@unpublished{SeitzJungnickelKleiberetal.2024, author = {Seitz, Florian and Jungnickel, Tina and Kleiber, Nicole and Kretschmer, Jens and Dietzsch, Julia and Adelmann, Juliane and Bohnsack, Katherine E. and Bohnsack, Markus T. and H{\"o}bartner, Claudia}, title = {Atomic mutagenesis of N\(^6\)-methyladenosine reveals distinct recognition modes by human m\(^6\)A reader and eraser proteins}, series = {Journal of the American Chemical Society}, journal = {Journal of the American Chemical Society}, doi = {10.1021/jacs.4c00626}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-352376}, year = {2024}, abstract = {N\(^6\)-methyladenosine (m\(^6\)A) is an important modified nucleoside in cellular RNA associated with multiple cellular processes and is implicated in diseases. The enzymes associated with the dynamic installation and removal of m\(^6\)A are heavily investigated targets for drug research, which requires detailed knowledge of the recognition modes of m\(^6\)A by proteins. Here, we use atomic mutagenesis of m\(^6\)A to systematically investigate the mechanisms of the two human m\(^6\)A demethylase enzymes FTO and ALKBH5 and the binding modes of YTH reader proteins YTHDF2/DC1/DC2. Atomic mutagenesis refers to atom-specific changes that are introduced by chemical synthesis, such as the replacement of nitrogen by carbon atoms. Synthetic RNA oligonucleotides containing site-specifically incorporated 1-deaza-, 3-deaza-, and 7-deaza-m\(^6\)A nucleosides were prepared by solid-phase synthesis and their RNA binding and demethylation by recombinant proteins were evaluated. We found distinct differences in substrate recognition and transformation and revealed structural preferences for the enzymatic activity. The deaza m\(^6\)A analogues introduced in this work will be useful probes for other proteins in m\(^6\)A research.}, language = {en} } @unpublished{Dandekar2023, author = {Dandekar, Thomas}, title = {A modified inflation cosmology relying on qubit-crystallization: rare qubit interactions trigger qubit ensemble growth and crystallization into "real" bit-ensembles and emergent time}, doi = {10.25972/OPUS-32177}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-321777}, pages = {42}, year = {2023}, abstract = {In a modified inflation scenario we replace the "big bang" by a condensation event in an eternal all-compassing big ocean of free qubits in our modified cosmology. Interactions of qubits in the qubit ocean are rare. If they happen, they provide a nucleus for a new universe as the qubits become decoherent and freeze-out into defined bit ensembles. Second, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth) - the crystal unit cell guarantees same symmetries everywhere. Hence, the textbook inflation scenario to explain the same laws of nature in our domain is replaced by the crystal unit cell of the crystal formed. We give here only the perspective or outline of this modified inflation theory, as the detailed mathematical physics behind this has still to be formulated and described. Interacting qubits solidify, quantum entropy decreases (but increases in the ocean around). The interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, but more importantly can explain well by such a type of cosmological crystallization instead of inflation the early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: no annihilation of antimatter necessary, rather the unit cell of our crystal universe has a matter handedness avoiding anti-matter. We prove a triggering of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, this means that in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below h dash liquidity left). However, the E8 symmetry of heterotic string theory has six rolled-up, small dimensions which help to keep the qubit crystal together and will never expand. Finally, we give first energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field in the crystal. Hence, vacuum energy gets low inside the qubit crystal. Condensed mathematics may advantageously help to model free (many states denote the same qubit) and bound qubits in phase space.}, language = {en} } @unpublished{NeitzBessiKuperetal.2023, author = {Neitz, Hermann and Bessi, Irene and Kuper, Jochen and Kisker, Caroline and H{\"o}bartner, Claudia}, title = {Programmable DNA interstrand crosslinking by alkene-alkyne [2+2] photocycloaddition}, series = {Journal of the American Chemical Society}, journal = {Journal of the American Chemical Society}, edition = {submitted version}, doi = {10.1021/jacs.3c01611}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-311822}, year = {2023}, abstract = {Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (\(^{Phe}\)dU). The crosslinking ability of \(^{Phe}\)dU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2+2] cycloaddition within the DNA duplex, resulting in efficient formation of a \(^{Phe}\)dU-dimer after short irradiation times of a few seconds. A \(^{Phe}\)dU dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.