Prashant K. Purohit

Enhanced Piezoelectricity and Stretchability in Energy Harvesting Devices Fabricated from Buckled PZT Ribbons

The development of a method for integrating highly efficient energy conversion materials onto soft, biocompatible substrates could yield breakthroughs in implantable or wearable energy harvesting systems. Of particular interest are devices which can conform to irregular, curved surfaces, and operate in vital environments that may involve both flexing and stretching modes. Previous studies have shown significant advances in the integration of highly efficient piezoelectric nanocrystals on flexible and bendable substrates. Yet, such inorganic nanomaterials are mechanically incompatible with the extreme elasticity of elastomeric substrates. Here, we present a novel strategy for overcoming these limitations, by generating wavy piezoelectric ribbons on silicone rubber. Our results show that the amplitudes in the waves accommodate order-of-magnitude increases in maximum tensile strain without fracture. Further, local probing of the buckled ribbons reveals an enhancement in the piezoelectric effect of up to 70%, thus representing the highest reported piezoelectric response on a stretchable medium. These results allow for the integration of energy conversion devices which operate in stretching mode via reversible deformations in the wavy/buckled ribbons.

Multiscale Mechanics of Fibrin Polymer: Gel Stretching with Protein Unfolding and Loss of Water

<< Focusing on Fibrin Vascular injury initiates biochemical reactions that cause the blood protein, fibrin, to polymerize and help to stop bleeding and support wound healing. Fibrin can also be a scaffold for thrombi that lead to cardiovascular diseases. To maintain homeostasis, fibrin clots must be stiff, plastic, and, so that the network can be decompsed, permeable. Brown et al. (p. 741) investigated the behavior of fibrin clots at the macroscopic, single-fiber, and molecular scale. At relatively low strains, fibers aligned and formed bundles, and at higher strains, protein unfolding occurred. An integrated model provides a molecular basis for fibrin elasticity and extensibility. Protein unfolding in stretched fibrin blood clots creates porous gels that can withstand high strains. Blood clots and thrombi consist primarily of a mesh of branched fibers made of the protein fibrin. We propose a molecular basis for the marked extensibility and negative compressibility of fibrin gels based on the structural and mechanical properties of clots at the network, fiber, and molecular levels. The force required to stretch a clot initially rises linearly and is accompanied by a dramatic decrease in clot volume and a peak in compressibility. These macroscopic transitions are accompanied by fiber alignment and bundling after forced protein unfolding. Constitutive models are developed to integrate observations at spatial scales that span six orders of magnitude and indicate that gel extensibility and expulsion of water are both manifestations of protein unfolding, which is not apparent in other matrix proteins such as collagen.

Forces during Bacteriophage DNA Packaging and Ejection

The conjunction of insights from structural biology, solution biochemistry, genetics, and single-molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a beneficiary of these experimental techniques is the study of viruses. In this article we describe how the insights obtained from such experiments can be utilized to construct physical models of processes in the viral life cycle. We focus on dsDNA bacteriophages and show that the bending elasticity of DNA and its electrostatics in solution can be combined to determine the forces experienced during packaging and ejection of the viral genome. Furthermore, we quantitatively analyze the effect of fluid viscosity and capsid expansion on the forces experienced during packaging. Finally, we present a model for DNA ejection from bacteriophages based on the hypothesis that the energy stored in the tightly packed genome within the capsid leads to its forceful ejection. The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure.

Mechanics of DNA packaging in viruses

A new generation of single-molecule experiments has opened up the possibility of reexamining many of the fundamental processes of biochemistry and molecular biology from a unique and quantitative perspective. One technique producing a host of intriguing results is the use of optical tweezers to measure the mechanical forces exerted by molecular motors during key processes such as the transcription of DNA or the packing of a viral genome into its capsid. The objective of the current article is to respond to such measurements on viruses and to use the theory of elasticity and a simple model of charge and hydration forces to derive the force required to pack DNA into a viral capsid as a function of the fraction of the viral genome that has been packed. The results are found to be in excellent accord with recent measurements and complement previous theoretical work. Because the packing of DNA in viral capsids occurs under circumstances of high internal pressure, we also compute how much pressure a capsid can sustain without rupture.

