Critical evaluation of the computational methods used in the forced polymer translocation

In forced polymer translocation, the average translocation time, $\tau$, scales with respect to pore force, $f$, and polymer length, $N$, as $\tau \sim f^{-1} N^{\beta}$. We demonstrate that an artifact in Metropolis Monte Carlo method resulting in breakage of the force scaling with large $f$ may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent $\beta \le 1 + \nu$ is not universal, but depends on $f$. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and $\beta$ to arise solely from the initial polymer configuration

Cluster decomposition of full configuration interaction wave functions: a tool for chemical interpretation of systems with strong correlation

Approximate full configuration interaction (FCI) calculations have recently become tractable for systems of unforeseen size thanks to stochastic and adaptive approximations to the exponentially scaling FCI problem. The result of an FCI calculation is a weighted set of electronic configurations, which can also be expressed in terms of excitations from a reference configuration. The excitation amplitudes contain information on the complexity of the electronic wave function, but this information is contaminated by contributions from disconnected excitations, i.e. those excitations that are just products of independent lower-level excitations. The unwanted contributions can be removed via a cluster decomposition procedure, making it possible to examine the importance of connected excitations in complicated multireference molecules which are outside the reach of conventional algorithms. We present an implementation of the cluster decomposition analysis and apply it to both true FCI wave functions, as well as wave functions generated from the adaptive sampling CI (ASCI) algorithm. The cluster decomposition is useful for interpreting calculations in chemical studies, as a diagnostic for the convergence of various excitation manifolds, as well as as a guidepost for polynomially scaling electronic structure models. Applications are presented for (i) the double dissociation of water, (ii) the carbon dimer, (iii) the {\pi} space of polyacenes, as well as (iv) the chromium dimer. While the cluster amplitudes exhibit rapid decay with increasing rank for the first three systems, even connected octuple excitations still appear important in Cr$_2$, suggesting that spin-restricted single-reference coupled-cluster approaches may not be tractable for some problems in transition metal chemistry.Comment: 15 pages, 5 figure

Nanoplasmonics simulations at the basis set limit through completeness-optimized, local numerical basis sets

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate that the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.Comment: 11 pages, 6 figure

Measurements of muon flux in the Pyh\"asalmi underground laboratory

The cosmic-ray induced muon flux was measured at several depths in the Pyh\"asalmi mine (Finland) using a plastic scintillator telescope mounted on a trailer. The flux was determined at four different depths underground at 400 m (980 m.w.e), at 660 m (1900 m.w.e), at 990 m (2810 m.w.e) and at 1390 m (3960 m.w.e) with the trailer, and also at the ground surface. In addition, previously measured fluxes from depths of 90 m (210 m.w.e) and 210 m (420 m.w.e) are shown. A relation was obtained for the underground muon flux as a function of the depth. The measured flux follows well the general behaviour and is consistent with results determined in other underground laboratories.Comment: 8 pages, 2 figures. Submitted to Nuclear Instrum. Methods

Dynamics of forced biopolymer translocation

We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore potentials in experiments and biological systems. Scaling of translocation time with polymer length varies with pore force and friction. Hydrodynamics affects this scaling and significantly reduces translocation times.Comment: Published in: http://www.iop.org/EJ/article/0295-5075/85/5/58006/epl_85_5_58006.htm

Preregistration Classification of Mobile LIDAR Data Using Spatial Correlations

We explore a novel paradigm for light detection and ranging (LIDAR) point classification in mobile laser scanning (MLS). In contrast to the traditional scheme of performing classification for a 3-D point cloud after registration, our algorithm operates on the raw data stream classifying the points on-the-fly before registration. Hence, we call it preregistration classification (PRC). Specifically, this technique is based on spatial correlations, i.e., local range measurements supporting each other. The proposed method is general since exact scanner pose information is not required, nor is any radiometric calibration needed. Also, we show that the method can be applied in different environments by adjusting two control parameters, without the results being overly sensitive to this adjustment. As results, we present classification of points from an urban environment where noise, ground, buildings, and vegetation are distinguished from each other, and points from the forest where tree stems and ground are classified from the other points. As computations are efficient and done with a minimal cache, the proposed methods enable new on-chip deployable algorithmic solutions. Broader benefits from the spatial correlations and the computational efficiency of the PRC scheme are likely to be gained in several online and offline applications. These range from single robotic platform operations including simultaneous localization and mapping (SLAM) algorithms to wall-clock time savings in geoinformation industry. Finally, PRC is especially attractive for continuous-beam and solid-state LIDARs that are prone to output noisy data

