Related papers: Optimal metabolic pathway activation
Optimizing paths on networks is crucial for many applications, from subway traffic to Internet communication. As global path optimization that takes account of all path-choices simultaneously is computationally hard, most existing routing…
While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior…
We investigate how to control optimally a traffic flow through a junction on the line by acting only on speed reduction or traffic light at the junction. We show the existence of an optimal control and, under structure assumptions, provide…
The effective use of limited resources for controlling spreading processes on networks is of prime significance in diverse contexts, ranging from the identification of "influential spreaders" for maximizing information dissemination and…
In proliferating cell populations, adaptive changes to biochemical reactions can change a cell's division time, which in turn can change the population size. However, biochemical reactions are subject to noise, and therefore the conditions…
Locomotion is essential for living cells. It enables bacteria and algae to explore space for food, cancer to spread, and immune system to fight infections. Motile cells display trajectories of intriguing complexity, from regular (e.g.…
We investigate dynamics of activated escape in periodically modulated systems. The trajectories followed in escape form diffusion broadened tubes, which are periodically repeated in time. We show that these tubes can be directly observed…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Unraveling the structure of complex biological networks and relating it to their functional role is an important task in systems biology. Here we attempt to characterize the functional organization of the large-scale metabolic networks of…
The question of how "smart" active agents, like insects, microorganisms, or future colloidal robots need to steer to optimally reach or discover a target, such as an odor source, food, or a cancer cell in a complex environment has recently…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
A simple model is studied for the chemotactic movement of biological cells in the presence of a periodic chemical wave. It incorporates the feature of adaptation that may play an important role in allowing for ``rectified" chemotaxis:…
The control of active colloidal particles via optical traps is a cornerstone for research of matter at the micron and nanometer scale. A central challenge in this domain is the derivation of optimal transport protocols that minimize the…
Transport of molecules across membrane channels is investigated theoretically using exactly solvable discrete stochastic site-binding models. It is shown that the interaction potential between molecules and the channel has a strong effect…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
In this paper we present a method for automatically generating optimal robot trajectories satisfying high level mission specifications. The motion of the robot in the environment is modeled as a general transition system, enhanced with…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
For a small system like a colloidal particle or a single biomolecule embedded in a heat bath, the optimal protocol of an external control parameter minimizes the mean work required to drive the system from one given equilibrium state to…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…