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Quantum dynamics of a spin-1 condensate in a double-well potential
No full textWe study quantum dynamics of a Bose-Einstein condensate of spin-1 atoms inside a double-well potential. Under the single spatial mode approximation for condensate wave functions localized within each of the two wells, we examine quantum entanglement and pseudo-spin-squeezing properties in both the Rabi and Josephson regimes. Quantum fluctuations is found to be more stable leading to robust multipartite entanglement in the lower end of the Josephson regime, or the mean field self-trapped region. Substantial multipartite entanglement is witnessed not only due to pseudo-spin-squeezing by the axis-twisting interaction but also from redistribution of mode-entangled atoms between the wells by the tunneling coupling
Calculating the local solvent chemical potential in crystal hydrates
No full textDetermining solvation patterns in biological systems is crucial in investigating the functional role water may play in structural stabilization and molecular recognition. Determining whether a particular position would be occupied by a solvent molecule requires the local thermodynamics to be known. In this work we introduce a simple and inexpensive approach based on grand canonical molecular simulations to determine the occupancy factors of the cavities. The method is applied to the test case of the sodium salt of hyaluronic acid. The results agree very well with experimental results and demonstrate the success of the method
Finite-size effects in the dynamics and thermodynamics of two-dimensional Coulomb clusters
No full textThe dynamics and thermodynamics of melting in two-dimensional Coulomb clusters is revisited using molecular dynamics and Monte Carlo simulations. Several parameters are considered, including the Lindemann index, the largest Lyapunov exponent, and the diffusion constant. In addition to the orientational and radial melting processes, isomerizations and complex size effects are seen to occur in a very similar way to atomic and molecular clusters. The results are discussed in terms of the energy landscape represented through disconnectivity graphs, with proper attention paid to the broken ergodicity problems in simulations. Clusters bound by 1/r(3) and e(-kappa r)/r forces, and heterogeneous clusters made of singly and doubly charged species, are also studied, as well as the evolution toward larger systems
Infinitely robust order and local order-parameter tulips in Apollonian networks with quenched disorder
No full textFor a variety of quenched random spin systems on an Apollonian network, including ferromagnetic and antiferromagnetic bond percolation and the Ising spin glass, we find the persistence of ordered phases up to infinite temperature over the entire range of disorder. We develop a renormalization-group technique that yields highly detailed information, including the exact distributions of local magnetizations and local spin-glass order parameters, which turn out to exhibit, as function of temperature, complex and distinctive tulip patterns
Reentrant and forward phase diagrams of the anisotropic three-dimensional Ising spin glass
No full textThe spatially uniaxially anisotropic d=3 Ising spin glass is solved exactly on a hierarchical lattice. Five different ordered phases, namely, ferromagnetic, columnar, layered, antiferromagnetic, and spin-glass phases, are found in the global phase diagram. The spin-glass phase is more extensive when randomness is introduced within the planes than when it is introduced in lines along one direction. Phase diagram cross sections, with no Nishimori symmetry, with Nishimori symmetry lines, or entirely imbedded into Nishimori symmetry, are studied. The boundary between the ferromagnetic and spin-glass phases can be either reentrant or forward, that is either receding from or penetrating into the spin-glass phase, as temperature is lowered. However, this boundary is always reentrant when the multicritical point terminating it is on the Nishimori symmetry line
Supercoil formation in DNA denaturation
No full textWe generalize the Poland-Scheraga model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional stress induced by denaturation enforces the formation of supercoils whose writhe absorbs the linking number expelled by the loops. Our model predicts that when the entropy parameter of a loop satisfies c <= 2, denaturation transition does not take place. On the other hand, for c>2, a first-order denaturation transition is consistent with our model and may take place in the actual system, as in the case with no supercoils. These results are in contrast with other treatments of circular DNA melting where denaturation is assumed to be accompanied by an increase in twist rather than writhe on the bound segments
