A5006405122- Micro and Nano Robotics
- Cellular Mechanics and Interactions
- Mathematical Biology Tumor Growth
- Gene Regulatory Network Analysis
- Slime Mold and Myxomycetes Research
- Markov Chains and Monte Carlo Methods
- Diffusion and Search Dynamics
- Simulation Techniques and Applications
- Molecular Communication and Nanonetworks
- Microbial Metabolic Engineering and Bioproduction
- Cell Image Analysis Techniques
- Mass Spectrometry Techniques and Applications
- T-cell and B-cell Immunology
- Cellular Automata and Applications
- Single-cell and spatial transcriptomics
- Cancer Cells and Metastasis
- Congenital heart defects research
- Angiogenesis and VEGF in Cancer
- Machine Learning and Algorithms
- Microtubule and mitosis dynamics
- Gaussian Processes and Bayesian Inference
- Inhalation and Respiratory Drug Delivery
- Polymer Surface Interaction Studies
- Evolution and Genetic Dynamics
- Zebrafish Biomedical Research Applications
Technische Universität Dresden
2007-2023
DSI Informationstechnik (Germany)
2012
We characterize cell motion in experiments and show that the transition to collective colonies of gliding bacterial cells confined a monolayer appears through organization into larger moving clusters. Collective by nonequilibrium cluster formation is detected for critical packing fraction around 17%. This characterized scale-free power-law cluster-size distribution, with an exponent $0.88\ifmmode\pm\else\textpm\fi{}0.07$, appearance giant number fluctuations. Our findings are quantitative...
Abstract Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations reaction-diffusion systems. It allows rapid development multiscale in biological terms mathematical expressions rather than programming code. Its graphical user interface supports entire workflow from model construction to visualization, archiving batch processing. Availability implementation: Binary packages are available at...
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging reproduce reuse simulations, in part, because the numerous formats methods for simulating various subsystems scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find use simulation tools, we developed BioSimulators (https://biosimulators.org), central registry of capabilities...
During embryonic vasculogenesis, endothelial precursor cells of mesodermal origin known as angioblasts assemble into a characteristic network pattern. Although considerable amount markers and signals involved in this process have been identified, the mechanisms underlying coalescence reticular pattern remain unclear. Various recent studies hypothesize that autocrine regulation chemoattractant vascular growth factor (VEGF) is responsible for formation networks vitro. However, hypothesis does...
Formation of spatial patterns cells is a recurring theme in biology and often depends on regulated cell motility. Motility the rod-shaped bacterium Myxococcus xanthus two motility machineries, type IV pili (giving rise to S-motility) gliding apparatus A-motility). Cell by occasional reversals. Moving M. can organize into spreading colonies or spore-filled fruiting bodies, depending their nutritional status. To ultimately understand these pattern-formation processes contributions as well...
The cellular Potts model (CPM) is a powerful computational method for simulating collective spatiotemporal dynamics of biological cells. To drive the dynamics, CPMs rely on physics-inspired Hamiltonians. However, as first principles remain elusive in biology, these Hamiltonians only approximate full complexity real multicellular systems. address this limitation, we propose NeuralCPM, more expressive that can be trained directly observational data. At core NeuralCPM lies Neural Hamiltonian,...
Collective cell migration is an important process during biological development and tissue repair but may turn malignant tumor invasion. Mathematical computational models are essential to unravel the mechanisms of self-organization that underlie emergence collective from interactions among individual cells. Recently, guidance-by-followers was identified as one such underlying mechanism in embryo zebrafish. This poses question how guidance stimuli integrated when multiple cells interact...
Biological tissues are dynamic and highly organized. Multi-scale models helpful tools to analyse understand the processes determining tissue dynamics. These usually depend on parameters that need be inferred from experimental data achieve a quantitative understanding, predict response perturbations, evaluate competing hypotheses. However, even advanced inference approaches such as approximate Bayesian computation (ABC) difficult apply due computational complexity of simulation multi-scale...
The continuous phasing technique was successfully used to obtain a high degree of cell cycle synchrony in cultures the model organism Ralstonia eutropha JMP 134 (today reclassified into Cupriavidus necator). responses were evaluated with flow cytometric determinations DNA contents and size (by fluorescence forward scatter measurements, respectively, after staining DNA-binding dye 4',6-diamidino-2'-phenylindole, DAPI), concentration, nucleic acid binding LDS-751. strain cultivated on mineral...
Formation of fibrillar fibronectin networks is a major process during embryogenesis and tissue formation, but the molecular details fibril assembly remain poorly understood. Based on current ideas fibrillogenesis, stochastic model was developed to enlighten mechanism formation paired nanofibrils by adherent endothelial cells, which has been observed recently. The development clusters fibrils investigated means Monte Carlo simulations, including diffusion-controlled aggregation myosin-driven...
Abstract Motivation Biological tissues are dynamic and highly organized. Multi-scale models helpful tools to analyze understand the processes determining tissue dynamics. These usually depend on parameters that need be inferred from experimental data achieve a quantitative understanding, predict response perturbations, evaluate competing hypotheses. However, even advanced inference approaches such as Approximate Bayesian Computation (ABC) difficult apply due computational complexity of...
Abstract Cytomegalovirus (CMV) has evolved a unique virus-host relationship in the salivary glands (SGs) to sustain prolonged viral replication and hence chances for horizontal transmission. Previous reports have established decisive role IFN γ producing CD4 + T cells control murine CMV (MCMV) infection SGs; however, micro-anatomical information regarding their mode of action is largely missing. Here, we provide spatiotemporal analysis defined antiviral immune actions that eventually...
Considering the cost effectiveness, elasticity, and flexibility of virtualized cloud environments, porting HPC applications to those environments executing them within these settings is becoming more popular. For this purpose, traditional have be redesigned as applications. An analysis performance environment in-dispensable, if should efficiently executed in environment.
Abstract Cell motility has important influence on cell interactions and functionality for various biological aspects. Deciphering these dynamics often relies live-cell microscopy measurements, which partly have to deal with limitations that could impair a reliable quantification of their motility. Especially given complex environments tissue structures, limited observation periods, cells moving in out focus impaired calibration axes lead loss tracks insufficient tracking within several...
Abstract Collective cell migration is an important process during biological development and tissue repair, but may turn malignant tumor invasion. Mathematical computational models are essential to unravel the mechanisms of self-organization that underlie emergence collective from interactions among individual cells. Recently, guidance-by-followers was identified as one such underlying mechanism in zebrafish embryo. This poses question how guidance stimuli integrated when multiple cells...
Human airway epithelium (HAE) represents the primary site of viral infection for SARS-CoV-2. Comprising different cell populations, a lot research has been aimed at deciphering major types and dynamics that determine disease progression severity. However, type-specific replication kinetics, as well contribution cellular composition respiratory to pathology are still not fully understood. Although experimental advances, including Air-liquid interface (ALI) cultures reconstituted...