Create accountLogin

Recent searches

No recent searches

Search options

Only available when logged in.
mastodon.world is one of the many independent Mastodon servers you can use to participate in the fediverse.
Generic Mastodon server for anyone to use.

Administered by:

Server stats:

10K
active users

mastodon.world: AboutStatusProfiles directoryPrivacy policy

Mastodon: AboutGet the appKeyboard shortcutsView source codev4.3.7

#dynamics

40 posts12 participants0 posts today
Public
Rxiv mechanobio

📰 "Boundary Effects and Oxygen Deficiency-Driven Pattern Transitions in Algal Bioconvection"
arxiv.org/abs/2504.12362 #Physics.Flu-Dyn #Physics.Bio-Ph #Dynamics #Cell

arXiv logo
arXiv.orgBoundary Effects and Oxygen Deficiency-Driven Pattern Transitions in Algal BioconvectionSuspensions of motile microorganisms can spontaneously give rise to large scale fluid motion, known as bioconvection, which is characterized by dense, cell-rich downwelling plumes interspersed with broad upwelling regions. In this study, we investigate bioconvection in shallow suspensions of Chlamydomonas reinhardtii cells confined within spiral-shaped boundaries, combining detailed experimental observations with 3D simulations. Under open liquid-air interface conditions, cells accumulate near the surface due to negative gravitaxis, forming spiral shaped density patterns that subsequently fragment into lattice-like structures and give rise to downwelling plumes. Space-time analyses reveal coherent rotational dynamics, with inward-moving patterns near the spiral core and bidirectional motion farther from the center. Introducing confinement by sealing the top boundary with an air-impermeable transparent wall triggers striking transitions in the bioconvection patterns, driven by oxygen depletion: initially stable structures reorganize into new patterns with reduced characteristic wavelengths. Complementary 3D simulations, based on the incompressible Navier-Stokes equations and incorporating negative buoyancy and active stress from swimming cells, capture the initial pattern formation and its subsequent instability, reproducing the fragmentation of spiral-shaped accumulations into downwelling plumes and the emergence of strong vortical flows, nearly an order of magnitude faster than individual cell swimming speeds. However, these models do not capture the oxygen-driven pattern transitions observed experimentally. Our findings reveal that confinement geometry, oxygen dynamics, and metabolic transitions critically govern bioconvection pattern evolution, offering new strategies to control microbial self-organization and flow through environmental and geometric design.
Public
Rxiv mechanobio

📰 "Negative feedback and oscillations in a model for mRNA translation"
arxiv.org/abs/2504.12926 #Q-Bio.Qm #Dynamics #Q-Bio.Mn #Cell

arXiv logo
arXiv.orgNegative feedback and oscillations in a model for mRNA translationThe ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during translation. In this case, the particles model ribosomes and each site corresponds to a consecutive group of codons. Networks of interconnected RFMs have been used to model and analyze large-scale translation in the cell and, in particular, the effects of competition for shared resources. Here, we analyze the RFM with a negative feedback connection from the protein production rate to the initiation rate. This models, for example, the production of proteins that inhibit the translation of their own mRNA. Using tools from the theory of 2-cooperative dynamical systems, we provide a simple condition guaranteeing that the closed-loop system admits at least one non-trivial periodic solution. When this condition holds, we also explicitly characterize a large set of initial conditions such that any solution emanating from this set converges to a non-trivial periodic solution. Such a solution corresponds to a periodic pattern of ribosome densities along the mRNA, and to a periodic pattern of protein production.
Public
Rxiv mechanobio

📰 "The Dissipation Theory of Aging: A Quantitative Analysis Using a Cellular Aging Map"
arxiv.org/abs/2504.13044 #Physics.Bio-Ph #Q-Bio.Qm #Dynamics #Cs.Lg #Cell

arXiv logo
arXiv.orgThe Dissipation Theory of Aging: A Quantitative Analysis Using a Cellular Aging MapWe propose a new theory for aging based on dynamical systems and provide a data-driven computational method to quantify the changes at the cellular level. We use ergodic theory to decompose the dynamics of changes during aging and show that aging is fundamentally a dissipative process within biological systems, akin to dynamical systems where dissipation occurs due to non-conservative forces. To quantify the dissipation dynamics, we employ a transformer-based machine learning algorithm to analyze gene expression data, incorporating age as a token to assess how age-related dissipation is reflected in the embedding space. By evaluating the dynamics of gene and age embeddings, we provide a cellular aging map (CAM) and identify patterns indicative of divergence in gene embedding space, nonlinear transitions, and entropy variations during aging for various tissues and cell types. Our results provide a novel perspective on aging as a dissipative process and introduce a computational framework that enables measuring age-related changes with molecular resolution.
Public
Rxiv mechanobio

📰 "Hemodynamic Markers: CFD-Based Prediction of Cerebral Aneurysm Rupture Risk"
arxiv.org/abs/2504.10524 #Physics.Med-Ph #Physics.Bio-Ph #Dynamics #Q-Bio.Qm #Cell

arXiv logo
arXiv.orgHemodynamic Markers: CFD-Based Prediction of Cerebral Aneurysm Rupture RiskThis study investigates the influence of aneurysm evolution on hemodynamic characteristics within the sac region. Using computational fluid dynamics (CFD), blood flow through the parent vessel and aneurysm sac was analyzed to assess the impact on wall shear stress (WSS), time-averaged wall shear stress (TAWSS), and the oscillatory shear index (OSI), key indicators of rupture risk. Additionally, Relative Residence Time (RRT) and Endothelial Cell Activation Potential (ECAP) were examined to provide a broader understanding of the aneurysm's hemodynamic environment. Six distinct cerebral aneurysm (CA) models, all from individuals of the same gender, were selected to minimize gender-related variability. Results showed that unruptured cases exhibited higher WSS and TAWSS, along with lower OSI and RRT values patterns consistent with stable flow conditions supporting vascular integrity. In contrast, ruptured cases had lower WSS and TAWSS, coupled with elevated OSI and RRT, suggesting disturbed and oscillatory flow commonly linked to aneurysm wall weakening. ECAP was also higher in ruptured cases, indicating increased endothelial activation under unstable flow. Notably, areas with the highest OSI and RRT often aligned with vortex centers, reinforcing the association between disturbed flow and aneurysm instability. These findings highlight the value of combining multiple hemodynamic parameters for rupture risk assessment. Including RRT and ECAP provides deeper insight into flow endothelium-interactions, offering a stronger basis for evaluating aneurysm stability and guiding treatment decisions.
ExploreLive feeds
About