Dynamical and Mechanical Properties of Biological Systems
Biological systems exhibit a plethora of fascinating dynamical and mechanical phenomena that are yet to be fully explored or understood. For example, a living cell can transition between fluid-like and solid-like states by altering the interactions between proteins that constitute a biopolymer network or gel called the cytoskeleton. Even more remarkable is their ability to generate contractile forces and flows due to the action of motor proteins or using polymerisation dynamics. We are interested in characterising these responses, modelling them using physical principles, and in understanding the connection between these responses and cellular functions (or disfunction). To achieve this, we not only develop and employ novel instruments to quantitatively probe cell mechanical responses, but also collaborate intensely with theoreticians and biologists across the globe.
Mechanical responses of axons:
Axons are thin and long tubular extensions of neuronal cells which enable them to form networks with other neurons and to transmit signals across long distances. Both in the peripheral nerves and in the brain (which is as soft as jelly), axons are highly susceptible to mechanical damage. We are interested in understanding how the structural organisation of the axonal cytoskeleton imparts unique mechanical properties which help axons withstand sudden deformations. We are also interested in active dynamics of axons which lead to contractile responses. We probe these responses using an optical fiber based Micro-Extensional Rheometer which we designed and developed at RRI.
Shape instabilities of axons:
The nervous system is highly vulnerable to a wide range of neurodegenerative conditions. Axons, because they extend long distances from the cell body, are particularly vulnerable. Degenerating axons exhibit propagating shape instabilities, known as axonal beading to biologists and pearling instability to physicists, which eventually leads to axonal atrophy. We study the dynamics of such morphological transformations by inducing them in the lab using biochemical means. We are interested in the cytoskeletal and membrane mechanisms that drive such processes.
Axonal membrane dynamics:
We have recently started investigating axonal membrane dynamics using a home-built optical tweezers. We are interested in membrane tension regulation in axons and in the interaction between the plasma membrane and the underlying cytoskeleton. Recently, we had shown that the coupling between axonal membrane and cytoskeleton may be very different from that of other cell types.
Quantification of cell-substrate adhesion:
A quantitative understanding of how cells adhere to substrates is important in problems ranging from cancer metastasis to developing medical implants. We have recently developed a microscope mountable shear device which can quantify cell-substrate adhesion. We have also developed a stochastic model based on the Bell model for force-induced detachment of ligands to gain a better understanding of the physical processes that govern cell adhesion. Both the experimental technique and the theoretical analysis is being improved to incorporate the dynamic nature of cell adhesion which involves feedback processes.
Mechanical properties of spider silk:
Spider silk has fascinating mechanical properties like high tensile strength as well as extensibility, and has been studied extensively. Recently, we explored the rheological properties of dragline spider silk obtained from social spiders using the Micro- Extensional Rheometer we have developed. We explore strain softening and stiffening responses of silk fibers using an oscillatory strain protocol and extract frequency dependencies and relaxation time responses using a step strain protocol. We are now interested in trying to explain the time dependencies and the non-linear elastic responses using theoretical models.
Below we give a list of home-built instruments, most of which we have designed and developed for investigating mechanical properties of living cells and other soft materials. Details can be found in the publication links given in the captions or can be obtained by contacting us.
Cell monolayer rheology:
An adaptor to a commercial rheometer designed to perform rheological measurements on a monolayer of living cells. The levelling screws and the laser pointer allow for precise alignment of the two glass plates using interference fringes of equal thickness. The cells adhere to both fibronectin coated glass plates (verifiable using a built in inverted microscope). Small oscillations can be applied to shear the cells without detaching them. A hole in the bottom plate allows for the introduction of pharmacological agents during measurement. This method gives population averaged viscoelastic properties using standard shear rheology protocols.
Link to publication.
Axon viscoelasticity:
(a) Experimental setup developed to study mechanical responses of axons. Here an optical fiber is used as a force sensing cantilever. The base of the cantilever can be displaced using piezo with nano-meter precision and the resulting force on the cantilever can be measured using a Position Sensitive Detector (PSD) to sub-nano-Newton accuracy. A feedback algorithm controls the piezo to perform constant strain measurements. (b) Schematic showing how an axon is stretched. (c) The different parameters used to calculate the tension (T) along the axon from the force (F) experienced by the cantilever.
Link to publication.
Extension rheology of non-Newtonian fluids:
Experimental arrangement showing how extensional rheology can be performed at microscopic scale using an optical fiber as a force transducing cantilever. The laser light exiting the flexible fiber (cantilever) and the rigid fiber are imaged on to a camera and a Position Sensitive Detector to measure displacements and stress. Measurements can be made using an imposed exponential strain or an oscillatory strain as per need.
Link to publication.
Non-linear elasticity of spider silk:
Experimental arrangement used to measure mechanical properties of spider silk. See Axon viscoelasticity section above for details.
Link to publication.
Low cost fluid shear cell:
A low cost microscope mountable fluid shear cell developed to study cell detachment dynamics under shear flow. The instrument is made using the out-runner motor from a discarded computer hard disc, driven using an electronic speed controller used for hobby aircrafts and an Arduino interface. A feedback system maintains constant RPM irrespective of load. It is compact and can be mounted on any standard inverted microscope, including confocal systems. We used this fluid shear cell to study cell detachment dynamics.
Link to publication.
Optical tweezers:
Our home-built optical tweezers used for studying viscoelastic properties of cell membrane.
