26,087 results match your criteria simulations provide


Fine-scale genetic diversity and putative ecotypes of oxymonad protists co-inhabiting the hindgut of Reticulitermes speratus.

Mol Ecol 2021 Dec 5. Epub 2021 Dec 5.

School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.

The hindgut of lower termites is generally co-inhabited by multiple morphologically identifiable protist species. However, it is unclear how many protist species truly coexist in this miniaturized environment, and moreover, it is difficult to define the fundamental unit of protist diversity. Species delineation of termite gut protists has therefore been guided without a theory-based concept of species. Read More

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December 2021

Efficient approaches for large-scale GWAS with genotype uncertainty.

G3 (Bethesda) 2021 Dec 4. Epub 2021 Dec 4.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.

Introduction: Association studies using genetic data from SNP-chip based imputation or low depth sequencing data provide a cost-efficient design for large-scale association studies. We explore methods for performing association studies applicable to such genetic data and investigate how using different priors when estimating genotype probabilities affects the association results.

Methods: Our proposed method, ANGSD-asso's latent model, models the unobserved genotype as a latent variable in a generalised linear model framework. Read More

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December 2021

Theoretical study of Myriocin binding mechanism targeting Serine Palmitoyltransferase.

Chem Biol Drug Des 2021 Dec 3. Epub 2021 Dec 3.

School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China.

Sphingolipids (SLs) are vital for cells as forming membrane and transducing signals. The first step for de novo biosynthesis of SLs is catalyzed by the pyridoxal-5'-phosphate (PLP)-dependent enzyme Serine palmitoyltransferase (SPT), which has been proven to be a promising drug target for treating various diseases. However, there are few SPT-specific inhibitors have been identified so far. Read More

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December 2021

Statistical testing in transcriptomic-neuroimaging studies: A how-to and evaluation of methods assessing spatial and gene specificity.

Hum Brain Mapp 2021 Dec 4. Epub 2021 Dec 4.

Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

Multiscale integration of gene transcriptomic and neuroimaging data is becoming a widely used approach for exploring the molecular underpinnings of large-scale brain organization in health and disease. Proper statistical evaluation of determined associations between imaging-based phenotypic and transcriptomic data is key in these explorations, in particular to establish whether observed associations exceed "chance level" of random, nonspecific effects. Recent approaches have shown the importance of statistical models that can correct for spatial autocorrelation effects in the data to avoid inflation of reported statistics. Read More

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December 2021

Modelling of Hepatitis E virus RNA-dependent RNA polymerase genotype 3 from a chronic patient and interaction analysis by molecular docking with Ribavirin.

J Biomol Struct Dyn 2021 Dec 3:1-17. Epub 2021 Dec 3.

Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.

Hepatitis E Virus (HEV) infection is an emergent zoonotic disease, where chronic hepatitis E associated to solid organ transplant (SOT) recipients, related to genotype 3, is the clinical manifestation of major concern. In this setting, ribavirin (RBV) treatment is the only available therapy, though drug-resistant variants could emerge leading to a therapeutic failure. Crystallographic structures have not been reported for most of the HEV proteins, including the RNA-polymerase (RdRp). Read More

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December 2021

Molecular insights into the uptake of SiO nanoparticles on phospholipid membrane: Effect of surface properties and particle size.

Colloids Surf B Biointerfaces 2021 Nov 27;210:112250. Epub 2021 Nov 27.

Key Lab of Colloid and Interface Chemistry, Shandong University, Jinan 250100, China. Electronic address:

Silica (SiO) nanoparticles (NPs) have attracted much attention due to the potential for a wide range of applications and they have been confirmed to be hazardous to humans. Partitioning to phospholipid bilayers is an important way for their bioaccumulation. However, the detailed mechanism of SiO NPs uptake by membrane phospholipids remains uncertain. Read More

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November 2021

Modeling Performance of Open Surgical Cases.

