Biomedical subjects

Yitzhak Rabin

Publications and source records attributed to Yitzhak Rabin.

7 recordsLinked to original sources

PubMed2005

Where is the sodium in self-assembled monolayers of single-stranded DNA?

Monolayers of single-stranded DNA (ssDNA) immobilized on surfaces form the basis of a number of important biotechnology applications, including DNA microarrays and biosensors. The organization of ssDNA as layer on a solid substrate allows one to investigate various properties of the DNA in a controlled manner and to use DNA for analytical applications as well as for exploring futuristic schemes for molecular electronics. It is commonly assumed that the adsorbed DNA layer contains some structural water and the cations. Here we show, based on XPS studies, that when monolayers of ssDNA are formed from sodium phosphate buffer and washed thoroughly, no Na+ signal is detected. A finite concentration of ions is observed when the DNA is made from a solution of Mg2+ ions, but it is still only a fifth of what it would be if all the phosphate ions were fully neutralized by the metal cations.

DNA, Single-Stranded↗

PubMed2005

DNA in nanopores: counterion condensation and coion depletion.

Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and nearly complete depletion of coions from the pore is observed. The implications of our results for experiments on DNA translocation through alpha-hemolysin nanopores are discussed.

Computer Simulation↗

PubMed2004

Nanopore unzipping of individual DNA hairpin molecules.

We have used the nanometer scale alpha-Hemolysin pore to study the unzipping kinetics of individual DNA hairpins under constant force or constant loading rate. Using a dynamic voltage control method, the entry rate of polynucleotides into the pore and the voltage pattern applied to induce hairpin unzipping are independently set. Thus, hundreds of unzipping events can be tested in a short period of time (few minutes), independently of the unzipping voltage amplitude. Because our method does not entail the physical coupling of the molecules under test to a force transducer, very high throughput can be achieved. We used our method to study DNA unzipping kinetics at small forces, which have not been accessed before. We find that in this regime the static unzipping times decrease exponentially with voltage with a characteristic slope that is independent of the duplex region sequence, and that the intercept depends strongly on the duplex region energy. We also present the first nanopore dynamic force measurements (time varying force). Our results are in agreement with the approximately logV dependence at high V (where V is the loading rate) observed by other methods. The extension of these measurements to lower loading rates reveals a much weaker dependence on V.

DNA↗

PubMed2004

Distribution functions for filaments under tension.

We develop a biased Monte Carlo simulation technique to measure the distribution functions of the extension and the end-to-end distance of fluctuating filaments stretched by external force. The method is applicable for arbitrary ratio of the persistence length to the contour length and for arbitrary forces, and also for the case of steric constraints, such as an external wall. The fundamental idea underlying the algorithm is to account explicitly for the length-scale dependence of the effective elastic moduli. We find that orientational fluctuations and wall effects produce non-Gaussian distributions for nearly rigid filaments in the small to intermediate force regime. The simulation results are tested against analytic expressions for the force-extension curves, both in the semiflexible and nearly stiff limits.

Journal Article↗

PubMed2003

Stretching instability of helical springs.

We show that when a gradually increasing tensile force is applied to the ends of a helical spring with sufficiently large ratios of radius to pitch and twist to bending rigidity, the end-to-end distance undergoes a sequence of discontinuous stretching transitions. Subsequent decrease of the force leads to steplike contraction, and hysteresis is observed. For finite helices, the number of these transitions increases with the number of helical turns but only one stretching and one contraction instability survive in the limit of an infinite helix. We calculate the critical line that separates the region of parameters in which the deformation is continuous from that in which stretching instabilities occur.

Cholesterol↗

PubMed2002

Metastable lattice of droplets in phase separating polymer blends.

Phase separation in a polymer mixture with an off-critical composition is described by a Ginzburg-Landau Hamiltonian that contains both cubic and quartic terms in the deviation of composition from its mean value in the homogeneous phase. Our analysis suggests that when a blend is brought in the vicinity of the spinodal, the initial homogeneous phase becomes unstable against the formation of a metastable lattice of spherical droplets whose lifetime diverges in the limit of infinite molecular weight. The composition of the droplets approaches that of the background phase and their size diverges with the approach to the critical point, but the composition contrast is enhanced and droplet radii become comparable to polymer dimensions, away from criticality. The connection between our predictions and the results of recent neutron scattering experiments is discussed, and new experiments that could probe the proposed droplet lattice are proposed.

Journal Article↗

PubMed2002

Frenet algorithm for simulations of fluctuating continuous elastic filaments.

We present an algorithm for generating the equilibrium configurations of fluctuating continuous elastic filaments, based on a combination of statistical mechanics and differential geometry. We use this to calculate the distribution function of the end-to-end distance of filaments with nonvanishing spontaneous curvature and show that for small twist and large bending rigidities there is an intermediate temperature range in which the filament becomes nearly completely stretched. We show that volume interactions can be incorporated into our algorithm, demonstrating this through the calculation of the effect of excluded volume on the end-to-end distance of the filament.

Journal Article↗