Convected level set method for the numerical simulation of fluid buckling

‘Fluid buckling’ is a phenomenon characterized mainly by the existence of fluid toroidal oscillations during flow. It appears when a high viscosity fluid flows vertically against a flat surface and may occur in industrial applications, as in injection molding of a propergol in complex‐shaped cavities. These coiling or folding oscillations appear during the mold filling stage, leading to air entrapment. To understand and to model this free surface flow problem, a convected level set method is proposed. First, a sinus filter is applied to the distance function to get a smooth truncation far from the interface. Second, the reinitialization is embedded in the transport equation model, avoiding it as a separate step during calculation. In order to validate the method, numerical results are presented on classical interface capturing benchmarks. Finally, results are shown on two‐dimensional and three‐dimensional viscous jet buckling problems. Copyright © 2010 John Wiley & Sons, Ltd.     

Influence of mesh deformation on the quality of large eddy simulations

The influence of mesh motion on the quality of large eddy simulation (LES) was studied in the present article. A three‐dimensional, turbulent pipe flow (Re_τ=360) was considered as a test case. Simulations with both stretching and static meshes were carried out in order to understand how mesh motion affects the turbulence statistics. The spatial filtering of static and moving mesh direct numerical simulation (DNS) data showed how an ideal LES would perform, while the comparison of DNS cases with static and moving meshes revealed that no significant numerical errors arise from the mesh motion when the simulation is fully resolved. The comparison of the filtered fields of the DNS with a moving mesh with the corresponding LES fields revealed different responses to mesh motion from different numerical approaches. A straightforward test was applied in order to verify that the moving mesh works consistently in LES: when the mesh is stretched in the streamwise direction, the moving mesh results should be in between the two extremal resolutions between which the mesh is stretched. Numerical investigations using four different LES approaches were carried out. In addition to the Smagorinsky model, three implicit LES approaches were used: linear interpolation (non‐dissipative), the Gamma limiter (dissipative), and the scale‐selective discretisation (slightly dissipative). The results indicate that while the Smagorinsky and the scale‐selective discretisation approaches produce results consistent with the resolution of the non‐static mesh, the implicit LES with linear interpolation or the Gamma scheme do not. Copyright © 2016 John Wiley & Sons, Ltd.     

Side-branch resonators modelling with Green׳s function methods

This paper deals with strategies for computing efficiently the propagation of sound waves in ducts containing passive components. In many cases of practical interest, these components are acoustic cavities which are connected to the duct. Though standard Finite Element software could be used for the numerical prediction of sound transmission through such a system, the method is known to be extremely demanding, both in terms of data preparation and computation, especially in the mid-frequency range. To alleviate this, a numerical technique that exploits the benefit of the FEM and the BEM approach has been devised. First, a set of eigenmodes is computed in the cavity to produce a numerical impedance matrix connecting the pressure and the acoustic velocity on the duct wall interface. Then an integral representation for the acoustic pressure in the main duct is used. By choosing an appropriate Green?s function for the duct, the integration procedure is limited to the duct–cavity interface only. This allows an accurate computation of the scattering matrix of such an acoustic system with a numerical complexity that grows very mildly with the frequency. Typical applications involving Helmholtz and Herschel–Quincke resonators are presented.     

Differentiability in the Sobolev space W^{1,n-1}

Let \(\Omega \subset {\mathbb {R}}^{n}\) be a domain, \(n \ge 2\) . We show that a continuous, open and discrete mapping \(f \in W_{\mathrm{loc }}^{1,n-1}(\Omega , {\mathbb {R}}^{n})\) with integrable inner distortion is differentiable almost everywhere on \(\Omega \) . As a corollary we get that the branch set of such a mapping has measure zero.     

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.     

Small-angle scattering study of structural changes in the microfibril network of nanocellulose during enzymatic hydrolysis

The hydrolysis of nanofibrillated cellulose (NFC), consisting of individual cellulose fibrils, was followed using small-angle scattering techniques in order to reveal changes in the substrate structure caused by cellulose degrading enzymes. In particular, the nanoscale structure of the network of cellulose fibrils was characterized with the combination of small-angle neutron scattering and small-angle x-ray scattering. In the nanocellulose with higher xylan content, the interfibrillar distance was shown to remain unchanged during enzymatic degradation, whereas the distance increased in the nanocellulose with lower xylan content. The limiting effect of xylan on the hydrolysis and a faster hydrolysis of the more thoroughly fibrillated segments of the NFC network could be observed. Despite the extensive fibrillation of the raw material, however, the hydrolysis was eventually limited by the aggregated and heterogeneous structure of the substrate.     

Lab‐on‐a‐Chip Reactor Imaging with Unprecedented Chemical Resolution by Hadamard‐Encoded Remote Detection NMR

The development of microfluidic processes requires information‐rich detection methods. Here we introduce the concept of remote detection exchange NMR spectroscopy (RD‐EXSY), and show that, along with indirect spatial information extracted from time‐of‐flight data, it provides unique information about the active regions, reaction pathways, and intermediate products in a lab‐on‐a‐chip reactor. Furthermore, we demonstrate that direct spatial resolution can be added to RD‐EXSY efficiently by applying the principles of Hadamard spectroscopy.     

Fluorescent protein-based FRET sensor for intracellular monitoring of redox status in bacteria at single cell level

Monitoring of intracellular redox status in a bacterial cell provides vital information about the physiological status of the cell, which can be exploited in several applications such as metabolic engineering and computational modeling. Fluorescent protein-based genetically encoded sensors can be used to monitor intracellular oxidation/reduction status. This study reports the development of a redox sensor for intracellular measurements using fluorescent protein pairs and the phenomenon of Förster resonance energy transfer (FRET). For the development of the sensor, fluorescent proteins Citrine and Cerulean were genetically modified to carry reactive cysteine residues on the protein surface close to the chromophore and a constructed FRET pair was fused using a biotinylation domain as a linker. In oxidized state, the FRET pairs are in close proximity by labile disulfide bond formation resulting in higher FRET efficiency. In reducing environment, the FRET is diminished due to the increased distance between FRET pairs providing large dynamic measurement range to the sensor. Intracellular studies in Escherichia coli mutants revealed the capability of the sensor in detecting real-time redox variations at single cell level. The results were validated by intensity based and time resolved measurements. The functional immobilization of the fluorescent protein-based FRET sensor at solid surfaces for in vitro applications was also demonstrated. Graphical Abstract

Schematic representation of FRET-based redox sensor     

Quantum chemical modeling of chiral catalysis. Part 14. On the coordination of carbonyl compounds to diaza-, oxaza- and dioxaluminolidines of potential use as chiral controllers in organic synthetic chemistry

Conformers of 4-coordinate adducts of carbonyl compounds and diaza-, oxaza- and dioxaluminolidines were investigated by means of ab initio MO methods (RHF). Formaldehyde was used as a model of carbonyl compounds. Relative stabilities of the conformers indicate formation of syn adducts of carbonyl compounds and aluminolidines (C_C=O and aluminolidine ring syn about the Al---O_C=O bond) to be favoured over that of the corresponding anti ones (all syn/anti ratios higher than 99:1, 6–31G//6–31G). The energetic preference for the formation of syn adducts of oxazaaluminolidines was about twice as high as that of diaza- or dioxaluminolidines of which the syn/anti selectivities were found to be practically equal.