144 citations · 810 across the 34 of their papers we have counts for
8 papers · 1 filter
Synaptic spine head morphodynamics from graph grammar rules for actin dynamics
Matthew Hur, Thomas Bartol, Padmini Rangamani +2
There is a morphodynamic component to synaptic learning by which changes in dendritic (postsynaptic) spine head size are associated with the strengthening or weakening of the synap…
Increasing certainty in systems biology models using Bayesian multimodel inference
Nathaniel Linden-Santangeli, Jin Zhang, Boris Kramer +1
Mathematical models are indispensable to the system biology toolkit for studying the structure and behavior of intracellular signaling networks. A common approach to modeling is to…
Spatial modeling algorithms for reactions and transport (SMART) in biological cells
Emmet A. Francis, Justin G. Laughlin, Jørgen S. Dokken +4
Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mat…
SMART: Spatial Modeling Algorithms for Reaction and Transport
Justin G. Laughlin, Jørgen S. Dokken, Henrik N. T. Finsberg +4
Recent advances in microscopy and 3D reconstruction methods have allowed for characterization of cellular morphology in unprecedented detail, including the irregular geometries of…
Modeling membrane curvature generation using mechanics and machine learning
Sage Malingen, Padmini Rangamani
The deformation of cellular membranes regulates trafficking processes, such as exocytosis and endocytosis. Classically, the Helfrich continuum model is used to characterize the for…
Bayesian Parameter Estimation for Dynamical Models in Systems Biology
Nathaniel J. Linden, Boris Kramer, Padmini Rangamani
Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical compone…
Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematics and revealed by a three dimensional computational framework
Debabrata Auddya, Xiaoxuan Zhang, Rahul Gulati +4
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and function…
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle +5
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the abil…