6,693 research outputs found
Efficiency at maximum power of interacting molecular machines
We investigate the efficiency of systems of molecular motors operating at
maximum power. We consider two models of kinesin motors on a microtubule: for
both the simplified and the detailed model, we find that the many-body
exclusion effect enhances the efficiency at maximum power of the many-motor
system, with respect to the single motor case. Remarkably, we find that this
effect occurs in a limited region of the system parameters, compatible with the
biologically relevant range.Comment: To appear in Phys. Rev. Let
Molecular Electroporation and the Transduction of Oligoarginines
Certain short polycations, such as TAT and polyarginine, rapidly pass through
the plasma membranes of mammalian cells by an unknown mechanism called
transduction as well as by endocytosis and macropinocytosis. These
cell-penetrating peptides (CPPs) promise to be medically useful when fused to
biologically active peptides. I offer a simple model in which one or more CPPs
and the phosphatidylserines of the inner leaflet form a kind of capacitor with
a voltage in excess of 180 mV, high enough to create a molecular electropore.
The model is consistent with an empirical upper limit on the cargo peptide of
40--60 amino acids and with experimental data on how the transduction of a
polyarginine-fluorophore into mouse C2C12 myoblasts depends on the number of
arginines in the CPP and on the CPP concentration. The model makes three
testable predictions.Comment: 15 pages, 5 figure
Non-equilibrium mechanics and dynamics of motor activated gels
The mechanics of cells is strongly affected by molecular motors that generate
forces in the cellular cytoskeleton. We develop a model for cytoskeletal
networks driven out of equilibrium by molecular motors exerting transient
contractile stresses. Using this model we show how motor activity can
dramatically increase the network's bulk elastic moduli. We also show how motor
binding kinetics naturally leads to enhanced low-frequency stress fluctuations
that result in non-equilibrium diffusive motion within an elastic network, as
seen in recent \emph{in vitro} and \emph{in vivo} experiments.Comment: 21 pages, 8 figure
Shocks in asymmetric simple exclusion processes of interacting particles
In this paper, we study shocks and related transitions in asymmetric simple
exclusion processes of particles with nearest neighbor interactions. We
consider two kinds of inter-particle interactions. In one case, the
particle-hole symmetry is broken due to the interaction. In the other case,
particles have an effective repulsion due to which the particle-current-density
drops down near the half filling. These interacting particles move on a one
dimensional lattice which is open at both the ends with injection of particles
at one end and withdrawal of particles at the other. In addition to this, there
are possibilities of attachments or detachments of particles to or from the
lattice with certain rates. The hydrodynamic equation that involves the exact
particle current-density of the particle conserving system and additional terms
taking care of the attachment-detachment kinetics is studied using the
techniques of boundary layer analysis.Comment: 10 pages, 8 figure
Ergodic and Nonergodic Anomalous Diffusion in Coupled Stochastic Processes
Inspired by problems in biochemical kinetics, we study statistical properties
of an overdamped Langevin process whose friction coefficient depends on the
state of a similar, unobserved process. Integrating out the latter, we derive
the long time behaviour of the mean square displacement. Anomalous diffusion is
found. Since the diffusion exponent can not be predicted using a simple scaling
argument, anomalous scaling appears as well. We also find that the coupling can
lead to ergodic or non-ergodic behaviour of the studied process. We compare our
theoretical predictions with numerical simulations and find an excellent
agreement. The findings caution against treating biochemical systems coupled
with unobserved dynamical degrees of freedom by means of standard, diffusive
Langevin descriptions
The LMA Classic™ as a conduit for tracheal intubation in adult patients: a review and practical guide
Unexpected difficulty in maintaining an open airway following induction of anaesthesia remains an ever-present hazard. Repetitive attempts at direct laryngoscopy and intubation are generally acknowledged to be inappropriate. The LMA Classic™ is recognised as a rescue ventilation device in failed intubation scenarios and its specific role is well defined in international airway management protocols. Should clinical conditions dictate the need for tracheal intubation following placement of an LMA Classic™, it may be retained to serve as a conduit for intubation. Utilising the LMA Classic™ as a conduit for intubation is considered a rescue manoeuvre, only resorted to when conventional methods such as direct laryngoscopy have failed. Therefore, it is important that this approach to intubation has a high success rate and that airway management specialists are familiar with the different available options, the relevant limitations and the pitfalls. A short description of the components of the LMA Classic™, specifically relating to its function as an intubating conduit, is provided in this review. Its limitations as a conduit are then listed, followed by a description of the most popular techniques of intubation via the LMA Classic™. By adhering to a number of basic principles outlined in this review, limitations may be overcome, pitfalls avoided, and an escape conduit added for the anaesthetist who is faced with a difficult-to-intubate airway.Keywords: laryngeal mask airway; intubation; intubating conduit; bougie; catheter; guidewire; failed intubation; difficult airwa
Development of an automatic system to monitor the performance of a dense medium (mineral) separation process
Includes bibliographical references.Dense Medium Separation (DMS) is a process used extensively in the minerals processing industry to separate dense from less dense material in a dense fluid. It may be considered to be a simple “sink-float” separation process. DMS is used on a large scale in South African coal, iron ore and diamond operations. There are, however, no commercially available systems that can determine the separation efficiency of a DMS process on-line. This presents severe problems to those operating DMS processes. The present study attempts to provide a measurement technique for on-line application
Clustering Coefficients of Protein-Protein Interaction Networks
The properties of certain networks are determined by hidden variables that
are not explicitly measured. The conditional probability (propagator) that a
vertex with a given value of the hidden variable is connected to k of other
vertices determines all measurable properties. We study hidden variable models
and find an averaging approximation that enables us to obtain a general
analytical result for the propagator. Analytic results showing the validity of
the approximation are obtained. We apply hidden variable models to
protein-protein interaction networks (PINs) in which the hidden variable is the
association free-energy, determined by distributions that depend on
biochemistry and evolution. We compute degree distributions as well as
clustering coefficients of several PINs of different species; good agreement
with measured data is obtained. For the human interactome two different
parameter sets give the same degree distributions, but the computed clustering
coefficients differ by a factor of about two. This shows that degree
distributions are not sufficient to determine the properties of PINs.Comment: 16 pages, 3 figures, in Press PRE uses pdflate
How does torsional rigidity affect the wrapping transition of a semiflexible chain around a spherical core?
We investigated the effect of torsional rigidity of a semiflexible chain on
the wrapping transition around a spherical core, as a model of nucleosome, the
fundamental unit of chromatin. Through molecular dynamics simulation, we show
that the torsional effect has a crucial effect on the chain wrapping around the
core under the topological constraints. In particular, the torsional stress (i)
induces the wrapping/unwrapping transition, and (ii) leads to a unique complex
structure with an antagonistic wrapping direction which never appears without
the topological constraints. We further examine the effect of the stretching
stress for the nucleosome model, in relation to the unique characteristic
effect of the torsional stress on the manner of wrapping
Time scale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria
We report molecular dynamics simulations of the segregation of two
overlapping chains in cylindrical confinement. We find that the entropic
repulsion between the chains can be sufficiently strong to cause segregation on
a time scale that is short compared to the one for diffusion. This result
implies that entropic driving forces are sufficiently strong to cause rapid
bacterial chromosome segregation.Comment: Minor changes. Added some references, corrected the labels in figure
6 and reformatted in two columns. Also added reference to published version
in PR
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