Photonic band gap via quantum coherence in vortex lattices of Bose-Einstein condensates
No full textWe investigate the optical response of an atomic Bose-Einstein condensate with a vortex lattice. We find that it is possible for the vortex lattice to act as a photonic crystal and create photonic band gaps, by enhancing the refractive index of the condensate via a quantum coherent scheme. If high enough index contrast between the vortex core and the atomic sample is achieved, a photonic band gap arises depending on the healing length and the lattice spacing. A wide range of experimentally accessible parameters are examined and band gaps in the visible region of the electromagnetic spectrum are found. We also show how directional band gaps can be used to directly measure the rotation frequency of the condensate
Time-dependent pseudo-Hermitian Hamiltonians defining a unitary quantum system and uniqueness of the metric operator
No full textThe quantum measurement axiom dictates that physical observables and in particular the Hamiltonian must be diagonalizable and have a real spectrum. For a time-independent Hamiltonian (with a discrete spectrum) these conditions ensure the existence of a positive-definite inner product that renders the Hamiltonian self-adjoint. Unlike for a time-independent Hamiltonian, this does not imply the unitarity of the Schrodinger time-evolution for a general time-dependent Hamiltonian. We give an additional necessary and sufficient condition for the unitarity of time-evolution. In particular, we obtain the general form of a two-level Hamiltonian that fulfills this condition. We show that this condition is geometrical in nature and that it implies the reality of the adiabatic geometric phase angles. We also address the problem of the uniqueness of the metric operator
Born-Infeld axion-dilaton electrodynamics and electromagnetic confinement
No full textA generalization of Born-Infeld non-linear vacuum electrodynamics involving axion and dilaton fields is constructed with couplings dictated by electromagnetic duality and SL(2, IR) symmetries in the weak field limit. Besides the Newtonian gravitational constant the model contains a single fundamental coupling parameter b(0). In the absence of axion and dilaton interactions it reduces in the limit b(0) bar right arrow infinity to Maxwell's linear vacuum theory while for finite b(0) it reduces to the original Born-Infeld model. The spherically symmetric static sector of the theory is explored in a flat background spacetime in the Jordan frame where numerical evidence suggests the existence of axion-dilaton bound states possessing confined electric flux
Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study
No full textBackground: Histone demethylase, JMJD2A, specifically recognizes and binds to methylated lysine residues at histone H3 and H4 tails (especially trimethylated H3K4 (H3K4me3), trimethylated H3K9 (H3K9me3) and di, trimethylated H4K20 (H4K20me2, H4K20me3)) via its tandem tudor domains. Crystal structures of JMJD2A-tudor binding to H3K4me3 and H4K20me3 peptides are available whereas the others are not. Complete picture of the recognition of the four histone peptides by the tandem tudor domains yet remains to be clarified. Methodology/Principal Findings: We report a detailed molecular dynamics simulation and binding energy analysis of the recognition of JMJD2A-tudor with four different histone tails. 25 ns fully unrestrained molecular dynamics simulations are carried out for each of the bound and free structures. We investigate the important hydrogen bonds and electrostatic interactions between the tudor domains and the peptide molecules and identify the critical residues that stabilize the complexes. Our binding free energy calculations show that H4K20me2 and H3K9me3 peptides have the highest and lowest affinity to JMJD2A-tudor, respectively. We also show that H4K20me2 peptide adopts the same binding mode with H4K20me3 peptide, and H3K9me3 peptide adopts the same binding mode with H3K4me3 peptide. Decomposition of the enthalpic and the entropic contributions to the binding free energies indicate that the recognition of the histone peptides is mainly driven by favourable van der Waals interactions. Residue decomposition of the binding free energies with backbone and side chain contributions as well as their energetic constituents identify the hotspots in the binding interface of the structures. Conclusion: Energetic investigations of the four complexes suggest that many of the residues involved in the interactions are common. However, we found two receptor residues that were related to selective binding of the H3 and H4 ligands. Modifications or mutations on one of these residues can selectively alter the recognition of the H3 tails or the H4 tails