Search results for "Simulation."
showing 10 items of 4779 documents
Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics
2021
Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP2(18–62)) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time…
Missing value imputation in proximity extension assay-based targeted proteomics data
2020
Targeted proteomics utilizing antibody-based proximity extension assays provides sensitive and highly specific quantifications of plasma protein levels. Multivariate analysis of this data is hampered by frequent missing values (random or left censored), calling for imputation approaches. While appropriate missing-value imputation methods exist, benchmarks of their performance in targeted proteomics data are lacking. Here, we assessed the performance of two methods for imputation of values missing completely at random, the previously top-benchmarked ‘missForest’ and the recently published ‘GSimp’ method. Evaluation was accomplished by comparing imputed with remeasured relative concentrations…
A practical protocol for calibration of nutrient removal wastewater treatment models
2011
Activated sludge models can be very useful for designing and managing wastewater treatment plants (WWTPs). However, as with every model, they need to be calibrated for correct and reliable application. Activated sludge model calibration is still a crucial point that needs appropriate guidance. Indeed, although calibration protocols have been developed, the model calibration still represents the main bottleneck to modelling. This paper presents a procedure for the calibration of an activated sludge model based on a comprehensive sensitivity analysis and a novel step-wise Monte Carlo-based calibration of the subset of influential parameters. In the proposed procedure the complex calibration i…
Enablers of the successful implementation of simulation exercises: a qualitative study among nurse teachers in undergraduate nursing education
2021
Abstract Background Simulation exercises are increasingly being used as a teaching method in the field of undergraduate nursing education. Thus, the present study sought to identify, describe and discuss enablers of the successful implementation of simulation exercises in undergraduate nursing education. Methods This study had a qualitative descriptive design and involved individual interviews conducted between November and December 2018 with six nurse teachers from three different university campuses in Norway. The transcribed interviews were analysed by means of a qualitative thematic analysis. Results The majority of the interviewees wanted to offer more simulation exercises as part of t…
Automated anaesthesia record systems, observations on future trends of development.
1995
The introduction of electronic anaesthesia documentation systems was attempted as early as in 1979, although their efficient application has become reality only in the past few years. Today, documentation technology is offered by most of the monitor manufacturers and new systems are being developed by various working groups. The advantages of the electronic protocol are apparent: Continuous high quality documentation, comparability of data due to the availability of a anaesthesia data bank, reduction of the workload of the anaesthesia staff and availability of new additional information. Disadvantages of the electronic protocol have also been discussed. Typically, by going through the proce…
Teaching mechanical oscillations using an integrate curriculum
1997
Abstract A set of teaching materials dealing with harmonic oscillations was developed as part of a research project investigating the influence of different pedagogical tools on physics learning. The materials incorporate simulation software and laboratory activities associated with Teacher and Student Units. The project involved research groups at seven Italian universities and the materials have been trialled in high schools nation‐wide. This paper describes the experimental protocol for the use of these materials in pilot classes and the evaluation of student learning and teacher training results. The intervention was found to improve physics education at school praxis level and to promo…
Measurement of multi-jet cross sections in proton-proton collisions at a 7 TeV center-of-mass energy
2011
Inclusive multi-jet production is studied in proton–proton collisions at a center-of-mass energy of 7 TeV, using the ATLAS detector. The data sample corresponds to an integrated luminosity of 2.4 pb−1. Results on multi-jet cross sections are presented and compared to both leading-order plus parton-shower Monte Carlo predictions and to next-to-leading-order QCD calculations.
Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer
2016
In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its…
Statistical properties of the site-frequency spectrum associated with lambda-coalescents.
2013
Abstract Statistical properties of the site-frequency spectrum associated with Λ-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Λ-coalescents for data sets too large for full-likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values that give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a…
On the collision property of chaotic iterations based post-treatments over cryptographic pseudorandom number generators
2018
International audience; There is not a proper mathematical definition of chaos, we have instead a quite big amount of definitions, each of one describes chaos in a more or less general context. Taking in account this, it is clear why it is hard to design an algorithm that produce random numbers, a kind of algorithm that could have plenty of concrete appliceautifat (anul)d bions. However we must use a finite state machine (e.g. a laptop) to produce such a sequence of random numbers, thus it is convenient, for obvious reasons, to redefine those aimed sequences as pseudorandom; also problems arise with floating point arithmetic if one wants to recover some real chaotic property (i.e. propertie…