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 X phage 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.

Self-assembled monolayers (SAMs) formed from alkanethiols on thin films of gold were exposed to a beam of metastable argon atoms through a stencil mask. The changes in the organizational structure of the alkyl chains in the SAM that resulted from exposure were characterized using reflection-absorption infrared spectroscopy. All spectroscopic evidence suggested that the SAM become disordered after exposure to metastable argon atoms and that no apparent oxidation of the alkane chain occurred. The alkanethiolates in the regions of a SAM of dodecanethiolate damaged by the atom beam Exchanged readily upon immersion in a solution of 16-mercaptohexadecanoic acid. The exchange reaction was selective for the regions of the SAM exposed to metastable argon atoms with patterns containing critical dimensions of < 50 nm. A thin (<5 nm) polymeric multilayer was covalently linked to the carboxylic acid groups in the exposed regions of the SAM. The polymeric layer served as an improved resist against a commercial KI/I-2-based etchant used to transfer the pattern into the thin film of gold.

Single molecule techniques to measure biological molecules and reactions have provided an alternative way to probe and visualize bond characteristics and reaction dynamics. However, these techniques, such as atomic force microscopy, optical tweezers, and micropipettes often require expensive and complicated equipment and are very time intensive, because each measurement gives the results of one-single reaction or a property of one-single molecule. Here, we report on a technique that allows for massively parallel measurements on many individual single molecules in microfluidic systems. We demonstrate the effectiveness of a simple, robust, inexpensive apparatus, by using it to differentiate between deoxyribonucleic acid (DNA) assemblies that are merely annealed from others that are ligated, and by measuring the rate at which annealed DNA denatures as function of temperature. (C) 2002 American Institute of Physics.

We propose a simple method for the deterministic generation of an arbitrary continuous quantum state of the center-of-mass of an atom. The method's spatial resolution gradually increases with the interaction time with no apparent fundamental limitations. Such de Broglie wave-front engineering of the atomic density can find applications in Atom Lithography, and we discuss possible implementations of our scheme in atomic beam experiments.

Soft lithography offers a convenient set of methods for the transfer of patterns to planar and nonplanar substrates. Microelectrodeposition can transform thin metal patterns into self-supporting microstructures, weld components together, and strengthen microstructures after deformations. Together, soft lithography and electrochemistry provide synergistic technologies and the basis for a strategy for converting planar patterns into three-dimensional (3D) microstructures with complex topologies. This strategy is illustrated in the formation of folded tetrahedra, square-based pyramids, cylinders with joints, "pop-up" cubes, and linked chains and knots.

Two concepts for use in the fabrication of three-dimensional (3D) microstructures with complex topologies are described. Both routes begin with a two-dimensional (2D) pattern and transform it into a 3D microstructure, The concepts are illustrated by use of soft lithographic techniques to transfer 2D patterns to cylindrical (pseudo-3D) substrates. Subsequent steps-application of uniaxial strain, connection of patterns on intersecting surfaces-transform these patterns into free-standing, 3D, noncylindrically symmetrical microstructures. Microelectrodeposition provides an additive method that strengthens thin metal designs produced by patterning, welds nonconnected structures, and enables the high-strain deformations required in one method to be carried out successfully.

The spatially dependent de-excitation of a beam of metastable argon atoms, traveling through an optical standing wave, produced a periodic array of localized metastable atoms with position and momentum spreads approaching the limit stated by the Heisenberg uncertainty principle. Silicon and silicon dioxide substrates placed in the path of the atom beam were patterned by the metastable atoms. The de-excitation of metastable atoms upon collision with the surface promoted the deposition of a carbonaceous film from a vapor-phase hydrocarbon precursor, The resulting patterns were imaged both directly and after chemical etching. Thus, quantum-mechanical steady-state atom distributions can be used for sub-0.1-micrometer lithography.

Lithography can be performed with beams of neutral atoms in metastable excited states to pattern self-assembled monolayers (SAMs) of alkanethiolates on gold. An estimated exposure of a SAM of dodecanethiolate (DDT) to 15 to 20 metastable argon atoms per DDT molecule damaged the SAM sufficiently to allow penetration of an aqueous solution of ferricyanide to the surface of the gold. This solution etched the gold and transformed the patterns in the SAMs into structures of gold; these structures had edge resolution of less than 100 nanometers. Regions of SAMs as large as 2 square centimeters were patterned by exposure to a beam of metastable argon atoms. these observations suggest that this system may be useful in new forms of micro- and nanolithography.

A sodium atomic beam is deflected by two optical standing-wave fields which excite near resonance Raman transitions. Observed deflections are consistent with theoretical predictions of a long-range dc component of the force on a three-level atom in the LAMBDA-configuration. The low laser intensities (and small detunings) used, combined with observed evidence of damping in the three-level LAMBDA-system, may ultimately lead to the design of high-density, all optical traps wherein the atoms would be mostly in the dark state.

We investigate the force on a two-level atom interacting with intense monochromatic laser fields which are combinations of standing and traveling waves. We present a continued-fraction solution to the optical Bloch equations. Using this solution to calculate the force on an atom, we have examined the slowing and cooling of a thermal Na atomic beam. We find that the addition of a traveling wave to an intense standing wave can significantly improve the slowing rate and simultaneously decrease the final velocity of the cooled beam.

We show that light can be used as a lens to focus a collimated neutral atomic beam to submicron dimensions during deposition onto a substrate. We have used an optical standing wave at 589 nm as an array of cylindrical lenses to focus a perpendicular sodium beam into a grating on a substrate, with a periodicity of 294.3 +/- 0.3 nm. This result is the first direct evidence of submicron focusing of atoms by light, and represents a fundamentally new scheme for submicron lithography.

A new method for laterally manipulating the morphology of a thin film is presented, which uses the force exerted by light to deflect neutral atoms in an atomic beam during deposition. We have evaluated the dependence of the thickness of a thin metal film on the frequency, intensity, and the spatial structure of the light field, and find that the stimulated component of the force is suitable for laterally organizing atoms from centimeter to submicron dimensions.

We derive expressions for the damping rate for a two-level atom trapped in the antinodes of an optical interference pattern. We find that the decay rate is much slower than the rate for untrapped atoms in optical molasses. Although the velocity of untrapped atoms decays exponentially in time, the velocity of trapped atoms decays only as t-1/2. We show that the slow damping rate can be circumvented by the addition of a traveling-wave component to the molasses standing wave and discuss how these results can be extended to multilevel atoms.