24 research outputs found
Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness
DNA and other biopolymers differ from classical polymers due to their
torsional stiffness. This property changes the statistical character of their
conformations under tension from a classical random walk to a problem we call
the `torsional directed walk'. Motivated by a recent experiment on single
lambda-DNA molecules [Strick et al., Science 271 (1996) 1835], we formulate the
torsional directed walk problem and solve it analytically in the appropriate
force regime. Our technique affords a direct physical determination of the
microscopic twist stiffness C and twist-stretch coupling D relevant for DNA
functionality. The theory quantitatively fits existing experimental data for
relative extension as a function of overtwist over a wide range of applied
force; fitting to the experimental data yields the numerical values C=120nm and
D=50nm. Future experiments will refine these values. We also predict that the
phenomenon of reduction of effective twist stiffness by bend fluctuations
should be testable in future single-molecule experiments, and we give its
analytic form.Comment: Plain TeX, harvmac, epsf; postscript available at
http://dept.physics.upenn.edu/~nelson/index.shtm
Critical exponents for random knots
The size of a zero thickness (no excluded volume) polymer ring is shown to
scale with chain length in the same way as the size of the excluded volume
(self-avoiding) linear polymer, as , where . The
consequences of that fact are examined, including sizes of trivial and
non-trivial knots.Comment: 4 pages, 0 figure
Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations
We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N [subscript G] is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε ε[subscript s] with slow internal dynamics. The cohesion strength ε[subscript s] of this freezing transition depends on N G . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N [subscript G] . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi
The Flexibility of DNA Double Crossover Molecules
Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. They are found as intermediates in meiosis and they have been used extensively in structural DNA nanotechnology for the construction of one-dimensional and two-dimensional arrays and in a DNA nanomechanical device. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half-turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, facilitating their characterization in a ligation cyclization assay. Hence, we have estimated the flexibility of antiparallel DNA double crossover molecules by means of ligation-closure experiments. We are able to show that these molecules are approximately twice as rigid as linear duplex DNA