Observability and Synchronization of Neuron Models

Observability is the property that enables to distinguish two different locations in $n$-dimensional state space from a reduced number of measured variables, usually just one. In high-dimensional systems it is therefore important to make sure that the variable recorded to perform the analysis conveys good observability of the system dynamics. In the case of networks composed of neuron models, the observability of the network depends nontrivially on the observability of the node dynamics and on the topology of the network. The aim of this paper is twofold. First, a study of observability is conducted using four well-known neuron models by computing three different observability coefficients. This not only clarifies observability properties of the models but also shows the limitations of applicability of each type of coefficients in the context of such models. Second, a multivariate singular spectrum analysis (M-SSA) is performed to detect phase synchronization in networks composed by neuron models. This tool, to the best of the authors' knowledge has not been used in the context of networks of neuron models. It is shown that it is possible to detect phase synchronization i)~without having to measure all the state variables, but only one from each node, and ii)~without having to estimate the phase

A new SSI algorithm for LPTV systems: Application to a hinged-bladed helicopter

Many systems such as turbo-generators, wind turbines and helicopters show intrinsic time-periodic behaviors. Usually, these structures are considered to be faithfully modeled as linear time-invariant (LTI). In some cases where the rotor is anisotropic, this modeling does not hold and the equations of motion lead necessarily to a linear periodically time- varying (referred to as LPTV in the control and digital signal field or LTP in the mechanical and nonlinear dynamics world) model. Classical modal analysis methodologies based on the classical time-invariant eigenstructure (frequencies and damping ratios) of the system no more apply. This is the case in particular for subspace methods. For such time-periodic systems, the modal analysis can be described by characteristic exponents called Floquet multipliers. The aim of this paper is to suggest a new subspace-based algorithm that is able to extract these multipliers and the corresponding frequencies and damping ratios. The algorithm is then tested on a numerical model of a hinged-bladed helicopter on the ground

Input-dependent structural identifiability of nonlinear systems

A dynamic model is structurally identifiable if it is possible to infer its unknown parameters by observing its output. Structural identifiability depends on the system dynamics, output, and input, as well as on the specific values of initial conditions and parameters. Here we present a symbolic method that characterizes the input that a model requires to be structurally identifiable. It determines which derivatives must be non-zero in order to have a sufficiently exciting input. Our approach considers structural identifiability as a generalization of nonlinear observability and incorporates extended Lie derivatives. The methodology assesses structural identifiability for time-varying inputs and, additionally, it can be used to determine the input profile that is required to make the parameters structurally locally identifiable. Furthermore, it is sometimes possible to replace an experiment with time-varying input with multiple experiments with constant inputs. We implement the resulting method as a MATLAB toolbox named STRIKE-GOLDD2. This tool can assist in the design of new experiments for the purpose of parameter estimation

A mathematical model for breath gas analysis of volatile organic compounds with special emphasis on acetone

Recommended standardized procedures for determining exhaled lower respiratory nitric oxide and nasal nitric oxide have been developed by task forces of the European Respiratory Society and the American Thoracic Society. These recommendations have paved the way for the measurement of nitric oxide to become a diagnostic tool for specific clinical applications. It would be desirable to develop similar guidelines for the sampling of other trace gases in exhaled breath, especially volatile organic compounds (VOCs) which reflect ongoing metabolism. The concentrations of water-soluble, blood-borne substances in exhaled breath are influenced by: (i) breathing patterns affecting gas exchange in the conducting airways; (ii) the concentrations in the tracheo-bronchial lining fluid; (iii) the alveolar and systemic concentrations of the compound. The classical Farhi equation takes only the alveolar concentrations into account. Real-time measurements of acetone in end-tidal breath under an ergometer challenge show characteristics which cannot be explained within the Farhi setting. Here we develop a compartment model that reliably captures these profiles and is capable of relating breath to the systemic concentrations of acetone. By comparison with experimental data it is inferred that the major part of variability in breath acetone concentrations (e.g., in response to moderate exercise or altered breathing patterns) can be attributed to airway gas exchange, with minimal changes of the underlying blood and tissue concentrations. Moreover, it is deduced that measured end-tidal breath concentrations of acetone determined during resting conditions and free breathing will be rather poor indicators for endogenous levels. Particularly, the current formulation includes the classical Farhi and the Scheid series inhomogeneity model as special limiting cases.Comment: 38 page

Observability of Minimal Cell Models

Identifying and modeling of biological systems is very useful to understand cell's dynamic. To know what really happens inside the cell we need to observe the state of a cell. In fact observability is a structural property of a control system defined as the possibility to deduce the state of the system from observing its input-output behavior. Any complex cell model is a combination of some minimal models which are simpler than complex cell model because they have two dimensions. These models can describe the behavior of the cell. The property of observability for nonlinear systems is very useful in analyzing such systems. This paper deals with the observability of minimal cell models. Based on the fact that the minimal cell models are nonlinear, analyzing the property of these models need nonlinear methods. The method has been used for observability is Lie Derivative. The results indicate observability of minimal cell models

No entailing laws, but enablement in the evolution of the biosphere

Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phenotypes, niches, ecosystems. We wish to argue that the evolution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon discussing the variability of the very "contexts of life": the interactions between organisms, biological niches and ecosystems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead of time the "niches" which constitute the boundary conditions on selection. More generally, by the mathematical unprestatability of the "phase space" (space of possibilities), no laws of motion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound conceptual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of (theoretical) symmetries as invariant preserving transformations will allow us to understand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of "enablement". This will restrict causal analyses to differential cases (a difference that causes a difference). Mutations or other causal differences will allow us to stress that "non conservation principles" are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as symmetries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to "extended criticality" as a conceptual frame for a better understanding of the living state of matter

Machine learning and mapping algorithms applied to proteomics problems

Proteins provide evidence that a given gene is expressed, and machine learning algorithms can be applied to various proteomics problems in order to gain information about the underlying biology. This dissertation applies machine learning algorithms to proteomics data in order to predict whether or not a given peptide is observable by mass spectrometry, whether a given peptide can serve as a cell penetrating peptide, and then utilizes the peptides observed through mass spectrometry to aid in the structural annotation of the chicken genome. Peptides observed by mass spectrometry are used to identify proteins, and being able to accurately predict which peptides will be seen can allow researchers to analyze to what extent a given protein is observable. Cell penetrating peptides can possibly be utilized to allow targeted small molecule delivery across cellular membranes and possibly serve a role as drug delivery peptides. Peptides and proteins identified through mass spectrometry can help refine computational gene models and improve structural genome annotations