TY - JOUR AB - Abstract RNA editing processes are strikingly different in animals and plants. Up to thousands of specific cytidines are converted into uridines in plant chloroplasts and mitochondria whereas up to millions of adenosines are converted into inosines in animal nucleo-cytosolic RNAs. It is unknown whether these two different RNA editing machineries are mutually incompatible. RNA-binding pentatricopeptide repeat (PPR) proteins are the key factors of plant organelle cytidine-to-uridine RNA editing. The complete absence of PPR mediated editing of cytosolic RNAs might be due to a yet unknown barrier that prevents its activity in the cytosol. Here, we transferred two plant mitochondrial PPR-type editing factors into human cell lines to explore whether they could operate in the nucleo-cytosolic environment. PPR56 and PPR65 not only faithfully edited their native, co-transcribed targets but also different sets of off-targets in the human background transcriptome. More than 900 of such off-targets with editing efficiencies up to 91%, largely explained by known PPR-RNA binding properties, were identified for PPR56. Engineering two crucial amino acid positions in its PPR array led to predictable shifts in target recognition. We conclude that plant PPR editing factors can operate in the entirely different genetic environment of the human nucleo-cytosol and can be intentionally re-engineered towards new targets. AU - Lesch, Elena AU - Schilling, Maximilian T AU - Brenner, Sarah AU - Yang, Yingying AU - Gruss, Oliver J AU - Knoop, Volker AU - Schallenberg-Rüdinger, Mareike ID - 50149 IS - 17 JF - Nucleic Acids Research KW - Genetics SN - 0305-1048 TI - Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells VL - 50 ER - TY - JOUR AB - Recent advances in numerical methods significantly pushed forward the understanding of electrons coupled to quantized lattice vibrations. At this stage, it becomes increasingly important to also account for the effects of physically inevitable environments. In particular, we study the transport properties of the Hubbard-Holstein Hamiltonian that models a large class of materials characterized by strong electron-phonon coupling, in contact with a dissipative environment. Even in the one-dimensional and isolated case, simulating the quantum dynamics of such a system with high accuracy is very challenging due to the infinite dimensionality of the phononic Hilbert spaces. For this reason, the effects of dissipation on the conductance properties of such systems have not been investigated systematically so far. We combine the non-Markovian hierarchy of pure states method and the Markovian quantum jumps method with the newly introduced projected purified density-matrix renormalization group, creating powerful tensor-network methods for dissipative quantum many-body systems. Investigating their numerical properties, we find a significant speedup up to a factor $\sim 30$ compared to conventional tensor-network techniques. We apply these methods to study dissipative quenches, aiming for an in-depth understanding of the formation, stability, and quasi-particle properties of bipolarons. Surprisingly, our results show that in the metallic phase dissipation localizes the bipolarons, which is reminiscent of an indirect quantum Zeno effect. However, the bipolaronic binding energy remains mainly unaffected, even in the presence of strong dissipation, exhibiting remarkable bipolaron stability. These findings shed light on the problem of designing real materials exhibiting phonon-mediated high-$T_\mathrm{C}$ superconductivity. AU - Moroder, Mattia AU - Grundner, Martin AU - Damanet, François AU - Schollwöck, Ulrich AU - Mardazad, Sam AU - Flannigan, Stuart AU - Köhler, Thomas AU - Paeckel, Sebastian ID - 50146 JF - Physical Review B 107, 214310 (2023) TI - Stable bipolarons in open quantum systems ER - TY - JOUR AB - We develop a general decomposition of an ensemble of initial density profiles in terms of an average state and a basis of modes that represent the event-by-event fluctuations of the initial state. The basis is determined such that the probability distributions of the amplitudes of different modes are uncorrelated. Based on this decomposition, we quantify the different types and probabilities of event-by-event fluctuations in Glauber and Saturation models and investigate how the various modes affect different characteristics of the initial state. We perform simulations of the dynamical evolution with KoMPoST and MUSIC to investigate the impact of the modes on final-state observables and their correlations. AU - Borghini, Nicolas AU - Borrell, Marc AU - Feld, Nina AU - Roch, Hendrik AU - Schlichting, Sören AU - Werthmann, Clemens ID - 50148 JF - Phys. Rev. C 107 (2023) 034905 TI - Statistical analysis of initial state and final state response in heavy-ion collisions ER - TY - JOUR AU - Schade, Robert AU - Kenter, Tobias AU - Elgabarty, Hossam AU - Lass, Michael AU - Schütt, Ole AU - Lazzaro, Alfio AU - Pabst, Hans AU - Mohr, Stephan AU - Hutter, Jürg AU - Kühne, Thomas AU - Plessl, Christian ID - 33684 JF - Parallel Computing KW - Artificial Intelligence KW - Computer Graphics and Computer-Aided Design KW - Computer Networks and Communications KW - Hardware and Architecture KW - Theoretical Computer Science KW - Software SN - 0167-8191 TI - Towards electronic structure-based ab-initio molecular dynamics simulations with hundreds of millions of atoms VL - 111 ER - TY - JOUR AB -

The effect of traces of ethanol in supercritical carbon dioxide on the mixture's thermodynamic properties is studied by molecular simulations and Taylor dispersion measurements.

