Related papers: Reconstructing the kinetic chemotaxis kernel using…
Auto-chemotaxis, the directed movement of cells along gradients in chemicals they secrete, is central to the formation of complex spatiotemporal patterns in biological systems. Since the introduction of the Keller--Segel model, numerous…
Bacterial cells exhibit a diverse array of shapes and sizes, largely governed by their cell walls in conjunction with cytoskeletal proteins and internal turgor pressure. The present study develops a theoretical framework for modeling the…
Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modelling meticulously executed. Furthermore, to enable the…
External control of the swimming speed of `active particles' can be used to self assemble designer structures in situ on the micrometer to millimeter scale. We demonstrate such reconfigurable templated active self assembly in a fluid…
If the 20th century was known for the computational revolution, what will the 21st be known for? Perhaps the recent strides in the nascent fields of molecular programming and biological computation will help bring about the 'Coming Era of…
The analysis of human microbiome data is often based on dimension-reduced graphical displays and clustering derived from vectors of microbial abundances in each sample. Common to these ordination methods is the use of biologically motivated…
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…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
Investigation of dynamic processes in cell biology very often relies on the observation in two dimensions of 3D biological processes. Consequently, the data are partial and statistical methods and models are required to recover the…
Chemotaxis receptors in E. coli form clusters at the cell poles and also laterally along the cell body, and this clustering plays an important role in signal transduction. Recently, experiments using flourrescence imaging have shown that,…
Optical molecular tomographic imaging is to reconstruct the concentration distribution of photon-molecular probes in a small animal from measured photon fluence rates. The localization and quantification of molecular probes is related to…
A direct formulation of linear elasticity of cell complexes based on discrete exterior calculus is presented. The primary unknown are displacements, represented by primal vector-valued 0-cochain. Displacement differences and internal forces…
The notion of a (polynomial) kernelization from parameterized complexity is a well-studied model for efficient preprocessing for hard computational problems. By now, it is quite well understood which parameterized problems do or…
A mathematical model is proposed for shape evolution and locomotion of fish epidermal keratocytes on elastic substrates. The model is based on mechanosensing concepts: cells apply contractile forces onto the elastic substrate, while cell…
The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while…
We study the long-time behaviour of a run and tumble model which is a kinetic-transport equation describing bacterial movement under the effect of a chemical stimulus. The experiments suggest that the non-uniform tumbling kernels are…
We present a data-driven algorithm for efficiently computing stochastic control policies for general joint chance constrained optimal control problems. Our approach leverages the theory of kernel distribution embeddings, which allows…
Extending the classic works of Berg and Purcell on the biophysics of bacterial chemotaxis, we find the optimal chemotactic strategy for the peritrichous bacterium E. Coli in the high and low signal to noise ratio limits. The optimal…
We study a chemotaxis-growth system with nonlinear local and nonlocal reactions and gradient-dependent damping. Under suitable conditions on the system parameters and spatial dimension, we prove that solutions exist globally in time and…