}, language = {en} } @unpublished{Dandekar2023, author = {Dandekar, Thomas}, title = {Analysing the phase space of the standard model and its basic four forces from a qubit phase transition perspective: implications for large-scale structure generation and early cosmological events}, doi = {10.25972/OPUS-29858}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-298580}, pages = {42}, year = {2023}, abstract = {The phase space for the standard model of the basic four forces for n quanta includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. We replace the "big bang" by a condensation event (interacting qubits become decoherent) and inflation by a crystallization event - the crystal unit cell guarantees same symmetries everywhere. Interacting qubits solidify and form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, large-scale structure of voids and filaments, supercluster formation, galaxy formation, dominance of matter and life-friendliness. We prove qubit interactions to be 1,2,4 or 8 dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. We give energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field. Hence, vacuum energy gets low only inside the qubit crystal. Condensed mathematics may advantageously model free / bound qubits in phase space.}, language = {en} } @unpublished{FerschMalyRueheetal.2023, author = {Fersch, Daniel and Mal{\´y}, Pavel and R{\"u}he, Jessica and Lisinetskii, Victor and Hensen, Matthias and W{\"u}rthner, Frank and Brixner, Tobias}, title = {Single-Molecule Ultrafast Fluorescence-Detected Pump-Probe Microscopy}, doi = {10.25972/OPUS-31348}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-313485}, year = {2023}, abstract = {We introduce fluorescence-detected pump-probe microscopy by combining a wavelength-tunable ultrafast laser with a confocal scanning fluorescence microscope, enabling access to the femtosecond time scale on the micrometer spatial scale. In addition, we obtain spectral information from Fourier transformation over excitation pulse-pair time delays. We demonstrate this new approach on a model system of a terrylene bisimide (TBI) dye embedded in a PMMA matrix and acquire the linear excitation spectrum as well as time-dependent pump-probe spectra simultaneously. We then push the technique towards single TBI molecules and analyze the statistical distribution of their excitation spectra. Furthermore, we demonstrate the ultrafast transient evolution of several individual molecules, highlighting their different behavior in contrast to the ensemble due to their individual local environment. By correlating the linear and nonlinear spectra, we assess the effect of the molecular environment on the excited-state energy.}, subject = {Fluoreszenz}, language = {en} } @unpublished{NeitzHoebartner2023, author = {Neitz, Hermann and H{\"o}bartner, Claudia}, title = {A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker}, series = {Chemical Communications}, journal = {Chemical Communications}, edition = {submitted version}, doi = {10.1039/D3CC03796G}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328255}, year = {2023}, abstract = {We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detectio of a specific DNA sequence.}, language = {en} } @unpublished{DietzschJayachandranMuelleretal.2023, author = {Dietzsch, Julia and Jayachandran, Ajay and Mueller, Stefan and H{\"o}bartner, Claudia and Brixner, Tobias}, title = {Excitonic coupling of RNA-templated merocyanine dimer studied by higher-order transient absorption spectroscopy}, series = {Chemical Communications}, journal = {Chemical Communications}, edition = {submitted version}, doi = {10.1039/D3CC02024J}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-327772}, year = {2023}, abstract = {We report the synthesis and spectroscopic analysis of RNA containing the barbituric acid merocyanine rBAM2 as a nucleobase surrogate. Incorporation into RNA strands by solid-phase synthesis leads to fluorescence enhancement compared to the free chromophore. In addition, linear absorption studies show the formation of an excitonically coupled H-type dimer in the hybridized duplex. Ultrafast third- and fifth-order transient absorption spectroscopy of this non-fluorescent dimer suggests immediate (sub-200 fs) exciton transfer and annihilation due to the proximity of the rBAM2 units.}, language = {en} } @unpublished{SaalSwainSchmiedeletal.2023, author = {Saal, Fridolin and Swain, Asim and Schmiedel, Alexander and Holzapfel, Marco and Lambert, Christoph and Ravat, Prince}, title = {Push-Pull [7]Helicene Diimide: Excited-State Charge Transfer and Solvatochromic Circularly Polarised Luminescence}, edition = {submitted version}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345207}, year = {2023}, abstract = {In this communication we describe a helically chiral push-pull molecule named 9,10-dimethoxy-[7]helicene diimide, displaying fluorescence (FL) and circularly polarised luminescence (CPL) over nearly the entire visible spectrum dependent on solvent polarity. The synthesised molecule exhibits an unusual solvent polarity dependence of FL quantum yield and nonradiative rate constant, as well as remarkable gabs and glum values along with high configurational stability.