AU - Chatwell, René Spencer AU - Guevara-Carrion, Gabriela AU - Gaponenko, Yuri AU - Shevtsova, Valentina AU - Vrabec, Jadran ID - 32240 IS - 4 JF - Physical Chemistry Chemical Physics KW - Physical and Theoretical Chemistry KW - General Physics and Astronomy SN - 1463-9076 TI - Diffusion of the carbon dioxide–ethanol mixture in the extended critical region VL - 23 ER - TY - JOUR AU - Kaczmarek, Olaf AU - Mazur, Lukas AU - Sharma, Sayantan ID - 46122 IS - 9 JF - Physical Review D SN - 2470-0010 TI - Eigenvalue spectra of QCD and the fate of UA(1) breaking towards the chiral limit VL - 104 ER - TY - JOUR AU - Altenkort, Luis AU - Eller, Alexander M. AU - Kaczmarek, O. AU - Mazur, Lukas AU - Moore, Guy D. AU - Shu, H.-T. ID - 46124 IS - 1 JF - Physical Review D SN - 2470-0010 TI - Heavy quark momentum diffusion from the lattice using gradient flow VL - 103 ER - TY - JOUR AB - Abstract The defining feature of active particles is that they constantly propel themselves by locally converting chemical energy into directed motion. This active self-propulsion prevents them from equilibrating with their thermal environment (e.g. an aqueous solution), thus keeping them permanently out of equilibrium. Nevertheless, the spatial dynamics of active particles might share certain equilibrium features, in particular in the steady state. We here focus on the time-reversal symmetry of individual spatial trajectories as a distinct equilibrium characteristic. We investigate to what extent the steady-state trajectories of a trapped active particle obey or break this time-reversal symmetry. Within the framework of active Ornstein–Uhlenbeck particles we find that the steady-state trajectories in a harmonic potential fulfill path-wise time-reversal symmetry exactly, while this symmetry is typically broken in anharmonic potentials. AU - Dabelow, Lennart AU - Bo, Stefano AU - Eichhorn, Ralf ID - 32243 IS - 3 JF - Journal of Statistical Mechanics: Theory and Experiment KW - Statistics KW - Probability and Uncertainty KW - Statistics and Probability KW - Statistical and Nonlinear Physics SN - 1742-5468 TI - How irreversible are steady-state trajectories of a trapped active particle? VL - 2021 ER - TY - JOUR AU - Altenkort, Luis AU - Eller, Alexander M. AU - Kaczmarek, O. AU - Mazur, Lukas AU - Moore, Guy D. AU - Shu, H.-T. ID - 46123 IS - 11 JF - Physical Review D SN - 2470-0010 TI - Sphaleron rate from Euclidean lattice correlators: An exploration VL - 103 ER - TY - JOUR AU - Alhaddad, Samer AU - Förstner, Jens AU - Groth, Stefan AU - Grünewald, Daniel AU - Grynko, Yevgen AU - Hannig, Frank AU - Kenter, Tobias AU - Pfreundt, Franz‐Josef AU - Plessl, Christian AU - Schotte, Merlind AU - Steinke, Thomas AU - Teich, Jürgen AU - Weiser, Martin AU - Wende, Florian ID - 24788 JF - Concurrency and Computation: Practice and Experience KW - tet_topic_hpc SN - 1532-0626 TI - The HighPerMeshes framework for numerical algorithms on unstructured grids ER -