arXiv subjects

Mara Prentiss

Publications and source records attributed to Mara Prentiss.

11 recordsLinked to original sources

arXiv2012

The Tension on dsDNA Bound to ssDNA/RecA Filaments May Play an Important Role in Driving Efficient and Accurate Homology Recognition and Strand Exchange

It is well known that during homology recognition and strand exchange the double stranded DNA (dsDNA) in DNA/RecA filaments is highly extended, but the functional role of the extension has been unclear. We present an analytical model that calculates the distribution of tension in the extended dsDNA during strand exchange. The model suggests that the binding of additional dsDNA base pairs to the DNA/RecA filament alters the tension in dsDNA that was already bound to the filament, resulting in a non-linear increase in the mechanical energy as a function of the number of bound base pairs. This collective mechanical response may promote homology stringency and underlie unexplained experimental results.

physics.bio-ph↗

arXiv2010

Atom interferometry using wavepackets with constant spatial displacements

We demonstrate a standing wave light pulse sequence that places atoms into a superposition of displaced wavepackets with precisely controlled displacements that remain constant for times as long as 1 s. The separated wavepackets are subsequently recombined resulting in atom interference patterns that probe energy differences of approximately 10^-34 J, and can provide acceleration measurements that are insensitive to platform vibrations.

physics.atom-ph↗

arXiv2009

Macroscopic magnetic guide for cold atoms

We demonstrate a macroscopic magnetic guide for cold atoms with suppressed longitudinal field curvature which is highly desired for atom interferometry. The guide is based on macroscopic copper tape coils in a copropagating currents geometry, where the atoms are located between the coils few cm away from each surface. The symmetric geometry provides a much lower magnetic field curvature per fixed length that promises longer coherence time for atom interferometers. A double-tape design of each coil allows a smooth translation of guided atoms without addition of an external bias field. The guide is also immune from the current and thermal noise by virtue of the turns averaging and a large working distance, respectively. We present the experimental results of guide application to atom interferometry.

physics.atom-ph↗

arXiv2007

Demonstration of a moving guide based atom interferometer for rotation sensing

We demonstrate area-enclosing atom interferometry based on a moving guide. Light pulses along the free propagation direction of a magnetic guide are applied to split and recombine the confined atomic matter-wave, while the atoms are translated back and forth along a second direction in 50 ms. The interferometer is estimated to resolve ten times the earth rotation rate per interferometry cycle. We demonstrate a ``folded figure 8'' interfering configuration for creating a compact, large-area atom gyroscope with multiple-turn interfering paths.

physics.atom-ph↗

arXiv2007

DNA unzipping phase diagram calculated via replica theory

We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We study a model for a long molecule of dsDNA, and compute the equilibrium phase diagram for the experiment in which the molecule is unzipped under force. We consider a perfect-matching dsDNA model, in which the loops are volume-excluding chains with arbitrary loop exponent c. We include stacking interactions, hydrogen bonds, and main-chain entropy, including sequence heterogeneity at the level of random sequences. We use the replica method to calculate the equilibrium properties of the system. As a function of temperature, we obtain the minimal force at which the molecule separates completely. This critical force curve is a line in the temperature-force phase diagram that marks the regions where the molecule exists primarily as a helix, versus the region where the molecule exists as two separate strands. Near melting, the critical force curve of our random-sequence model is very different from that of the homogeneous version of our model. For both sequence models, the critical force falls to zero at the melting temperature with a power law having exponent alpha. For the homogeneous model, alpha is 1/2 almost exactly, while for the random model, alpha is about 0.9. The shape of the critical force determines how the helix fraction falls to zero at melting, and thus classifies the melting transition as a type of phase transition.

