6,198 results match your criteria realistic dynamics

Effect of RNA on Morphology and Dynamics of Membraneless Organelles.

J Phys Chem B 2021 May 10. Epub 2021 May 10.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.

Membraneless organelles (MLOs) are spatiotemporally regulated structures that concentrate multivalent proteins or RNA, often in response to stress. The proteins enriched within MLOs are often classified as high-valency "scaffolds" or low-valency "clients", with the former being associated with a phase-separation promoting role. In this study, we employ a minimal model for P-body components, with a defined protein-protein interaction network, to study their phase separation at biologically realistic low protein concentrations. Read More

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Dynamics of a stochastic COVID-19 epidemic model with jump-diffusion.

Adv Differ Equ 2021 1;2021(1):228. Epub 2021 May 1.

Department of Mathematical Sciences, Clemson University, Clemson, South Carolina 29634 USA.

For a stochastic COVID-19 model with jump-diffusion, we prove the existence and uniqueness of the global positive solution. We also investigate some conditions for the extinction and persistence of the disease. We calculate the threshold of the stochastic epidemic system which determines the extinction or permanence of the disease at different intensities of the stochastic noises. Read More

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Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity.

Acc Chem Res 2021 May 7. Epub 2021 May 7.

Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France.

ConspectusThe computational modeling of realistic extended systems, relevant in, e.g., Chemistry and Biophysics, is a fundamental problem of paramount importance in contemporary research. Read More

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Microstates in complex and dynamical environments: Unraveling situational awareness in critical helicopter landing maneuvers.

Hum Brain Mapp 2021 May 4. Epub 2021 May 4.

Hospital Israelita Albert Einstein, São Paulo, Brazil.

Understanding decision-making in complex and dynamic environments is relevant for designing strategies targeting safety improvements and error rate reductions. However, studies evaluating brain dynamics in realistic situations are scarce in the literature. Given the evidence that specific microstates may be associated with perception and attention, in this work we explored for the first time the application of the microstate model in an ecological, dynamic and complex scenario. Read More

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The atomic structure and dynamics at the CaCO vaterite-water interface: A classical molecular dynamics study.

J Chem Phys 2021 Apr;154(16):164504

Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.

Classical molecular and lattice dynamics were applied to explore the structure and dynamics of water on different surfaces of vaterite, the least abundant calcium carbonate polymorph. Surfaces were generated starting from the three possible structural models for vaterite (monoclinic, hexagonal/trigonal, and triclinic) and pre-screened using their surface energies in an implicit solvent. Surfaces with energies lower than 0. Read More

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Temperature Dynamics of MAPbI and PbI Photolysis: Revealing the Interplay between Light and Heat, Two Enemies of Perovskite Photovoltaics.

J Phys Chem Lett 2021 May 3:4362-4367. Epub 2021 May 3.

The Institute for Problems of Chemical Physics of the Russian Academy of Sciences, Semenov Prospect 1, Chernogolovka 142432, Russia.

Regardless of the impressive photovoltaic performances demonstrated for lead halide perovskite solar cells, their practical implementation is severely impeded by the low device stability. Complex lead halides are sensitive to both light and heat, which are unavoidable under realistic solar cell operational conditions. Suppressing these intrinsic degradation pathways requires a thorough understanding of their mechanistic aspects. Read More

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Ultra-acute exposure to cadmium does not impair whitefish sperm motility.

J Fish Biol 2021 May 2. Epub 2021 May 2.

Department of Biology, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland.

Cadmium (Cd) exposure can impair the traits of aquatic animals associated with reproduction. In natural lakes Cd is typically detected at concentrations below 0.001 mg L . Read More

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Aerodynamic effects and performance improvements of running in drafting formations.

J Biomech 2021 Apr 22;122:110457. Epub 2021 Apr 22.

ADIDAS, Herzogenaurach DE-91074, Germany.

Drafting as a process to reduce drag and to benefit from the presence of other competitors is applied in various sports with several recent examples of competitive running in formations. In this study, the aerodynamics of a realistic model of a female runner is calculated by computational fluid dynamics (CFD) simulations at four running speeds of 15 km h, 18 km h, 21 km h, and 36 km h. Aerodynamic power fractions of the total energy expenditure are found to be in the range of 2. Read More

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Towards homogenization of liquid plug distribution in reconstructed 3D upper airways of the preterm infant.

J Biomech 2021 Apr 22;122:110458. Epub 2021 Apr 22.

Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel. Electronic address:

Liquid plug therapies are commonly instilled in premature babies suffering from infant respiratory distress syndrome (IRDS) by a procedure called surfactant replacement therapy (SRT) in which a surfactant-laden bolus is instilled endotracheally in the neonatal lungs, dramatically reducing mortality and morbidity in neonatal populations. Since data are frequently limited, the optimal method for surfactant delivery has yet to be established towards more standardized guidelines. Here, we explore the dynamics of liquid plug transport using an anatomically-relevant, true-scale in vitro 3D model of the upper airways of a premature infant. Read More

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Mitigation effect of face shield to reduce SARS-CoV-2 airborne transmission risk: Preliminary simulations based on computed tomography.

Environ Res 2021 Apr 29;198:111229. Epub 2021 Apr 29.

Department of Otolaryngology, Gdansk Medical University, Gdansk, Poland.

We aimed to develop a model to quantitatively assess the potential effectiveness of face shield (visor) in reducing airborne transmission risk of the novel coronavirus SARS-CoV-2 during the current COVID-19 pandemic using the computational fluid dynamics (CFD) method. The studies with and without face shield in both an infected and healthy person have been considered in indoor environment simulation. In addition to the influence of the face shield and the synchronization of the breathing process while using the device, we also simulated the effect of small air movements on the SARS-CoV-2 infection rate (outdoor environment simulation). Read More

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Comparing metapopulation dynamics of infectious diseases under different models of human movement.

Proc Natl Acad Sci U S A 2021 May;118(18)

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA 98121.

Newly available datasets present exciting opportunities to investigate how human population movement contributes to the spread of infectious diseases across large geographical distances. It is now possible to construct realistic models of infectious disease dynamics for the purposes of understanding global-scale epidemics. Nevertheless, a remaining unanswered question is how best to leverage the new data to parameterize models of movement, and whether one's choice of movement model impacts modeled disease outcomes. Read More

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An Experimental Approach to Study the Effects of Realistic Environmental Mixture of Linuron and Propamocarb on Zebrafish Synaptogenesis.

Int J Environ Res Public Health 2021 Apr 27;18(9). Epub 2021 Apr 27.

Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.

The reasons behind the extensive use of pesticides include the need to destroy vector organisms and promote agricultural production in order to sustain population growth. Exposure to pesticides is principally occupational, even if their persistence in soil, surface water and food brings the risk closer to the general population, hence the demand for risk assessment, since these compounds exist not only as individual chemicals but also in form of mixtures. In light of this, zebrafish represents a suitable model for the evaluation of toxicological effects. Read More

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Mikto-Arm Stars as Soft-Patchy Particles: From Building Blocks to Mesoscopic Structures.

Polymers (Basel) 2021 Apr 1;13(7). Epub 2021 Apr 1.

Computation-Based Science and Technology Research Center, The Cyprus Institute, 20 Constantinou Kavafi Str., Nicosia 2121, Cyprus.

We present an atomistic molecular dynamics study of self-assembled mikto-arm stars, which resemble patchy-like particles. By increasing the number of stars in the system, we propose a systematic way of examining the mutual orientation of these fully penetrable patchy-like objects. The individual stars maintain their patchy-like morphology when creating a mesoscopic (macromolecular) self-assembled object of more than three stars. Read More

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Direct Comparison of Bayesian and Fermi Deconvolution Approaches for Myocardial Blood Flow Quantification: and Clinical Validations.

Front Physiol 2021 12;12:483714. Epub 2021 Apr 12.

Univ Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne, CNRS, Inserm, CREATIS, UMR 5220, U1294, Lyon, France.

Cardiac magnetic resonance myocardial perfusion imaging can detect coronary artery disease and is an alternative to single-photon emission computed tomography or positron emission tomography. However, the complex, non-linear MR signal and the lack of robust quantification of myocardial blood flow have hindered its widespread clinical application thus far. Recently, a new Bayesian approach was developed for brain imaging and evaluation of perfusion indexes (Kudo et al. Read More

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Finite-element simulation of photoinduced strain dynamics in silicon thin plates.

Struct Dyn 2021 Mar 15;8(2):024103. Epub 2021 Apr 15.

RIKEN Center for Emergent Matter Science, Wako, Saitama 351-0198, Japan.

In this paper, we investigate the femtosecond-optical-pulse-induced strain dynamics in relatively thin (100 nm) and thick (10 000 nm) silicon plates based on finite-element simulations. In the thin sample, almost spatially homogeneous excitation by the optical pulse predominantly generates a standing wave of the lowest-order acoustic resonance mode along the out-of-plane direction. At the same time, laterally propagating plate waves are emitted at the sample edge through the open edge deformation. Read More

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An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation.

