A continuous model for microtubule dynamics with catastrophe, rescue and nucleation processes

Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in the polymerization of microtubules from tubulin dimers. Our model is an extension of various mathematical models developed earlier formulated in order to capture and unify the various aspects of tubulin polymerization including the dynamic instability, growth of microtubules to saturation, time-localized periods of nucleation and depolymerization as well as synchronized oscillations exhibited by microtubules under various experimental conditions. Our model, while attempting to use a minimal number of adjustable parameters, covers a broad range of behaviors and has predictive features discussed in the paper. We have analyzed the resultant behaviors of the microtubules changing each of the parameter values at a time and observing the emergence of various dynamical regimes.Comment: 25 pages, 12 figure

Modeling the Effects of Drug Binding on the Dynamic Instability of Microtubules

We propose a stochastic model that accounts for the growth, catastrophe and rescue processes of steady state microtubules assembled from MAP-free tubulin. Both experimentally and theoretically we study the perturbation of microtubule dynamic instability by S-methyl-D-DM1, a synthetic derivative of the microtubule-targeted agent maytansine and a potential anticancer agent. We find that to be an effective suppressor of microtubule dynamics a drug must primarily suppress the loss of GDP tubulin from the microtubule tip.Comment: 17 pages, 11 figures, to appear in Phys. Bio

High-Temperature Expansions of Bures and Fisher Information Priors

For certain infinite and finite-dimensional thermal systems, we obtain --- incorporating quantum-theoretic considerations into Bayesian thermostatistical investigations of Lavenda --- high-temperature expansions of priors over inverse temperature beta induced by volume elements ("quantum Jeffreys' priors) of Bures metrics. Similarly to Lavenda's results based on volume elements (Jeffreys' priors) of (classical) Fisher information metrics, we find that in the limit beta -> 0, the quantum-theoretic priors either conform to Jeffreys' rule for variables over [0,infinity], by being proportional to 1/beta, or to the Bayes-Laplace principle of insufficient reason, by being constant. Whether a system adheres to one rule or to the other appears to depend upon its number of degrees of freedom.Comment: Six pages, LaTeX. The title has been shortened (and then further modified), at the suggestion of a colleague. Other minor change

Analytic structure factors and pair-correlation functions for the unpolarized homogeneous electron gas

We propose a simple and accurate model for the electron static structure factors (and corresponding pair-correlation functions) of the 3D unpolarized homogeneous electron gas. Our spin-resolved pair-correlation function is built up with a combination of analytic constraints and fitting procedures to quantum Monte Carlo data, and, in comparison to previous attempts (i) fulfills more known integral and differential properties of the exact pair-correlation function, (ii) is analytic both in real and in reciprocal space, and (iii) accurately interpolates the newest, extensive diffusion-Monte Carlo data of Ortiz, Harris and Ballone [Phys. Rev. Lett. 82, 5317 (1999)]. This can be of interest for the study of electron correlations of real materials and for the construction of new exchange and correlation energy density functionals.Comment: 14 pages, 5 figures, submitted to Phys. Rev.

Cellular automata modelling of slime mould actin network signalling

© 2016, The Author(s). Actin is a cytoskeletal protein which forms dense, highly interconnected networks within eukaryotic cells. A growing body of evidence suggests that actin-mediated intra- and extracellular signalling is instrumental in facilitating organism-level emergent behaviour patterns which, crucially, may be characterised as natural expressions of computation. We use excitable cellular automata modelling to simulate signal transmission through cell arrays whose topology was extracted from images of Watershed transformation-derived actin network reconstructions; the actin networks sampled were from laboratory experimental observations of a model organism, slime mould Physarum polycephalum. Our results indicate that actin networks support directional transmission of generalised energetic phenomena, the amplification and trans-network speed of which of which is proportional to network density (whose primary determinant is the anatomical location of the network sampled). Furthermore, this model also suggests the ability of such networks for supporting signal-signal interactions which may be characterised as Boolean logical operations, thus indicating that a cell’s actin network may function as a nanoscale data transmission and processing network. We conclude by discussing the role of the cytoskeleton in facilitating intracellular computing, how computation can be implemented in such a network and practical considerations for designing ‘useful’ actin circuitry

