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

List Models of Procedure Learning

This paper presents a new theory of the initial stages of skill acquisition and then employs the theory to model current and future training programs for fight management systems (FMSs) in modern commercial airliners like the Boeing 777 and the Airbus A320. The theoretical foundations for the theory are a new synthesis of the literature on human memory and the latest version of the ACT-R theory of skill acquisition

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

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

Quantitative analysis of several random lasers

We prescribe the minimal set of experimental data and parameters that should be reported for random-laser experiments and models. This prescript allows for a quantitative comparison between different experiments, and for a criterion whether a model predicts the outcome of an experiment correctly. In none of more than 150 papers on random lasers that we found these requirements were fulfilled. We have nevertheless been able to analyze a number of published experimental results and recent experiments of our own. Using our method we determined that the most intriguing property of the random laser (spikes) is in fact remarkably similar for different random lasers.Comment: 3 pages, 1 figur

In Situ Localization and Characterization of Active Proteases in Chronically Inflamed and Healthy Human Gingival Tissues

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141400/1/jper1303.pd

Towards Better Integrators for Dissipative Particle Dynamics Simulations

Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compressibility and the diffusion coefficient. We assess the quality of these integration schemes, including variants based on a recently suggested self-consistent approach, and examine their relative performance. Implications of integrator-induced effects are discussed.Comment: 4 pages, 3 figures, 2 tables, accepted for publication in Phys. Rev. E (Rapid Communication), tentative publication issue: 01 Dec 200

Have greenhouse gases intensified the contrast between wet and dry regions?

While changes in land precipitation during the last 50 years have been attributed in part to human influences, results vary by season, are affected by data uncertainty and do not account for changes over ocean. One of the more physically robust responses of the water cycle to warming is the expected amplification of existing patterns of precipitation minus evaporation. Here, precipitation changes in wet and dry regions are analyzed from satellite data for 1988–2010, covering land and ocean. We derive fingerprints for the expected change from climate model simulations that separately track changes in wet and dry regions. The simulations used are driven with anthropogenic and natural forcings combined, and greenhouse gas forcing or natural forcing only. Results of detection and attribution analysis show that the fingerprint of combined external forcing is detectable in observations and that this intensification of the water cycle is partly attributable to greenhouse gas forcing

The Sustainable Path to a Circular Bioeconomy

This is the final version. Available on open access from Elsevier via the DOI in this recordCircular bioeconomy is gaining prominence in academic, policy, and industry contexts, linking circular economy and bioeconomy agendas in service of sustainability. However, it is at risk of developing in narrow, unsustainable ways. A sustainable path to circular bioeconomies must embrace diverse expert and stakeholder input, multiple solutions, and noneconomic value.European Union Horizon 2020University of NottinghamEngineering and Physical Sciences Research Council (EPSRC)Biotechnology and Biological Sciences Research Council (BBSRC)Economic and Social Research Council (ESRC)University of ManchesterResearch EnglandHub for Biotechnology in the Built Environment, Newcastle Universit