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#dynamics

3 posts3 participants0 posts today
Public
Rxiv mechanobio

📰 "Modular integration of neural connectomics, dynamics and biomechanics for identification of behavioral sensorimotor pathways in Caenorhabditis elegans"
arxiv.org/abs/2504.18073 #Extra-Cellular #Mechanical #Q-Bio.Qm #Dynamics #Q-Bio.Nc

arXiv logo
arXiv.orgModular integration of neural connectomics, dynamics and biomechanics for identification of behavioral sensorimotor pathways in Caenorhabditis elegansComputational approaches which emulate in-vivo nervous system are needed to investigate mechanisms of the brain to orchestrate behavior. Such approaches must integrate a series of biophysical models encompassing the nervous system, muscles, biomechanics to allow observing the system in its entirety while supporting model variations. Here we develop modWorm: a modular modeling framework for the nematode C. elegans. modWorm allows for construction of a model as an integrated series of configurable, exchangeable modules each describing specific biophysical processes across different modalities. Utilizing modWorm, we propose a base neuro-mechanical model for C. elegans built upon the complete connectome. The model integrates a series of 7 modules: i) intra-cellular dynamics, ii) electrical and iii) chemical extra-cellular neural dynamics, iv) translation of neural activity to muscle calcium dynamics, v) muscle calcium dynamics to muscle forces, vi) muscle forces to body postures and vii) proprioceptive feedback. We validate the base model by in-silico injection of constant currents into neurons known to be associated with locomotion behaviors and by applying external forces to the body. Applications of in-silico neural stimuli experimentally known to modulate locomotion show that the model can recapitulate natural behavioral responses such as forward and backward locomotion as well as mid-locomotion responses such as avoidance and turns. Furthermore, through in-silico ablation surveys, the model can infer novel neural circuits involved in sensorimotor behaviors. To further dissect mechanisms of locomotion, we utilize modWorm to introduce empirical based model variations and model optimizations to elucidate their effects on simulated locomotion. Our results show that modWorm can be utilized to identify neural circuits which control, mediate and generate natural behavior.
Public
COPASI

A new COPASI version 4.45 was released.

New features:
- tool to parse arbitrary ODEs into reaction-based model.
- menu entry allowing definition and running of external tools (scripts ,etc)

Many bug fixes, including:
- better scaling for MCA in the presence of small compartment volumes
- fixed intervals for time courses running backwards (negative time)
- improvement in steady state criteria in models with conserved moieties
- Improved parsing SED-ML & SBML

copasi.org/Download/
#SystemsBiology #Chemistry #Simulation #Dynamics

copasi.orgCOPASI: DownloadCOPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
Public
Philo Sophies

#Zoomposium with Prof. Dr. #Thomas #Klinger: “The sun on earth - #nuclearfusion as an #energy source”

This time we talk with Thomas Klinger, who has been a “Scientific Member” of the #MaxPlanckSociety since 2001 and is Director of the “#Stellarator #Dynamics and #Transport” division at the Institute for #PlasmaPhysics in Greifswald. There he heads the highly successful #Wendelstein7X project.

youtu.be/8bNqFmmXebk

More at: philosophies.de/index.php/2024

portrait of Thomas Klinger
Public *
Samuel Alizon

It is still possible to #register for the 32nd International #dynamics & #evolution of human #viruses #conference that will be held from May 6-9, 2025 in the beautiful #abbaye of #Royaumont (north of Paris, France).

dynamicsevolution.org/event/5/

There is even room left for #childcare (from 8:30 to 17:00)!

The full program is available online with a great line up of speakers (@TanjaStadler, @chaoranchen, @firefoxx66, @famulare, ,...).

dynamicsevolution.org/event/5/

entrance of the abbaye of Royaumont at night
Public
Philo Sophies

#Zoomposium with Prof. Dr. #Thomas #Klinger: “The sun on earth - #nuclear fusion as an #energy source”

This time we talk about the #dis-/advantages of #nuclearfusiontechnology with Thomas Klinger, who has been a “Scientific Member” of the #MaxPlanckSociety since 2001 and is Director of the “#Stellarator #Dynamics and #Transport” division at the Institute for #PlasmaPhysics. There he heads the highly successful #Wendelstein7X project.

