Search results for " simulations."

Training machine learning models with synthetic data improves the prediction of ventricular origin in outflow tract ventricular arrhythmias

2022

In order to determine the site of origin (SOO) in outflow tract ventricular arrhythmias (OTVAs) before an ablation procedure, several algorithms based on manual identification of electrocardiogram (ECG) features, have been developed. However, the reported accuracy decreases when tested with different datasets. Machine learning algorithms can automatize the process and improve generalization, but their performance is hampered by the lack of large enough OTVA databases. We propose the use of detailed electrophysiological simulations of OTVAs to train a machine learning classification model to predict the ventricular origin of the SOO of ectopic beats. We generated a synthetic database of 12-l…

Influence of bed roughness on flow and turbulence structure around a partially-buried, isolated freshwater mussel

2023

The present study uses eddy-resolving numerical simulations to investigate how bed roughness affects flow and turbulence structure around an isolated, partially-buried mussel (Unio elongatulus) aligned with the incoming flow. The rough-bed simulations resolve the flow past the exposed part of a gravel bed, whose surface is obtained from a laboratory experiment that also provides some additional data for validation of the numerical model. Results are also discussed for the limiting case of a horizontal smooth bed. Additionally, the effects of varying the level of burial of the mussel inside the substrate and the discharge through the two mussel siphons are investigated via a set of simulatio…

B–T phase diagram of Pd/Fe/Ir(111) computed with parallel tempering Monte Carlo

2017

We use an atomistic spin model derived from density functional theory calculations for the ultra-thin film Pd/Fe/Ir(111) to show that temperature induces coexisting non-zero skyrmion and antiskyrmion densities. We apply the parallel tempering Monte Carlo method in order to reliably compute thermodynamical quantities and the B-T phase diagram in the presence of frustrated exchange interactions. We evaluate the critical temperatures using the topological susceptibility. We show that the critical temperatures depend on the magnetic field in contrast to previous work. In total, we identify five phases: spin spiral, skyrmion lattice, ferromagnetic phase, intermediate region with finite topologic…

Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations.

2017

Abstract The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a tot…

Larval fish assemblages in the central Mediterranean Sea: spatio spatio-temporal dynamics and biological effect on early life stage of Sardinella aur…

HSV-1 Glycoprotein D and Its Surface Receptors: Evaluation of Protein–Protein Interaction and Targeting by Triazole-Based Compounds through In Silico…

2023

Protein–protein interactions (PPI) represent attractive targets for drug design. Thus, aiming at a deeper insight into the HSV-1 envelope glycoprotein D (gD), protein–protein docking and dynamic simulations of gD-HVEM and gD-Nectin-1 complexes were performed. The most stable complexes and the pivotal key residues useful for gD to anchor human receptors were identified and used as starting points for a structure-based virtual screening on a library of both synthetic and designed 1,2,3-triazole-based compounds. Their binding properties versus gD interface with HVEM and Nectin-1 along with their structure-activity relationships (SARs) were evaluated. Four [1,2,3]triazolo[4,5-b]pyridines were i…

A Comprehensive Model for Hydraulic Analysis and Wetting Patterns Simulation under Subsurface Drip Laterals

2022

In the absence of suitable specialized models to simulate the soil wetting patterns in subsurface drip irrigation systems considering the hydraulic conditions along the laterals, a new model was developed and named a “comprehensive model” in this study. This model couples the subsurface drip irrigation lateral characteristics with the soil hydraulic properties and utilizes the Hydrus-3D software as a complementary section of the model to simulate the wetting front beneath the lateral. To evaluate the model, three 16 mm drip-line pipes of 62 m length with 20, 40, and 50 cm spacing emitters and 2 to 5 L/h discharge were buried at 0.2 m depth in a soil box containing clay loamy soil. Then, the…

Might as well jump: Sound affects muscle activation in skateboarding

2014

The aim of the study is to reveal the role of sound in action anticipation and performance, and to test whether the level of precision in action planning and execution is related to the level of sensorimotor skills and experience that listeners possess about a specific action. Individuals ranging from 18 to 75 years of age - some of them without any skills in skateboarding and others experts in this sport - were compared in their ability to anticipate and simulate a skateboarding jump by listening to the sound it produces. Only skaters were able to modulate the forces underfoot and to apply muscle synergies that closely resembled the ones that a skater would use if actually jumping on a ska…

Ultrasound measurements in bone using an array transducer

2014

Best Practices in Constant pH MD Simulations: Accuracy and Sampling

2022

Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput.2022, DOI: 10.1021/acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on…