28,594 research outputs found
Intracellular transport driven by cytoskeletal motors: General mechanisms and defects
Cells are strongly out-of-equilibrium systems driven by continuous energy
supply. They carry out many vital functions requiring active transport of
various ingredients and organelles, some being small, others being large. The
cytoskeleton, composed of three types of filaments, determines the shape of the
cell and plays a role in cell motion. It also serves as a road network for the
so-called cytoskeletal motors. These molecules can attach to a cytoskeletal
filament, perform directed motion, possibly carrying along some cargo, and then
detach. It is a central issue to understand how intracellular transport driven
by molecular motors is regulated, in particular because its breakdown is one of
the signatures of some neuronal diseases like the Alzheimer.
We give a survey of the current knowledge on microtubule based intracellular
transport. We first review some biological facts obtained from experiments, and
present some modeling attempts based on cellular automata. We start with
background knowledge on the original and variants of the TASEP (Totally
Asymmetric Simple Exclusion Process), before turning to more application
oriented models. After addressing microtubule based transport in general, with
a focus on in vitro experiments, and on cooperative effects in the
transportation of large cargos by multiple motors, we concentrate on axonal
transport, because of its relevance for neuronal diseases. It is a challenge to
understand how this transport is organized, given that it takes place in a
confined environment and that several types of motors moving in opposite
directions are involved. We review several features that could contribute to
the efficiency of this transport, including the role of motor-motor
interactions and of the dynamics of the underlying microtubule network.
Finally, we discuss some still open questions.Comment: 74 pages, 43 figure
The Grand-Canonical Asymmetric Exclusion Process and the One-Transit Walk
The one-dimensional Asymmetric Exclusion Process (ASEP) is a paradigm for
nonequilibrium dynamics, in particular driven diffusive processes. It is
usually considered in a canonical ensemble in which the number of sites is
fixed. We observe that the grand-canonical partition function for the ASEP is
remarkably simple. It allows a simple direct derivation of the asymptotics of
the canonical normalization in various phases and of the correspondence with
One-Transit Walks recently observed by Brak et.al.Comment: Published versio
Maximizing Protein Translation Rate in the Ribosome Flow Model: the Homogeneous Case
Gene translation is the process in which intracellular macro-molecules,
called ribosomes, decode genetic information in the mRNA chain into the
corresponding proteins. Gene translation includes several steps. During the
elongation step, ribosomes move along the mRNA in a sequential manner and link
amino-acids together in the corresponding order to produce the proteins.
The homogeneous ribosome flow model(HRFM) is a deterministic computational
model for translation-elongation under the assumption of constant elongation
rates along the mRNA chain. The HRFM is described by a set of n first-order
nonlinear ordinary differential equations, where n represents the number of
sites along the mRNA chain. The HRFM also includes two positive parameters:
ribosomal initiation rate and the (constant) elongation rate. In this paper, we
show that the steady-state translation rate in the HRFM is a concave function
of its parameters. This means that the problem of determining the parameter
values that maximize the translation rate is relatively simple. Our results may
contribute to a better understanding of the mechanisms and evolution of
translation-elongation. We demonstrate this by using the theoretical results to
estimate the initiation rate in M. musculus embryonic stem cell. The underlying
assumption is that evolution optimized the translation mechanism.
For the infinite-dimensional HRFM, we derive a closed-form solution to the
problem of determining the initiation and transition rates that maximize the
protein translation rate. We show that these expressions provide good
approximations for the optimal values in the n-dimensional HRFM already for
relatively small values of n. These results may have applications for synthetic
biology where an important problem is to re-engineer genomic systems in order
to maximize the protein production rate
When is a bottleneck a bottleneck?
Bottlenecks, i.e. local reductions of capacity, are one of the most relevant
scenarios of traffic systems. The asymmetric simple exclusion process (ASEP)
with a defect is a minimal model for such a bottleneck scenario. One crucial
question is "What is the critical strength of the defect that is required to
create global effects, i.e. traffic jams localized at the defect position".
Intuitively one would expect that already an arbitrarily small bottleneck
strength leads to global effects in the system, e.g. a reduction of the maximal
current. Therefore it came as a surprise when, based on computer simulations,
it was claimed that the reaction of the system depends in non-continuous way on
the defect strength and weak defects do not have a global influence on the
system. Here we reconcile intuition and simulations by showing that indeed the
critical defect strength is zero. We discuss the implications for the analysis
of empirical and numerical data.Comment: 8 pages, to appear in the proceedings of Traffic and Granular Flow
'1
Analyzing Linear Communication Networks using the Ribosome Flow Model
The Ribosome Flow Model (RFM) describes the unidirectional movement of
interacting particles along a one-dimensional chain of sites. As a site becomes
fuller, the effective entry rate into this site decreases. The RFM has been
used to model and analyze mRNA translation, a biological process in which
ribosomes (the particles) move along the mRNA molecule (the chain), and decode
the genetic information into proteins.
Here we propose the RFM as an analytical framework for modeling and analyzing
linear communication networks. In this context, the moving particles are
data-packets, the chain of sites is a one dimensional set of ordered buffers,
and the decreasing entry rate to a fuller buffer represents a kind of
decentralized backpressure flow control. For an RFM with homogeneous link
capacities, we provide closed-form expressions for important network metrics
including the throughput and end-to-end delay. We use these results to analyze
the hop length and the transmission probability (in a contention access mode)
that minimize the end-to-end delay in a multihop linear network, and provide
closed-form expressions for the optimal parameter values
Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms
Traffic-like collective movements are observed at almost all levels of
biological systems. Molecular motor proteins like, for example, kinesin and
dynein, which are the vehicles of almost all intra-cellular transport in
eukayotic cells, sometimes encounter traffic jam that manifests as a disease of
the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the
collagen fibrils of the extracellular matrix of vertebrates, has also been
observed in recent experiments. Traffic-like movements of social insects like
ants and termites on trails are, perhaps, more familiar in our everyday life.
Experimental, theoretical and computational investigations in the last few
years have led to a deeper understanding of the generic or common physical
principles involved in these phenomena. In particular, some of the methods of
non-equilibrium statistical mechanics, pioneered almost a hundred years ago by
Einstein, Langevin and others, turned out to be powerful theoretical tools for
quantitaive analysis of models of these traffic-like collective phenomena as
these systems are intrinsically far from equilibrium. In this review we
critically examine the current status of our understanding, expose the
limitations of the existing methods, mention open challenging questions and
speculate on the possible future directions of research in this
interdisciplinary area where physics meets not only chemistry and biology but
also (nano-)technology.Comment: 33 page Review article, REVTEX text, 29 EPS and PS figure
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