youtu.be/8bNqFmmXebk

More at: philosophies.de/index.php/2024

portrait of Thomas Klinger
Public
💧🌏 Greg Cocks

Interpretable Physics-Informed Graph Neural Networks For Flood Forecasting
--
doi.org/10.1111/mice.13484 <-- shared paper
--
github.com/MehdiTaghizadehUVa/ <-- shared GitHub repository
--
#GIS #spatial #mapping #FloodForecasting #GraphNeuralNetworks #PhysicsInformedAI #Hydrology #ClimateResilience #ScientificMachineLearning #CivilEngineering #HydroGraphNet #PhyiscsNeMo #hydrology #water #flood #flooding #spatialanalysis #spatiotemporal #climatechange #model #modeling #machinelearning #AI #extremeweather #prediction #forecasting #planning #humanimpacts #loss #lossoflife #publicsafety #cost #economics #infrastructure #risk #hazard #disaster #mitigation #preparedness #naturaldisaster #HydroGraphNet #floodforecasting #dynamics #remotesensing #earthobservation

Public
Rxiv mechanobio

📰 "A Navier-Stokes-Peridynamics hybrid algorithm for the coupling of compressible flows and fracturing materials"
arxiv.org/abs/2504.11006 #Physics.Comp-Ph #Dynamics #Cell

arXiv logo
arXiv.orgA Navier-Stokes-Peridynamics hybrid algorithm for the coupling of compressible flows and fracturing materialsModeling and simulation of fluid-structure interactions are crucial to the success of aerospace engineering. This work addresses a novel hybrid algorithm that models the close coupling between compressible flows and deformable materials using a mesoscopic approach. Specifically, the high-speed flows are described by the gas-kinetic scheme, which is a robust Navier-Stokes alternative solver built on the molecular kinetic theory. The deformation, damage, and fracture of materials are depicted using the bond-based peridynamics, which serves as coarse-grained molecular dynamics to construct non-local extensions of classical continuum mechanics. The evolution of fluids and materials are closely coupled using the ghost-cell immersed boundary method. Within each time step, the solutions of flow and solid fields are updated simultaneously, and physics-driven boundary conditions are exchanged for each other via ghost cells. Extensive numerical experiments, including crack propagation in a pre-cracked plate, subsonic flow around the NACA0012 airfoil, supersonic flow around the circular cylinder, and shock wave impacting on the elastic panel, are performed to validate the algorithm. The simulation results demonstrate the unique advantages of current hybrid algorithm in solving fracture propagation induced by high-speed flows.
Public
Charo del Genio

New paper, just out.

Often, in real-world situations, one does not know the full structure of a network. However, at the same time, one can often observe some interactions that take place on it, and may be interested in knowing its full structure. For example, one may be detecting some partial criminal activity and may want to determine the whole organization. We consider higher-order networks, which are structures with many-body interactions, and specifically simplicial complexes, and show that one can reconstruct a whole network almost perfectly simply by observing the transient of the dynamics that takes place on it. In fact, we give 3 different algorithms to do it, with different complexities and accuracies, so you can choose which one suits you best.

Nine plots, arranged in a 3-by-3 grid. The columns, left to right, correspond to three real-world data sets, marked "Malawi", "SFHH" and "LH10", left to right. The rows, from top to bottom, correspond to the three algorithms introduced in the article, namely PBP, GLO and GLOC. Each plot show how the F1 score, on the y axis, very quickly approaches almost 100% for 1-simplices and 2-simplices as the size of the observation set, on the x axis, increases. In general, GLO and GLOC perform better than PBP.
#physics#mathematics#networks
Public
Rxiv mechanobio

📰 "Influence of erythrocyte density on aggregability as a marker of cell age: Dissociation dynamics in extensional flow"
arxiv.org/abs/2409.08877 #Physics.Bio-Ph #Mechanical #Dynamics #Cell

arXiv.orgInfluence of erythrocyte density on aggregability as a marker of cell age: Dissociation dynamics in extensional flowBlood rheology and microcirculation are strongly influenced by red blood cell (RBC) aggregation. The aggregability of RBCs can vary significantly due to factors such as their mechanical and membrane surface properties, which are affected by cell aging in vivo. In this study, we investigate RBC aggregability as a function of their density, a marker of cell age and mechanical properties, by separating RBCs from healthy donors into different density fractions using Percoll density gradient centrifugation. We examine the dissociation rates of aggregates in a controlled medium supplemented with Dextran, employing an extensional flow technique based on hyperbolic microfluidic constrictions and image analysis, assisted by a convolutional neural network (CNN). In contrast to other techniques, our microfluidic experimental approach highlights the behavior of RBC aggregates in dynamic flow conditions relevant to microcirculation. Our results demonstrate that aggregate dissociation is strongly correlated with cell density and that aggregates formed from the denser fractions of RBCs are significantly more robust than those from the average cell population. This study provides insight into the effect of RBC aging in vivo on their mechanical properties and aggregability, underscoring the importance of further exploration of RBC aggregation in the context of cellular senescence and its potential implications for hemodynamics. Additionally, it suggests that this technique can complement existing methods for improved evaluation of RBC aggregability in health and disease.
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