Sticky issues in turbulent transport.

We investigate the role of partial stickiness among particles or with a surface for turbulent transport. For the former case, we re-derive known results for the case of the compressible Kraichnan model by using a method based on bi-orthogonality for the expansion of the propagator in terms of left and right eigenvectors. In particular, we show that enforcing the constraints of orthogonality and normalization yields results that were previously obtained by a rigorous, yet possibly less intuitive method.

Seeking and sharing information in collective olfactory search.

Searching for a target is a task of fundamental importance for many living organisms. Long-distance search guided by olfactory cues is a prototypical example of such a process. The searcher receives signals that are sparse and very noisy, making the task extremely difficult.

Erratum: Flow Navigation by Smart Microswimmers via Reinforcement Learning [Phys. Rev. Lett. 118, 158004 (2017)].

This corrects the article DOI: 10.1103/PhysRevLett.118.

Tempo is the key.

Walking flies find the source of attractive odors by changing how frequently they stop and turn in response to the smell.

Collective olfactory search in a turbulent environment.

Finding the source of an odor dispersed by a turbulent flow is a vital task for many organisms. When many individuals concurrently perform the same olfactory search task, sharing information about other members' decisions can potentially boost the performance. But how much of this information is actually exploitable for the collective task? Here we show, in a model of a swarm of agents inspired by moth behavior, that there is an optimal way to blend the private information about odor and wind detections with the public information about other agents' heading direction.

Learning to flock through reinforcement.

Flocks of birds, schools of fish, and insect swarms are examples of the coordinated motion of a group that arises spontaneously from the action of many individuals. Here, we study flocking behavior from the viewpoint of multiagent reinforcement learning. In this setting, a learning agent tries to keep contact with the group using as sensory input the velocity of its neighbors.

Generosity, selfishness and exploitation as optimal greedy strategies for resource sharing.

Resource sharing outside the kinship bonds is rare. Besides humans, it occurs in chimpanzee, wild dogs and hyenas, as well as in vampire bats. Resource sharing is an instance of animal cooperation, where an animal gives away part of the resources that it owns for the benefit of a recipient.

Glider soaring via reinforcement learning in the field.

Soaring birds often rely on ascending thermal plumes (thermals) in the atmosphere as they search for prey or migrate across large distances. The landscape of convective currents is rugged and shifts on timescales of a few minutes as thermals constantly form, disintegrate or are transported away by the wind. How soaring birds find and navigate thermals within this complex landscape is unknown.

Exploring the function of bacterial chemotaxis.

Bacterial chemotaxis is a classical subject: our knowledge of its molecular pathway has grown very detailed, and experimental observations, as well as mathematical models of the dynamics of chemotactic populations, have a history of several decades. This should not lead to the conclusion that only minor details are left to be understood. Indeed, it is believed that bacterial chemotaxis is under selection for efficiency, yet the underlying functional forces remain largely unknown.

Flow Navigation by Smart Microswimmers via Reinforcement Learning.

Smart active particles can acquire some limited knowledge of the fluid environment from simple mechanical cues and exert a control on their preferred steering direction. Their goal is to learn the best way to navigate by exploiting the underlying flow whenever possible. As an example, we focus our attention on smart gravitactic swimmers.

Cell-size distribution in epithelial tissue formation and homeostasis.

How cell growth and proliferation are orchestrated in living tissues to achieve a given biological function is a central problem in biology. During development, tissue regeneration and homeostasis, cell proliferation must be coordinated by spatial cues in order for cells to attain the correct size and shape. Biological tissues also feature a notable homogeneity of cell size, which, in specific cases, represents a physiological need.

Learning to soar in turbulent environments.

Birds and gliders exploit warm, rising atmospheric currents (thermals) to reach heights comparable to low-lying clouds with a reduced expenditure of energy. This strategy of flight (thermal soaring) is frequently used by migratory birds. Soaring provides a remarkable instance of complex decision making in biology and requires a long-term strategy to effectively use the ascending thermals.

The Role of Adaptation in Bacterial Speed Races.

Evolution of biological sensory systems is driven by the need for efficient responses to environmental stimuli. A paradigm among prokaryotes is the chemotaxis system, which allows bacteria to navigate gradients of chemoattractants by biasing their run-and-tumble motion. A notable feature of chemotaxis is adaptation: after the application of a step stimulus, the bacterial running time relaxes to its pre-stimulus level.

Three-dimensional chemotaxis-driven aggregation of tumor cells.

