Related papers: Active skeleton for bacteria modeling
To model the morphogenesis of rod-shaped bacterial micro-colony, several individual-based models have been proposed in the biophysical literature. When studying the shape of micro-colonies, most models present interaction forces such as…
Incorporating cells within active biomaterial scaffolds is a promising strategy to develop forefront materials that can autonomously sense, respond, and alter the scaffold in response to environmental cues or internal cell circuitry. Using…
We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…
The hydrodynamic interactions among bacterial cell bodies, flagella, and surrounding boundaries are essential for understanding bacterial motility in complex environments. In this study, we demonstrate that each slender flagellum can be…
Near field hydrodynamic interactions are essential to determine many important emergent behaviors observed in active suspensions, but have not been successfully modeled so far. In this work we propose an effective model capable of…
General skinning techniques aim to deform the surface of an articulated model following the pose change of a skeleton. Their rapidity makes them ideal tools for real-time animation purposes. However, popular skinning algorithms are simple,…
We use moving light patterns to control the motion of {\it Escherichia coli} bacteria whose motility is photo-activated. Varying the pattern speed controls the magnitude and direction of the bacterial flux, and therefore the accumulation of…
Computer simulations can aid in understanding how collective materials properties emerge from interactions between simple constituents. Here, we introduce a coarse-grained model that enables simulation of networks of actin filaments, myosin…
The swimming properties of an E. coli-type model bacterium are investigated by mesoscale hy- drodynamic simulations, combining molecular dynamics simulations of the bacterium with the multiparticle particle collision dynamics method for the…
The basic problem of shape complementarity analysis appears fundamental to applications as diverse as mechanical design, assembly automation, robot motion planning, micro- and nano-fabrication, protein-ligand binding, and rational drug…
Tracking many cells in time-lapse 3D image sequences is an important challenging task of bioimage informatics. Motivated by a study of brain-wide 4D imaging of neural activity in C. elegans, we present a new method of multi-cell tracking.…
The field of active matter explores the behaviors of self propelled agents out of equilibrium, with active suspensions, such as swimming bacteria in solutions, serving as impactful models. These systems exhibit spatio-temporal patterns akin…
We present a new approach for modelling musculoskeletal anatomy. Unlike previous methods, we do not model individual muscle shapes as geometric primitives (polygonal meshes, NURBS etc.). Instead, we adopt a volumetric segmentation approach…
Mesoscopic active systems exhibit various unique behaviours - absent in passive systems - due to the forces generated by the corresponding constituents by converting their available free energies. However, estimating these forces - which…
Cell motility in higher organisms (eukaryotes) is crucial to biological functions ranging from wound healing to immune response, and also implicated in diseases such as cancer. For cells crawling on hard surfaces, significant insights into…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because…
A preliminary iterative 3D meso-scale structural model of the femur was developed, in which bar and shell elements were used to represent trabecular and cortical bone respectively. The cross-sectional areas of the bar elements and the…
The development of traction-force microscopy, in the past two decades, has created the unprecedented opportunity of performing direct mechanical measurements on living cells as they adhere or crawl on uniform or micro-patterned substrates.…
Active Brownian particles (ABPs) are termed out to be a successful way of modeling the moving microorganism on the substrate. In recent studies, it is shown that such organisms can sense the characteristics of the substrate. Motivated by…