22,813 research outputs found
Cell death and life in cancer: mathematical modeling of cell fate decisions
Tumor development is characterized by a compromised balance between cell life
and death decision mechanisms, which are tighly regulated in normal cells.
Understanding this process provides insights for developing new treatments for
fighting with cancer. We present a study of a mathematical model describing
cellular choice between survival and two alternative cell death modalities:
apoptosis and necrosis. The model is implemented in discrete modeling formalism
and allows to predict probabilities of having a particular cellular phenotype
in response to engagement of cell death receptors. Using an original parameter
sensitivity analysis developed for discrete dynamic systems, we determine the
critical parameters affecting cellular fate decision variables that appear to
be critical in the cellular fate decision and discuss how they are exploited by
existing cancer therapies
Platonic model of mind as an approximation to neurodynamics
Hierarchy of approximations involved in simplification of microscopic theories, from sub-cellural to the whole brain level, is presented. A new approximation to neural dynamics is described, leading to a Platonic-like model of mind based on psychological spaces. Objects and events in these spaces correspond to quasi-stable states of brain dynamics and may be interpreted from psychological point of view. Platonic model bridges the gap between neurosciences and psychological sciences. Static and dynamic versions of this model are outlined and Feature Space Mapping, a neurofuzzy realization of the static version of Platonic model, described. Categorization experiments with human subjects are analyzed from the neurodynamical and Platonic model points of view
Introduction to Focus Issue : Dynamics in Systems Biology
Peer reviewedPublisher PD
COMPUTER SIMULATION AND COMPUTABILITY OF BIOLOGICAL SYSTEMS
The ability to simulate a biological organism by employing a computer is related to the
ability of the computer to calculate the behavior of such a dynamical system, or the "computability" of the system.* However, the two questions of computability and simulation are not equivalent. Since the question of computability can be given a precise answer in terms of recursive functions, automata theory and dynamical systems, it will be appropriate to consider it first. The more elusive question of adequate simulation of biological systems by a computer will be then addressed and a possible connection between the two answers given will be considered. A conjecture is formulated that suggests the possibility of employing an algebraic-topological, "quantum" computer (Baianu, 1971b)
for analogous and symbolic simulations of biological systems that may include chaotic processes that are not, in genral, either recursively or digitally computable. Depending on the biological network being modelled, such as the Human Genome/Cell Interactome or a trillion-cell Cognitive Neural Network system, the appropriate logical structure for such simulations might be either the Quantum MV-Logic (QMV) discussed in recent publications (Chiara, 2004, and references cited therein)or Lukasiewicz Logic Algebras that were shown to be isomorphic to MV-logic algebras (Georgescu et al, 2001)
Using synchronous Boolean networks to model several phenomena of collective behavior
In this paper, we propose an approach for modeling and analysis of a number
of phenomena of collective behavior. By collectives we mean multi-agent systems
that transition from one state to another at discrete moments of time. The
behavior of a member of a collective (agent) is called conforming if the
opinion of this agent at current time moment conforms to the opinion of some
other agents at the previous time moment. We presume that at each moment of
time every agent makes a decision by choosing from the set {0,1} (where
1-decision corresponds to action and 0-decision corresponds to inaction). In
our approach we model collective behavior with synchronous Boolean networks. We
presume that in a network there can be agents that act at every moment of time.
Such agents are called instigators. Also there can be agents that never act.
Such agents are called loyalists. Agents that are neither instigators nor
loyalists are called simple agents. We study two combinatorial problems. The
first problem is to find a disposition of instigators that in several time
moments transforms a network from a state where a majority of simple agents are
inactive to a state with a majority of active agents. The second problem is to
find a disposition of loyalists that returns the network to a state with a
majority of inactive agents. Similar problems are studied for networks in which
simple agents demonstrate the contrary to conforming behavior that we call
anticonforming. We obtained several theoretical results regarding the behavior
of collectives of agents with conforming or anticonforming behavior. In
computational experiments we solved the described problems for randomly
generated networks with several hundred vertices. We reduced corresponding
combinatorial problems to the Boolean satisfiability problem (SAT) and used
modern SAT solvers to solve the instances obtained
Joint perceptual decision-making: a case study in explanatory pluralism.
Traditionally different approaches to the study of cognition have been viewed as competing explanatory frameworks. An alternative view, explanatory pluralism, regards different approaches to the study of cognition as complementary ways of studying the same phenomenon, at specific temporal and spatial scales, using appropriate methodological tools. Explanatory pluralism has been often described abstractly, but has rarely been applied to concrete cases. We present a case study of explanatory pluralism. We discuss three separate ways of studying the same phenomenon: a perceptual decision-making task (Bahrami et al., 2010), where pairs of subjects share information to jointly individuate an oddball stimulus among a set of distractors. Each approach analyzed the same corpus but targeted different units of analysis at different levels of description: decision-making at the behavioral level, confidence sharing at the linguistic level, and acoustic energy at the physical level. We discuss the utility of explanatory pluralism for describing this complex, multiscale phenomenon, show ways in which this case study sheds new light on the concept of pluralism, and highlight good practices to critically assess and complement approaches
Revisiting the Complexity of Stability of Continuous and Hybrid Systems
We develop a framework to give upper bounds on the "practical" computational
complexity of stability problems for a wide range of nonlinear continuous and
hybrid systems. To do so, we describe stability properties of dynamical systems
using first-order formulas over the real numbers, and reduce stability problems
to the delta-decision problems of these formulas. The framework allows us to
obtain a precise characterization of the complexity of different notions of
stability for nonlinear continuous and hybrid systems. We prove that bounded
versions of the stability problems are generally decidable, and give upper
bounds on their complexity. The unbounded versions are generally undecidable,
for which we give upper bounds on their degrees of unsolvability
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