Yitzhak Rabin

Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient.

Solid-state nanopores are sensors capable of analyzing individual unlabelled DNA molecules in solution. While the critical information obtained from nanopores (e.g., DNA sequence) is the signal collected during DNA translocation, the throughput of the method is determined by the rate at which molecules arrive and thread into the pores. Here we study the process of DNA capture into nanofabricated silicon nitride pores of molecular dimensions. For fixed analyte concentrations we find an increase in capture rate as the DNA length increases from 800 to 8,000 basepairs, a length-independent capture rate for longer molecules, and increasing capture rates when ionic gradients are established across the pore. In addition, we show that application of a 20-fold salt gradient enables detection of picomolar DNA concentrations at high throughput. The salt gradients enhance the electric field, focusing more molecules into the pore, thereby advancing the possibility of analyzing unamplified DNA samples using nanopores.

Modeling the conductance and DNA blockade of solid-state nanopores

We present measurements and theoretical modeling of the ionic conductance G of solid-state nanopores with 5-100 nm diameters, with and without DNA inserted into the pore. First, we show that it is essential to include access resistance to describe the conductance, in particular for larger pore diameters. We then present an exact solution for G of an hourglass-shaped pore, which agrees very well with our measurements without any adjustable parameters, and which is an improvement over the cylindrical approximation. Subsequently we discuss the conductance blockade ΔG due to the insertion of a DNA molecule into the pore, which we study experimentally as a function of pore diameter. We find that ΔG decreases with pore diameter, contrary to the predictions of earlier models that forecasted a constant ΔG. We compare three models for ΔG, all of which provide good agreement with our experimental data.

An Elastic Analysis of Listeria monocytogenes Propulsion

The bacterium Listeria monocytogenes uses the energy of the actin polymerization to propel itself through infected tissues. In steady state, it continuously adds new polymerized filaments to its surface, pushing on its tail, which is made from previously cross-linked actin filaments. In this paper we introduce an elastic model to describe how the addition of actin filaments to the tail results in the propulsive force on the bacterium. Filament growth on the bacterial surface produces stresses that are relieved at the back of the bacterium as it moves forward. The model leads to a natural competition between growth from the sides and growth from the back of the bacterium, with different velocities and strengths for each. This competition can lead to the periodic motion observed in a Listeria mutant.

Crumpled Globule Model of the Three-Dimensional Structure of DNA

We argue that in order to maintain the biological function of DNA confined inside the cell nucleus, its spatial structure has to be unknotted, of the so-called crumpled globule type. The fixation of a particular realization of this non-equilibrium structure by attractive interactions between specific units imposes a connection between the spatial structure of DNA and the statistical distribution of these units along the chain contour. This suggests that both primary sequence and spatial structure of native DNA were formed simultaneously by a self-similar evolution process. The predictions of our model are compared with recent observations of long-range correlations in intron-containing genes and non-transcribed regulatory elements and further experimental tests are proposed.

Fast Translocation of Proteins through Solid State Nanopores

Measurements on protein translocation through solid-state nanopores reveal anomalous (non-Smoluchowski) transport behavior, as evidenced by extremely low detected event rates; that is, the capture rates are orders of magnitude smaller than what is theoretically expected. Systematic experimental measurements of the event rate dependence on the diffusion constant are performed by translocating proteins ranging in size from 6 to 660 kDa. The discrepancy is observed to be significantly larger for smaller proteins, which move faster and have a lower signal-to-noise ratio. This is further confirmed by measuring the event rate dependence on the pore size and concentration for a large 540 kDa protein and a small 37 kDa protein, where only the large protein follows the expected behavior. We dismiss various possible causes for this phenomenon and conclude that it is due to a combination of the limited temporal resolution and low signal-to-noise ratio. A one-dimensional first-passage time-distribution model supports this and suggests that the bulk of the proteins translocate on time scales faster than can be detected. We discuss the implications for protein characterization using solid-state nanopores and highlight several possible routes to address this problem.

