A variational growth approach to topology optimization

In this contribution we present an overview of our work on a novel approach to topology optimization based on growth processes [1, 2, 3]. A compliance parameter to describe the spatial distribution of mass is introduced. It serves as an internal variable for which an associated evolution equation is derived using Hamilton’s principle. The well-known problem of checkerboarding is faced with energy regularization techniques. Numerical examples are given for demonstration purposes

Rapid in vitro prototyping of O-methyltransferases for pathway applications in Escherichia coli

O-methyltransferases are ubiquitous enzymes involved in biosynthetic pathways for secondary metabolites such as bacterial antibiotics, human catecholamine neurotransmitters, and plant phenylpropanoids. While thousands of putative O-methyltransferases are found in sequence databases, few examples are functionally characterized. From a pathway engineering perspective, however, it is crucial to know the substrate and product ranges of the respective enzymes to fully exploit their catalytic power. In this study, we developed an in vitro prototyping workflow that allowed us to screen ~30 enzymes against five substrates in three days with high reproducibility. We combined in vitro transcription/translation of the genes of interest with a microliter-scale enzymatic assay in 96-well plates. The substrate conversion was indirectly measured by quantifying the consumption of the S-adenosyl-L-methionine co-factor by time-resolved fluorescence resonance energy transfer rather than time-consuming product analysis by chromatography. This workflow allowed us to rapidly prototype thus-far uncharacterized O-methyltransferases for future use as biocatalysts

A Method for Gradient Enhancement of Continuum Damage Models

A method for the regularization of continuum damage material models based on gradient-type enhancement of the free-energy functional is presented. Direct introduction of the gradient of the damage variable would require C1 interpolation of the displacements, which is a complicated task to achieve with quadrilateral elements. Therefore a new variable field is introduced, which makes the model non-local in nature, while preserving C0 interpolation order of the variables at the same time. The strategy is formulated as a pure minimization problem, therefore the LBB-condition does not apply in this case. However, we still take the interpolation of the displacement field one order higher than the interpolation of the field of additional (non-local) variables. That leads to increased accuracy and removes the post-processing step necessary to obtain consistent results in the case of equal interpolation order. Several numerical examples which show the performance of the proposed gradient enhancement are presented. The pathological mesh dependence of the damage model is efficiently removed, together with the difficulties of numerical calculations in the softening range. Calculations predict a development of the damage variable which is mesh-objective for fixed internal material length

Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate

Virophages can parasitize giant DNA viruses and may provide adaptive anti-giant virus defense in unicellular eukaryotes. Under laboratory conditions, the virophage mavirus integrates into the nuclear genome of the marine flagellate Cafeteria burkhardae and reactivates upon superinfection with the giant virus CroV. In natural systems, however, the prevalence and diversity of host-virophage associations has not been systematically explored. Here, we report dozens of integrated virophages in four globally sampled C. burkhardae strains that constitute up to 2% of their host genomes. These endogenous mavirus-like elements (EMALEs) separated into eight types based on GC-content, nucleotide similarity, and coding potential and carried diverse promoter motifs implicating interactions with different giant viruses. Between host strains, some EMALE insertion loci were conserved indicating ancient integration events, whereas the majority of insertion sites were unique to a given host strain suggesting that EMALEs are active and mobile. Furthermore, we uncovered a unique association between EMALEs and a group of tyrosine recombinase retrotransposons, revealing yet another layer of parasitism in this nested microbial system. Our findings show that virophages are widespread and dynamic in wild Cafeteria populations, supporting their potential role in antiviral defense in protists

Electron-boson glue function derived from electronic Raman scattering

Raman scattering cross sections depend on photon polarization. In the cuprates nodal and antinodal directions are weighted more strongly in $B_{2g}$ and $B_{1g}$ symmetry, respectively. On the other hand in angle-resolved photoemission spectroscopy (ARPES), electronic properties are measured along well-defined directions in momentum space rather than their weighted averages. In contrast, the optical conductivity involves a momentum average over the entire Brillouin zone. Newly measured Raman response data on high-quality Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ single crystals up to high energies have been inverted using a modified maximum entropy inversion technique to extract from $B_{1g}$ and $B_{2g}$ Raman data corresponding electron-boson spectral densities (glue) are compared to the results obtained with known ARPES and optical inversions. We find that the $B_{2g}$ spectrum agrees qualitatively with nodal direction ARPES while the $B_{1g}$ looks more like the optical spectrum. A large peak around $30 - 40\,$meV in $B_{1g}$, much less prominent in $B_{2g}$, is taken as support for the importance of $(\pi,\pi)$ scattering at this frequency.Comment: 7 pages, 3 figure

Genome sequencing and molecular networking analysis of the wild fungusAnthostomella pineareveal its ability to produce a diverse range of secondary metabolites

Background Filamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority of fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild fungal isolate that we identified as Anthostomella pinea. The fungus belongs to a complex polyphyletic genus in the family of Xylariaceae, which is known to comprise endophytic and pathogenic fungi that produce a plethora of interesting secondary metabolites. Despite that, Anthostomella is largely understudied and only two species have been fully sequenced and characterized at a genomic level.Results In this work, we used long-read sequencing to obtain the complete 53.7 Mb genome sequence including the full mitochondrial DNA. We performed extensive structural and functional annotation of coding sequences, including genes encoding enzymes with potential applications in biotechnology. Among others, we found that the genome of A. pinea encodes 91 biosynthetic gene clusters, more than 600 CAZymes, and 164 P450s. Furthermore, untargeted metabolomics and molecular networking analysis of the cultivation extracts revealed a rich secondary metabolism, and in particular an abundance of sesquiterpenoids and sesquiterpene lactones. We also identified the polyketide antibiotic xanthoepocin, to which we attribute the anti–Gram-positive effect of the extracts that we observed in antibacterial plate assays.Conclusions Taken together, our results provide a first glimpse into the potential of Anthstomella pinea to provide new bioactive molecules and biocatalysts and will facilitate future research into these valuable metabolites

Comment on "Superconducting gap anisotropy vs. doping level in high-T_c cuprates" by C. Kendziora et al, PRL 77, 727 (1996)

In a recent paper Kendziora et al concluded that the superconducting gap in overdoped Bi-2212 is isotropic. From data obtained from electronic Raman scattering measurements, their conclusion was based on the observation that pair breaking peaks occured at approximately the same frequency in different scattering geometries and that the normalized scattering intensity at low energies was strongly depleted. We discuss a different interpretation of the raw data and present new data which is consistent with a strongly anisotropic gap with nodes. The spectra can be successfully described by a model for Raman scattering in a d_{x^{2}-y^{2}} superconductor with spin fluctuations and impurity scattering included.Comment: 1 page revtex plus 1 postscript figur

Finite element simulation of strain localization in inelastic solids by energy relaxation

A new approach for the treatment of strain localization in inelastic material is proposed. It is based on energy minimization principles associated with micro-structure developments. Shear bands are treated as micro-shearing of rank-one laminates.  It is assumed that the thickness of the shear band represented by its volume fraction tends to zero, and the energy inside the shear band is a function of the norm of the strain field. The existence of shear bands in the structure leads to an ill-posed problem which can be solved by means of energy relaxation. The performance of the proposed concept is demonstrated through numerical simulation of tension test under plane strain conditions. Numerical results show that mesh sensitivity can be completely removed