Giovanni Zocchi

An Experimental Study of the Saffman Taylor Instability

When a gas is pushed into a viscous fluid through a Hele-Shaw cell, one observes, after a long transient, the formation of a finger which propagates steadily along the channel. This simple situation defines the Saffman Taylor1 problem. In spite of its simplicity, the limiting sizes of those fingers at large velocities and their stability has not been understood for a long time. A particularly striking fact observed in the experiments is that fingers occupy about one-half of the channel width at large velocities. In the model of Saffman and Taylor1, where surface tension is neglected, all finger sizes are allowed. Moreover, fingers of size 1/2 are found linearly unstable, which is also in direct conflict with experiment. The problem was then to understand how surface tension acts to select finger sizes and to ensure stability.

Coherent structures in turbulent convection, an experimental study

We present results from a visualization experiment in Rayleigh-Benard convection in water at high Rayleigh number. We distinguish three kinds of coherent structures in the flow: waves along the boundary layers, plumes, and spiraling swirls. The waves originate from the interaction of plumes with the boundary layers. The spiraling swirls appear to be the result of a shear instability of the viscous boundary layer. We describe the “life cycle” of these structures in the cell, and when we focus on the waves and characterize them quantitatively using local temperature measurements.

An experimental study of laminar plumes

We present an experimental study of the scaling laws for the front (or cap) of an isolated, laminar starting plume. The scaling relations are formulated and measured experimentally over a range of power, fluids, and heaters. The results are that the cap rises at constant velocity, grows diffusively in width, and its temperature depends inversely on height. This extends analytic results by Batchelor (1954) for the column (stem) below the front. The source size determines initial conditions for the cap, but does not affect it in the far field. The shape of the front is fitted by a model of potential flow. The interaction between plume caps is complex, but with simple underlying dynamics. We conjecture that some of our conclusions can be applied to a distribution of plumes, as in soft turbulent convection.

Statistics of Turbulence between Two Counterrotating Disks in Low-Temperature Helium Gas

Turbulent flows, driven between two counterrotating disks in low-temperature helium gas, are investigated experimentally. The statistical characteristics of the flows are studied for various values of Rλ, ranging between 100 and 2100. The inertial range is investigated, and various quantities, such as the probability density function and the exponents of the structure functions, are determined. We find that the characteristics of the inertial range are essentially the same as those obtained in grid and jet turbulence.

Single-molecule detection of DNA hybridization

We demonstrate the detection of nanometer-scale conformational changes of single DNA oligomers through a micromechanical technique. The quantity monitored is the displacement of a micrometer-size bead tethered to a surface by the probe molecule undergoing the conformational change. This technique allows probing of conformational changes within distances beyond the range of fluorescence resonance energy transfer. We apply the method to detect single hybridization events of label-free target oligomers. Hybridization of the target is detected through the conformational change of the probe.

Controlling Proteins Through Molecular Springs

We argue that the mechanical control of proteins-the notion of controlling chemical reactions and processes by mechanics-is conceptually interesting. We give a brief review of the main accomplishments so far, leading to our present approach of using DNA molecular springs to exert controlled stresses on proteins. Our focus is on the physical principles that underlie both artificial mechanochemical devices and natural mechanisms of allostery.

Statistical mechanics of warm and cold unfolding in proteins

Abstract:We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm unfolding, thus qualitatively reproducing the known thermodynamics of proteins.

The Dynamics and Interaction of Laminar Thermal Plumes

We present an experimental study of the dynamics and interactions of laminar plumes emitted from a localized heat source. The observations are explained by a simple model of the flow structure around a plume. Using sources and sinks in a uniform flow, we reproduce the experimental shapes and extract the scaling behavior of the size of the plume. The model describes the initial stage of the interaction between plumes.

Force Measurements on Single Molecular Contacts through Evanescent Wave Microscopy

We introduce a new method to apply controlled forces on single molecules. The motion of a micron-sized bead attached to a solid surface through a single molecular contact is tracked by evanescent wave microscopy as a force is exerted through a flow. We report measurements of the streptavidin-biotin bond rupture force obtained with this technique. We also obtain detailed measurements of the balance of forces involved in detaching an adhering bead with a flow. A small lateral force translates into a much bigger normal force on the attachment point. This effect is relevant for the interpretation of common cell adhesion assays.

Statistical mechanics of base stacking and pairing in DNA melting

We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low pH this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.