Viscosity of dilute polyelectrolyte solutions

We have developed an apparatus which enables us to perform accurate measurements of the shear viscosity of low ionic strength, dilute polyelectrolytesolutions, down to polymer concentrations below one part per million. We have shown that a theoretical expression for the viscosity of such solutions can be derived using the mode–mode coupling approximation to the hydrodynamics of charged Brownian spheres. Very good agreement between the predicted and observed polymer and salt concentration and molecular weight dependence of the viscosity is observed in the low‐added salt, dilute solution range. Furthermore, it appears that the theory gives a qualitatively correct description of the viscosity of semidilute solutions, indicating that independent of polyion concentration, the hydrodynamics of low ionic strength polyelectrolytesolutions is dominated by electrostatic repulsion between polyions.

Soft order in physical systems

Considers how physicists apply intuition to problems that appear to defy rigorous analysis, contrary to conventional notions of science, and come up with believable answers. Four review papers on general topics are followed by 23 research reports treating such areas as polymer physics, crystallograp

Kinetics and mechanism of DNA uptake into the cell nucleus

Gene transfer to eukaryotic cells requires the uptake of exogenous DNA into the cell nucleus. Except during mitosis, molecular access to the nuclear interior is limited to passage through the nuclear pores. Here we demonstrate the nuclear uptake of extended linear DNA molecules by a combination of fluorescence microscopy and single-molecule manipulation techniques, using the latter to follow uptake kinetics of individual molecules in real time. The assays were carried out on nuclei reconstituted in vitro from extracts of Xenopus eggs, which provide both a complete complement of biochemical factors involved in nuclear protein import, and unobstructed access to the nuclear pores. We find that uptake of DNA is independent of ATP or GTP hydrolysis, but is blocked by wheat germ agglutinin. The kinetics are much slower than would be expected from hydrodynamic considerations. A fit of the data to a simple model suggests femto-Newton forces and a large friction relevant to the uptake process.

Statistical physics of polymer gels

Abstract This work presents a comprehensive analysis of the statistical mechanics of randomly cross-linked polymer gels, starting from a microscopic model of a network made of instantaneously cross-linked Gaussian chains with excluded volume, and ending with the derivation of explicit expressions for the thermodynamic functions and for the density correlation functions which can be tested by experiments. Using replica field theory we calculate the mean field density in replica space and show that this solution contains statistical information about the behavior of individual chains in the network. The average monomer positions change affinely with macroscopic deformation and fluctuations about these positions are limited to length scales of the order of the mesh size. We prove that a given gel has a unique state of microscopic equilibrium which depends on the temperature, the solvent, the average monomer density and the imposed deformation. This state is characterized by the set of the average positions of all the monomers or, equivalently, by a unique inhomogeneous monomer density profile. Gels are thus the only known example of equilibrium solids with no long-range order. We calculate the RPA density correlation functions that describe the statistical properties of small deviations from the average density, due to both static spatial heterogeneities (which characterize the inhomogeneous equilibrium state) and thermal fluctuations (about this equilibrium). We explain how the deformation-induced anisotropy of the inhomogeneous equilibrium density profile is revealed by small angle neutron scattering and light scattering experiments, through the observation of the butterfly effect. We show that all the statistical information about the structure of polymer networks is contained in two parameters whose values are determined by the conditions of synthesis: the density of cross-links and the heterogeneity parameter. We find that the structure of instantaneously cross-linked gels becomes increasingly inhomogeneous with the approach to the cross-link saturation threshold at which the heterogeneity parameter diverges. Analytical expressions for the correlators of deformed gels are derived in both the long wavelength and the short wavelength limits and an exact expression for the total static structure factor, valid for arbitrary wavelengths, is obtained for gels in the state of preparation. We adapt the RPA results to gels permeated by free labelled chains and to gels in good solvents (in the latter case, excluded volume effects are taken into account exactly) and make predictions which can be directly tested by scattering and thermodynamic experiments. Finally, we discuss the limitations and the possible extensions of our work.

Flow‐induced scission of isolated macromolecules

We review experimental results on the degradation of stretched polymer molecules in strong extensional flow fields. Atactic polystyrene and polyethylene oxide both show closely central scission along the backbone of the chain. We present a theoretical approach based upon a modified thermally activated barrier to scission model. This successfully describes the scission process as a function of molecular weight and stiffness and strain rate.