Simul Healthc 2021 Dec;16(6):e188-e193

From the Department of Industrial and Systems Engineering (D.P.A., R.G.R.); Department of Surgery (S.R.P.Q., C.C.G.), Clinical Sciences Center; Department of Urology (B.V.L.); and Duane H. and Dorothy M. Bluemke Professor in the College of Engineering (R.G.R.), University of Wisconsin-Madison, Madison, WI; Department of Surgery (L.L.F.), Penn Medicine - University of Pennsylvania Health System, Philadelphia, PA; City of Hope National Comprehensive Cancer Center (B.L.M), Duarte, CA.

Introduction: Previous efforts used digital video to develop computer-generated assessments of surgical hand motion economy and fluidity of motion. This study tests how well previously trained assessment models match expert ratings of suturing and tying video clips recorded in a new operating room (OR) setting.

Methods: Enabled through computer vision of the hands, this study tests the applicability of assessments born out of benchtop simulations to in vivo suturing and tying tasks recorded in the OR. Read More

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December 2021

Simulating Collider Physics on Quantum Computers Using Effective Field Theories.

Phys Rev Lett 2021 Nov;127(21):212001

NHETC, Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA and Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

Simulating the full dynamics of a quantum field theory over a wide range of energies requires exceptionally large quantum computing resources. Yet for many observables in particle physics, perturbative techniques are sufficient to accurately model all but a constrained range of energies within the validity of the theory. We demonstrate that effective field theories (EFTs) provide an efficient mechanism to separate the high energy dynamics that is easily calculated by traditional perturbation theory from the dynamics at low energy and show how quantum algorithms can be used to simulate the dynamics of the low energy EFT from first principles. Read More

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November 2021

Möbius Strip Microlasers: A Testbed for Non-Euclidean Photonics.

Phys Rev Lett 2021 Nov;127(20):203901

Laboratoire Lumière, Matière et Interfaces (LuMIn) CNRS, ENS Paris-Saclay, Université Paris-Saclay, CentraleSupélec, 91190 Gif-sur-Yvette, France.

We report on experiments with Möbius strip microlasers, which were fabricated with high optical quality by direct laser writing. A Möbius strip, i.e. Read More

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November 2021

Effective Resource Competition Model for Species Coexistence.

Phys Rev Lett 2021 Nov;127(20):208101

Dipartimento di Fisica e Astronomia Galileo Galilei, Università degli Studi di Padova, via Marzolo 8, 35131 Padova, Italy.

Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider a consumer-resource model in which a coarse-graining procedure accounts for a variety of ecological mechanisms and leads to effective spatial effects which favor species coexistence. Read More

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November 2021

Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations.

Phys Chem Chem Phys 2021 Dec 3. Epub 2021 Dec 3.

Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.

Collision-induced dissociation experiments of hydrated molecular species can provide a wealth of important information. However, they often need a theoretical support to extract chemical information. In the present article, in order to provide a detailed description of recent experimental measurements [Braud , , 2019, , 014303], collision simulations between low-energy protonated uracil water clusters (HO)UH and an Ar atom were performed using a quantum mechanics/molecular mechanics formalism based on the self-consistent-charge density-functional based tight-binding method. Read More

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December 2021

Exploring Dihydroflavonol-4-reductase reactivity and selectivity by QM/MM-MD simulations.

Chembiochem 2021 Dec 2. Epub 2021 Dec 2.

Universite Cote d'Azur, institut de Chimie de NIce, 28 avenue Valrose, 06100, Nice, FRANCE.

Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds to be used in pharmacology. Therefore, unravelling the mechanisms of flavonoids biosynthesis is a current hot challenge for the scientific community. Read More

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December 2021

Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer Simulations.

Front Immunol 2021 11;12:730099. Epub 2021 Nov 11.

Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.

SARS-CoV-2 infects humans and causes Coronavirus disease 2019 (COVID-19). The S1 domain of the spike glycoprotein of SARS-CoV-2 binds to human angiotensin-converting enzyme 2 (hACE2) its receptor-binding domain, while the S2 domain facilitates fusion between the virus and the host cell membrane for entry. The spike glycoprotein of circulating SARS-CoV-2 genomes is a mutation hotspot. Read More

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November 2021

Mimicking atmospheric photochemical modelling with a deep neural network.

Atmos Res 2022 Jan;265:1-11

State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.