Computer-based Eye-tracking Analysis of King-Devick Test Differentiates Persons with Idiopathic Normal Pressure Hydrocephalus from Cognitively Unimpaired

Publisher Copyright: © 2022 Lippincott Williams and Wilkins. All rights reserved.Background: Functional defects in eye movements and reduced reading speed in neurodegenerative diseases represent a potential new biomarker to support clinical diagnosis. We investigated whether computer-based eye-tracking (ET) analysis of the King-Devick (KD) test differentiates persons with idiopathic normal pressure hydrocephalus (iNPH) from cognitively unimpaired [control (CO)] and persons with Alzheimer's disease (AD). Methods: We recruited 68 participants (37 CO, 10 iNPH, and 21 AD) who underwent neurological examination, the Consortium to Establish a Registry for Alzheimer's Disease neuropsychological test battery (CERAD-NB), and a Clinical Dementia Rating interview. The KD reading test was performed using computer-based ET. We analyzed the total time used for the reading test, number of errors, durations of fixation and saccade, and saccade amplitudes. Results: The iNPH group significantly differed from the CO group in the KD test mean total time (CO 69.3 s, iNPH 87.3 s; P≤0.009) and eye-tracking recording of the mean saccade amplitude (CO 3.6 degree, iNPH 3.2 degree; P≤0.001). The AD group significantly differed from the CO group in each tested parameter. No significant differences were detected between the iNPH and AD groups. Conclusion: For the first time, we demonstrated altered reading ability and saccade amplitudes in patients with iNPH.Peer reviewe

Shortening of Saccades as a Possible Easy-to-Use Biomarker to Detect Risk of Alzheimer's Disease

Background: Wide-ranging functional defects in eye movements have been reported in Alzheimer's disease (AD) dementia. The detection of abnormal eye movements and reading problems may identify persons at risk of AD when clear clinical symptoms are lacking. Objective: To examine whether computer-based eye-tracking (ET) analysis of King-Devick (KD) test results differentiates cognitively healthy persons from persons with minor problems in cognitive testing or diagnosed mild AD. Methods: We recruited 78 participants (57 non-demented, 21 with mild AD) who underwent neurological examination, the Consortium to Establish a Registry for Alzheimer's Disease neuropsychological test battery (CERAD-NB), and a Clinical Dementia Rating (CDR) interview. The non-demented participants were further divided into control (normal CERAD subtests, mean MMSE= 28) and objective mild cognitive impairment (MCI; decline in at least one CERAD memory score, mean MMSE= 27) groups. The KD reading test was performed using computer-based ET. The total time used for the reading test, errors made, fixation and saccade durations, and saccade amplitudes were analyzed. Results: We found significant differences between the control, objective MCI, and AD groups in regard to the mean saccade amplitude (3.58, 3.33, and 3.21 ms, respectively, p < 0.03) and duration (27.1, 25.3, and 24.8 ms, respectively, p < 0.05). The KD error scores in the AD group differed significantly (p < 0.01) from the other groups. Conclusion: Computed ET analysis of the KD test may help detect persons with objective MCI early when clear clinical symptoms are lacking. The portable device for ET is easy to use in primary health care memory clinics.Peer reviewe

Effectiveness of interventions for preventing injuries in the construction industry: results of an updated Cochrane systematic review

Various interventions to prevent occupational injuries in the construction industry have been proposed and studied. This continuing updated Cochrane review systematically summarizes the most current scientific evidence on the effectiveness of interventions to prevent injuries associated with construction work. Search terms that covered the concepts of ‘construction workers’, ‘injury’, ’safety’ and ‘study design’ were used to identify intervention studies in five electronic databases up to April 2017. Acceptable study designs included randomized controlled trials (RCT), controlled before–after studies (CBA) and interrupted time series (ITS). In total 17 studies, 14 ITS and three CBA studies, from the US (6), UK (2), Italy (3), Denmark (1), Finland (1), Austria (1) Germany (1) Spain (1), Belgium (1) met the inclusion criteria. Most studies were at high risk of bias. There is very low-quality evidence that introducing regulations as such may or may not result in a decrease in fatal and non-fatal injuries. There is also very low-quality evidence that regionally oriented safety campaigns, training, inspections or the introduction of occupational health services may not reduce non-fatal injuries in construction companies. There is very low-quality evidence that company-oriented safety interventions such as a multifaceted safety campaign, a multifaceted drug workplace programme and subsidies for replacement of scaffoldings may reduce non-fatal injuries among construction workers