PubMed Health⌕ Search

Biomedical subjects

Daniel Branton

Publications and source records attributed to Daniel Branton.

6 recordsLinked to original sources

Eddies in a bottleneck: an arbitrary Debye length theory for capillary electroosmosis.

Using an applied electrical field to drive fluid flows becomes desirable as channels become smaller. Although most discussions of electroosmosis treat the case of thin Debye layers, here electroosmotic flow (EOF) through a constricted cylinder is presented for arbitrary Debye lengths (kappa(-1)) using a long wavelength perturbation of the cylinder radius. The analysis uses the approximation of small potentials. The varying diameter of the cylinder produces radially and axially varying effective electric fields, as well as an induced pressure gradient. We predict the existence of eddies for certain constricted geometries and propose the possibility of electrokinetic trapping in these regions. We also present a leading-order criterion which predicts central eddies in very narrow constrictions at the scale of the Debye length. Eddies can be found both in the center of the channel and along the perimeter, and the presence of the eddies is a consequence of the induced pressure gradient that accompanies electrically driven flow into a narrow constriction.

Electrophoresis, Capillary↗

Nanometer patterning with ice.

Nanostructures can be patterned with focused electron or ion beams in thin, stable, conformal films of water ice grown on silicon. We use these patterns to reliably fabricate sub-20 nm wide metal lines and exceptionally well-defined, sub-10 nanometer beam-induced chemical surface transformations. We argue more generally that solid-phase condensed gases of low sublimation energy are ideal materials for nanoscale patterning, and water, quite remarkably, may be among the most useful.

Chromium↗

DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis.

Broad-spectrum analysis of DNA and RNA samples is of increasing importance in the growing field of biotechnology. We show that nanopore measurements may be used to assess the purity, phosphorylation state, and chemical integrity of nucleic acid preparations. In contrast with gel electrophoresis and mass spectrometry, an unprecedented dynamic range of DNA sizes and concentrations can be evaluated in a single data acquisition process that spans minutes. Because the molecule information is quantized and digitally recorded with single-molecule resolution, the sensitivity of the system can be adjusted in real time to detect trace amounts of a particular DNA species.

DNA↗

Unzipping kinetics of double-stranded DNA in a nanopore.

We studied the unzipping of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. Polymerase chain reaction analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.

DNA↗

Single molecule measurements of DNA transport through a nanopore.

We examined the voltage-driven movement of single-stranded DNA molecules in a membrane channel or "nanopore". Using single channel recording methods and a statistical analysis of many single molecule events, we determined how voltage influences capture and translocation in the nanopore. We verified that the mean time between capture events follows a simple exponential distribution, whereas the translocation times follow a unique distribution that is partly Gaussian and partly exponential. Measurements of polymer sequence effects demonstrated that translocation duration is heavily influenced by specific or nonspecific purine-channel interactions. The single molecule approach we used revealed molecular interactions that can influence both capture rates and translocation velocities in a manner that enriches naive barrier crossing models.

DNA, Single-Stranded↗

Characterization of nucleic acids by nanopore analysis.

Single-stranded DNA and RNA molecules in solution can be driven through a nanoscopic pore by an applied electric field. As each molecule occupies the pore, a characteristic blockade of ionic current is produced. Information about length, composition, structure, and dynamic motion of the molecule can be deduced from modulations of the current blockade.

Biopolymers↗