Shape morphing and topology optimization of fluid channels by explicit boundary tracking

An integrated shape morphing and topology optimization approach based on the deformable simplicial complex methodology is developed to address Stokes and Navier‐Stokes flow problems. The optimized geometry is interpreted by a set of piecewise linear curves embedded in a well‐formed triangular mesh, resulting in a physically well‐defined interface between fluid and impermeable regions. The shape evolution is realized by deforming the curves while maintaining a high‐quality mesh through adaption of the mesh near the structural boundary, rather than performing global remeshing. Topological changes are allowed through hole merging or splitting of islands. The finite element discretization used provides smooth and stable optimized boundaries for simple energy dissipation objectives. However, for more advanced problems, boundary oscillations are observed due to conflicts between the objective function and the minimum length scale imposed by the meshing algorithm. A surface regularization scheme is introduced to circumvent this issue, which is specifically tailored for the deformable simplicial complex approach. In contrast to other filter‐based regularization techniques, the scheme does not introduce additional control variables, and at the same time, it is based on a rigorous sensitivity analysis. Several numerical examples are presented to demonstrate the applicability of the approach.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

Combined Subcutaneous Fat Aspirate and Skin Tru-Cut Biopsy for Amyloid Screening in Patients with Suspected Systemic Amyloidosis

Screening for systemic amyloidosis is typically carried out with abdominal fat aspirates with varying reported sensitivities. Fat aspirates are preferred for use in primary screening instead of organ biopsies as they are less invasive and thereby minimize the potential risk of complications. At Odense Amyloidosis Center, we performed a prospective study on whether the combined use of fat aspirate and tru-cut skin biopsy could increase the diagnostic sensitivity. Both fat aspirates and skin biopsies were screened with Congo Red staining, and positive biopsies were subsequently subtyped using immunoelectron microscopy and mass spectrometry. Seventy-six patients were included. In total, 24 patients had systemic amyloidosis (11 AL, 12 wtATTR, 1 AA), and 6 patients had localized amyloidosis. Combined fat aspirate and skin biopsy were Congo Red-positive in 15 patients (overall sensitivity (OS) 62.5%). Fat aspirates were positive in 14 patients (OS 58.3%), and the skin biopsy was positive in 5 patients (OS 20.8%). In only one patient did the skin biopsy add extra diagnostic information. The sensitivity differed between AL and ATTR amyloidosis—81.8% and 41.7%, respectively. Using skin biopsy as the only screening method is not recommended.     

Quantitative Derivation of the Gross‐Pitaevskii Equation

Starting from first‐principle many‐body quantum dynamics, we show that the dynamics of Bose‐Einstein condensates can be approximated by the time‐dependent nonlinear Gross‐Pitaevskii equation, giving a bound on the rate of the convergence. Initial data are constructed on the bosonic Fock space applying an appropriate Bogoliubov transformation on a coherent state with expected number of particles N. The Bogoliubov transformation plays a crucial role; it produces the correct microscopic correlations among the particles. Our analysis shows that, on the level of the one‐particle reduced density, the form of the initial data is preserved by the many‐body evolution, up to a small error that vanishes as N^?1/2 in the limit of large N.© 2015 Wiley Periodicals, Inc.     

Implementation of a separate fluid-neutral energy equation in SOLPS-ITER and its impact on the validity range of advanced fluid-neutral models

In plasma edge transport codes for nuclear fusion devices, fluid-neutral models offer an interesting alternative to the currently used kinetic Monte Carlo simulations, especially for cases of high ion-neutral collisionality. In this paper, we elaborate a separate neutral energy equation in the state-of-the-art SOLPS-ITER code suite, which previously assumed perfect ion-neutral temperature equilibration. Furthermore, we study the coupled plasma-neutral solutions for a range of divertor operating regimes, proving the validity of these fluid-neutral models for high-recycling and detached regimes.     

DFT Study of the Molybdenum‐Catalyzed Deoxydehydration of Vicinal Diols

The mechanism of the molybdenum‐catalyzed deoxydehydration (DODH) of vicinal diols has been investigated using density functional theory. The proposed catalytic cycle involves condensation of the diol with an Mo^VI oxo complex, oxidative cleavage of the diol resulting in an Mo^IV complex, and extrusion of the alkene. We have compared the proposed pathway with several alternatives, and the results have been corroborated by comparison with the molybdenum‐catalyzed sulfoxide reduction recently published by Sanz et al. and with experimental observations for the DODH itself. Improved understanding of the mechanism should expedite future optimization of molybdenum‐catalyzed biomass transformations.