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

Mode Repulsion and Mode Coupling in Random Lasers

We studied experimentally and theoretically the interaction of lasing modes in random media. In a homogeneously broadened gain medium, cross gain saturation leads to spatial repulsion of lasing modes. In an inhomogeneously broadened gain medium, mode repulsion occurs in the spectral domain. Some lasing modes are coupled through photon hopping or electron absorption and reemission. Under pulsed pumping, weak coupling of two modes leads to synchronization of their lasing action. Strong coupling of two lasing modes results in anti-phased oscillations of their intensities.Comment: 13 pages, 4 figure

The effect of universal maternal antenatal iron supplementation on neurodevelopment in offspring : a systematic review and meta-analysis

Funding One author (CJ) was funded by the Ministry of Health, Government of Sri Lanka. Availability of data and materials Supporting data can be obtained from the corresponding author.Peer reviewedPublisher PD

Spontaneous Glioblastoma Spheroid Infiltration of Early-Stage Cerebral Organoids Models Brain Tumor Invasion.

Organoid methodology provides a platform for the ex vivo investigation of the cellular and molecular mechanisms underlying brain development and disease. The high-grade brain tumor glioblastoma multiforme (GBM) is considered a cancer of unmet clinical need, in part due to GBM cell infiltration into healthy brain parenchyma, making complete surgical resection improbable. Modeling the process of GBM invasion in real time is challenging as it requires both tumor and neural tissue compartments. Here, we demonstrate that human GBM spheroids possess the ability to spontaneously infiltrate early-stage cerebral organoids (eCOs). The resulting formation of hybrid organoids demonstrated an invasive tumor phenotype that was distinct from noncancerous adult neural progenitor (NP) spheroid incorporation into eCOs. These findings provide a basis for the modeling and quantification of the GBM infiltration process using a stem-cell-based organoid approach, and may be used for the identification of anti-GBM invasion strategies

Who needs a stapling device for haemorrhoidectomy, if one has the radiofrequency device?

Peer reviewedPublisher PD

Factors influencing the catalytic oxidation of benzyl alcohol using supported phosphine-capped gold nanoparticles

Open Access Article. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.Two phosphine-stabilised gold clusters, Au101(PPh3)21Cl5 and Au9(PPh3)8(NO3)3, were deposited and activated on anatase TiO2 and fumed SiO2. These catalysts showed an almost complete oxidation of benzyl alcohol (>90%) within 3 hours at 80 °C and 3 bar O2 in methanol with a high substrate-to-metal molar ratio of 5800 and turn-over frequency of 0.65 s−1. Factors influencing catalytic activity were investigated, including metal–support interaction, effects of heat treatments, chemical composition of gold clusters, the size of gold nanoparticles and catalytic conditions. It was found that the anions present in gold clusters play a role in determining the catalytic activity in this reaction, with NO3− diminishing the catalytic activity. High catalytic activity was attributed to the formation of large gold nanoparticles (>2 nm) that coincides with partial removal of ligands which occurs during heat treatment and catalysis. Selectivity towards the formation of methyl benzoate can be tuned by selection of the reaction temperature. The catalysts were characterised using transmission electron microscopy, UV-vis diffuse reflectance spectroscopy and X-ray photoelectron spectroscopy