35 research outputs found
Transport on a Lattice with Dynamical Defects
Many transport processes in nature take place on substrates, often considered
as unidimensional lanes. These unidimensional substrates are typically
non-static: affected by a fluctuating environment, they can undergo
conformational changes. This is particularly true in biological cells, where
the state of the substrate is often coupled to the active motion of
macromolecular complexes, such as motor proteins on microtubules or ribosomes
on mRNAs, causing new interesting phenomena. Inspired by biological processes
such as protein synthesis by ribosomes and motor protein transport, we
introduce the concept of localized dynamical sites coupled to a driven lattice
gas dynamics. We investigate the phenomenology of transport in the presence of
dynamical defects and find a novel regime characterized by an intermittent
current and subject to severe finite-size effects. Our results demonstrate the
impact of the regulatory role of the dynamical defects in transport, not only
in biology but also in more general contexts
Mixed population of competing TASEPs with a shared reservoir of particles
We introduce a mean-field theoretical framework to describe multiple totally
asymmetric simple exclusion processes (TASEPs) with different lattice lengths,
entry and exit rates, competing for a finite reservoir of particles. We present
relations for the partitioning of particles between the reservoir and the
lattices: these relations allow us to show that competition for particles can
have non-trivial effects on the phase behavior of individual lattices. For a
system with non-identical lattices, we find that when a subset of lattices
undergoes a phase transition from low to high density, the entire set of
lattice currents becomes independent of total particle number. We generalize
our approach to systems with a continuous distribution of lattice parameters,
for which we demonstrate that measurements of the current carried by a single
lattice type can be used to extract the entire distribution of lattice
parameters. Our approach applies to populations of TASEPs with any distribution
of lattice parameters, and could easily be extended beyond the mean-field case.Comment: 12 pages, 8 figure
Multiple phase transitions in a system of exclusion processes with limited reservoirs of particles and fuel carriers
The TASEP is a paradigmatic model from non-equilibrium statistical physics,
which describes particles hopping along a lattice of discrete sites. The TASEP
is applicable to a broad range of different transport systems, but does not
consider the fact that in many such systems the availability of resources
required for the transport is limited. In this paper we extend the TASEP to
include the effect of a limited number of two different fundamental transport
resources: the hopping particles, and the "fuel carriers", which provide the
energy required to drive the system away from equilibrium. As as consequence,
the system's dynamics are substantially affected: a "limited resources" regime
emerges, where the current is limited by the rate of refuelling, and the usual
coexistence line between low and high particle density opens into a broad
region on the phase plane. Due to the combination of a limited amount of both
resources, multiple phase transitions are possible when increasing the exit
rate beta for a fixed entry rate alpha. This is a new feature that can only be
obtained by the inclusion of both kinds of limited resources. We also show that
the fluctuations in particle density in the LD and HD phases are unaffected by
fluctuations in the number of loaded fuel carriers, except by the fact that
when these fuel resources become limited, the particle hopping rate is severely
reduced
The Dynamics of Supply and Demand in mRNA Translation
We study the elongation stage of mRNA translation in eukaryotes and find that, in contrast to the assumptions of previous models, both the supply and the demand for tRNA resources are important for determining elongation rates. We find that increasing the initiation rate of translation can lead to the depletion of some species of aa-tRNA, which in turn can lead to slow codons and queueing. Particularly striking “competition” effects are observed in simulations of multiple species of mRNA which are reliant on the same pool of tRNA resources. These simulations are based on a recent model of elongation which we use to study the translation of mRNA sequences from the Saccharomyces cerevisiae genome. This model includes the dynamics of the use and recharging of amino acid tRNA complexes, and we show via Monte Carlo simulation that this has a dramatic effect on the protein production behaviour of the system
Effects of dialysis technique on the acute hypotension: a model-based study
The patient's tendency to develop acute hemodialysis-induced hypotension can be influenced by the choice of hemodialysis technique (dialysate composition, filter, convection/diffusion ratio, etc.). We examined the hypothesis that the dialysis technique affects the pressure behavior during the sessions complicated by hypotension by altering the short-term compensatory reflexes to hemodialysis-induced hypovolemia. Hypotension-prone subjects were studied both during sessions of conventional bicarbonate dialysis (BD) and during sessions of acetate-free biofiltration (AFB) complicated by hypotension (8 BD vs 8 AFB). (a) During BD hypotension occurred, on average, about 70 min earlier than in AFB treatments (hypotension time: 120 \ub1 66 min in BD vs 193 \ub1 26 min in AFB, p < 0.01), and (b) patients exhibited a major susceptibility to blood volume reduction (blood volume reduction at hypotension time: 127.17 \ub1 3.26% in BD vs 1210.88 \ub1 2.46% in AFB, p < 0.05). A mathematical model was used to analyze the efficacy of reflex compensatory mechanisms during hemodialysis sessions. Data analysis using the model indicated that during BD sessions all the compensatory mechanisms were almost inoperative, whereas during the AFB sessions residual compensatory reflexes were active. Model simulation demonstrated that hypotension occurred later in AFB because the residual compensatory capacity in AFB was able to maintain arterial pressure for higher blood volume reductions