Evaluating the Applicability of the Fokker-Planck Equation in Polymer Translocation: A Brownian Dynamics Study

Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N=21-61. The rate of translocation is controlled by a tunable friction coefficient, gamma_{0p}, for monomers inside the nanopore. In the case of unforced translocation, the mean translocation time scales with polymer length N as ~ (N-N_p)^alpha, where N_p is the average number of monomers in the nanopore. The exponent approaches the value alpha=2 when the pore friction is sufficiently high, in accord with the prediction for the case of the quasi-static regime where pore friction dominates. In the case of forced translocation, the polymer chain is stretched and compressed on the cis and trans sides, respectively, for low gamma_{0p}. However, the chain approaches conformational quasi-equilibrium for sufficiently large gamma_{0p}. In this limit the observed scaling of with driving force and chain length supports the FP prediction that is proportional to N/f_d for sufficiently strong driving force. Monte Carlo simulations are used to calculate translocation free energy functions for the system. The free energies are used with the Fokker-Planck equation to calculate translocation time distributions. At sufficiently high gamma_{0p}, the predicted distributions are in excellent agreement with those calculated from the BD simulations. Thus, the FP equation provides a valid description of translocation dynamics for sufficiently high pore friction for the range of polymer lengths considered here. Increasing N will require a corresponding increase in pore friction to maintain the validity of the FP approach. Outside the regime of low N and high pore friction, the polymer is out of equilibrium, and the FP approach is not valid.Comment: 13 pages, 11 figure

Polymer Translocation Dynamics in the Quasi-Static Limit

Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean translocation time scales with polymer length N according to \propto (N-N_p)^2, where N_p is the average number of monomers in the nanopore; this scaling is an indication of a quasi-static regime in which polymer-nanopore friction dominates. We use a multiple-histogram method to calculate the variation of the free energy with Q, a coordinate used to quantify the degree of translocation. The free energy functions are used with the Fokker-Planck formalism to calculate translocation time distributions in the quasi-static regime. These calculations also require a friction coefficient, characterized by a quantity N_{eff}, the effective number of monomers whose dynamics are affected by the confinement of the nanopore. This was determined by fixing the mean of the theoretical distribution to that of the distribution obtained from MC dynamics simulations. The theoretical distributions are in excellent quantitative agreement with the distributions obtained directly by the MC dynamics simulations for physically meaningful values of N_{eff}. The free energy functions for narrow-pore systems exhibit oscillations with an amplitude that is sensitive to the nanopore length. Generally, larger oscillation amplitudes correspond to longer translocation times.Comment: 13 pages, 13 figure

Particle In Cell Simulation of Combustion Synthesis of TiC Nanoparticles

A coupled continuum-discrete numerical model is presented to study the synthesis of TiC nanosized aggregates during a self-propagating combustion synthesis (SHS) process. The overall model describes the transient of the basic mechanisms governing the SHS process in a two-dimensional micrometer size geometry system. At each time step, the continuum (micrometer scale) model computes the current temperature field according to the prescribed boundary conditions. The overall system domain is discretized with a desired number of uniform computational cells. Each cell contains a convenient number of computation particles which represent the actual particles mixture. The particle-in-cell (discrete) model maps the temperature field from the (continuum) cells to the respective internal particles. Depending on the temperature reached by the cell, the titanium particles may undergo a solid-liquid transformation. If the distance between the carbon particle and the liquid titanium particles is within a certain tolerance they will react and a TiC particle will be formed in the cell. Accordingly, the molecular dynamic method will update the location of all particles in the cell and the amount of transformation heat accounted by the cell will be entered into the source term of the (continuum) heat conduction equation. The new temperature distribution will progress depending on the cells which will time-by-time undergo the chemical reaction. As a demonstration of the effectiveness of the overall model some paradigmatic examples are shown.Comment: submitted to Computer Physics Communication

