Related papers: Perfect adaptation in eukaryotic gradient sensing …
Collective migration of eukaryotic cells is often guided by chemotaxis, and is critical in several biological processes, such as cancer metastasis, wound healing, and embryogenesis. Understanding collective chemotaxis has challenged…
A current challenge in atomistic machine learning is that of efficiently predicting the response of the electron density under electric fields. We address this challenge with symmetry-adapted kernel functions that are specifically derived…
Chemotaxis and reactions are fundamental processes in biology, often intricately intertwined. Chemotaxis, in particular, can be crucial in maintaining and accelerating a reaction. In this work, we extend the investigation initiated by…
Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…
During the past century, biologists and mathematicians investigated two mechanisms underlying bacteria motion: the run phase during which bacteria move in straight lines and the tumble phase in which they change their orientation. When…
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past…
Temperature sensing is a ubiquitous cell behavior, but the fundamental limits to the precision of temperature sensing are poorly understood. Unlike in chemical concentration sensing, the precision of temperature sensing is not limited by…
Calibration refers to the estimation of unknown parameters which are present in computer experiments but not available in physical experiments. An accurate estimation of these parameters is important because it provides a scientific…
A stochastic version of the Barkai-Leibler model of chemotaxis receptors in {\it E. coli} is studied here to elucidate the effects of intrinsic network noise in their conformational dynamics. It was originally proposed to explain the robust…
Cell migration in vivo is often guided by chemical signals. Such chemotaxis, such as performed by immune cells migrating to a wound site, is complicated by the complex geometry inside living tissues. In this study, we extend our theoretical…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of…
A key problem of eukaryotic cell motility is the signaling mechanism of chemoattractant gradient sensing. Recent experiments have revealed the molecular correlate of gradient sensing: Frontness molecules, such as PI3P and Rac, localize at…
Enzymes are essential to maintain organisms alive. Some of the reactions they catalyze are associated with a change in reagents chirality, hence their activity can be tracked by using optical means. However, illumination affects enzyme…
Living cells sense their environment through the binding of extra-cellular molecular ligands to cell surface receptors. Puzzlingly, vast numbers of signaling pathways exhibit a high degree of cross talk between different signals whereby…
We study the problem of calibrating a quantum receiver for optical coherent states when transmitted on a quantum optical channel with variable transmissivity, a common model for long-distance optical-fiber and free/deep-space optical…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown,…
Cell adhesion proteins typically form stable clusters that anchor the cell membrane to its environment. Several works have suggested that cell membrane protein clusters can emerge from a local feedback between the membrane curvature and the…
In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical…
Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein…