising model played for equilibrium statistical mechanics. It is also the starting point for the second approach, which attempts to include more realistic ingredients in order to be more applicable to systems in nature. Restricting ourselves to the area of biophysics and cellular biology, we review a number of models that are relevant for transport phenomena.
PDFs: Non-equilibrium statistical mechanics.pdf
PNGs: Non-equilibrium statistical mechanics.png (361.05 KB)
Research categories: Nonequilibrium physics


Macrospin Tunneling and Magnetopolaritons with Nanomechanical Interference
Macrospin Tunneling and Magnetopolaritons with Nanomechanical Interference A. A. Kovalev, L. X. Hayden, G. E. W. Bauer, and Y. Tserkovnyak, Phys. Rev. Lett. 106, 147203 (2011) (Editors’ Suggestion and Viewpoint in Physics)
Alexey A. Kovalev, Lorien X. Hayden, Gerrit E. W. Bauer, Yaroslav Tserkovnyak
We theoretically address the quantum dynamics of a nanomechanical resonator coupled to the macrospin of a magnetic nanoparticle by both instanton and perturbative approaches. We demonstrate suppression of the tunneling between opposite magnetizations and destruction of magnetopolaritons (coherent magnetomechanical oscillations) by nanomechanical interference. The predictions can be verified experimentally by a molecular magnet attached to a nanomechanical bridge.
JPEGs: PastedGraphic-1.jpg (471.77 KB)
PDFs: kovalevPRL11.pdf (3.66 MB)
Research categories: Nonequilibrium physics