Adam E. Cohen

Thermal fluctuations agitate molecules in solution over a broad range of times and distances. By passively watching the shape fluctuations of a thermally driven biomolecule, one can infer properties of the underlying interactions that determine the motion. We applied this concept to single molecules of fluorescently labeled λ-DNA, a key model system for polymer physics. In contrast to most other single-molecule DNA experiments, we examined the unstretched, equilibrium state of DNA by using an anti-Brownian electrokinetic trap to confine the center of mass of the DNA without perturbing its internal dynamics. We analyze the long-wavelength conformational normal modes, calculate their spring constants, and measure linear and nonlinear couplings between modes. The modes show strong signs of nonlinear hydrodynamics, a feature of the underlying equations of polymer dynamics that has not previously been reported and is neglected in the widely used Rouse and Zimm approximations.

An anti-Brownian electrophoretic trap is used to create arbitrary two-dimensional force fields for individual nanoscale objects in solution. The trap couples fluorescence microscopy with digital particle tracking and real-time feedback to generate a position-dependent electrophoretic force on a single nanoparticle. The force may vary over nanometer distances and millisecond times and need not be the gradient of a potential. As illustrations of this technique, I study Brownian motion in harmonic, power-law, and double-well potentials.

We study theoretically the conformation and force-extension curve of a semiflexible polymer in a spatially uniform ac electric field. The polymer backbone minimizes its energy by aligning along one of two orientations parallel to the field. In a strong ac field, hairpin kinks develop between regions of opposite alignment. These kinks are mathematically described as sine-Gordon solitons. We calculate the equation of state of the one-dimensional kink gas, which yields the force-extension curve of the polymer. A sufficiently strong ac field causes the polymer to extend spontaneously to almost its full contour length. The theory is applied to recent experiments on dielectrophoretic stretching of DNA.