Impact of Cholesterol on Voids in Phospholipid Membranes

Free volume pockets or voids are important to many biological processes in cell membranes. Free volume fluctuations are a prerequisite for diffusion of lipids and other macromolecules in lipid bilayers. Permeation of small solutes across a membrane, as well as diffusion of solutes in the membrane interior are further examples of phenomena where voids and their properties play a central role. Cholesterol has been suggested to change the structure and function of membranes by altering their free volume properties. We study the effect of cholesterol on the properties of voids in dipalmitoylphosphatidylcholine (DPPC) bilayers by means of atomistic molecular dynamics simulations. We find that an increasing cholesterol concentration reduces the total amount of free volume in a bilayer. The effect of cholesterol on individual voids is most prominent in the region where the steroid ring structures of cholesterol molecules are located. Here a growing cholesterol content reduces the number of voids, completely removing voids of the size of a cholesterol molecule. The voids also become more elongated. The broad orientational distribution of voids observed in pure DPPC is, with a 30% molar concentration of cholesterol, replaced by a distribution where orientation along the bilayer normal is favored. Our results suggest that instead of being uniformly distributed to the whole bilayer, these effects are localized to the close vicinity of cholesterol molecules

Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences

Local transmission of chikungunya virus (CHIKV) was first detected in the Americas in December 2013, after which it spread rapidly throughout the Caribbean islands and American mainland, causing a major chikungunya fever epidemic. Previous phylogenetic analysis of CHIKV from a limited number of countries in the Americas suggests that an Asian genotype strain was responsible, except in Brazil where both Asian and East/Central/South African (ECSA) lineage strains were detected. In this study, we sequenced thirty-three complete CHIKV genomes from viruses isolated in 2014 from fourteen Caribbean islands, the Bahamas and two mainland countries in the Americas. Phylogenetic analyses confirmed that they all belonged to the Asian genotype and clustered together with other Caribbean and mainland sequences isolated during the American outbreak, forming an 'Asian/American' lineage defined by two amino acid substitutions, E2 V368A and 6K L20M, and divided into two well-supported clades. This lineage is estimated to be evolving at a mean rate of 5 x 10-4 substitutions per site per year (95% higher probability density, 2.9-7.9 x 10-4) and to have arisen from an ancestor introduced to the Caribbean (most likely from Oceania) in about March 2013, 9 months prior to the first report of CHIKV in the Americas. Estimation of evolutionary rates for individual gene regions and selection analyses indicate that (in contrast to the Indian Ocean Lineage that emerged from the ECSA genotype followed by adaptive evolution and with a significantly higher substitution rate) the evolutionary dynamics of the Asian/American lineage are very similar to the rest of the Asian genotype and natural selection does not appear to have played a major role in its emergence. However, several codon sites with evidence of positive selection were identified within the non-structural regions of Asian genotype sequences outside of the Asian/American lineage

Detection of non-thermal X-ray emission in the lobes and jets of Cygnus A

This article has been published in Monthly Notices of the Royal Astronomical Society © 2018 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. 21 pages, 8 figuresWe present a spectral analysis of the lobes and X-ray jets of Cygnus A, using more than 2 Ms of $\textit{Chandra}$ observations. The X-ray jets are misaligned with the radio jets and significantly wider. We detect non-thermal emission components in both lobes and jets. For the eastern lobe and jet, we find 1 keV flux densities of $71_{-10}^{+10}$ nJy and $24_{-4}^{+4}$ nJy, and photon indices of $1.72_{-0.03}^{+0.03}$ and $1.64_{-0.04}^{+0.04}$ respectively. For the western lobe and jet, we find flux densities of $50_{-13}^{+12}$ nJy and $13_{-5}^{+5}$ nJy, and photon indices of $1.97_{-0.10}^{+0.23}$ and $1.86_{-0.12}^{+0.18}$ respectively. Using these results, we modeled the electron energy distributions of the lobes as broken power laws with age breaks. We find that a significant population of non-radiating particles is required to account for the total pressure of the eastern lobe. In the western lobe, no such population is required and the low energy cutoff to the electron distribution there needs to be raised to obtain pressures consistent with observations. This discrepancy is a consequence of the differing X-ray photon indices, which may indicate that the turnover in the inverse-Compton spectrum of the western lobe is at lower energies than in the eastern lobe. We modeled the emission from both jets as inverse-Compton emission. There is a narrow region of parameter space for which the X-ray jet can be a relic of an earlier active phase, although lack of knowledge about the jet's electron distribution and particle content makes the modelling uncertain.Peer reviewedFinal Published versio

