Ices in Star-Forming Regions: First Results from VLT-ISAAC

The first results from a VLT-ISAAC program on L- and M-band infrared spectroscopy of deeply-embedded young stellar objects are presented. The advent of 8-m class telescopes allows high S/N spectra of low-luminosity sources to be obtained. In our first observing run, low- and medium-resolution spectra have been measured toward a dozen objects, mostly in the Vela and Chamaeleon molecular clouds. The spectra show strong absorption of H2O and CO ice, as well as weak features at `3.47' and 4.62 mu. No significant solid CH3OH feature at 3.54 mu is found, indicating that the CH3OH/H2O ice abundance is lower than toward some massive protostars. Various evolutionary diagnostics are investigated for a set of sources in Vela.Comment: 8 pages, 4 figures, to appear in The Origins of Stars and Planets: the VLT View, eds. J. Alves, M. McCaughrean (Springer Verlag

Algebraic totality, towards completeness

Finiteness spaces constitute a categorical model of Linear Logic (LL) whose objects can be seen as linearly topologised spaces, (a class of topological vector spaces introduced by Lefschetz in 1942) and morphisms as continuous linear maps. First, we recall definitions of finiteness spaces and describe their basic properties deduced from the general theory of linearly topologised spaces. Then we give an interpretation of LL based on linear algebra. Second, thanks to separation properties, we can introduce an algebraic notion of totality candidate in the framework of linearly topologised spaces: a totality candidate is a closed affine subspace which does not contain 0. We show that finiteness spaces with totality candidates constitute a model of classical LL. Finally, we give a barycentric simply typed lambda-calculus, with booleans ${\mathcal{B}}$ and a conditional operator, which can be interpreted in this model. We prove completeness at type ${\mathcal{B}}^n\to{\mathcal{B}}$ for every n by an algebraic method

A Computation of the Maximal Order Type of the Term Ordering on Finite Multisets

We give a sharpening of a recent result of Aschenbrenner and Pong about the maximal order type of the term ordering on the finite multisets over a wpo. Moreover we discuss an approach to compute maximal order types of well-partial orders which are related to tree embeddings

Effective dynamics using conditional expectations

The question of coarse-graining is ubiquitous in molecular dynamics. In this article, we are interested in deriving effective properties for the dynamics of a coarse-grained variable $\xi(x)$, where $x$ describes the configuration of the system in a high-dimensional space $\R^n$, and $\xi$ is a smooth function with value in $\R$ (typically a reaction coordinate). It is well known that, given a Boltzmann-Gibbs distribution on $x \in \R^n$, the equilibrium properties on $\xi(x)$ are completely determined by the free energy. On the other hand, the question of the effective dynamics on $\xi(x)$ is much more difficult to address. Starting from an overdamped Langevin equation on $x \in \R^n$, we propose an effective dynamics for $\xi(x) \in \R$ using conditional expectations. Using entropy methods, we give sufficient conditions for the time marginals of the effective dynamics to be close to the original ones. We check numerically on some toy examples that these sufficient conditions yield an effective dynamics which accurately reproduces the residence times in the potential energy wells. We also discuss the accuracy of the effective dynamics in a pathwise sense, and the relevance of the free energy to build a coarse-grained dynamics

How the Kano model contributes to Kansei engineering in services

Recent studies show that products and services hold great appeal if they are attractively designed to elicit emotional feelings from customers. Kansei engineering (KE) has good potential to provide a competitive advantage to those able to read and translate customer affect and emotion in actual product and services. This study introduces an integrative framework of the Kano model and KE, applied to services. The Kano model was used and inserted into KE to exhibit the relationship between service attribute performance and customer emotional response. Essentially, the Kano model categorises service attribute quality into three major groups (must-be [M], one-dimensional [O] and attractive [A]). The findings of a case study that involved 100 tourists who stayed in luxury 4- and 5-star hotels are presented. As a practical matter, this research provides insight on which service attributes deserve more attention with regard to their significant impact on customer emotional needs. Statement of Relevance: Apart from cognitive evaluation, emotions and hedonism play a big role in service encounters. Through a focus on delighting qualities of service attributes, this research enables service providers and managers to establish the extent to which they prioritise their improvement efforts and to always satisfy their customer emotions beyond expectation. Keywords: Kansei engineering, emotional feelings, Kano model, service

In Vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis

Background Effectiveness of ART regimens strongly depends upon complex interactions between the selective pressure of drugs and the evolution of mutations that allow or restrict drug resistance. Methods Four clinical isolates from NRTI-exposed, NNRTI-naive subjects were passaged in increasing concentrations of NVP in combination with 1 µM 3 TC and 2 µM ADV to assess selective pressures of multi-drug treatment. A novel parameter inference procedure, based on a stochastic viral growth model, was used to estimate phenotypic resistance and fitness from in vitro combination passage experiments. Results Newly developed mathematical methods estimated key phenotypic parameters of mutations arising through selective pressure exerted by 3 TC and NVP. Concentrations of 1 µM 3 TC maintained the M184V mutation, which was associated with intrinsic fitness deficits. Increasing NVP concentrations selected major NNRTI resistance mutations. The evolutionary pathway of NVP resistance was highly dependent on the viral genetic background, epistasis as well as stochasticity. Parameter estimation indicated that the previously unrecognized mutation L228Q was associated with NVP resistance in some isolates. Conclusion Serial passage of viruses in the presence of multiple drugs may resemble the selection of mutations observed among treated individuals and populations in vivo and indicate evolutionary preferences and restrictions. Phenotypic resistance estimated here “in silico” from in vitro passage experiments agreed well with previous knowledge, suggesting that the unique combination of “wet-” and “dry-lab” experimentation may improve our understanding of HIV-1 resistance evolution in the future

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and non-trivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.Comment: 23 pages, 12 figure

A weak characterization of slow variables in stochastic dynamical systems

We present a novel characterization of slow variables for continuous Markov processes that provably preserve the slow timescales. These slow variables are known as reaction coordinates in molecular dynamical applications, where they play a key role in system analysis and coarse graining. The defining characteristics of these slow variables is that they parametrize a so-called transition manifold, a low-dimensional manifold in a certain density function space that emerges with progressive equilibration of the system's fast variables. The existence of said manifold was previously predicted for certain classes of metastable and slow-fast systems. However, in the original work, the existence of the manifold hinges on the pointwise convergence of the system's transition density functions towards it. We show in this work that a convergence in average with respect to the system's stationary measure is sufficient to yield reaction coordinates with the same key qualities. This allows one to accurately predict the timescale preservation in systems where the old theory is not applicable or would give overly pessimistic results. Moreover, the new characterization is still constructive, in that it allows for the algorithmic identification of a good slow variable. The improved characterization, the error prediction and the variable construction are demonstrated by a small metastable system

Fermion-Boson Interactions and Quantum Algebras

Quantum Algebras (q-algebras) are used to describe interactions between fermions and bosons. Particularly, the concept of a su_q(2) dynamical symmetry is invoked in order to reproduce the ground state properties of systems of fermions and bosons interacting via schematic forces. The structure of the proposed su_q(2) Hamiltonians, and the meaning of the corresponding deformation parameters, are discussed.Comment: 20 pages, 10 figures. Physical Review C (in press