A reduction technique for weighted grouping problems

Weighted grouping problems are shown to have an equivalent reduced form, which is often considerably smaller than the original problem. Although the reduction may be small for randomly generated problems, real-life problems often contain non-random properties that greatly increase the effect of reduction. We give an efficient algorithm to build the reduced problem instance, and analyse the expected amount of reduction for certain statistical distributions and real-life data. In addition, we briefly discuss the effect of reduction on traditional solving methods of the grouping problem. The results show clearly the usefulness of problem reduction: it is computationally cheap to apply and may make the reduced problem solvable in a practical time whilst the original one is not. The method is readily applicable to the job grouping problem of printed circuit board (PCB) printing industry.     

A Protonated Water Cluster as a Transient Proton‐Loading Site in Cytochrome c Oxidase

Cytochrome c oxidase (CcO) is a redox‐driven proton pump that powers aerobic respiratory chains. We show here by multi‐scale molecular simulations that a protonated water cluster near the active site is likely to serve as the transient proton‐loading site (PLS) that stores a proton during the pumping process. The pK_a of this water cluster is sensitive to the redox states of the enzyme, showing distinct similarities to other energy converting proton pumps.     

Energetics and dynamics of proton transfer reactions along short water wires

Proton transfer (pT) reactions in biochemical processes are often mediated by chains of hydrogen-bonded water molecules. We use hybrid density functional calculations to study pT along quasi one-dimensional water arrays that connect an imidazolium-imidazole proton donor-acceptor pair. We characterize the structures of intermediates and transition states, the energetics, and the dynamics of the pT reactions, including vibrational contributions to kinetic isotope effects. In molecular dynamics simulations of pT transition paths, we find that for short water chains with four water molecules, the pT reactions are semi-concerted. The formation of a high-energy hydronium intermediate next to the proton-donating group is avoided by a simultaneous transfer of a proton from the donor to the first water molecule, and from the first water molecule into the water chain. Lowering the dielectric constant of the environment and increasing the water chain length both reduce the barrier for pT. We study the effect of the driving force on the energetics of the pT reaction by changing the proton affinity of the donor and acceptor groups through halogen and methyl substitutions. We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Br?nsted slopes of one and zero, respectively.     

Hydrogen-bond strengths by magnetically induced currents

We present here a "non-invasive" computational method to estimate the strength of individual hydrogen bonds using magnetically induced currents. The method is calibrated using H-bonding dimers, and applied on Watson-Crick DNA base pairs and proton wires in carbonic anhydrase.     

Arabinoxylan structure affects the reinforcement of films by microfibrillated cellulose

The chemical structure of rye arabinoxylan (rAX) was systematically modified, exploiting selective enzymes to mimic different naturally occurring xylans, i.e., its degree of substitution (DS) was decreased using α-l-arabinofuranosidase, and a controlled decrease in the degree of polymerization (DP) was performed using endo-1,4-β-d-xylanase. The arabinose to xylose ratio was decreased from 0.45 to 0.27 and the weight-average molar mass was decreased from 184,000 to 49,000 g/mol. The resulting samples were used to prepare films, as such, and with 15% (wt. − %) softwood-derived microfibrillated cellulose (MFC) to obtain novel plant-derived biocomposite materials. The enzymatic tailoring of rAX increased the crystallinity of films, evidenced by X-ray diffraction studies, and the addition of MFC to the debranched, low DS rAX induced the formation of ordered structures visible with polarizing optical microscopy. MFC decreased the moisture uptake of films and increased the relative humidity of softening of the films, detected with moisture scanning dynamic mechanical analysis. For the first time, the chemical structure of xylan was proven to significantly affect the reinforcement potential of nano-sized cellulose, as the tensile strength of films from high DP rAXs, but not that of low DP rAXs, clearly increased with the addition of MFC. At the same time, MFC only increased the Young’s modulus of films from rAX with high arabinose content, regardless of DP.     

Estimating head-related transfer functions of human subjects from pressure-velocity measurements

Direct measurements of individual head-related transfer functions (HRTFs) with a probe microphone at the eardrum are unpleasant, risky, and unreliable and therefore have not been widely used. Instead, the HRTFs are commonly measured from the blocked ear canal entrance, which excludes the effects of the individual ear canals and eardrums. This paper presents a method that allows obtaining individually correct magnitude frequency responses of HRTFs at the eardrum from pressure-velocity (PU) measurements at the ear canal entrance with a miniature PU sensor. The HRTFs of 25 test subjects with nine directions of sound incidence were estimated using real anechoic measurements and an energy-based estimation method. To validate the approach, measurements were also conducted with probe microphones near the eardrums as well as at blocked ear canal entrances. Comparisons between the different methods show that the method presented is a valid and reliable technique for obtaining magnitude frequency responses of HRTFs. The HRTF filters designed using the PU measurements are also shown to yield more correct frequency responses at the eardrum than the filters designed using measurements from the blocked ear canal entrance.     

Phase transition and gravitational wave phenomenology of scalar conformal extensions of the Standard Model

Thermal corrections in classically conformal models typically induce a strong first-order electroweak phase transition, thereby resulting in a stochastic gravitational background that could be detectable at gravitational wave observatories. After reviewing the basics of classically conformal scenarios, in this paper we investigate the phase transition dynamics in a thermal environment and the related gravitational wave phenomenology within the framework of scalar conformal extensions of the Standard Model. We find that minimal extensions involving only one additional scalar field struggle to reproduce the correct phase transition dynamics once thermal corrections are accounted for. Next-to-minimal models, instead, yield the desired electroweak symmetry breaking and typically result in a very strong gravitational wave signal.     

Electron impact induced fragmentations of some 2,2-disubstituted 1,3-dithiolanes

Electron impact induced fragmentations of the title compounds were studied by exact mass measurement and metastable ion analysis. Sulphur atoms within the ring effectively stabilize the positive charge. In most cases the loss of the larger substituent, and not the other, methyl group, gives rise to the base peak in the spectrum. Examination of competing metastable transitions shows that generally this is also the lowest activation energy primary process. In general primary ring cleavage reactions are not important unless there is a heteroatom in the substituent that can assist this cleavage.     

Total synthesis of thiostrepton. Retrosynthetic analysis and construction of key building blocks

The first phase of the total synthesis of thiostrepton (1), a highly complex thiopeptide antibiotic, is described. After a brief introduction to the target molecule and its structural motifs, it is shown that retrosynthetic analysis of thiostrepton reveals compounds 23, 24, 26, 28, and 29 as potential key building blocks for the projected total synthesis. Concise and stereoselective constructions of all these intermediates are then described. The synthesis of the dehydropiperidine core 28 was based on a biosynthetically inspired aza-Diels-Alder dimerization of an appropriate azadiene system, an approach that was initially plagued with several problems which were, however, resolved satisfactorily by systematic investigations. The quinaldic acid fragment 24 and the thiazoline-thiazole segment 26 were synthesized by a series of reactions that included asymmetric and other stereoselective processes. The dehydroalanine tail precursor 23 and the alanine equivalent 29 were also prepared from the appropriate amino acids. Finally, a method was developed for the direct coupling of the labile dehydropiperidine key building block 28 to the more advanced and stable peptide intermediate 27 through capture with the highly reactive alanine equivalent 67 under conditions that avoided the initially encountered destructive ring contraction process.