Related papers: Optimal metabolic pathway activation
The coordinated and efficient distribution of limited resources by individual decisions is a fundamental, unsolved problem. When individuals compete for road capacities, time, space, money, goods, etc., they normally make decisions based on…
This paper explores a number of questions regarding optimal strategies evolved by viruses upon entry into a vertebrate host. The infected cell life cycle consists of a non-productively infected stage in which it is producing virions but not…
It has recently been shown that the minimum energy solution of the control problem for a linear system produces a control trajectory that is nonlocal. An issue then arises when the dynamics represents a linearization of the underlying…
In this paper, we address an optimal distributed control problem for a non-local model of phase-field type, describing the evolution of tumour cells in presence of a nutrient. The model couples a non-local and viscous Cahn-Hilliard equation…
Enzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo enhanced diffusion in the presence of their corresponding…
Biological systems display impressive capabilities in effectively responding to environmental signals in real time. There is increasing evidence that organisms may indeed be employing near optimal Bayesian calculations in their…
In this work, we investigate the optimal control problem for continuous-time Markov decision processes with the random impact of the environment. We provide conditions to show the existence of optimal controls under finite-horizon criteria.…
We study a statistical model describing the steady state distribution of the fluxes in a metabolic network. The resulting model on continuous variables can be solved by the cavity method. In particular analytical tractability is possible…
A spatio-temporal evolution of chemicals appearing in a reversible enzyme reaction and modelled by a four component reaction-diffusion system with the reaction terms obtained by the law of mass action is considered. The large time behaviour…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
In this paper, a reaction-diffusion system modeling injection of a chemotherapeutic drug on the surface of a living tissue during a treatment for cancer patients is studied. The system describes the interaction of the chemotherapeutic drug…
One of simplest examples of navigation found in nature is run-and-tumble chemotaxis. Tumbles reorient cells randomly, and cells can drift toward attractants or away from repellents by biasing the frequency of these events. The post-tumble…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
A problem studied in Systems Biology is how to find shortest paths in metabolic networks. Unfortunately, simple (i.e., graph theoretic) shortest paths do not properly reflect biochemical facts. An approach to overcome this issue is to use…
We give a framework for molecular multiphoton excitation process induced by an optimally designed electric field. The molecule is initially prepared in a coherent superposition state of two of its eigenfunctions. The relative phase of the…
We model the joint distribution of choice probabilities and decision times in binary choice tasks as the solution to a problem of optimal sequential sampling, where the agent is uncertain of the utility of each action and pays a constant…
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies…
We investigate the distributed planning of robot trajectories for optimal execution of cooperative tasks with time windows. In this setting, each task has a value and is completed if sufficiently many robots are simultaneously present at…
Current molecular dynamic simulations of biomolecules using multiple time steps to update the slowingly changing force are hampered by an instability occuring at time step equal to half the period of the fastest vibrating mode. This has…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…