2,900 research outputs found
Entanglement entropy and macroscopic quantum states with dipolar bosons in a triple-well potential
We study interacting dipolar atomic bosons in a triple-well potential within
a ring geometry. This system is shown to be equivalent to a three-site
Bose-Hubbard model. We analyze the ground state of dipolar bosons by varying
the effective on-site interaction. This analysis is performed both numerically
and analytically by using suitable coherent-state representations of the ground
state. The latter exhibits a variety of forms ranging from the su(3) coherent
state in the delocalization regime to a macroscopic cat-like state with fully
localized populations, passing for a coexistence regime where the ground state
displays a mixed character. We characterize the quantum correlations of the
ground state from the bi-partition perspective. We calculate both numerically
and analytically (within the previous coherent-state representation) the
single-site entanglement entropy which, among various interesting properties,
exhibits a maximum value in correspondence to the transition from the cat-like
to the coexistence regime. In the latter case, we show that the ground-state
mixed form corresponds, semiclassically, to an energy exhibiting two
almost-degenerate minima.Comment: 9 pages, 2 figure
Parallel computing and molecular dynamics of biological membranes
In this talk I discuss the general question of the portability of Molecular
Dynamics codes for diffusive systems on parallel computers of the APE family.
The intrinsic single precision arithmetics of the today available APE platforms
does not seem to affect the numerical accuracy of the simulations, while the
absence of integer addressing from CPU to individual nodes puts strong
constraints on the possible programming strategies. Liquids can be very
satisfactorily simulated using the "systolic" method. For more complex systems,
like the biological ones at which we are ultimately interested in, the "domain
decomposition" approach is best suited to beat the quadratic growth of the
inter-molecular computational time with the number of elementary components of
the system. The promising perspectives of using this strategy for extensive
simulations of lipid bilayers are briefly reviewed.Comment: 4 pages LaTeX, 2 figures included, espcrc2.sty require
Ab initio simulations of Cu binding sites in the N-terminal region of PrP
The prion protein (PrP) binds Cu2+ ions in the octarepeat domain of the
N-terminal tail up to full occupancy at pH=7.4. Recent experiments show that
the HGGG octarepeat subdomain is responsible for holding the metal bound in a
square planar coordination. By using first principle ab initio molecular
dynamics simulations of the Car-Parrinello type, the Cu coordination mode to
the binding sites of the PrP octarepeat region is investigated. Simulations are
carried out for a number of structured binding sites. Results for the complexes
Cu(HGGGW)+(wat), Cu(HGGG) and the 2[Cu(HGGG)] dimer are presented. While the
presence of a Trp residue and a H2O molecule does not seem to affect the nature
of the Cu coordination, high stability of the bond between Cu and the amide
Nitrogens of deprotonated Gly's is confirmed in the case of the Cu(HGGG)
system. For the more interesting 2[Cu(HGGG)] dimer a dynamically entangled
arrangement of the two monomers, with intertwined N-Cu bonds, emerges. This
observation is consistent with the highly packed structure seen in experiments
at full Cu occupancy.Comment: 4 pages, conference proceedin
A simple atomistic model for the simulation of the gel phase of lipid bilayers
In this paper we present the results of a large-scale numerical investigation
of structural properties of a model of cell membrane, simulated as a bilayer of
flexible molecules in vacuum. The study was performed by carrying out extensive
Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two
systems of different sizes (2x32 and 2x256 molecules), over a fairly large set
of temperatures and densities, using parallel platforms and more standard
serial computers. Depending on the dimension of the system, the dynamics was
followed for physical times that go from few hundred of picoseconds for the
largest system to 5--10 nanoseconds for the smallest one. We find that the
bilayer remains stable even in the absence of water and neglecting Coulomb
interactions in the whole range of temperatures and densities we have
investigated. The extension of the region of physical parameters that we have
explored has allowed us to study significant points in the phase diagram of the
bilayer and to expose marked structural changes as density and temperature are
varied, which are interpreted as the system passing from a crystal to a gel
phase.Comment: 41 pages, 13 figure
Mott Insulator to Superfluid transition in Bose-Bose mixtures in a two-dimensional lattice
We perform a numeric study (Worm algorithm Monte Carlo simulations) of
ultracold two-component bosons in two-dimensional optical lattices. We study
how the Mott insulator to superfluid transition is affected by the presence of
a second superfluid bosonic species. We find that, at fixed interspecies
interaction, the upper and lower boundaries of the Mott lobe are differently
modified. The lower boundary is strongly renormalized even for relatively low
filling factor of the second component and moderate (interspecies) interaction.
The upper boundary, instead, is affected only for large enough filling of the
second component. Whereas boundaries are renormalized we find evidence of
polaron-like excitations. Our results are of interest for current experimental
setups.Comment: 4 pages, 3 figures, accepted as PRA Rapid Communicatio
Ground-state Properties of Small-Size Nonlinear Dynamical Lattices
We investigate the ground state of a system of interacting particles in small
nonlinear lattices with M > 2 sites, using as a prototypical example the
discrete nonlinear Schroedinger equation that has been recently used
extensively in the contexts of nonlinear optics of waveguide arrays, and
Bose-Einstein condensates in optical lattices. We find that, in the presence of
attractive interactions, the dynamical scenario relevant to the ground state
and the lowest-energy modes of such few-site nonlinear lattices reveals a
variety of nontrivial features that are absent in the large/infinite lattice
limits: the single-pulse solution and the uniform solution are found to coexist
in a finite range of the lattice intersite coupling where, depending on the
latter, one of them represents the ground state; in addition, the single-pulse
mode does not even exist beyond a critical parametric threshold. Finally, the
onset of the ground state (modulational) instability appears to be intimately
connected with a non-standard (``double transcritical'') type of bifurcation
that, to the best of our knowledge, has not been reported previously in other
physical systems.Comment: 7 pages, 4 figures; submitted to PR
A benchmark for stocking rate management in a highly variable climate
Resting pastures and adjusting stocking rate to match carrying capacity are recommended for managing year-to-year variability in forage supply. Within the Queensland Government Drought and Climate Adaptation Program, grazing benchmark properties are being established to help validate the FORAGE modelling framework. Data from well-managed properties that are in good condition provide a reference for comparison with modelled long- term carrying capacity estimates. We report on the stocking rate strategies used by an experienced grazier for one of these benchmark properties
Measuring shared electrons in extended molecular systems: Covalent bonds from plane-wave representation of wave function
In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions
A lightweight BPMN extension for business process-oriented requirements engineering
Process-oriented requirements engineering approaches are often required to deal with the effective adaptation of existing processes in order to easily introduce new or updated requirements. Such approaches are based on the adoption of widely used notations, such as the one introduced by the Business Process Model and Notation (BPMN) standard. However, BPMN models do not convey enough information on the involved entities and how they interact with process activities, thus leading to ambiguities, as well as to incomplete and inconsistent requirements definitions. This paper proposes an approach that allows stakeholders and software analysts to easily merge and integrate behavioral and data properties in a BPMN model, so as to fully exploit the potential of BPMN without incurring into the aforementioned limitation. The proposed approach introduces a lightweight BPMN extension that specifically addresses the annotation of data properties in terms of constraints, i.e., pre- and post-conditions that the different process activities must satisfy. The visual representation of the annotated model conveys all the information required both by stakeholders, to understand and validate requirements, and by software analysts and developers, to easily map these updates to the corresponding software implementation. The presented approach is illustrated by use of two running examples, which have also been used to carry out a preliminary validation activity
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