Zuse Institute Berlin

Dynamics of systems with varying number of particles: from Liouville equations to general master equations for open systems. Publication (co)authored by Zuse Institute members. In: SciPost Physics, doi.org/10.21468/Sci...

Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach by Inan Bostanci and Tim Conrad

Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach. Publication (co)authored by Zuse Institute members. In: Journal of Artificial Societies and Social Simulation, doi.org/10.18564/jas...

Resonance modes in microstructured photonic waveguides: efficient and accurate computation based on AAA rational approximation We present a framework for the efficient and accurate computation of resonance modes in photonic waveguides. The framework is based on AAA rational approximation with the application of special light ...

Resonance modes in microstructured photonic waveguides: Efficient and accurate computation based on AAA rational approximation. Publication (co)authored by Zuse Institute members. In: Nanophotonics, doi.org/10.1515/nano...

A case study of the use of logical data analysis in the Workmen’s Village in Tell el-Amarna, Egypt The search for patterns in archaeological contexts is crucial to understanding ancient civilizations, including the organization of their societies and economies. This study focuses on the interdiscip...

A Case Study of the Use of Logical Data Analysis in the Workmen's Village in Tell el-Amarna, Egypt. Publication (co)authored by Zuse Institute members. In: it - Information Technology, doi.org/10.1515/itit...

Optics for terawatt-scale photovoltaics: review and perspectives Photovoltaics, a mature technology, is set to play a vital role in achieving a carbon-free energy system. This article examines the pivotal role of optics in advancing photovoltaics. We identify key s...

Optics for terawatt-scale photovoltaics: review and perspectives. Publication (co)authored by Zuse Institute members. In: Adv. Opt. Photonics, doi.org/10.1364/AOP....

Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition - BMC Bioinformatics Background The dynamics of many gene regulatory networks (GRNs) is characterized by the occurrence of metastable phenotypes and stochastic phenotype switches. The chemical master equation (CME) is the...

Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition. Publication (co)authored by Zuse Institute members. In: BMC Bioinformatics, doi.org/10.1186/s128...

Approximating Particle-Based Clustering Dynamics by Stochastic PDEs | SIAM Journal on Applied Dynamical Systems Abstract. This work proposes stochastic partial differential equations (SPDEs) as a practical tool to replicate clustering effects of more detailed particle-based dynamics. Inspired by membrane-mediat...

Approximating particle-based clustering dynamics by stochastic PDEs. Publication (co)authored by Zuse Institute members. In: SIAM Journal on Applied Dynamical Systems, doi.org/10.1137/24M1...

On finding optimal collective variables for complex systems by minimizing the deviation between effective and full dynamics. Publication (co)authored by Zuse Institute members. In: Multiscale Modeling and Simulation, doi.org/10.1137/24M1...

Splitting the conditional gradient algorithm. Publication (co)authored by Zuse Institute members. In: SIAM Journal on Optimization, doi.org/10.1137/24M1...

Independently engaging protein tethers of different length enhance synaptic vesicle trafficking to the plasma membrane Abstract figure legend The independent assembly of the protein tethers synaptotagmin (Syt1/2), Munc13 and the SNAREs (upper) affects the stochastic movement of a synaptic vesicle (SV) with respect to...

Independently engaging protein tethers of different length enhance synaptic vesicle trafficking to the plasma membrane. Publication (co)authored by Zuse Institute members. In: The Journal of Physiology, doi.org/10.1113/JP28...

The helmeted hornbill casque is reinforced by a bundle of exceptionally thick, rod-like trabeculae. Publication (co)authored by Zuse Institute members. In: Annals of the New York Academy of Sciences, doi.org/10.1111/nyas...

A Scalable System for Visual Analysis of Ocean Data pyParaOcean is a system for interactive exploration and visual analysis of ocean data. The system leverages the functionalities of ParaView to enable scalable visualizations of data available from hi...

A Scalable System for Visual Analysis of Ocean Data. Publication (co)authored by Zuse Institute members. In: Computer Graphics Forum, doi.org/10.1111/cgf....

Macroscopic Stochastic Model for Economic Cycle Dynamics. Publication (co)authored by Zuse Institute members. In: Physical Review Letters, doi.org/10.1103/Phys...

A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain We present a correlated light and electron microscopy (CLEM) dataset from a 7-day-old larval zebrafish, integrating confocal imaging of genetically labeled excitatory ( vglut2a ) and inhibitory ( gad1...

A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain. Publication (co)authored by Zuse Institute members. In: bioRxiv, doi.org/10.1101/2025...

Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish Evidence accumulation is a fundamental neural computation essential for adaptive behavior, yet its synaptic implementation remains unclear. Addressing this challenge critically depends on linking neur...

Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish. Publication (co)authored by Zuse Institute members. In: bioRxiv, doi.org/10.1101/2025...

