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M S Chapman

Publications and source records attributed to M S Chapman.

At least 19 recordsLinked to original sources
PubMed2006

Dipolar effect in coherent spin mixing of two atoms in a single optical lattice site.

We show that atomic dipolar effects are detectable in the system that recently demonstrated two-atom coherent spin dynamics within individual lattice sites of a Mott state. Based on a two-state approximation for the two-atom internal states and relying on a variational approach, we have estimated the spin dipolar effect. Despite the absolute weakness of the dipole-dipole interaction, it is shown that it leads to experimentally observable effects in the spin mixing dynamics.

Journal Article↗
PubMed2006

Controlled splitting of an atomic wave packet.

We propose a simple scheme capable of adiabatically splitting an atomic wave packet using two independent translating traps. Implemented with optical dipole traps, our scheme allows a high degree of flexibility for atom interferometry arrangements and highlights its potential as an efficient and high fidelity atom optical beam splitter.

Journal Article↗
PubMed2006

PIPATH: an optimized algorithm for generating alpha-helical structures from PISEMA data.

An optimized algorithm for finding structures and assignments of solid-state NMR PISEMA data obtained from alpha-helical membrane proteins is presented. The description of this algorithm, PIPATH, is followed by an analysis of its performance on simulated PISEMA data derived from synthetic and experimental structures. pipath transforms the assignment problem into a path-finding problem for a directed graph, and then uses techniques of graph theory to efficiently find candidate assignments from a very large set of possibilities.

Algorithms↗
PubMed2006

Quantum telecommunication based on atomic cascade transitions.

A quantum repeater at telecommunications wavelengths with long-lived atomic memory is proposed, and its critical elements are experimentally demonstrated using a cold atomic ensemble. Via atomic cascade emission, an entangled pair of 1.53 microm and 780 nm photons is generated. The former is ideal for long-distance quantum communication, and the latter is naturally suited for mapping to a long-lived atomic memory. Together with our previous demonstration of photonic-to-atomic qubit conversion, both of the essential elements for the proposed telecommunications quantum repeater have now been realized.

Journal Article↗
PubMed2006

Intensity and mosaic spread analysis from PISEMA tensors in solid-state NMR.

The solid-state NMR experiment PISEMA, is a technique for determining structures of proteins, especially membrane proteins, from oriented samples. One method for determining the structure is to find orientations of local molecular frames (peptide planes) with respect to the unit magnetic field direction, B0. This is done using equations that compute the coordinates of this vector in the frames. This requires an analysis of the PISEMA function and its degeneracies. As a measure of the sensitivity of peptide plane orientations to the data, we use these equations to derive a formula for the intensity function in the powder pattern. With this function and other measures, we investigate the effect of small changes in peptide plane orientations depending on the location of the resonances in the powder pattern spectrum. This gives us an indication of the change in lineshape due to mosaic spread and a way to interpret these in terms of an orientational error bar.

Ion Channels↗
PubMed2005

Dynamical instability and domain formation in a spin-1 Bose-Einstein condensate.

We interpret the recently observed spatial domain formation in spin-1 atomic condensates as a result of dynamical instability. Within the mean field theory, a homogeneous condensate is dynamically unstable (stable) for ferromagnetic (antiferromagnetic) atomic interactions. We find that this dynamical instability naturally leads to spontaneous domain formation as observed in several recent experiments for condensates with rather small numbers of atoms. For trapped condensates, our numerical simulations compare quantitatively to the experimental results, thus largely confirming the physical insight from our analysis of the homogeneous case.

Journal Article↗
PubMed2004

Observation of spinor dynamics in optically trapped 87Rb Bose-Einstein condensates.

We measure spin mixing of F=1 and F=2 spinor condensates of 87Rb atoms confined in an optical trap. We determine the spin mixing time to be typically less than 600 ms and observe spin population oscillations. The equilibrium spin configuration in the F=1 manifold is measured for different magnetic fields and found to show ferromagnetic behavior for low field gradients. An F=2 condensate is created by microwave excitation from the F=1 manifold, and this spin-2 condensate is observed to decay exponentially with time constant 250 ms. Despite the short lifetime in the F=2 manifold, spin mixing of the condensate is observed within 50 ms.

Journal Article↗
PubMed2001

Storage ring for neutral atoms.

We have demonstrated a storage ring for ultracold neutral atoms. Atoms with mean velocities of 1 m/s corresponding to kinetic energies of approximately 100 neV are confined to a 2 cm diameter ring by magnetic forces produced by two current-carrying wires. Up to 10(6) atoms are loaded at a time in the ring, and seven revolutions are clearly observed. Additionally, we have demonstrated multiple loading of the ring and deterministic manipulation of the longitudinal velocity distribution of the atoms using applied laser pulses. Applications of this ring include large area atom interferometers and monochromatic atomic beam generation.

Journal Article↗
PubMed2001

All-optical formation of an atomic Bose-Einstein condensate.

We have created a Bose-Einstein condensate (BEC) of 87Rb atoms directly in an optical trap. We employ a quasielectrostatic dipole force trap formed by two crossed CO2 laser beams. Loading directly from a sub-Doppler laser-cooled cloud of atoms results in initial phase space densities of approximately 1/200. Evaporatively cooling through the BEC transition is achieved by lowering the power in the trapping beams over approximately 2 s. The resulting condensates are F = 1 spinors with 3.5x10(4) atoms distributed between the m(F) = (-1,0,1) states.

