828 results match your criteria: "Institute for Advanced Simulation[Affiliation]"

Adaptive-precision potentials for large-scale atomistic simulations.

J Chem Phys

March 2025

Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, Jülich, Germany.

Large-scale atomistic simulations rely on interatomic potentials, providing an efficient representation of atomic energies and forces. Modern machine-learning (ML) potentials provide the most precise representation compared to electronic structure calculations, while traditional potentials provide a less precise but computationally much faster representation and, thus, allow simulations of larger systems. We present a method to combine a traditional and a ML potential into a multi-resolution description, leading to an adaptive-precision potential with an optimum of performance and precision in large, complex atomistic systems.

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False vacuum decay-the transition from a metastable quantum state to a true vacuum state-plays an important role in quantum field theory and non-equilibrium phenomena such as phase transitions and dynamical metastability. The non-perturbative nature of false vacuum decay and the limited experimental access to this process make it challenging to study, leaving several open questions regarding how true vacuum bubbles form, move and interact. Here we observe quantized bubble formation in real time, a key feature of false vacuum decay dynamics, using a quantum annealer with 5,564 superconducting flux qubits.

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Aggregation and disaggregation of red blood cells: Depletion versus bridging.

Biophys J

April 2025

Theoretical Physics of Living Matter, Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany. Electronic address:

The aggregation of red blood cells (RBCs) is a complex phenomenon that strongly impacts blood flow and tissue perfusion. Despite extensive research for more than 50 years, physical mechanisms that govern RBC aggregation are still under debate. Two proposed mechanisms are based on bridging and depletion interactions between RBCs due to the presence of macromolecules in blood plasma.

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The System for Measuring Overlap with Gas (SMOG2) at the LHCb detector enables the study of fixed-target ion-ion collisions at relativistic energies (sqrt[s_{NN}]∼100  GeV in the center of mass). With input from ab initio calculations of the structure of ^{16}O and ^{20}Ne, we compute 3+1D hydrodynamic predictions for the anisotropic flow of Pb+Ne and Pb+O collisions to be tested with upcoming LHCb data. This will allow the detailed study of quark-gluon plasma formation as well as experimental tests of the predicted nuclear shapes.

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Background: Repetitive transcranial magnetic stimulation (rTMS) is well known for its ability to induce synaptic plasticity, yet its impact on structural and functional remodeling within stimulated networks remains unclear. This study investigates the cellular and network-level mechanisms of rTMS-induced plasticity using a clinically approved 600-pulse intermittent theta burst stimulation (iTBS600) protocol applied to organotypic brain tissue cultures.

Methods: We applied iTBS600 to entorhino-hippocampal organotypic tissue cultures and conducted a 24-hour analysis using c-Fos immunostaining, whole-cell patch-clamp recordings, time-lapse imaging of dendritic spines, and calcium imaging.

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A study of light Λ hypernuclei in chiral effective field theory is presented. For the first time, chiral ΛNN and ΣNN three-body forces are included consistently. The calculations are performed within the no-core shell model.

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In the acquisition of Magnetic Resonance (MR) images shorter scan times lead to higher image noise. Therefore, automatic image denoising using deep learning methods is of high interest. In this work, we concentrate on image denoising of MR images containing line-like structures such as roots or vessels.

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Behavioural repertoires in moving crowds: an observational approach.

R Soc Open Sci

February 2025

Faculty of Behavioral and Social Sciences, University of Groningen, Groningen, The Netherlands.

The wide variety of behaviour found in crowds is a challenge for current models of crowd movement behaviour. To aid the development of a new generation of models, this paper develops a systematic observational approach based on social psychological knowledge about how humans recognize and use social meaning and structures. To develop this approach, we studied the movement behaviour of participants in a pedestrian crowd experiment, more specifically in four experimental runs ( = 351) of crowd situations, videotaped from a top-view perspective.

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Self-propelled particles that are subject to noise are a well-established generic model system for active matter. A homogeneous alignment field can be used to orient the direction of the self-propulsion velocity and to model systems like phoretic Janus particles with a magnetic dipole moment or magnetotactic bacteria in an external magnetic field. Computer simulations are used to predict the phase behavior and dynamics of self-propelled Brownian particles in a homogeneous alignment field in two dimensions.

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In magnetic systems, angular momentum is carried by spin and orbital degrees of freedom. Nonlocal devices, comprising heavy-metal nanowires on magnetic insulators like yttrium iron garnet (YIG), enable angular momentum transport via magnons. These magnons are polarized by spin accumulation at the interface through the spin Hall effect (SHE) and detected via the inverse SHE (iSHE).

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Explicit expressions for the leading chiral hyperon-nucleon-nucleon three-body forces have been derived by Petschauer et al (Phys Rev C93:014001, 2016). An important prerequisite for including these three-body forces in few- and many-body calculations is the accuracy and efficiency of their partial-wave decomposition. A careful benchmark of the NN potential matrix elements, computed using two robust and efficient partial-wave decomposition methods, is presented.

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Translocation across barriers and through constrictions is a mechanism that is often used in vivo for transporting material between compartments. A specific example is apicomplexan parasites invading host cells through the tight junction that acts as a pore, and a similar barrier crossing is involved in drug delivery using lipid vesicles penetrating intact skin. Here, we use triangulated membranes and energy minimization to study the translocation of vesicles through pores with fixed radii.

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Ab initio calculation of hyper-neutron matter.