}, language = {en} } @unpublished{Dandekar2023, author = {Dandekar, Thomas}, title = {Protein folding and crystallization applied to qubit interactions and fundamental physics yields a modified inflation model for cosmology}, doi = {10.25972/OPUS-34615}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346156}, pages = {42}, year = {2023}, abstract = {Protein folding achieves a clear solution structure in a huge parameter space (the so-called protein folding problem). Proteins fold in water, and get by this a highly ordered structure. Finally, inside a protein crystal for structure resolution, you have everywhere the same symmetries as there is everywhere the same unit cell. We apply this to qubit interactions to do fundamental physics: in a modified cosmology, we replace the big bang by a condensation event in an eternal all-encompassing ocean of free qubits. Interactions of qubits in the qubit ocean are quite rare but provide a nucleus or seed for a new universe (domain) as the qubits become decoherent and freeze-out into defined bit ensembles. Second, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth). The crystal unit cell guarantees same symmetries everywhere inside the crystal. The textbook inflation scenario to explain the same laws of nature in our domain is replaced by the unit cell of the crystal formed. Interacting qubits solidify, quantum entropy decreases (but increases in the ocean around). In a modified inflation scenario, the interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. Then standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements. We explain by cosmological crystallization instead of inflation: early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: the unit cell of our crystal universe has a matter handedness avoiding anti-matter. We prove initiation of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below Planck quantum there is liquidity left). The E8 symmetry of heterotic string theory has six curled-up, small dimensions which help to keep the qubit crystal together and will never expand. Mathematics focusses on the Hurwitz proof applied to qubit interaction, a toy model of qubit interaction and repulsive forces of qubits. Vacuum energy gets appropriate low inside the crystal. We give first energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction/confinement and gravity are derived from the qubit-interaction field.}, language = {en} } @unpublished{WarmdtFrischRatzetal.2023, author = {Warmdt, Julia and Frisch, Henrik and Ratz, Christoph and Pohlmann-Rother, Sanna}, title = {Digital lesen und erz{\"a}hlen. Eine Projektwoche f{\"u}r den inklusiven Anfangsunterricht}, series = {F{\"o}rdermagazin Grundschule}, journal = {F{\"o}rdermagazin Grundschule}, edition = {accepted version}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328443}, year = {2023}, abstract = {Das Digital Storytelling bietet Sch{\"u}ler:innen im inklusiven Anfangsunterricht vielf{\"a}ltige M{\"o}glichkeiten der Teilhabe am Unterricht. Lesen Sie in diesem Beitrag, wie die Kinder eine digitale Geschichte auf unterschiedliche Art rezipieren und weitererz{\"a}hlen k{\"o}nnen.}, subject = {Bilderbuch}, language = {de} } @unpublished{ScheitlMieczkowskiSchindelinetal.2022, author = {Scheitl, Carolin P. M. and Mieczkowski, Mateusz and Schindelin, Hermann and H{\"o}bartner, Claudia}, title = {Structure and mechanism of the methyltransferase ribozyme MTR1}, series = {Nature Chemical Biology}, journal = {Nature Chemical Biology}, edition = {submitted version}, doi = {10.1038/s41589-022-00976-x}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-272170}, year = {2022}, abstract = {RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the site-specific synthesis of 1-methyladenosine (m\(^1\)A) in RNA, using O\(^6\)-methylguanine (m\(^6\)G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 {\AA}, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m1A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.}, language = {en} } @unpublished{SednevLiaqatHoebartner2022, author = {Sednev, Maksim V. and Liaqat, Anam and H{\"o}bartner, Claudia}, title = {High-Throughput Activity Profiling of RNA-Cleaving DNA Catalysts by Deoxyribozyme Sequencing (DZ-seq)}, series = {Journal of the American Chemical Society}, journal = {Journal of the American Chemical Society}, doi = {10.1021/jacs.1c12489}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-258520}, year = {2022}, abstract = {RNA-cleaving deoxyribozymes have found broad application as useful tools for RNA biochemistry. However, tedious in vitro selection procedures combined with laborious characterization of individual candidate catalysts hinder the discovery of novel catalytic motifs. Here, we present a new high-throughput sequencing method, DZ-seq, which directly measures activity and localizes cleavage sites of thousands of deoxyribozymes. DZ-seq exploits A-tailing followed by reverse transcription with an oligo-dT primer to capture the cleavage status and sequences of both deoxyribozyme and RNA substrate. We validated DZ-seq by conventional analytical methods and demonstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA targets or the analysis of RNA modification states.