Optimizing Replica Exchange Moves For Molecular Dynamics

In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.Comment: 4 pages, 3 figures; revised version (1 figure added), PRE in pres

Inversion of exciton level splitting in quantum dots

The demonstration of degeneracy of exciton spin states is an important step toward the production of entangled photon pairs from the biexciton cascade. We measure the fine structure of exciton and biexciton states for a large number of single InAs quantum dots in a GaAs matrix; the energetic splitting of the horizontally and vertically polarized components of the exciton doublet is shown to decrease as the exciton confinement decreases, crucially passing through zero and changing sign. Thermal annealing is shown to reduce the exciton confinement, thereby increasing the number of dots with splitting close to zero

Optically tunable nuclear magnetic resonance in a single quantum dot

We report optically detected nuclear magnetic resonance (ODNMR) measurements on small ensembles of nuclear spins in single GaAs quantum dots. Using ODNMR we make direct measurements of the inhomogeneous Knight field from a photoexcited electron which acts on the nuclei in the dot. The resulting shifts of the NMR peak can be optically controlled by varying the electron occupancy and its spin orientation, and lead to strongly asymmetric line shapes at high optical excitation. The all-optical control of the NMR line shape will enable position-selective control of small groups of nuclear spins inside a dot

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

Uncoupled excitons in semiconductor microcavities detected in resonant Raman scattering

We present an outgoing resonant Raman-scattering study of a GaAs/AlGaAs based microcavity embedded in a p-i-n junction. The p-i-n junction allows the vertical electric field to be varied, permitting control of exciton-photon detuning and quenching of photoluminescence which otherwise obscures the inelastic light scattering signals. Peaks corresponding to the upper and lower polariton branches are observed in the resonant Raman cross sections, along with a third peak at the energy of uncoupled excitons. This third peak, attributed to disorder activated Raman scattering, provides clear evidence for the existence of uncoupled exciton reservoir states in microcavities in the strong-coupling regime

The new physics of non-equilibrium condensates: insights from classical dynamics

We discuss the dynamics of classical Dicke-type models, aiming to clarify the mechanisms by which coherent states could develop in potentially non-equilibrium systems such as semiconductor microcavities. We present simulations of an undamped model which show spontaneous coherent states with persistent oscillations in the magnitude of the order parameter. These states are generalisations of superradiant ringing to the case of inhomogeneous broadening. They correspond to the persistent gap oscillations proposed in fermionic atomic condensates, and arise from a variety of initial conditions. We show that introducing randomness into the couplings can suppress the oscillations, leading to a limiting dynamics with a time-independent order parameter. This demonstrates that non-equilibrium generalisations of polariton condensates can be created even without dissipation. We explain the dynamical origins of the coherence in terms of instabilities of the normal state, and consider how it can additionally develop through scattering and dissipation.Comment: 10 pages, 4 figures, submitted for a special issue of J. Phys.: Condensed Matter on "Optical coherence and collective phenomena in nanostructures". v2: added discussion of links to exact solution

Fast preparation of single hole spin in InAs/GaAs quantum dot in Voigt geometry magnetic field

The preparation of a coherent heavy-hole spin via ionization of a spin-polarized electron-hole pair in an InAs/GaAs quantum dot in a Voigt geometry magnetic field is investigated. For a dot with a 17 ueV bright-exciton fine-structure splitting, the fidelity of the spin preparation is limited to 0.75, with optimum preparation occurring when the effective fine-structure of the bright-exciton matches the in-plane hole Zeeman energy. In principle, higher fidelities can be achieved by minimizing the bright-exciton fine-structure splitting.Comment: 8 pages, 10 figs, published PRB 85 155310 (2012

Angle-resonant stimulated polariton amplifier

We experimentally demonstrate resonant coupling between photons and excitons in microcavities which can efficiently generate enormous single-pass optical gains approaching 100. This new parametric phenomenon appears as a sharp angular resonance of the incoming pump beam, at which the moving excitonic polaritons undergo very large changes in momentum. Ultrafast stimulated scattering is clearly identified from the exponential dependence on pump intensity. This device utilizes boson amplification induced by stimulated energy relaxation

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein

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