14,458 research outputs found
The macroscopic effects of microscopic heterogeneity
Over the past decade, advances in super-resolution microscopy and
particle-based modeling have driven an intense interest in investigating
spatial heterogeneity at the level of single molecules in cells. Remarkably, it
is becoming clear that spatiotemporal correlations between just a few molecules
can have profound effects on the signaling behavior of the entire cell. While
such correlations are often explicitly imposed by molecular structures such as
rafts, clusters, or scaffolds, they also arise intrinsically, due strictly to
the small numbers of molecules involved, the finite speed of diffusion, and the
effects of macromolecular crowding. In this chapter we review examples of both
explicitly imposed and intrinsic correlations, focusing on the mechanisms by
which microscopic heterogeneity is amplified to macroscopic effect.Comment: 20 pages, 5 figures. To appear in Advances in Chemical Physic
A phenomenological approach to the simulation of metabolism and proliferation dynamics of large tumour cell populations
A major goal of modern computational biology is to simulate the collective
behaviour of large cell populations starting from the intricate web of
molecular interactions occurring at the microscopic level. In this paper we
describe a simplified model of cell metabolism, growth and proliferation,
suitable for inclusion in a multicell simulator, now under development
(Chignola R and Milotti E 2004 Physica A 338 261-6). Nutrients regulate the
proliferation dynamics of tumor cells which adapt their behaviour to respond to
changes in the biochemical composition of the environment. This modeling of
nutrient metabolism and cell cycle at a mesoscopic scale level leads to a
continuous flow of information between the two disparate spatiotemporal scales
of molecular and cellular dynamics that can be simulated with modern computers
and tested experimentally.Comment: 58 pages, 7 figures, 3 tables, pdf onl
The Evolution of Reaction-diffusion Controllers for Minimally Cognitive Agents
No description supplie
A framework for the local information dynamics of distributed computation in complex systems
The nature of distributed computation has often been described in terms of
the component operations of universal computation: information storage,
transfer and modification. We review the first complete framework that
quantifies each of these individual information dynamics on a local scale
within a system, and describes the manner in which they interact to create
non-trivial computation where "the whole is greater than the sum of the parts".
We describe the application of the framework to cellular automata, a simple yet
powerful model of distributed computation. This is an important application,
because the framework is the first to provide quantitative evidence for several
important conjectures about distributed computation in cellular automata: that
blinkers embody information storage, particles are information transfer agents,
and particle collisions are information modification events. The framework is
also shown to contrast the computations conducted by several well-known
cellular automata, highlighting the importance of information coherence in
complex computation. The results reviewed here provide important quantitative
insights into the fundamental nature of distributed computation and the
dynamics of complex systems, as well as impetus for the framework to be applied
to the analysis and design of other systems.Comment: 44 pages, 8 figure
Spatiotemporal visualization of subcellular dynamics of carbon nanotubes
To date, there is no consensus on the relationship between the physicochemical characteristics of carbon nanotubes (CNTs) and their biological behavior; however, there is growing evidence that the versatile characteristics make their biological fate largely unpredictable and remain an issue of limited knowledge. Here we introduce an experimental methodology for tracking and visualization of post-uptake behavior and the intracellular fate of CNTs based on the spatial distribution of diffusion values throughout the plant cell. By using raster scan image correlation spectroscopy (RICS), we were able to generate highly quantitative spatial maps of CNTs diffusion in different cell compartments. The spatial map of diffusion values revealed that the uptake of CNTs is associated with important subcellular events such as carrier-mediated vacuolar transport and autophagy. These results show that RICS is a useful methodology to elucidate the intracellular behavior mechanisms of carbon nanotubes and potentially other fluorescently labeled nanoparticles, which is of relevance for the important issues related to the environmental impact and health hazards
Design for a Darwinian Brain: Part 1. Philosophy and Neuroscience
Physical symbol systems are needed for open-ended cognition. A good way to
understand physical symbol systems is by comparison of thought to chemistry.
Both have systematicity, productivity and compositionality. The state of the
art in cognitive architectures for open-ended cognition is critically assessed.
I conclude that a cognitive architecture that evolves symbol structures in the
brain is a promising candidate to explain open-ended cognition. Part 2 of the
paper presents such a cognitive architecture.Comment: Darwinian Neurodynamics. Submitted as a two part paper to Living
Machines 2013 Natural History Museum, Londo
Verticalization of bacterial biofilms
Biofilms are communities of bacteria adhered to surfaces. Recently, biofilms
of rod-shaped bacteria were observed at single-cell resolution and shown to
develop from a disordered, two-dimensional layer of founder cells into a
three-dimensional structure with a vertically-aligned core. Here, we elucidate
the physical mechanism underpinning this transition using a combination of
agent-based and continuum modeling. We find that verticalization proceeds
through a series of localized mechanical instabilities on the cellular scale.
For short cells, these instabilities are primarily triggered by cell division,
whereas long cells are more likely to be peeled off the surface by nearby
vertical cells, creating an "inverse domino effect". The interplay between cell
growth and cell verticalization gives rise to an exotic mechanical state in
which the effective surface pressure becomes constant throughout the growing
core of the biofilm surface layer. This dynamical isobaricity determines the
expansion speed of a biofilm cluster and thereby governs how cells access the
third dimension. In particular, theory predicts that a longer average cell
length yields more rapidly expanding, flatter biofilms. We experimentally show
that such changes in biofilm development occur by exploiting chemicals that
modulate cell length.Comment: Main text 10 pages, 4 figures; Supplementary Information 35 pages, 15
figure
- …