A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants

First published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23 (1996) published by the American Mathematical Society.Presented at DIMACS Workshop on Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, March 20-21, 1995.A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al

Melt viscosities of lattice polymers using a Kramers potential treatment

Kramers relaxation times $\tau_{K}$ and relaxation times $\tau_{R}$ and $\tau_{G}$ for the end-to-end distances and for center of mass diffusion are calculated for dense systems of athermal lattice chains. $\tau_{K}$ is defined from the response of the radius of gyration to a Kramers potential which approximately describes the effect of a stationary shear flow. It is shown that within an intermediate range of chain lengths N the relaxation times $\tau_{R}$ and $\tau_{K}$ exhibit the same scaling with N, suggesting that N-dependent melt-viscosities for non-entangled chains can be obtained from the Kramers equilibrium concept.Comment: submitted to: Journal of Chemical Physic

On-chip electrically controlled routing of photons from a single quantum dot

Electrical control of on-chip routing of photons emitted by a single InAs/GaAs self-assembled quantum dot (SAQD) is demonstrated in a photonic crystal cavity-waveguide system. The SAQD is located inside an H1 cavity, which is coupled to two photonic crystal waveguides. The SAQD emission wavelength is electrically tunable by the quantum-confined Stark effect. When the SAQD emission is brought into resonance with one of two H1 cavity modes, it is preferentially routed to the waveguide to which that mode is selectively coupled. This proof of concept provides the basis for scalable, low-power, high-speed operation of single-photon routers for use in integrated quantum photonic circuits

Effect of interactions on vortices in a nonequilibrium polariton condensate

We demonstrate the creation of vortices in a macroscopically occupied polariton state formed in a semiconductor microcavity. A weak external laser beam carrying orbital angular momentum (OAM) is used to imprint a vortex on the condensate arising from the polariton optical parametric oscillator (OPO). The vortex core radius is found to decrease with increasing pump power, and is determined by polariton-polariton interactions. As a result of OAM conservation in the parametric scattering process, the excitation consists of a vortex in the signal and a corresponding antivortex in the idler of the OPO. The experimental results are in good agreement with a theoretical model of a vortex in the polariton OPO

Vortices in resonant polariton condensates in semiconductor microcavities

Covering general theoretical concepts and the research to date, this book demonstrates that Bose-Einstein condensation is a truly universal phenomenon

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

Fermi-Edge Singularities in AlxGa1-xAs Quantum Wells : Extrinsic Versus Many-Body Scattering Processes

A Fano resonance mechanism is evidenced to control the formation of optical Fermi-edge singularities in multi-subband systems such as remotely doped AlxGa1-xAs heterostructures. Using Fano parameters, we probe the physical nature of the interaction between Fermi-sea electrons and empty conduction subbands. We show that processes of extrinsic origin like alloy-disorder prevail easily at 2D over multiple diffusions from charged valence holes expected by many-body scenarios.Comment: 4 pages, 3 figures, accepted for publication in Physical Review Letter

Continuous wave observation of massive polariton redistribution by stimulated scattering in semiconductor microcavities

A massive redistribution of the polariton occupancy to two specific wave vectors is observed under conditions of continuous wave excitation of a semiconductor microcavity. The “condensation” of the polaritons to the two specific states arises from stimulated scattering at final state occupancies of order unity. The stimulation phenomena, arising due to the bosonic character of the polariton quasiparticles, occur for conditions of resonant excitation of the lower polariton branch. High energy nonresonant excitation, as in most previous work, instead leads to conventional lasing in the vertical cavity structure

Negative electrostatic contribution to the bending rigidity of charged membranes and polyelectrolytes screened by multivalent counterions

Bending rigidity of a charged membrane or a charged polyelectrolyte screened by monovalent counterions is known to be enhanced by electrostatic effects. We show that in the case of screening by multivalent counterions the electrostatic effects reduce the bending rigidity. This inversion of the sign of the electrostatic contribution is related to the formation of two-dimensional strongly correlated liquids (SCL) of counterions at the charged surface due to strong lateral repulsion between them. When a membrane or a polyelectrolyte is bent, SCL is compressed on one side and stretched on the other so that thermodynamic properties of SCL contribute to the bending rigidity. Thermodynamic properties of SCL are similar to those of Wigner crystal and are anomalous in the sense that the pressure, compressibility and screening radius of SCL are negative. This brings about substantial negative correction to the bending rigidity. For the case of DNA this effect qualitatively agrees with experiment.Comment: 8 pages, 2 figure