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