15,024 research outputs found
The Kinetic Basis of Morphogenesis
It has been shown recently (Shalygo, 2014) that stationary and dynamic
patterns can arise in the proposed one-component model of the analog
(continuous state) kinetic automaton, or kinon for short, defined as a
reflexive dynamical system with active transport. This paper presents
extensions of the model, which increase further its complexity and tunability,
and shows that the extended kinon model can produce spatio-temporal patterns
pertaining not only to pattern formation but also to morphogenesis in real
physical and biological systems. The possible applicability of the model to
morphogenetic engineering and swarm robotics is also discussed.Comment: 8 pages. Submitted to the 13th European Conference on Artificial Life
(ECAL-2015) on March 10, 2015. Accepted on April 28, 201
Morphogenesis and proportionate growth: A finite element investigation of surface growth with coupled diffusion
Modeling the spontaneous evolution of morphology in natural systems and its
preservation by proportionate growth remains a major scientific challenge. Yet,
it is conceivable that if the basic mechanisms of growth and the coupled
kinetic laws that orchestrate their function are accounted for, a minimal
theoretical model may exhibit similar growth behaviors. The ubiquity of surface
growth, a mechanism by which material is added or removed on the boundaries of
the body, has motivated the development of theoretical models, which can
capture the diffusion-coupled kinetics that govern it. However, due to their
complexity, application of these models has been limited to simplified
geometries. In this paper, we tackle these complexities by developing a finite
element framework to study the diffusion-coupled growth and morphogenesis of
finite bodies formed on uniform and flat substrates. We find that in this
simplified growth setting, the evolving body exhibits a sequence of distinct
growth stages that are reminiscent of natural systems, and appear spontaneously
without any externally imposed regulation or coordination. The computational
framework developed in this work can serve as the basis for future models that
are able to account for growth in arbitrary geometrical settings, and can shed
light on the basic physical laws that orchestrate growth and morphogenesis in
the natural world
Phase differences in reaction-diffusion-advection systems and applications to morphogenesis
The authors study the effect of advection on reaction-diffusion patterns. It is shown that the addition of advection to a two-variable reaction–diffusion system with periodic boundary conditions results in the appearance of a phase difference between the patterns of the two variables which depends on the difference between the advection coefficients. The spatial patterns move like a travelling wave with a fixed velocity which depends on the sum of the advection coefficients. By a suitable choice of advection coefficients, the solution can be made stationary in time. In the presence of advection a continuous change in the diffusion coefficients can result in two Turing-type bifurcations as the diffusion ratio is varied, and such a bifurcation can occur even when the inhibitor species does not diffuse. It is also shown that the initial mode of bifurcation for a given domain size depends on both the advection and diffusion coefficients. These phenomena are demonstrated in the numerical solution of a particular reaction–diffusion system, and finally a possible application of the results to pattern formation in Drosophila larvae is discussed
The Kinetic Basis of Self-Organized Pattern Formation
In his seminal paper on morphogenesis (1952), Alan Turing demonstrated that
different spatio-temporal patterns can arise due to instability of the
homogeneous state in reaction-diffusion systems, but at least two species are
necessary to produce even the simplest stationary patterns. This paper is aimed
to propose a novel model of the analog (continuous state) kinetic automaton and
to show that stationary and dynamic patterns can arise in one-component
networks of kinetic automata. Possible applicability of kinetic networks to
modeling of real-world phenomena is also discussed.Comment: 8 pages, submitted to the 14th International Conference on the
Synthesis and Simulation of Living Systems (Alife 14) on 23.03.2014, accepted
09.05.201
Tuning the kinetics of cadherin adhesion.
Cadherins are Ca(2+)-dependent cell-cell adhesion proteins that maintain the structural integrity of the epidermis; their principle function is to resist mechanical force. This review summarizes the biophysical mechanisms by which classical cadherins tune adhesion and withstand mechanical stress. We first relate the structure of classical cadherins to their equilibrium binding properties. We then review the role of mechanical perturbations in tuning the kinetics of cadherin adhesion. In particular, we highlight recent studies that show that cadherins form three types of adhesive bonds: catch bonds, which become longer lived and lock in the presence of tensile force; slip bonds, which become shorter lived when pulled; and ideal bonds, which are insensitive to tugging
Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster
Background: Reaction-diffusion systems are frequently used in systems biology to model developmental and signalling processes. In many applications, count numbers of the diffusing molecular species are very low, leading to the need to explicitly model the inherent variability using stochastic methods. Despite their importance and frequent use, parameter estimation for both deterministic and stochastic reaction-diffusion systems is still a challenging problem.
Results: We present a Bayesian inference approach to solve both the parameter and state estimation problem for stochastic reaction-diffusion systems. This allows a determination of the full posterior distribution of the parameters (expected values and uncertainty). We benchmark the method by illustrating it on a simple synthetic experiment. We then test the method on real data about the diffusion of the morphogen Bicoid in Drosophila melanogaster. The results show how the precision with which parameters can be inferred varies dramatically, indicating that the ability to infer full posterior distributions on the parameters can have important experimental design consequences.
Conclusions: The results obtained demonstrate the feasibility and potential advantages of applying a Bayesian approach to parameter estimation in stochastic reaction-diffusion systems. In particular, the ability to estimate credibility intervals associated with parameter estimates can be precious for experimental design. Further work, however, will be needed to ensure the method can scale up to larger problems
Synthetic Turing protocells: vesicle self-reproduction through symmetry-breaking instabilities
The reproduction of a living cell requires a repeatable set of chemical
events to be properly coordinated. Such events define a replication cycle,
coupling the growth and shape change of the cell membrane with internal
metabolic reactions. Although the logic of such process is determined by
potentially simple physico-chemical laws, the modeling of a full,
self-maintained cell cycle is not trivial. Here we present a novel approach to
the problem which makes use of so called symmetry breaking instabilities as the
engine of cell growth and division. It is shown that the process occurs as a
consequence of the breaking of spatial symmetry and provides a reliable
mechanism of vesicle growth and reproduction. Our model opens the possibility
of a synthetic protocell lacking information but displaying self-reproduction
under a very simple set of chemical reactions
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