}, language = {en} } @unpublished{Dandekar2022, author = {Dandekar, Thomas}, title = {Qubit transition into defined Bits: A fresh perspective for cosmology and unifying theories}, doi = {10.25972/OPUS-26641}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-266418}, pages = {42}, year = {2022}, abstract = {In this view point we do not change cosmology after the hot fireball starts (hence agrees well with observation), but the changed start suggested and resulting later implications lead to an even better fit with current observations (voids, supercluster and galaxy formation; matter and no antimatter) than the standard model with big bang and inflation: In an eternal ocean of qubits, a cluster of qubits crystallizes to defined bits. The universe does not jump into existence ("big bang") but rather you have an eternal ocean of qubits in free super-position of all their quantum states (of any dimension, force field and particle type) as permanent basis. The undefined, boiling vacuum is the real "outside", once you leave our everyday universe. A set of n Qubits in the ocean are "liquid", in very undefined state, they have all their m possibilities for quantum states in free superposition. However, under certain conditions the qubits interact, become defined, and freeze out, crystals form and give rise to a defined, real world with all possible time series and world lines. GR holds only within the crystal. In our universe all n**m quantum possibilities are nicely separated and crystallized out to defined bit states: A toy example with 6 qubits each having 2 states illustrates, this is completely sufficient to encode space using 3 bits for x,y and z, 1 bit for particle type and 2 bits for its state. Just by crystallization, space, particles and their properties emerge from the ocean of qubits, and following the arrow of entropy, time emerges, following an arrow of time and expansion from one corner of the toy universe to everywhere else. This perspective provides time as emergent feature considering entropy: crystallization of each world line leads to defined world lines over their whole existence, while entropy ensures direction of time and higher representation of high entropy states considering the whole crystal and all slices of world lines. The crystal perspective is also economic compared to the Everett-type multiverse, each qubit has its m quantum states and n qubits interacting forming a crystal and hence turning into defined bit states has only n**m states and not more states. There is no Everett-type world splitting with every decision but rather individual world trajectories reside in individual world layers of the crystal. Finally, bit-separated crystals come and go in the qubit ocean, selecting for the ability to lay seeds for new crystals. This self-organizing reproduction selects over generations also for life-friendliness. Mathematical treatment introduces quantum action theory as a framework for a general lattice field theory extending quantum chromo dynamics where scalar fields for color interaction and gravity have to be derived from the permeating qubit-interaction field. Vacuum energy should get appropriately low by the binding properties of the qubit crystal. Connections to loop quantum gravity, string theory and emergent gravity are discussed. Standard physics (quantum computing; crystallization, solid state physics) allow validation tests of this perspective and will extend current results.}, language = {en} } @unpublished{Wolf2021, author = {Wolf, Norbert Richard}, title = {Der Duden, die Genera und die Geschlechter}, series = {Vestnik of Samara University. History, pedagogics, philology}, journal = {Vestnik of Samara University. History, pedagogics, philology}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-241571}, pages = {26}, year = {2021}, abstract = {Anlass f{\"u}r diesen Aufsatz ist die Tatsache, dass die Duden-Redaktion bei zahlreichen Personenbezeichnungen das sog. ‚generische Maskulinum' wegdefiniert hat. Das Anfang 2021 erschienene online W{\"o}rterbuch gibt als Bedeutungserkl{\"a}rung des Substantiv Arzt folgende Beschreibung an: „m{\"a}nnliche Person, die nach Medizinstudium und klinischer Ausbildung die staatliche Zulassung (Approbation) erhalten hat, Kranke zu behandeln (Berufsbezeichnung)". Demgegen{\"u}ber hieß es im Duden Universalw{\"o}rterbuch von 2015: „jemand, der nach Medizinstudium und klinischer Ausbildung die staatliche Zulassung (Approbation) erhalten hat, Kranke zu behandeln (Berufsbezeichnung)" Der Aufsatz versucht, wieder einmal zu {\"u}berpr{\"u}fen, ob es das generische Maskulinum als geschlechts{\"u}bergreifende oder besser: geschlechtsneutrale Bezeichnung gibt oder ob es, nicht zuletzt aufgrund des jahrhundertelangen Einflusses des Patriarchats auf die Sprachentwicklung, sich doch um den Ausdruck m{\"a}nnlicher Vormacht handelt. Dabei werden sowohl das Problem ‚Genus' als auch der Begriff ‚generisch' untersucht und auf seine Bezeichnungsfunktion hin getestet. Schließlich soll auch {\"u}berpr{\"u}ft werden, ob die Sprache tats{\"a}chlich die Wirklichkeit widerspiegelt und ob die Sprache wirklich alle Ph{\"a}nomene in der außersprachlichen Realit{\"a}t benennen muss. Dazu kommt nat{\"u}rlich auch die Frage, ob die Duden-Redaktion ihre Kompetenzen richtig interpretiert (hat).}, language = {de} } @unpublished{Dandekar2021, author = {Dandekar, Thomas}, title = {Our universe may have started by Qubit decoherence}, doi = {10.25972/OPUS-23918}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239181}, pages = {54}, year = {2021}, abstract = {Our universe may have started by Qubit decoherence: In quantum computers, qubits have all their states undefined during calculation and become defined as output ("decoherence"). We study the transition from an uncontrolled, chaotic quantum vacuum ("before") to a clearly interacting "real world". In such a cosmology, the Big Bang singularity is replaced by a condensation event of interacting strings. This triggers a crystallization process. This avoids inflation, not fitting current observations: increasing long-range interactions limit growth and crystal symmetries ensure the same laws of nature and basic symmetries over the whole crystal. Tiny mis-arrangements provide nuclei of superclusters and galaxies and crystal structure allows arrangement of dark (halo regions) and normal matter (galaxy nuclei) for galaxy formation. Crystals come and go: an evolutionary cosmology is explored: entropic forces from the quantum soup "outside" of the crystal try to dissolve it. This corresponds to dark energy and leads to a "big rip" in 70 Gigayears. Selection for best growth and condensation events over generations of crystals favors multiple self-organizing processes within the crystal including life or even conscious observers in our universe. Philosophically this theory shows harmony with nature and replaces absurd perspectives of current cosmology. Independent of cosmology, we suggest that a "real world" (so our everyday macroscopic world) happens only inside a crystal. "Outside" there is wild quantum foam and superposition of all possibilities. In our crystallized world the vacuum no longer boils but is cooled down by the crystallization event, space-time exists and general relativity holds. Vacuum energy becomes 10**20 smaller, exactly as observed in our everyday world. We live in a "solid" state, within a crystal, the n quanta which build our world have all their different m states nicely separated. There are only nm states available for this local "multiverse". The arrow of entropy for each edge of the crystal forms one fate, one world-line or clear development of our world, while layers of the crystal are different system states. Mathematical leads from loop quantum gravity (LQG) point to required interactions and potentials. Interaction potentials for strings or loop quanta of any dimension allow a solid, decoherent state of quanta challenging to calculate. However, if we introduce here the heuristic that any type of physical interaction of strings corresponds just to a type of calculation, there is already since 1898 the Hurwitz theorem showing that then only 1D, 2D, 4D and 8D (octonions) allow complex or hypercomplex number calculations. No other hypercomplex numbers and hence dimensions or symmetries are possible to allow calculations without yielding divisions by zero. However, the richest solution allowed by the Hurwitz theorem, octonions, is actually the observed symmetry of our universe, E8. Standard physics such as condensation, crystallization and magnetization but also solid-state physics and quantum computing allow us to show an initial mathematical treatment of our new theory by LQG to describe the cosmological state transformations by equations, and, most importantly, point out routes to parametrization of free parameters looking at testable phenomena, experiments and formulas that describe processes of crystallization, protein folding, magnetization, solid-state physics and quantum computing. This is presented here for LQG, for string theory it would be more elegant but was too demanding to be shown here. Note: While my previous Opus server preprint "A new cosmology of a crystallization process (decoherence) from the surrounding quantum soup provides heuristics to unify general relativity and quantum physics by solid state physics" (https://doi.org/10.25972/OPUS-23076) deals with the same topics and basic formulas, this new version is improved: clearer in title, better introduction, more stringent in its mathematics and improved discussion of the implications including quantum computing, hints for parametrization and connections to LQG and other current cosmological efforts. This 5th of June 2021 version is again an OPUS preprint, but this will next be edited for Archives https://arxiv.org.