Search results for "Molecular network"
showing 10 items of 46 documents
On coincidence of feedback and global Stackelberg equilibria in a class of differential games
2021
This paper shows for a class of differential games that the global Stackelberg equilibrium (GSE) coincides with the feedback Stackelberg equilibrium (FSE), although the GSE assumes that the leader/regulator an- nounces at the initial time the regulatory instrument rule she will follow for the rest of the game, while in the FSE, the regulator at any time chooses the optimal level of the regulatory instrument rate. This coincidence is based on the fact that the FSE is calculated using dynamic programming what implies that although the regulator chooses the regulatory instrument rate level that maximizes social welfare, the first-order condition for the maximization of the right-hand side of t…
Organization and evolution of synthetic idiotypic networks
2012
We introduce a class of weighted graphs whose properties are meant to mimic the topological features of idiotypic networks, namely the interaction networks involving the B-core of the immune system. Each node is endowed with a bit-string representing the idiotypic specificity of the corresponding B cell and a proper distance between any couple of bit-strings provides the coupling strength between the two nodes. We show that a biased distribution of the entries in bit-strings can yield fringes in the (weighted) degree distribution, small-worlds features, and scaling laws, in agreement with experimental findings. We also investigate the role of ageing, thought of as a progressive increase in …
Well-resolved unusual alternating cyclic water tetramers embedded in a crystal host
2008
Infinite network involving two hydrogen-bonded tetrameric water rings (S4 and D2h) in a (4,4)-square grid crystal host
Theory of tailor automata
2019
Abstract In the paper, a fragment of the new theory of tailor automata is presented, within which a deterministic finite automaton was defined. The proposed automaton provides a theoretical model of an informally characterized biomolecular automaton. The idea of working of which is founded on the concept of alternating cut of some double-stranded fragments of DNA, with the use of a restriction enzyme and ligations of some double-stranded fragments of DNA, with the use of the ligase enzyme.
Hub-Centered Gene Network Reconstruction Using Automatic Relevance Determination
2012
Network inference deals with the reconstruction of biological networks from experimental data. A variety of different reverse engineering techniques are available; they differ in the underlying assumptions and mathematical models used. One common problem for all approaches stems from the complexity of the task, due to the combinatorial explosion of different network topologies for increasing network size. To handle this problem, constraints are frequently used, for example on the node degree, number of edges, or constraints on regulation functions between network components. We propose to exploit topological considerations in the inference of gene regulatory networks. Such systems are often…
Overload breakdown in models for photosynthesis
2015
In many models of the Calvin cycle of photosynthesis it is observed that there are solutions where concentrations of key substances belonging to the cycle tend to zero at late times, a phenomenon known as overload breakdown. In this paper we prove theorems about the existence and non-existence of solutions of this type and obtain information on which concentrations tend to zero when overload breakdown occurs. As a starting point we take a model of Pettersson and Ryde-Pettersson which seems to be prone to overload breakdown and a modification of it due to Poolman which was intended to avoid this effect.
Topics on n-ary algebras
2011
We describe the basic properties of two n-ary algebras, the Generalized Lie Algebras (GLAs) and, particularly, the Filippov (or n-Lie) algebras (FAs), and comment on their n-ary Poisson counterparts, the Generalized Poisson (GP) and Nambu-Poisson (N-P) structures. We describe the Filippov algebra cohomology relevant for the central extensions and infinitesimal deformations of FAs. It is seen that semisimple FAs do not admit central extensions and, moreover, that they are rigid. This extends the familiar Whitehead's lemma to all $n\geq 2$ FAs, n=2 being the standard Lie algebra case. When the n-bracket of the FAs is no longer required to be fully skewsymmetric one is led to the n-Leibniz (or…
The minimal model of Hahn for the Calvin cycle.
2018
There are many models of the Calvin cycle of photosynthesis in the literature. When investigating the dynamics of these models one strategy is to look at the simplest possible models in order to get the most detailed insights. We investigate a minimal model of the Calvin cycle introduced by Hahn while he was pursuing this strategy. In a variant of the model not including photorespiration it is shown that there exists exactly one positive steady state and that this steady state is unstable. For generic initial data either all concentrations tend to infinity at lates times or all concentrations tend to zero at late times. In a variant including photorespiration it is shown that for suitable v…
The Importance of Lipidomic Approach for Mapping and Exploring the Molecular Networks Underlying Physical Exercise: A Systematic Review
2021
Maintaining appropriate levels of physical exercise is an optimal way for keeping a good state of health. At the same time, optimal exercise performance necessitates an integrated organ system response. In this respect, physical exercise has numerous repercussions on metabolism and function of different organs and tissues by enhancing whole-body metabolic homeostasis in response to different exercise-related adaptations. Specifically, both prolonged and intensive physical exercise produce vast changes in multiple and different lipid-related metabolites. Lipidomic technologies allow these changes and adaptations to be clarified, by using a biological system approach they provide scientific u…
Relaxation of electronic excitations in LiNbO3crystals
2001
Transient absorption both in stoichiometric and Mg doped congruent LiNbO was observed after pulsed electron beam excitation. The luminescence spectra and decay kinetics in these materials show different excitonic relaxation possibilities. The dependence on sample stoichiometry is also discussed.