Link to publication.
Serene Rose David
Technical Assistant
Mohammad Arsalan Ashraf
PhD Student
Ashish Kumar Mishra
PhD Student
Sukh Veer
PhD Student
Madhusudhan
Visiting Student
Praveen Parthasarathi
Postdoctral Fellow
Current Collaborators
Andrew Callan-Jones
Université Paris-Diderot
Aurnab Ghose
IISER Pune
Gautam Menon
Ashoka Univ.
Namrata Gundiah
IISc Bengaluru
Jacques Prost
Institut Curie
Chirag Kalelkar
IIT Kharagpur
Roberto Bernal
University of Santiago, Chile
Past Members
Jaishabanu Ameeramja
Nishita Bhembre
Susav Pradhan
Renu Vishavkarma
Alka Bhat
Chirag Kalelkar
Seshagiri Rao
Anagha Datar
Roli Srivastava
Jagruti Pattadkal
Santanu Basu
Lt. to rt., Santanu, Renu, Pramod, Anagha, Kalpana (2008)
Lt. to rt., Renu, Giri, Santanu (2009)
Lt. to rt., Sushil, Pooja, Pramod, Susav, Arsalan, Sampada, Serene (2016)
Lt. to rt., Sushil, Jaisha, Serene, Nishita, Arsalan, Susav (2017)
Investigation of Soft and Living Matter using a Micro-Extensional Rheometer;
Journal of Physics-Condensed Matter (submitted 2020).
The axonal actin-spectrin lattice acts as shock absorbers to protect neurons from stretch-induced damage;
eLife, vol. 9, pp e51772, (2020)
Simpler form of the model can be found here
Strain softening and stiffening responses of spider silk fibers probed using Micro-Extension-Rheometer;
Soft Matter, vol. 16, pp 487 – 493, (2020).
The roles of microtubules and membrane tension in axonal beading, retraction, and atrophy;
Biophysical Journal, vol. 117, pp 880 (2019).
Biophysics of cell-substrate interactions under shear;
Frontiers in Cell and Developmental Biology, vol 7, article 251, (2019).
Dynamin independent endocytosis responds to and regulates membrane tension through a negative feedback loop;
Nature Communications, volume 28, (2018).
Cytoskeletal Mechanisms of Axonal Contractility;
Biophysical Journal volume 115, pp 713–724, (2018).
Modelling cell-substrate deadhesion dynamics under fluid shear;
Physical Biology, volume 15, pp 046006 (2018).
Oscillatory extensional rheology of microscale fluid filaments;
Rheologica Acta, Volume 56, pages113–122 (2017).
Dynamics of Membrane Tethers Reveal Novel Aspects of Cytoskeleton-Membrane Interactions in Axons;
Biophysical Journal, Volume 108, Issue 3, p489-497,2015 (2015).
Role of actin filaments in correlating nuclear shape and cell spreading;
Plos One, vol. 9, issue 9, e107895, Sep. 2014.
Optical fiber-based force transducer for microscale samples;
Review of Scientific Instruments, vol. 84, page 105107, year 2013.
The role of the cytoskeleton in volume regulation and beading transitions in PC12 neurites;
Biophysical Journal, vol . 99, pp. 3571 (2010).
Drag force as a tool to test active mechanical response of PC12 neurites;
Biophysical Journal, vol 98, pp. 515 (2010).
Coarsening through directed droplet coalescence in fluid-fluid phase separation;
Phy. Rev. E. 80, 011708 (2009).
Mechano-genetic coupling of Hydra symmetry breaking and driven Turing instability model;
Biophysical Journal, vol.96, pp. 1649 (2009).
An osmoregulatory basis for shape oscillations in regenerating Hydra;
Biophysical Journal, vol. 95, pp. 978-985 (2008).
Shape oscillations of non-adhering fibroblast cells;
Physical Biology, Vol 4, page 268 (2007).
Shear rheology of a cell monolayer;
New Journal of Physics, Vol 9, page 419 (2007).
Mechanical properties of axons;
Phys. Rev. Lett. 99 (2007) page 018301.
Rheological Properties of the Eukaryotic Cell Cytoskeleton;
Review, Physics Reports, 449 (2007), page 29.
Loss of Cell-Substrate Adhesion Leads to Spontaneous Shape Oscillations in Fibroblasts;
Physics Online Archive (2007)
Self Propulsion of Nematic Drops: Novel Phase Separation Dynamics in Impurity Doped Nematogens;
Phys. Rev. Lett. 97 (2006) page 115701.
Osmotically Driven Shape Transformations in Axons; (axonal beading or pearling instability)
Phys. Rev. Lett. 96 (2006) 048104.
A master relation defines the nonlinear viscoelasticity of single fibroblasts;
Biophysical Journal. 90 (2006) 3796.
A phenomenological model for the undulating twist grain boundary-C* phase;
Liquid Crystals, Page 525, Vol. 28, No. 4, April 2001.
Experimental studies on the undulated twist grain boundary-C* liquid crystal;
Ferroelectrics, Page 31, Vol. 244, 2000.
A three-dimensionally modulated structure in a chiral smectic-C liquid crystal;
Current Science, 761, vol. 73, no. 9, Nov. 1997.
Chiral symmetry breaking in three-dimensional smectic-C liquid crystal domains;
Phys. Rev. E (rapid communications), R4935, vol. 56, Nov. 1997.