Sci Bull (Beijing)

March 2025

Helmholtz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics, Universität Bonn, Bonn, D-53115, Germany; Institute for Advanced Simulation (IAS-4), Forschungszentrum Jülich, Jülich, D-52425, Germany; Center for Advanced Simulation and Analytics (CASA), Forschungszentru

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Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired by biological active systems, various types of autonomous synthetic nano- and micromachines have been designed, which provide the basis for multifunctional, highly responsive, intelligent active materials.

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Magneto-responsiveness in living organisms, exemplified by migratory birds navigating vast distances, offers inspiration for soft robots and human-computer interfaces. However, achieving both high magneto-responsiveness and resilient mechanical properties in synthetic materials has been challenging. Here, we develop magneto-iono-elastomers (MINEs), combining exceptional magnetization [2.

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The adsorption of ellipsoidal colloidal particles on liquid interfaces induces interfacial deformation, resulting in anisotropic interface-mediated interactions and the formation of superstructures. Soft prolate-shaped microgels at the air-water interface offer an ideal model for studying spontaneous capillary-driven self-assembly due to their tunable aspect ratio, controlled functionality, and softness. These microgels consist of a polystyrene core surrounded by a cross-linked, fluorescently labeled poly([Formula: see text]-isopropylmethylacrylamide) shell.

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Mast cell (MC)-driven allergic diseases are constantly expanding and require the development of novel pharmacological MC stabilizers. Allergen/antigen (Ag)-triggered activation via crosslinking of the high-affinity receptor for IgE (FcεRI) is fundamentally regulated by SRC family kinases, for example, LYN and FYN, exhibiting positive and negative functions. We report that KIRA6, an inhibitor for the endoplasmic reticulum stress sensor IRE1α, suppresses IgE-mediated MC activation by inhibiting both LYN and FYN.

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ω Meson from Lattice QCD.

Phys Rev Lett

November 2024

Helmholtz-Institut für Strahlen- und Kernphysik (Theorie) and Bethe Center for Theoretical Physics, Universität Bonn, 53115 Bonn, Germany.

Many excited states in the hadron spectrum have large branching ratios to three-hadron final states. Understanding such particles from first principles QCD requires input from lattice QCD with one-, two-, and three-meson interpolators as well as a reliable three-body formalism relating finite-volume spectra at unphysical pion mass values to the scattering amplitudes at the physical point. In this work, we provide the first-ever calculation of the resonance parameters of the ω meson from lattice QCD, including an update of the formalism through matching to effective field theories.

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Low efficiency of Janus microswimmers as hydrodynamic mixers.

Phys Rev E

October 2024

Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.

The generation of fluid flows by autophoretic microswimmers has been proposed as a mechanism to enhance mass transport and mixing at the micro- and nanoscale. Here, we experimentally investigate the ability of model 2D active baths of photocatalytic silica-titania Janus microspheres to enhance the diffusivity of tracer particles at different microswimmer densities below the onset of collective behavior. Inspired by the similarities between our experimental findings and previous results for biological microorganisms, we then model our Janus microswimmers using a general squirmer framework, specifically treating them as neutral squirmers.

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Spin Spiral State at a Ferromagnetic Gd Vacuum Interface.

Phys Rev Lett

November 2024

Physikalisches Institut, Experimentelle Physik II, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.

Centrosymmetric bulk magnets made of layered Gd intermetallics had been discovered recently to exhibit helical spin spirals with a wavelength of ≈2  nm that transform into skyrmion lattices at certain magnetic fields. Here we report on the observation of a spin spiral state at the Gd(0001) surface. Spin-polarized scanning tunneling microscopy images show striped regions with a periodicity of about 2 nm.

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From pole parameters to line shapes and branching ratios.

Eur Phys J C Part Fields

June 2024

Helmholtz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics, Universität Bonn, 53115 Bonn, Germany.

Resonances are uniquely characterized by their complex pole locations and the corresponding residues. In practice, however, resonances are typically identified experimentally as structures in invariant mass distributions, with branching fractions of resonances determined as ratios of count rates. To make contact between these quantities it is necessary to connect line shapes and resonance parameters.

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Understanding the strong interactions within baryonic systems beyond the up and down quark sector is pivotal for a comprehensive description of nuclear forces. This study explores the interactions involving hyperons, particularly the particle, within the framework of nuclear lattice effective field theory (NLEFT). By incorporating hyperons into the NLEFT framework, we extend our investigation into the sector, allowing us to probe the third dimension of the nuclear chart.

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Multi-electrode arrays covering several square millimeters of neural tissue provide simultaneous access to population signals such as extracellular potentials and spiking activity of one hundred or more individual neurons. The interpretation of the recorded data calls for multiscale computational models with corresponding spatial dimensions and signal predictions. Multi-layer spiking neuron network models of local cortical circuits covering about $1\,{\text{mm}^{2}}$ have been developed, integrating experimentally obtained neuron-type-specific connectivity data and reproducing features of observed in-vivo spiking statistics.

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The solute carrier 17 (SLC17) family contains anion transporters that accumulate neurotransmitters in secretory vesicles, remove carboxylated monosaccharides from lysosomes, or extrude organic anions from the kidneys and liver. We combined classical molecular dynamics simulations, Markov state modeling and hybrid first principles quantum mechanical/classical mechanical (QM/MM) simulations with experimental approaches to describe the transport mechanisms of a model bacterial protein, the D-galactonate transporter DgoT, at atomic resolution. We found that protonation of D46 and E133 precedes galactonate binding and that substrate binding induces closure of the extracellular gate, with the conserved R47 coupling substrate binding to transmembrane helix movement.

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