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 - N-body methods are one of the essential algorithmic building blocks of high-performance and parallel computing. Previous research has shown promising performance for implementing n-body simulations with pairwise force calculations on FPGAs. However, to avoid challenges with accumulation and memory access patterns, the presented designs calculate each pair of forces twice, along with both force sums of the involved particles. Also, they require large problem instances with hundreds of thousands of particles to reach their respective peak performance, limiting the applicability for strong scaling scenarios. This work addresses both issues by presenting a novel FPGA design that uses each calculated force twice and overlaps data transfers and computations in a way that allows to reach peak performance even for small problem instances, outperforming previous single precision results even in double precision, and scaling linearly over multiple interconnected FPGAs. For a comparison across architectures, we provide an equally optimized CPU reference, which for large problems actually achieves higher peak performance per device, however, given the strong scaling advantages of the FPGA design, in parallel setups with few thousand particles per device, the FPGA platform achieves highest performance and power efficiency.
AU - Menzel, Johannes
AU - Plessl, Christian
AU - Kenter, Tobias
ID - 28099
IS - 1
JF - ACM Transactions on Reconfigurable Technology and Systems
SN - 1936-7406
TI - The Strong Scaling Advantage of FPGAs in HPC for N-body Simulations
VL - 15
ER -
TY - CONF
AU - Meyer, Marius
ID - 27365
T2 - Proceedings of the 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies
TI - Towards Performance Characterization of FPGAs in Context of HPC using OpenCL Benchmarks
ER -
TY - CONF
AU - Nickchen, Tobias
AU - Heindorf, Stefan
AU - Engels, Gregor
ID - 20886
T2 - Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision
TI - Generating Physically Sound Training Data for Image Recognition of Additively Manufactured Parts
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 - GEN
AB - We push the boundaries of electronic structure-based \textit{ab-initio}
molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise
barely reachable with classical force-field methods or novel neural network and
machine learning potentials. We achieve this breakthrough by combining
innovations in linear-scaling AIMD, efficient and approximate sparse linear
algebra, low and mixed-precision floating-point computation on GPUs, and a
compensation scheme for the errors introduced by numerical approximations. The
core of our work is the non-orthogonalized local submatrix method (NOLSM),
which scales very favorably to massively parallel computing systems and
translates large sparse matrix operations into highly parallel, dense matrix
operations that are ideally suited to hardware accelerators. We demonstrate
that the NOLSM method, which is at the center point of each AIMD step, is able
to achieve a sustained performance of 324 PFLOP/s in mixed FP16/FP32 precision
corresponding to an efficiency of 67.7% when running on 1536 NVIDIA A100 GPUs.
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 D.
AU - Plessl, Christian
ID - 32244
T2 - arXiv:2104.08245
TI - Towards Electronic Structure-Based Ab-Initio Molecular Dynamics Simulations with Hundreds of Millions of Atoms
ER -
TY - GEN
AB - Optical travelling wave antennas offer unique opportunities to control and
selectively guide light into a specific direction which renders them as
excellent candidates for optical communication and sensing. These applications
require state of the art engineering to reach optimized functionalities such as
high directivity and radiation efficiency, low side lobe level, broadband and
tunable capabilities, and compact design. In this work we report on the
numerical optimization of the directivity of optical travelling wave antennas
made from low-loss dielectric materials using full-wave numerical simulations
in conjunction with a particle swarm optimization algorithm. The antennas are
composed of a reflector and a director deposited on a glass substrate and an
emitter placed in the feed gap between them serves as an internal source of
excitation. In particular, we analysed antennas with rectangular- and
horn-shaped directors made of either Hafnium dioxide or Silicon. The optimized
antennas produce highly directional emission due to the presence of two
dominant guided TE modes in the director in addition to leaky modes. These
guided modes dominate the far-field emission pattern and govern the direction
of the main lobe emission which predominately originates from the end facet of
the director. Our work also provides a comprehensive analysis of the modes,
radiation patterns, parametric influences, and bandwidths of the antennas that
highlights their robust nature.
AU - Farheen, Henna
AU - Leuteritz, Till
AU - Linden, Stefan
AU - Myroshnychenko, Viktor
AU - Förstner, Jens
ID - 32245
T2 - arXiv:2106.02468
TI - Optimization of optical waveguide antennas for directive emission of light
ER -
TY - GEN
AB - The interaction between quantum light and matter is being intensively studied
for systems that are enclosed in high-$Q$ cavities which strongly enhance the
light-matter coupling. However, for many applications, cavities with lower
$Q$-factors are preferred due to the increased spectral width of the cavity
mode. Here, we investigate the interaction between quantum light and matter
represented by a $\Lambda$-type three-level system in lossy cavities, assuming
that cavity losses are the dominant loss mechanism. We demonstrate that cavity
losses lead to non-trivial steady states of the electronic occupations that can
be controlled by the loss rate and the initial statistics of the quantum
fields. The mechanism of formation of such steady states can be understood on
the basis of the equations of motion. Analytical expressions for steady states
and their numerical simulations are presented and discussed.
AU - Rose, H.
AU - Tikhonova, O. V.
AU - Meier, T.
AU - Sharapova, P.
ID - 32236
T2 - arXiv:2109.00842
TI - Steady states of $Λ$-type three-level systems excited by quantum light in lossy cavities
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 -