The physics programme of the MoEDAL experiment at the LHC

The MoEDAL experiment at Point 8 of the LHC ring is the seventh and newest LHC experiment. It is dedicated to the search for highly-ionizing particle avatars of physics beyond the Standard Model, extending significantly the discovery horizon of the LHC. A MoEDAL discovery would have revolutionary implications for our fundamental understanding of the Microcosm. MoEDAL is an unconventional and largely passive LHC detector comprised of the largest array of Nuclear Track Detector stacks ever deployed at an accelerator, surrounding the intersection region at Point 8 on the LHC ring. Another novel feature is the use of paramagnetic trapping volumes to capture both electrically and magnetically charged highly-ionizing particles predicted in new physics scenarios. It includes an array of TimePix pixel devices for monitoring highly-ionizing particle backgrounds. The main passive elements of the MoEDAL detector do not require a trigger system, electronic readout, or online computerized data acquisition. The aim of this paper is to give an overview of the MoEDAL physics reach, which is largely complementary to the programs of the large multipurpose LHC detectors ATLAS and CMS

Structure–property relation and relevance of beam theories for microtubules: a coupled molecular and continuum mechanics study

Quasi-one-dimensional microtubules (MTs) in cells enjoy high axial rigidity but large transverse flexibility due to the inter-protofilament (PF) sliding. This study aims to explore the structure–property relation for MTs and examine the relevance of the beam theories to their unique features. A molecular structural mechanics (MSM) model was used to identify the origin of the inter-PF sliding and its role in bending and vibration of MTs. The beam models were then fitted to the MSM to reveal how they cope with the distinct mechanical responses induced by the inter-PF sliding. Clear evidence showed that the inter-PF sliding is due to the soft inter-PF bonds and leads to the length-dependent bending stiffness. The Euler beam theory is found to adequately describe MT deformation when the inter-PF sliding is largely prohibited. Nevertheless, neither shear deformation nor the nonlocal effect considered in the ‘more accurate’ beam theories can fully capture the effect of the inter-PF sliding. This reflects the distinct deformation mechanisms between an MT and its equivalent continuous body

Search for Magnetic Monopoles with the MoEDAL Forward Trapping Detector in 13 TeV Proton-Proton Collisions at the LHC

MoEDAL is designed to identify new physics in the form of long-lived highly ionizing particles produced in high-energy LHC collisions. Its arrays of plastic nuclear-track detectors and aluminium trapping volumes provide two independent passive detection techniques. We present here the results of a first search for magnetic monopole production in 13 TeV proton-proton collisions using the trapping technique, extending a previous publication with 8 TeV data during LHC Run 1. A total of 222 kg of MoEDAL trapping detector samples was exposed in the forward region and analyzed by searching for induced persistent currents after passage through a superconducting magnetometer. Magnetic charges exceeding half the Dirac charge are excluded in all samples and limits are placed for the first time on the production of magnetic monopoles in 13 TeV pp collisions. The search probes mass ranges previously inaccessible to collider experiments for up to five times the Dirac charge.Peer reviewe

Magnetic Monopole Search with the Full MoEDAL Trapping Detector in 13 TeV pp Collisions Interpreted in Photon-Fusion and Drell-Yan Production

MoEDAL is designed to identify new physics in the form of stable or pseudostable highly ionizing particles produced in high-energy Large Hadron Collider (LHC) collisions. Here we update our previous search for magnetic monopoles in Run 2 using the full trapping detector with almost four times more material and almost twice more integrated luminosity. For the first time at the LHC, the data were interpreted in terms of photon-fusion monopole direct production in addition to the Drell-Yan-like mechanism. The MoEDAL trapping detector, consisting of 794 kg of aluminum samples installed in the forward and lateral regions, was exposed to 4.0 fb(-1) of 13 TeV proton-proton collisions at the LHCb interaction point and analyzed by searching for induced persistent currents after passage through a superconducting magnetometer. Magnetic charges equal to or above the Dirac charge are excluded in all samples. Monopole spins 0, 1/2, and 1 are considered and both velocity-independent and-dependent couplings are assumed. This search provides the best current laboratory constraints for monopoles with magnetic charges ranging from two to five times the Dirac charge.Peer reviewe