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 -
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 - JOUR
AB - State-of-the-art methods in materials science such as artificial intelligence and data-driven techniques advance the investigation of photovoltaic materials.
AU - Mirhosseini, Hossein
AU - Kormath Madam Raghupathy, Ramya
AU - Sahoo, Sudhir K.
AU - Wiebeler, Hendrik
AU - Chugh, Manjusha
AU - Kühne, Thomas D.
ID - 32246
IS - 46
JF - Physical Chemistry Chemical Physics
KW - Physical and Theoretical Chemistry
KW - General Physics and Astronomy
SN - 1463-9076
TI - In silico investigation of Cu(In,Ga)Se2-based solar cells
VL - 22
ER -
TY - JOUR
AB - In scientific computing, the acceleration of atomistic computer simulations by means of custom hardware is finding ever-growing application. A major limitation, however, is that the high efficiency in terms of performance and low power consumption entails the massive usage of low precision computing units. Here, based on the approximate computing paradigm, we present an algorithmic method to compensate for numerical inaccuracies due to low accuracy arithmetic operations rigorously, yet still obtaining exact expectation values using a properly modified Langevin-type equation.
AU - Rengaraj, Varadarajan
AU - Lass, Michael
AU - Plessl, Christian
AU - Kühne, Thomas
ID - 12878
IS - 2
JF - Computation
TI - Accurate Sampling with Noisy Forces from Approximate Computing
VL - 8
ER -
TY - JOUR
AB - CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-theart ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post–Hartree–Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.
AU - Kühne, Thomas
AU - Iannuzzi, Marcella
AU - Ben, Mauro Del
AU - Rybkin, Vladimir V.
AU - Seewald, Patrick
AU - Stein, Frederick
AU - Laino, Teodoro
AU - Khaliullin, Rustam Z.
AU - Schütt, Ole
AU - Schiffmann, Florian
AU - Golze, Dorothea
AU - Wilhelm, Jan
AU - Chulkov, Sergey
AU - Mohammad Hossein Bani-Hashemian, Mohammad Hossein Bani-Hashemian
AU - Weber, Valéry
AU - Borstnik, Urban
AU - Taillefumier, Mathieu
AU - Jakobovits, Alice Shoshana
AU - Lazzaro, Alfio
AU - Pabst, Hans
AU - Müller, Tiziano
AU - Schade, Robert
AU - Guidon, Manuel
AU - Andermatt, Samuel
AU - Holmberg, Nico
AU - Schenter, Gregory K.
AU - Hehn, Anna
AU - Bussy, Augustin
AU - Belleflamme, Fabian
AU - Tabacchi, Gloria
AU - Glöß, Andreas
AU - Lass, Michael
AU - Bethune, Iain
AU - Mundy, Christopher J.
AU - Plessl, Christian
AU - Watkins, Matt
AU - VandeVondele, Joost
AU - Krack, Matthias
AU - Hutter, Jürg
ID - 16277
IS - 19
JF - The Journal of Chemical Physics
TI - CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations
VL - 152
ER -
TY - JOUR
AB - We address the general mathematical problem of computing the inverse p-th
root of a given matrix in an efficient way. A new method to construct iteration
functions that allow calculating arbitrary p-th roots and their inverses of
symmetric positive definite matrices is presented. We show that the order of
convergence is at least quadratic and that adaptively adjusting a parameter q
always leads to an even faster convergence. In this way, a better performance
than with previously known iteration schemes is achieved. The efficiency of the
iterative functions is demonstrated for various matrices with different
densities, condition numbers and spectral radii.
AU - Richters, Dorothee
AU - Lass, Michael
AU - Walther, Andrea
AU - Plessl, Christian
AU - Kühne, Thomas
ID - 21
IS - 2
JF - Communications in Computational Physics
TI - A General Algorithm to Calculate the Inverse Principal p-th Root of Symmetric Positive Definite Matrices
VL - 25
ER -
TY - JOUR
AU - Platzner, Marco
AU - Plessl, Christian
ID - 12871
JF - Informatik Spektrum
SN - 0170-6012
TI - FPGAs im Rechenzentrum
ER -
TY - JOUR
AU - Riebler, Heinrich
AU - Vaz, Gavin Francis
AU - Kenter, Tobias
AU - Plessl, Christian
ID - 7689
IS - 2
JF - ACM Trans. Archit. Code Optim. (TACO)
KW - htrop
TI - Transparent Acceleration for Heterogeneous Platforms with Compilation to OpenCL
VL - 16
ER -
TY - JOUR
AU - Mertens, Jan Cedric
AU - Boschmann, Alexander
AU - Schmidt, M.
AU - Plessl, Christian
ID - 6516
IS - 4
JF - Sports Engineering
SN - 1369-7072
TI - Sprint diagnostic with GPS and inertial sensor fusion
VL - 21
ER -
TY - JOUR
AU - Luk, Samuel M. H.
AU - Lewandowski, P.
AU - Kwong, N. H.
AU - Baudin, E.
AU - Lafont, O.
AU - Tignon, J.
AU - Leung, P. T.
AU - Chan, Ch. K. P.
AU - Babilon, M.
AU - Schumacher, Stefan
AU - Binder, R.
ID - 13348
IS - 1
JF - Journal of the Optical Society of America B
SN - 0740-3224
TI - Theory of optically controlled anisotropic polariton transport in semiconductor double microcavities
VL - 35
ER -
TY - JOUR
AB - Approximate computing has shown to provide new ways to improve performance
and power consumption of error-resilient applications. While many of these
applications can be found in image processing, data classification or machine
learning, we demonstrate its suitability to a problem from scientific
computing. Utilizing the self-correcting behavior of iterative algorithms, we
show that approximate computing can be applied to the calculation of inverse
matrix p-th roots which are required in many applications in scientific
computing. Results show great opportunities to reduce the computational effort
and bandwidth required for the execution of the discussed algorithm, especially
when targeting special accelerator hardware.
AU - Lass, Michael
AU - Kühne, Thomas
AU - Plessl, Christian
ID - 20
IS - 2
JF - Embedded Systems Letters
SN - 1943-0663
TI - Using Approximate Computing for the Calculation of Inverse Matrix p-th Roots
VL - 10
ER -