One of the most important steps in tumor progression involves the transformation from a differentiated epithelial phenotype to an aggressive, highly motile phenotype, where tumor cells invade neighboring tissues. Invasion can occur either by isolated mesenchymal cells or by aggregates that migrate collectively and do not lose completely the epithelial phenotype. Here, we show that, in a three-dimensional cancer cell culture, collective migration of cells eventually leads to aggregation in large clusters.

Estimating cellular parameters through optimization procedures: elementary principles and applications.

Construction of quantitative models is a primary goal of quantitative biology, which aims to understand cellular and organismal phenomena in a quantitative manner. In this article, we introduce optimization procedures to search for parameters in a quantitative model that can reproduce experimental data. The aim of optimization is to minimize the sum of squared errors (SSE) in a prediction or to maximize likelihood.

White-noise limit of nonwhite nonequilibrium processes.

The asymptotic behavior of a stochastic process subject to a colored noise is considered in the limit of vanishing correlation time of the noise. The interpretation of the multiplicative noise of the effective equation is investigated. The mathematically consistent formulation of the stochastic calculus for the limiting process is given.

Polarity, cell division, and out-of-equilibrium dynamics control the growth of epithelial structures.

The growth of a well-formed epithelial structure is governed by mechanical constraints, cellular apico-basal polarity, and spatially controlled cell division. Here we compared the predictions of a mathematical model of epithelial growth with the morphological analysis of 3D epithelial structures. In both in vitro cyst models and in developing epithelial structures in vivo, epithelial growth could take place close to or far from mechanical equilibrium, and was determined by the hierarchy of time-scales of cell division, cell-cell rearrangements, and lumen dynamics.

Entropic anomaly and maximal efficiency of microscopic heat engines.

The efficiency of microscopic heat engines in a thermally heterogenous environment is considered. We show that-as a consequence of the recently discovered entropic anomaly-quasistatic engines, whose efficiency is maximal in a fluid at uniform temperature, have in fact vanishing efficiency in the presence of temperature gradients. For slow cycles the efficiency falls off as the inverse of the period.

Anomalous thermodynamics at the microscale.

Particle motion at the microscale is an incessant tug-of-war between thermal fluctuations and applied forces on one side and the strong resistance exerted by fluid viscosity on the other. Friction is so strong that completely neglecting inertia--the overdamped approximation--gives an excellent effective description of the actual particle mechanics. In sharp contrast to this result, here we show that the overdamped approximation dramatically fails when thermodynamic quantities such as the entropy production in the environment are considered, in the presence of temperature gradients.

Nonlinearity, fluctuations, and response in sensory systems.

The statistics of fluctuations in biological sensing pathways and its relation to the response to environmental stimuli is investigated. We focus on bacterial chemotaxis, where detailed experiments and reliable models are available. We consider allosteric models of receptors' activity and derive analytically their steady-state probability distribution and correlation times.

Unraveling the influence of endothelial cell density on VEGF-A signaling.

Vascular endothelial growth factor-A (VEGF) is the master determinant for the activation of the angiogenic program leading to the formation of new blood vessels to sustain solid tumor growth and metastasis. VEGF specific binding to VEGF receptor-2 (VEGFR-2) triggers different signaling pathways, including phospholipase C-γ (PLC-γ) and Akt cascades, crucial for endothelial proliferation, permeability, and survival. By combining biologic experiments, theoretical insights, and mathematical modeling, we found that: (1) cell density influences VEGFR-2 protein level, as receptor number is 2-fold higher in long-confluent than in sparse cells; (2) cell density affects VEGFR-2 activation by reducing its affinity for VEGF in long-confluent cells; (3) despite reduced ligand-receptor affinity, high VEGF concentrations provide long-confluent cells with a larger amount of active receptors; (4) PLC-γ and Akt are not directly sensitive to cell density but simply transduce downstream the upstream difference in VEGFR-2 protein level and activation; and (5) the mathematical model correctly predicts the existence of at least one protein tyrosine phosphatase directly targeting PLC-γ and counteracting the receptor-mediated signal.

Noninvasive inference of the molecular chemotactic response using bacterial trajectories.

The quality of sensing and response to external stimuli constitutes a basic element in the selective performance of living organisms. Here we consider the response of Escherichia coli to chemical stimuli. For moderate amplitudes, the bacterial response to generic profiles of sensed chemicals is reconstructed from its response function to an impulse, which then controls the efficiency of bacterial motility.

Turbulence in more than two and less than three dimensions.

We investigate the behavior of turbulent systems in geometries with one compactified dimension. A novel phenomenological scenario dominated by the splitting of the turbulent cascade emerges both from the theoretical analysis of passive scalar turbulence and from direct numerical simulations of Navier-Stokes turbulence.