Zero-point vacancies in quantum solids

A Jastrow wave function (JWF) and a shadow wave function (SWF) describe a quantum solid with Bose--Einstein condensate; i.e. a supersolid. It is known that both JWF and SWF describe a quantum solid with also a finite equilibrium concentration of vacancies x_v. We outline a route for estimating x_v by exploiting the existing formal equivalence between the absolute square of the ground state wave function and the Boltzmann weight of a classical solid. We compute x_v for the quantum solids described by JWF and SWF employing very accurate numerical techniques. For JWF we find a very small value for the zero point vacancy concentration, x_v=(1.4\pm0.1) x 10^-6. For SWF, which presently gives the best variational description of solid 4He, we find the significantly larger value x_v=(1.4\pm0.1) x 10^-3 at a density close to melting. We also study two and three vacancies. We find that there is a strong short range attraction but the vacancies do not form a bound state.Comment: 19 pages, submitted to J. Low Temp. Phy

Biological effects of a root conditioning agent for dentin surface modification in vitro

Purpose: Connective tissue reattachment to periodontally damaged root surfaces is one of the most important goals of periodontal therapy. The aim of this study was to develop a root conditioning agent that can demineralize and detoxify the infected root surface. Methods: Dentin slices obtained from human teeth were treated with a novel root planing agent for 2 minutes and then washed with phosphate-buffered saline. Smear layer removal and type I collagen exposure were observed by scanning electron microscopy (SEM) and type I collagen immunostaining, respectively. Cell attachment and lipopolysaccharides (LPS) removal demonstrated the efficiency of the root conditioning agent. Results: SEM revealed that the smear layer was entirely removed and the dentinal tubules were opened by the experimental gel. Type I collagen was exposed on the surfaces of the dentin slices treated by the experimental gel, which were compared with dentin treated with other root planing agents. Dentin slices treated with the experimental gel showed the highest number of attached fibroblasts and flattened cell morphology. The agar diffusion assay demonstrated that the experimental gel also has effective antimicrobial activity. Escherichia coli LPS were effectively removed from well plates by the experimental gel. Conclusions: These results demonstrated that this experimental gel is a useful tool for root conditioning of infected root surfaces and can also be applied for detoxification of ailing implant surface threads. ⓒ 2010 Korean Academy of Periodontology.

Molecular determinants for subcellular trafficking of the malarial sheddase PfSUB2.

The malaria merozoite invades erythrocytes in the vertebrate host. Iterative rounds of asexual intraerythrocytic replication result in disease. Proteases play pivotal roles in erythrocyte invasion, but little is understood about their mode of action. The Plasmodium falciparum malaria merozoite surface sheddase, PfSUB2, is one such poorly characterized example. We have examined the molecular determinants that underlie the mechanisms by which PfSUB2 is trafficked initially to invasion-associated apical organelles (micronemes) and then across the surface of the free merozoite. We show that authentic promoter activity is important for correct localization of PfSUB2, likely requiring canonical features within the intergenic region 5' of the pfsub2 locus. We further demonstrate that trafficking of PfSUB2 beyond an early compartment in the secretory pathway requires autocatalytic protease activity. Finally, we show that the PfSUB2 transmembrane domain is required for microneme targeting, while the cytoplasmic domain is essential for surface translocation of the protease to the parasite posterior following discharge from micronemes. The interplay of pre- and post-translational regulatory elements that coordinate subcellular trafficking of PfSUB2 provides the parasite with exquisite control over enzyme-substrate interactions