Bose-Fermi Mixtures in Optical Lattices

Using mean field theory, we have studied Bose-Fermi mixtures in a one-dimensional optical lattice in the case of an attractive boson-fermion interaction. We consider that the fermions are in the degenerate regime and that the laser intensities are such that quantum coherence across the condensate is ensured. We discuss the effect of the optical lattice on the critical rotational frequency for vortex line creation in the Bose-Einstein condensate, as well as how it affects the stability of the boson-fermion mixture. A reduction of the critical frequency for nucleating a vortex is observed as the strength of the applied laser is increased. The onset of instability of the mixture occurs for a sizeably lower number of fermions in the presence of a deep optical lattice.Comment: 7 pages, 6 figures, revtex4, 14th International Laser Physics Workshop (LPHYS'05

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

Modelling and simulating change in reforesting mountain landscapes using a social-ecological framework

Natural reforestation of European mountain landscapes raises major environmental and societal issues. With local stakeholders in the Pyrenees National Park area (France), we studied agricultural landscape colonisation by ash (Fraxinus excelsior) to enlighten its impacts on biodiversity and other landscape functions of importance for the valley socio-economics. The study comprised an integrated assessment of land-use and land-cover change (LUCC) since the 1950s, and a scenario analysis of alternative future policy. We combined knowledge and methods from landscape ecology, land change and agricultural sciences, and a set of coordinated field studies to capture interactions and feedback in the local landscape/land-use system. Our results elicited the hierarchically-nested relationships between social and ecological processes. Agricultural change played a preeminent role in the spatial and temporal patterns of LUCC. Landscape colonisation by ash at the parcel level of organisation was merely controlled by grassland management, and in fact depended on the farmer's land management at the whole-farm level. LUCC patterns at the landscape level depended to a great extent on interactions between farm household behaviours and the spatial arrangement of landholdings within the landscape mosaic. Our results stressed the need to represent the local SES function at a fine scale to adequately capture scenarios of change in landscape functions. These findings orientated our modelling choices in the building an agent-based model for LUCC simulation (SMASH - Spatialized Multi-Agent System of landscape colonization by ASH). We discuss our method and results with reference to topical issues in interdisciplinary research into the sustainability of multifunctional landscapes

Superchemistry: dynamics of coupled atomic and molecular Bose-Einstein condensates

We analyze the dynamics of a dilute, trapped Bose-condensed atomic gas coupled to a diatomic molecular Bose gas by coherent Raman transitions. This system is shown to result in a new type of `superchemistry', in which giant collective oscillations between the atomic and molecular gas can occur. The phenomenon is caused by stimulated emission of bosonic atoms or molecules into their condensate phases

Macroscopic quantum tunneling of two-component Bose-Einstein condensates

We show theoretically the existence of a metastable state and the possibility of decay to the ground state through macroscopic quantum tunneling in two-component Bose-Einstein condensates with repulsive interactions. Numerical analysis of the coupled Gross-Pitaevskii equations clarifies the metastable states whose configuration preserves or breaks the symmetry of the trapping potential, depending on the interspecies interaction and the particle number. We calculate the tunneling decay rate of the metastable state by using the collective coordinate method under the WKB approximation. Then the height of the energy barrier is estimated by the saddle point solution. It is found that macroscopic quantum tunneling is observable in a wide range of particle numbers. Macroscopic quantum coherence between two distinct states is discussed; this might give an additional coherent property of two-component Bose condensed systems. Thermal effects on the decay rate are estimated.Comment: 11 pages, 10 figures, revtex

Dark soliton states of Bose-Einstein condensates in anisotropic traps

Dark soliton states of Bose-Einstein condensates in harmonic traps are studied both analytically and computationally by the direct solution of the Gross-Pitaevskii equation in three dimensions. The ground and self-consistent excited states are found numerically by relaxation in imaginary time. The energy of a stationary soliton in a harmonic trap is shown to be independent of density and geometry for large numbers of atoms. Large amplitude field modulation at a frequency resonant with the energy of a dark soliton is found to give rise to a state with multiple vortices. The Bogoliubov excitation spectrum of the soliton state contains complex frequencies, which disappear for sufficiently small numbers of atoms or large transverse confinement. The relationship between these complex modes and the snake instability is investigated numerically by propagation in real time.Comment: 11 pages, 8 embedded figures (two in color

Pinning of quantized vortices in helium drop by dopant atoms and molecules

Using a density functional method, we investigate the properties of liquid 4He droplets doped with atoms (Ne and Xe) and molecules (SF_6 and HCN). We consider the case of droplets having a quantized vortex pinned to the dopant. A liquid drop formula is proposed that accurately describes the total energy of the complex and allows one to extrapolate the density functional results to large N. For a given impurity, we find that the formation of a dopant+vortex+4He_N complex is energetically favored below a critical size N_cr. Our result support the possibility to observe quantized vortices in helium droplets by means of spectroscopic techniques.Comment: Typeset using Revtex, 3 pages and 5 figures (4 Postscript, 1 jpeg

Dynamics of collapsing and exploding Bose-Einstein condensed vortex state

Using the time-dependent mean-field Gross-Pitaevskii equation we study the dynamics of small repulsive Bose-Einstein condensed vortex states of ^{85}Rb atoms in a cylindrical trap with low angular momentum hbar L per atom (L <= 6), when the atomic interaction is suddenly turned attractive by manipulating the external magnetic field near a Feshbach resonance. Consequently, the condensate collapses and ejects atoms via explosion and a remnant condensate with a smaller number of atoms emerges that survives for a long time. Detail of this collapse and explosion is compared critically with a similar experiment performed with zero angular momentum (L=0). Suggestion for future experiment with vortex state is made.Comment: 8 REVTEX4 pages, 8 EPS figures, final version accepted in Phys. Rev. A after minor change

Molecular and cellular mechanisms underlying the evolution of form and function in the amniote jaw.

The amniote jaw complex is a remarkable amalgamation of derivatives from distinct embryonic cell lineages. During development, the cells in these lineages experience concerted movements, migrations, and signaling interactions that take them from their initial origins to their final destinations and imbue their derivatives with aspects of form including their axial orientation, anatomical identity, size, and shape. Perturbations along the way can produce defects and disease, but also generate the variation necessary for jaw evolution and adaptation. We focus on molecular and cellular mechanisms that regulate form in the amniote jaw complex, and that enable structural and functional integration. Special emphasis is placed on the role of cranial neural crest mesenchyme (NCM) during the species-specific patterning of bone, cartilage, tendon, muscle, and other jaw tissues. We also address the effects of biomechanical forces during jaw development and discuss ways in which certain molecular and cellular responses add adaptive and evolutionary plasticity to jaw morphology. Overall, we highlight how variation in molecular and cellular programs can promote the phenomenal diversity and functional morphology achieved during amniote jaw evolution or lead to the range of jaw defects and disease that affect the human condition

From thermal rectifiers to thermoelectric devices

We discuss thermal rectification and thermoelectric energy conversion from the perspective of nonequilibrium statistical mechanics and dynamical systems theory. After preliminary considerations on the dynamical foundations of the phenomenological Fourier law in classical and quantum mechanics, we illustrate ways to control the phononic heat flow and design thermal diodes. Finally, we consider the coupled transport of heat and charge and discuss several general mechanisms for optimizing the figure of merit of thermoelectric efficiency.Comment: 42 pages, 22 figures, review paper, to appear in the Springer Lecture Notes in Physics volume "Thermal transport in low dimensions: from statistical physics to nanoscale heat transfer" (S. Lepri ed.