Piezoelectric nanoribbons for monitoring cellular deformations

Methods for probing mechanical responses of mammalian cells to electrical excitations can improve our understanding of cellular physiology and function. The electrical response of neuronal cells to applied voltages has been studied in detail, but less is known about their mechanical response to electrical excitations. Studies using atomic force microscopes (AFMs) have shown that mammalian cells exhibit voltage-induced mechanical deflections at nanometre scales, but AFM measurements can be invasive and difficult to multiplex. Here we show that mechanical deformations of neuronal cells in response to electrical excitations can be measured using piezoelectric PbZr(x)Ti(1-x)O(3) (PZT) nanoribbons, and we find that cells deflect by 1 nm when 120 mV is applied to the cell membrane. The measured cellular forces agree with a theoretical model in which depolarization caused by an applied voltage induces a change in membrane tension, which results in the cell altering its radius so that the pressure remains constant across the membrane. We also transfer arrays of PZT nanoribbons onto a silicone elastomer and measure mechanical deformations on a cow lung that mimics respiration. The PZT nanoribbons offer a minimally invasive and scalable platform for electromechanical biosensing.

Protein unfolding accounts for the unusual mechanical behavior of fibrin networks

We describe the mechanical behavior of isotropic fibrin networks at the macroscopic scale in terms of the nanoscale force response of fibrin molecules that are its basic building blocks. We show that the remarkable extensibility and compressibility of fibrin networks have their origins in the unfolding of fibrin molecules. The force-stretch behavior of a single fibrin fiber is described using a two-state model in which the fiber has a linear force-stretch relation in the folded phase and behaves like a worm-like-chain in the unfolded phase. The nanoscale force-stretch response is connected to the macro-scale stress-stretch response by means of the eight-chain model. This model is able to capture the macroscopic response of a fibrin network in uniaxial tension and appears remarkably simple given the molecular complexity. We use the eight-chain model to explain why fibrin networks have negative compressibility and Poissons ratio greater than 1 due to unfolding of fibrin molecules.

Fibrin Clots Are Equilibrium Polymers That Can Be Remodeled Without Proteolytic Digestion

Fibrin polymerization is a necessary part of hemostasis but clots can obstruct blood vessels and cause heart attacks and strokes. The polymerization reactions are specific and controlled, involving strong knob-into-hole interactions to convert soluble fibrinogen into insoluble fibrin. It has long been assumed that clots and thrombi are stable structures until proteolytic digestion. On the contrary, using the technique of fluorescence recovery after photobleaching, we demonstrate here that there is turnover of fibrin in an uncrosslinked clot. A peptide representing the knobs involved in fibrin polymerization can compete for the holes and dissolve a preformed fibrin clot, or increase the fraction of soluble oligomers, with striking rearrangements in clot structure. These results imply that in vivo clots or thrombi are more dynamic structures than previously believed that may be remodeled as a result of local environmental conditions, may account for some embolization, and suggest a target for therapeutic intervention.

Effect of supercoiling on formation of protein-mediated DNA loops

DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic rod model of DNA to determine the free energy of forming short (50-100 basepair), protein mediated DNA loops. Superhelical stress in the DNA of living cells is a critical factor determining the energetics of loop formation, and we explicitly account for it in our calculations. The repressor protein itself is regarded as a rigid coupler; its geometry enters the problem through the boundary conditions it applies on the DNA. We show that a theory with these ingredients is sufficient to explain certain features observed in modulation of in vivo gene activity as a function of the distance between operator sites for the lac repressor. We also use our theory to make quantitative predictions for the dependence of looping on superhelical stress, which may be testable both in vivo and in single-molecule experiments such as the tethered particle assay and the magnetic bead assay.

Dynamics of strings made of phase-transforming materials

This paper presents a theory to describe the dynamical behavior of a string made of a phase-transforming material like a shape-memory alloy. The study of phase boundaries, the driving force acting on them and the kinetic relation governing their propagation is of central concern. The paper proposes a qualitative experimental test of the notion of a kinetic relation, as well as a simple experimental method for measuring it quantitatively. It presents a numerical method for studying general initial and boundary value problems in strings, and concludes by exploring the use of phase transforming strings to generate motion at very small scales.

Force steps during viral DNA packaging

Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent of single molecule biophysics techniques that have made it possible to exert piconewton forces on key macromolecules and observe their deformations at nanometer length scales, as well as to observe the mechanical action of macromolecules such as molecular motors. This has opened up immense possibilities for a new generation of mechanical investigations that will respond to such measurements in an attempt to develop a coherent theory for the mechanical behavior of macromolecules under conditions where thermal and chemical effects are on an equal footing with deterministic forces. This paper presents an application of the principles of mechanics to the problem of DNA packaging, one of the key events in the life cycle of bacterial viruses with special reference to the nature of the internal forces that are built up during the DNA packaging process.