Graph problems arising from parameter identification of discrete dynamical systems

This paper focuses on combinatorial feasibility and optimization problems that arise in the context of parameter identification of discrete dynamical systems. Given a candidate parametric model for a physical system and a set of experimental observations, the objective of parameter identification is to provide estimates of the parameter values for which the model can reproduce the experiments. To this end, we define a finite graph corresponding to the model, to each arc of which a set of parameters is associated. Paths in this graph are regarded as feasible only if the sets of parameters corresponding to the arcs of the path have nonempty intersection. We study feasibility and optimization problems on such feasible paths, focusing on computational complexity. We show that, under certain restrictions on the sets of parameters, some of the problems become tractable, whereas others are NP-hard. In a similar vein, we define and study some graph problems for experimental design, whose goal is to support the scientist in optimally designing new experiment

Statistical Mechanics and Information-Theoretic Perspectives on Complexity in the Earth System

Peer reviewedPublisher PD

Identification of control targets in Boolean molecular network models via computational algebra

Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. Experimentally, node manipulation requires technology to completely repress or fully activate a particular gene product while edge manipulations only require a drug that inactivates the interaction between two gene products. Results: This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network.Comment: 12 pages, 4 figures, 2 table

Quantum Gravity: Has Spacetime Quantum Properties?

The incompatibility between GR and QM is generally seen as a sufficient motivation for the development of a theory of Quantum Gravity. If - so a typical argumentation - QM gives a universally valid basis for the description of all natural systems, then the gravitational field should have quantum properties. Together with the arguments against semi-classical theories of gravity, this leads to a strategy which takes a quantization of GR as the natural avenue to Quantum Gravity. And a quantization of the gravitational field would in some sense correspond to a quantization of geometry. Spacetime would have quantum properties. But, this strategy will only be successful, if gravity is a fundamental interaction. - What, if gravity is instead an intrinsically classical phenomenon? Then, if QM is nevertheless fundamentally valid, gravity can not be a fundamental interaction. An intrinsically classical gravity in a quantum world would have to be an emergent, induced or residual, macroscopic effect, caused by other interactions. The gravitational field (as well as spacetime) would not have any quantum properties. A quantization of GR would lead to artifacts without any relation to nature. The serious problems of all approaches to Quantum Gravity that start from a direct quantization of GR or try to capture the quantum properties of gravity in form of a 'graviton' dynamics - together with the, meanwhile, rich spectrum of approaches to an emergent gravity and/or spacetime - make this latter option more and more interesting for the development of a theory of Quantum Gravity. The most advanced emergent gravity (and spacetime) scenarios are of an information-theoretical, quantum-computational type.Comment: 31 page