Related papers: Bacterial self-organisation and computation
Understanding how growth induces form is a longstanding biological question. Many studies concentrated on the shapes of plant cells, fungi or bacteria. Some others have shown the importance of the mechanical properties of bacterial walls…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
Machine learning applications in protein sciences have ushered in a new era for designing molecules in silico. Antibodies, which currently form the largest group of biologics in clinical use, stand to benefit greatly from this shift.…
Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…
In Schiebinger et al. (2017), the authors use optimal transport of measures on empirical distributions arising from biological experiments to relate the single cell RNA sequencing profiles for induced pluripotent stem cells differentiating.…
We investigate further the existence of solutions to kinetic models of chemotaxis. These are nonlinear transport-scattering equations with a quadratic nonlinearity which have been used to describe the motion of bacteria since the 80's when…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…
We provide an intuitive platform for engineering exciton transfer dynamics. We show that careful consideration of the spectral density, which describes the system-bath interaction, leads to opportunities to engineer the transfer of an…
Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…
The classical macroscopic chemotaxis equations have previously been derived from an individual-based description of the tactic response of cells that use a "run-and-tumble" strategy in response to environmental cues. Here we derive…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
A common feature of biological self-organization is how active agents communicate with each other or their environment via chemical signaling. Such communications, mediated by self-generated chemical gradients, have consequences for both…
A powerful experimental approach for investigating computation in networks of biological neurons is the use of cultured dissociated cortical cells grown into networks on a multi-electrode array. Such preparations allow investigation of…
Human pluripotent stem cells hold great promise for developments in regenerative medicine and drug design. The mathematical modelling of stem cells and their properties is necessary to understand and quantify key behaviours and develop…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
Active matter systems comprise self-propelled particles that move on a substrate while leaving chemical trails that influence other particles through chemotaxis (e.g., slime-depositing bacteria). Orientational chemotaxis manifests as a…
Motility is a fundamental survival strategy of bacteria to navigate porous environments. Swimming cells thrive in quiescent wetlands and sediments at the bottom of the marine water column, where they mediate many essential biogeochemical…
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 systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the…