On reduced inertial PDE models for Cucker–Smale flocking dynamics | Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences In particle systems, flocking refers to the phenomenon where particles’ individual velocities eventually align. The Cucker–Smale (CS) model is a well-known mathematical framework that describes this b...

On reduced inertial PDE models for Cucker-Smale flocking dynamics. Publication (co)authored by Zuse Institute members. In: Proceedings of the Royal Society A, doi.org/10.1098/rspa...

Risk aversion can promote cooperation. Publication (co)authored by Zuse Institute members. In: Journal of Physics: Complexity, doi.org/10.1088/2632...

Bayesian optimization for state engineering of quantum gases. Publication (co)authored by Zuse Institute members. In: Quantum Sci. Technol., doi.org/10.1088/2058...

Open reaction-diffusion systems: bridging probabilistic theory and simulations across scales. Publication (co)authored by Zuse Institute members. In: Journal of Physics A: Mathematical and Theoretical, doi.org/10.1088/1751...

An Application of Modified S-CLSVOF Method to Kelvin-Helmholtz Instability and Comparison with Theoretical Result. Publication (co)authored by Zuse Institute members. In: Journal of Chemical Engineering of Japan, doi.org/10.1080/0021...

Fluid flow inside slit-shaped nanopores: The role of surface morphology at the molecular scale Non-equilibrium molecular dynamics (NEMD) simulations of fluid flow have highlighted the peculiarities of nanoscale flows compared to classical fluid mechanics;

Fluid flow inside slit-shaped nanopores: the role of surface morphology at the molecular scale. Publication (co)authored by Zuse Institute members. In: The Journal of Chemical Physics, doi.org/10.1063/5.02...

Clustering time-evolving networks using the spatiotemporal graph Laplacian Time-evolving graphs arise frequently when modeling complex dynamical systems such as social networks, traffic flow, and biological processes. Developing techni

Clustering Time-Evolving Networks Using the Spatiotemporal Graph Laplacian. Publication (co)authored by Zuse Institute members. In: Chaos: An Interdisciplinary Journal of Nonlinear Science, doi.org/10.1063/5.02...

Rotation dynamics and torque efficiency of cometary nuclei. Publication (co)authored by Zuse Institute members. In: Astronomy & Astrophysics, doi.org/10.1051/0004...

Thermal environment and erosion of comet 67P/Churyumov-Gerasimenko. Publication (co)authored by Zuse Institute members. In: Astronomy and Astrophysics, doi.org/10.1051/0004...

The toxicity, uptake, and impact on galectin-3 mediated apoptosis of lactose functionalized PAMAM dendrimers Poly(amidoamine) (PAMAM) dendrimers functionalized with ligands that are designed to interact with biological receptors are important macromolecules for the elucidation and mediation of biological rec...

The toxicity, uptake, and impact on galectin-3 mediated apoptosis of lactose functionalized PAMAM dendrimers. Publication (co)authored by Zuse Institute members. In: Materials Advances, doi.org/10.1039/D4MA...

Blobby is a synaptic active zone assembly protein required for memory in Drosophila - Nature Communications The active zone is a brain signaling hub critical for synaptic information transfer and the encoding of behaviors. The authors identify Blobby as an assembly factor required for proper active zone nan...

Blobby is a synaptic active zone assembly protein required for memory in Drosophila. Publication (co)authored by Zuse Institute members. In: Nature Communications, doi.org/10.1038/s414...

Hydrogen Diffusion in Garnet: Insights From Atomistic Simulations With molecular dynamics simulation, two H diffusion regimes are found: (a) a H diffuser dominated regime and (b) a vacancy dominated regime The effect of atomic vibration of heavier atoms such as...

Hydrogen diffusion in garnet: insights from atomistic simulations. Publication (co)authored by Zuse Institute members. In: Geochemistry Geophysics Geosystems, doi.org/10.1029/2024...

Spectroscopic Ellipsometry of Plasmonic Gratings - Ideal Parameters for Sensing and Subpicometer Measurement Uncertainty. Publication (co)authored by Zuse Institute members. In: ACS Omega, doi.org/10.1021/acso...

Chiral Plasmonic Crystals Self-Assembled by DNA Origami Periodic lattices of high refractive index materials manipulate light in exceptional manners. Resulting remarkable properties range from photonic band gaps to chiral active matter, which critically de...

Chiral Plasmonic Crystals Self-Assembled by DNA Origami. Publication (co)authored by Zuse Institute members. In: J. Phys. Chem. C, doi.org/10.1021/acs....

Optimized Sensing on Gold Nanoparticles Created by Graded-Layer Magnetron Sputtering and Annealing. Publication (co)authored by Zuse Institute members. In: Sens. Actuators B Chem., doi.org/10.1016/j.sn...