cond-mat.soft↗

arXiv2005

Time domain deBroglie wave interferometry along a magnetic guide

Time domain deBroglie wave interferometry [Cahn et al, Phys. Rev. Lett. 79, 784] is applied to Rb87 atoms in a magnetic guide. A standing wave light field is carefully aligned along the guiding direction of the magnetic trapping potential from a soft-ferromagnetic 4-foil structure. A sequence of two standing wave pulses is applied to the magnetically trapped atoms. The backscattered light at the atomic density grating revival time is collected and detected via a heterodyning technique. In addition to the observed recoil oscillations that fit the interferometer theory for atoms in free space, we observe a decay of the interferometer contrast on a millisecond time scale with unexpected millisecond-scale oscillations. We find that the oscillating decay is explained by a residual variation of the linear trapping potential along the standing wave direction.

physics.atom-ph↗

arXiv2004

High efficiency symmetric beam splitter for cold atoms with a standing wave light pulse sequence

In a recent experiment [1], it was observed that a sequence of two standing wave square pulses can split a BEC at rest into +/- 2 h_bar k diffraction orders with almost 100% efficiency. By truncating the Raman-Nath equations to a 2-state model, we provide an intuitive picture that explains this double square pulse beamsplitter scheme. We further show it is possible to optimize a standingwave multi square pulse sequence to efficiently diffract an atom at rest to symmetric superposition of +/- 2n h_bar k diffraction order with n>1. The approach is considered to be qualitatively different from the traditional light pulse schemes in the Bragg or the Raman-Nath region, and can be extended to more complex atomic optical elements that produce various tailored output momentum states from a cold atom source.

physics.atom-ph↗

arXiv2004

An Atom Michelson Interferometer on a Chip Using a Bose-Einstein Condensate

An atom Michelson interferometer is implemented on an "atom chip." The chip uses lithographically patterned conductors and external magnetic fields to produce and guide a Bose-Einstein condensate. Splitting, reflecting, and recombining of condensate atoms are achieved by a standing-wave light field having a wave vector aligned along the atom waveguide. A differential phase shift between the two arms of the interferometer is introduced by either a magnetic-field gradient or with an initial condensate velocity. Interference contrast is still observable at 20% with atom propagation time of 10 ms.

cond-mat.other↗

arXiv2004

Bidirectional propagation of cold atoms in a "stadium" shaped magnetic guide

We demonstrate the bi-directional propagation of more than 10 7 atoms (87 Rb) around a "stadium" shaped magnetic ring that encloses an area of 10.9 cm 2, with a flux density exceeding 10 11 atoms sec -1 cm -2 . Atoms are loaded into the guide from a 2D + MOT at one side of the "stadium". An optical standing wave pulse is applied to increase the propagation velocity of atoms along the waveguide. The atom sample fills the entire ring in 200 ms when counterpropagating atom sections of the original atom cloud recombine at their initial positions after a full revolution. We discuss a possible extension of this result to a guided atom ring interferometer.

physics.atom-ph↗

arXiv2003

Observation of Caustics in the Trajectories of Cold Atoms in a Linear Magnetic Potential

We have studied the spatial and temporal dynamics of a cold atom cloud in the conservative force field of a ferromagnetic guide, after laser cooling has been switched off suddenly. We observe outgoing 'waves' that correspond to caustics of individual trajectories of trapped atoms. This provides detailed information on the magnetic field, the energy distribution and the spin states.

physics.atom-ph↗

arXiv2003

DNA unzipped under a constant force exhibits multiple metastable intermediates

Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the unzipped length as a function of time is characterized by jumps during which the strands separate rapidly, followed by long pauses where the number of separated base pairs remains constant. Here, we report previously uncharacterized observations of this striking behavior carried out on a number of identical single molecules simultaneously. When several single lphage molecules are subject to the same applied force, the pause positions are reproducible in each. This reproducibility shows that the positions and durations of the pauses in unzipping provide a sequence-dependent molecular fingerprint. For small forces, the DNA remains in a partially unzipped state for at least several hours. For larger forces, the separation is still characterized by jumps and pauses, but the double-stranded DNA will completely unzip in less than 30 min.

cond-mat.soft↗