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 -