Fast and accurate prediction of ambient ozone (O) formed from atmospheric photochemical processes is crucial for designing effective O pollution control strategies in the context of climate change. The chemical transport model (CTM) is the fundamental tool for O prediction and policy design, however, existing CTM-based approaches are computationally expensive, and resource burdens limit their usage and effectiveness in air quality management. Here we proposed a novel method (noted as DeepCTM) that using deep learning to mimic CTM simulations to improve the computational efficiency of photochemical modeling. Read More

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January 2022

Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract.

Sci Rep 2021 Dec 2;11(1):23270. Epub 2021 Dec 2.

UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Vidyanagari, Mumbai, 400098, India.

Crystallins are ubiquitous, however, prevalence is seen in eye lens. Eye lens crystallins are long-lived and structural intactness is required for maintaining lens transparency and protein solubility. Mutations in crystallins often lead to cataract. Read More

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December 2021

Evaluation of a New Virtual Reality Concept Teaching K-Wire Drilling With Force Feedback Simulated Haptic in Orthopedic Skills Training.

J Hand Surg Am 2021 Nov 30. Epub 2021 Nov 30.

Department of Trauma Surgery & Emergency Department, University Medical Center Regensburg, Regensburg, Germany; Centre for Hand- and Elbow Surgery, Microsurgery and Plastic Surgery, Schoen Clinic München Harlaching, Munich, Germany.

Purpose: Surgical simulations are becoming increasingly relevant in musculoskeletal training. They provide the opportunity to develop surgical skills in a controlled environment while reducing the risks for patients. For K-wire internal fixation in musculoskeletal surgery, a force feedback virtual reality (VR) simulator was developed. Read More

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November 2021

To Deconvolve, or Not to Deconvolve: Inferences of Neuronal Activities using Calcium Imaging Data.

J Neurosci Methods 2021 Nov 29:109431. Epub 2021 Nov 29.

Department of Statistics, University of California, CA, Irvine92697. Electronic address:

Background: With the increasing popularity of calcium imaging in neuroscience research, choosing the right methods to analyze calcium imaging data is critical to address various scientific questions. Unlike spike trains measured using electrodes, fluorescence intensity traces provide an indirect and noisy measurement of the underlying neuronal activities. The observed calcium traces are either analyzed directly or deconvolved to spike trains to infer neuronal activities. Read More

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November 2021

Technical Note: Providing proton fields down to the few-MeV level at clinical pencil beam scanning facilities for radiobiological experiments.

Med Phys 2021 Dec 1. Epub 2021 Dec 1.

West German Proton Therapy Centre Essen (WPE), Essen, 45147, Germany.

Purpose: The adequate performance of radiobiological experiments using clinical proton beams, typically requires substantial preparations to provide the appropriate setup for specific experiments. Providing radiobiologically interesting low-energy protons is a particular challenge, due to various physical effects that become more pronounced with larger absorber thickness and smaller proton energy. This work demonstrates the generation of decelerated low-energy protons from a clinical proton beam. Read More

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December 2021

Universal Two-Component Dynamics in Supercritical Fluids.

J Phys Chem B 2021 Dec 2. Epub 2021 Dec 2.

Dipartimento di Fisica e Astronomia, Università di Padova, 35131 Padova, Italy.

Despite the technological importance of supercritical fluids, controversy remains about the details of their microscopic dynamics. In this work, we study four supercritical fluid systems─water, Si, Te, and Lennard-Jones fluid─via classical molecular dynamics simulations. A universal two-component behavior is observed in the intermolecular dynamics of these systems, and the changing ratio between the two components leads to a crossover from liquidlike to gaslike dynamics, most rapidly around the Widom line. Read More

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December 2021

Drug Meets Monolayer: Understanding the Interactions of Sterol Drugs with Models of the Lung Surfactant Monolayer Using Molecular Dynamics Simulations.

Methods Mol Biol 2022 ;2402:103-121

School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.

The lung surfactant monolayer (LSM) is a thin layer of lipids and proteins that forms the air/water interface of the alveoli. The primary function of the LSM is to reduce the surface tension at the air/water interface during breathing. The LSM also forms the main biological barrier for any inhaled particles, including drugs, to treat lung diseases. Read More

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January 2022