Related papers: Reconstructing the kinetic chemotaxis kernel using…
It is widely recognized that reciprocal interactions between cells and their microenvironment, via mechanical forces and biochemical signaling pathways, regulate cell behaviors during normal development, homeostasis and disease progression…
Kinetic-transport equations that take into account the intra-cellular pathways are now considered as the correct description of bacterial chemotaxis by run and tumble. Recent mathematical studies have shown their interest and their…
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and…
In this paper we develop a kernel density estimation (KDE) approach to modeling and forecasting recurrent trajectories on a compact manifold. For the purposes of this paper, a trajectory is a sequence of coordinates in a phase space defined…
Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient…
Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices, all of these models assume central-force interactions between…
We discuss velocity-jump models for chemotaxis of bacteria with an internal state that allows the velocity jump rate to depend on the memory of the chemoattractant concentration along their path of motion. Using probabilistic techniques, we…
Run-and-tumble is a common but vital strategy that bacteria employ to explore environment suffused with boundaries, as well as to escape from entrapment. In this study we reveal how this strategy and the resulting dynamical behavior can be…
Models in systems biology are mathematical descriptions of biological processes that are used to answer questions and gain a better understanding of biological phenomena. Dynamic models represent the network through rates of the production…
An important feature of kernel mean embeddings (KME) is that the rate of convergence of the empirical KME to the true distribution KME can be bounded independently of the dimension of the space, properties of the distribution and smoothness…
In this work, we discuss model-independent reconstruction of the expansion history of the late Universe. We use Gaussian Process Regression (GPR) to reconstruct the evolution of various cosmological parameters such as Hubble parameter…
Mechanical cues from the extracellular microenvironment play a central role in regulating the structure, function and fate of living cells. Nevertheless, the precise nature of the mechanisms and processes underlying this crucial cellular…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
Bacterial migration through confined spaces is critical for several phenomena like: biofilm formation, bacterial transport in soils, and bacterial therapy against cancer . In the present work, \textit{E. coli} (strain K12-MG1655 WT)…
This paper addresses the problem of learning the impulse responses characterizing forward models by means of a regularized kernel-based Prediction Error Method (PEM). The common approach to accomplish that is to approximate the system with…
Controlling the phases of matter is a challenge that spans from condensed materials to biological systems. Here, by imposing a geometric boundary condition, we study controlled collective motion of Escherichia coli bacteria. A circular…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
The bacterium E.Coli swims in a zig-zag manner, in a series of straight runs and tumbles occurring alternately, with the run-durations dependent on the local spatial gradient of chemo-attractants/repellants. This enables the organism to…
We investigate the numerical discretization of a two-stream kinetic system with an internal state, such system has been introduced to model the motion of cells by chemotaxis. This internal state models the intracellular methylation level.…
Markov Chain Monte Carlo approach is frequently used within Bayesian framework to sample the target posterior distribution. Its efficiency strongly depends on the proposal used to build the chain. The best jump proposal is the one that…