}, language = {en} } @unpublished{HeidenreichGassenmaierAnkenbrandetal.2021, author = {Heidenreich, Julius F. and Gassenmaier, Tobias and Ankenbrand, Markus J. and Bley, Thorsten A. and Wech, Tobias}, title = {Self-configuring nnU-net pipeline enables fully automatic infarct segmentation in late enhancement MRI after myocardial infarction}, edition = {accepted version}, doi = {10.1016/j.ejrad.2021.109817}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-323418}, year = {2021}, abstract = {Purpose To fully automatically derive quantitative parameters from late gadolinium enhancement (LGE) cardiac MR (CMR) in patients with myocardial infarction and to investigate if phase sensitive or magnitude reconstructions or a combination of both results in best segmentation accuracy. Methods In this retrospective single center study, a convolutional neural network with a U-Net architecture with a self-configuring framework ("nnU-net") was trained for segmentation of left ventricular myocardium and infarct zone in LGE-CMR. A database of 170 examinations from 78 patients with history of myocardial infarction was assembled. Separate fitting of the model was performed, using phase sensitive inversion recovery, the magnitude reconstruction or both contrasts as input channels. Manual labelling served as ground truth. In a subset of 10 patients, the performance of the trained models was evaluated and quantitatively compared by determination of the S{\o}rensen-Dice similarity coefficient (DSC) and volumes of the infarct zone compared with the manual ground truth using Pearson's r correlation and Bland-Altman analysis. Results The model achieved high similarity coefficients for myocardium and scar tissue. No significant difference was observed between using PSIR, magnitude reconstruction or both contrasts as input (PSIR and MAG; mean DSC: 0.83 ± 0.03 for myocardium and 0.72 ± 0.08 for scars). A strong correlation for volumes of infarct zone was observed between manual and model-based approach (r = 0.96), with a significant underestimation of the volumes obtained from the neural network. Conclusion The self-configuring nnU-net achieves predictions with strong agreement compared to manual segmentation, proving the potential as a promising tool to provide fully automatic quantitative evaluation of LGE-CMR.}, language = {en} } @unpublished{HennigPrustyKauferetal.2021, author = {Hennig, Thomas and Prusty, Archana B. and Kaufer, Benedikt and Whisnant, Adam W. and Lodha, Manivel and Enders, Antje and Thomas, Julius and Kasimir, Francesca and Grothey, Arnhild and Herb, Stefanie and J{\"u}rges, Christopher and Meister, Gunter and Erhard, Florian and D{\"o}lken, Lars and Prusty, Bhupesh K.}, title = {Selective inhibition of microRNA processing by a herpesvirus-encoded microRNA triggers virus reactivation from latency}, edition = {submitted version}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-267858}, year = {2021}, abstract = {Herpesviruses have mastered host cell modulation and immune evasion to augment productive infection, life-long latency and reactivation thereof 1,2. A long appreciated, yet elusively defined relationship exists between the lytic-latent switch and viral non-coding RNAs 3,4. Here, we identify miRNA-mediated inhibition of miRNA processing as a novel cellular mechanism that human herpesvirus 6A (HHV-6A) exploits to disrupt mitochondrial architecture, evade intrinsic host defense and drive the latent-lytic switch. We demonstrate that virus-encoded miR-aU14 selectively inhibits the processing of multiple miR-30 family members by direct interaction with the respective pri-miRNA hairpin loops. Subsequent loss of miR-30 and activation of miR-30/p53/Drp1 axis triggers a profound disruption of mitochondrial architecture, which impairs induction of type I interferons and is necessary for both productive infection and virus reactivation. Ectopic expression of miR-aU14 was sufficient to trigger virus reactivation from latency thereby identifying it as a readily drugable master regulator of the herpesvirus latent-lytic switch. Our results show that miRNA-mediated inhibition of miRNA processing represents a generalized cellular mechanism that can be exploited to selectively target individual members of miRNA families. We anticipate that targeting miR-aU14 provides exciting therapeutic options for preventing herpesvirus reactivations in HHV-6-associated disorders like myalgic encephalitis/chronic fatigue syndrome (ME/CFS) and Long-COVID.}, language = {en} } @unpublished{WohlgemuthMitric2020, author = {Wohlgemuth, Matthias and Mitric, Roland}, title = {Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping}, series = {Physical Chemistry Chemical Physics}, journal = {Physical Chemistry Chemical Physics}, edition = {submitted version}, doi = {10.1039/D0CP02255A}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-209467}, year = {2020}, abstract = {Absorption of ultraviolet light is known as a major source of carcinogenic mutations of DNA. The underlying processes of excitation energy dissipation are yet not fully understood. In this work we provide a new and generally applicable route for studying the excitation energy transport in multi-chromophoric complexes at an atomistic level. The surface-hopping approach in the frame of the extended Frenkel exciton model combined with QM/MM techniques allowed us to simulate the photodynamics of the alternating (dAdT)10 : (dAdT)10 double-stranded DNA. In accordance with recent experiments, we find that the excited state decay is multiexponential, involving a long and a short component which are due to two distinct mechanisms: formation of long-lived delocalized excitonic and charge transfer states vs. ultrafast decaying localized states resembling those of the bare nucleobases. Our simulations explain all stages of the ultrafast photodynamics including initial photoexcitation, dynamical evolution out of the Franck-Condon region, excimer formation and nonradiative relaxation to the ground state.}, language = {en} } @unpublished{HumeniukBužančićHocheetal.2020, author = {Humeniuk, Alexander and Bužančić, Margarita and Hoche, Joscha and Cerezo, Javier and Mitric, Roland and Santoro, Fabrizio and Bonačić-Koutecky, Vlasta}, title = {Predicting fluorescence quantum yields for molecules in solution: A critical assessment of the harmonic approximation and the choice of the lineshape function}, series = {The Journal of Chemical Physics}, journal = {The Journal of Chemical Physics}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-199305}, year = {2020}, abstract = {For the rational design of new fluorophores, reliable predictions of fluorescence quantum yields from first principles would be of great help. However, efficient computational approaches for predicting transition rates usually assume that the vibrational structure is harmonic. While the harmonic approximation has been used successfully to predict vibrationally resolved spectra and radiative rates, its reliability for non-radiative rates is much more questionable. Since non-adiabatic transitions convert large amounts of electronic energy into vibrational energy, the highly excited final vibrational states deviate greatly from harmonic oscillator eigenfunctions. We employ a time-dependent formalism to compute radiative and non-radiative rates for transitions and study the dependence on model parameters. For several coumarin dyes we compare different adiabatic and vertical harmonic models (AS, ASF, AH, VG, VGF, VH), in order to dissect the importance of displacements, frequency changes and Duschinsky rotations. In addition we analyze the effect of different broadening functions (Gaussian, Lorentzian or Voigt). Moreover, to assess the qualitative influence of anharmonicity on the internal conversion rate, we develop a simplified anharmonic model. We adress the reliability of these models considering the potential errors introduced by the harmonic approximation and the phenomenological width of the broadening function.}, language = {en} } @unpublished{TitovHumeniukMitric2020, author = {Titov, Evgenii and Humeniuk, Alexander and Mitric, Roland}, title = {Comparison of moving and fixed basis sets for nonadiabatic quantum dynamics at conical intersections}, series = {Chemical Physics}, journal = {Chemical Physics}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-199225}, year = {2020}, abstract = {We assess the performance of two different types of basis sets for nonadiabatic quantum dynamics at conical intersections. The basis sets of both types are generated using Ehrenfest trajectories of nuclear coherent states. These trajectories can either serve as a moving (time-dependent) basis or be employed to sample a fixed (time-independent) basis. We demonstrate on the example of two-state two-dimensional and three-state five-dimensional models that both basis set types can yield highly accurate results for population transfer at intersections, as compared with reference quantum dynamics. The details of wave packet evolutions are discussed for the case of the two-dimensional model. The fixed basis is found to be superior to the moving one in reproducing nonlocal spreading and maintaining correct shape of the wave packet upon time evolution. Moreover, for the models considered, the fixed basis set outperforms the moving one in terms of computational efficiency.}, language = {en} }