Journal Article↗
PubMed2001

Conformational disorder of proteins assessed by real-space molecular dynamics refinement.

Motion is critical to the function of many proteins, but much more difficult to study than structure. Due to lack of easy alternatives, although there are inherent limitations, there have been several prior attempts to extract some information from the Bragg scattering in conventional diffraction patterns. Bragg diffraction reflects only a small proportion of a protein's motion and disorder, so fitted values likely underestimate reality. However, this work shows that the fitted estimates should be even smaller, because current methods of refinement over-fit the Bragg diffraction, leading to a component of the disorder that is not based on any experimental data, and could be characterized as a guess. Real-space refinement is less susceptible than other methods, but its application depends on the availability of very accurate experimental phases. A future challenge will be the collection of such data without resort to cryo-techniques, so that a physiologically relevant understanding can be achieved.

Amino Acid Sequence↗
PubMed2001

Imiquimod for plantar and periungual warts.

Plantar and periungual warts are notoriously difficult to eradicate. Two cases of nongenital warts in teenage girls are presented. Imiquimod was used in combination with cryotherapy for the periungual warts and with occlusion for the plantar warts. Both cases showed complete resolution and that imiquimod may be more effective on thicker keratinized (nongenital) skin when occluded or used in combination with cryotherapy.

Administration, Topical↗
PubMed2000

Atomic refinement using orientational restraints from solid-state NMR.

We describe a procedure for using orientational restraints from solid-state NMR in the atomic refinement of molecular structures. Minimization of an energy function can be performed through either (or both) least-squares minimization or molecular dynamics employing simulated annealing. The energy, or penalty, function consists of terms penalizing deviation from "ideal" parameters such as covalent bond lengths and terms penalizing deviation from orientational data. Thus, the refinement strives to produce a good fit to orientational data while maintaining good stereochemistry. The software is in the form of a module for the popular refinement package CNS and is several orders of magnitude faster than previous software for refinement with orientational data. The short computer time required for refinement removes one of the difficulties in protein structure determination with solid-state NMR.

Gramicidin↗
PubMed2000

Induced fit in arginine kinase.

Creatine kinase (CK) and arginine kinase (AK) are related enzymes that reversibly transfer a phosphoryl group between a guanidino compound and ADP. In the buffering of ATP energy levels, they are central to energy metabolism and have been paradigms of classical enzymology. Comparison of the open substrate-free structure of CK and the closed substrate-bound structure of AK reveals differences that are consistent with prior biophysical evidence of substrate-induced conformational changes. Large and small domains undergo a hinged 13 degrees rotation. Several loops become ordered and adopt different positions in the presence of substrate, including one (residues 309-319) that moves 15 A to fold over the substrates. The conformational changes appear to be necessary in aligning the two substrates for catalysis, in configuring the active site only when productive phosphoryl transfer is possible, and excluding water from the active site to avoid wasteful ATP hydrolysis.

Amino Acid Sequence↗
PubMed2000

Pigmented squamous cell carcinoma.

Pigmented squamous cell carcinomas have been reported in the oral and ocular mucosae, but rarely in the skin. We present a case of pigmented squamous cell carcinoma of the forehead and review the current English literature. Pigmented squamous cell carcinoma can be confused with pigmented basal cell carcinomas and melanoma, especially those melanomas associated with pseudoepitheliomatous hyperplasia and should be included in the differential diagnosis of atypical pigmented lesions.

Carcinoma, Squamous Cell↗
PubMed1999

Improved free R factors for cross-validation of macromolecular structure - importance for real-space refinement.

Improvements in free R cross-validation are based on changed scaling procedures and the use, in map calculation, of estimates of the validation amplitudes which are independent of the actual observed values. The deleterious effects of the omitted test data are mitigated by reduction of the test-set size, which is made possible by constraining test and working sets to share the same scaling coefficients, thereby reducing the degrees of freedom and the dependence of free R on data selection. Further improvements come with use of a modified free R factor, R freeTA. Instead of omitting the validation reflections from map calculation, their amplitudes are replaced by the average of resolution peers that is (nearly) independent of the actual cross-validation amplitudes. The improvements are relevant to model building, phase refinement by density modification and especially to real-space refinement. Although for real data at about 3 A resolution, free R factors of about 0.25 are affected little, the precision of the structure is improved by about 0.1 A. Tests with simulated data show that with good agreement between observed and calculated amplitudes (as in very high resolution studies or simulated refinement tests), free R factors can be improved by factors greater than two.

Crystallography, X-Ray↗
PubMed1999

Real-space molecular-dynamics structure refinement.

Real-space targets and molecular-dynamics search protocols have been combined to improve the convergence of macromolecular atomic refinement. This was accomplished by providing a local real-space target function for the molecular-dynamics program X-PLOR. With poor isomorphous replacement experimental phases, molecular dynamics does not improve real-space refinement. However, with high-quality anomalous diffraction phases convergence is improved at the start of refinement, and torsion-angle real-space molecular dynamics performs better than other available least-squares or maximum-likelihood methods in real or reciprocal space. It is shown that the improvements result from an optimization method that can escape local minima and from a reduction of overfitting through the implicit use of phases and through use of a local refinement in which errors in remote parts of the structure cannot be mutually compensating.

Hydroxymethylglutaryl CoA Reductases↗