Sci Rep 2021 Apr 27;11(1):9053. Epub 2021 Apr 27.

School of Biological Sciences, University of Reading, Reading, England.

The alpha-helix coiled-coils within talin's rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Read More

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Representing Tuberculosis Transmission with Complex Contagion: An Agent-Based Simulation Modeling Approach.

Med Decis Making 2021 Apr 27:272989X211007842. Epub 2021 Apr 27.

Department of Industrial and Systems Engineering, University of Wisconsin-Madison, Madison, WI, USA, PhD.

Objective: A recent study reported a tuberculosis (TB) outbreak in which, among newly infected individuals, exposure to additional active infections was associated with a higher probability of developing active disease. Referred to as , multiple reexposures to TB within a short period after initial infection is hypothesized to confer a greater likelihood of developing active infection in 1 y. The purpose of this article is to develop and validate an agent-based simulation model (ABM) to study the effect of complex contagion on population-level TB transmission dynamics. Read More

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Simulation of intravoxel incoherent perfusion signal using a realistic capillary network of a mouse brain.

NMR Biomed 2021 Apr 26:e4528. Epub 2021 Apr 26.

Institute for Biomedical Engineering, ETH and University of Zürich, Zürich, Switzerland.

We simulated the intravoxel incoherent perfusion magnetic resonance signal from the motion of blood particles in three realistic vascular network graphs, generated from the cortex of a mouse scanned using two-photon laser microscopy. We found a simulated pseudo-diffusion coefficient in good agreement with published in vivo measurements, and that all vessel types (artery, arterioles, capillaries, venules and veins) contribute to the IVIM signal. This improves our theoretical understanding of the IVIM perfusion method. Read More

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3D Modeling of Blood Flow in Simulated Abdominal Aortic Aneurysm.

Vasc Endovascular Surg 2021 Apr 27:15385744211012926. Epub 2021 Apr 27.

Tecnologico de Monterrey, School of Medicine and Health Sciences, Nuevo Leon, Mexico.

Background: Besides biological factors, abdominal aortic aneurysm rupture is also caused by mechanical parameters, which are constantly affecting the wall's tissue due to their abnormal values. The ability to evaluate these parameters could vastly improve the clinical treatment of patients with abdominal aortic aneurysms. The objective of this study was to develop and demonstrate a methodology to analyze the fluid dynamics that cause the wall stress distribution in abdominal aortic aneurysms, using accurate 3D geometry and a realistic, nonlinear, elastic biomechanical model using a computer-aided software. Read More

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A compartment modeling approach to reconstruct and analyze gender and age-grouped CoViD-19 Italian data for decision-making strategies.

J Biomed Inform 2021 Apr 24;118:103793. Epub 2021 Apr 24.

Department of Medical Biotechnologies, Bioengineering Lab, University of Siena, Siena, Italy; Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.

Background: Available national public data are often too incomplete and noisy to be used directly to interpret the evolution of epidemics over time, which is essential for making timely and appropriate decisions. The use of compartment models can be a worthwhile and attractive approach to address this problem. The present study proposes a model compartmentalized by sex and age groups that allows for more complete information on the evolution of the CoViD-19 pandemic in Italy. Read More

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Collective and synchronous dynamics of photonic spiking neurons.

Nat Commun 2021 04 23;12(1):2325. Epub 2021 Apr 23.

NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato Wakamiya, Atsugi, Kanagawa, 243-0198, Japan.

Nonlinear dynamics of spiking neural networks have recently attracted much interest as an approach to understand possible information processing in the brain and apply it to artificial intelligence. Since information can be processed by collective spiking dynamics of neurons, the fine control of spiking dynamics is desirable for neuromorphic devices. Here we show that photonic spiking neurons implemented with paired nonlinear optical oscillators can be controlled to generate two modes of bio-realistic spiking dynamics by changing optical-pump amplitude. Read More

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Reaction-diffusion in a growing 3D domain of skin scales generates a discrete cellular automaton.

Nat Commun 2021 04 23;12(1):2433. Epub 2021 Apr 23.

Laboratory of Artificial & Natural Evolution (LANE), Dept. of Genetics & Evolution, University of Geneva, Geneva, Switzerland.

We previously showed that the adult ocellated lizard skin colour pattern is effectively generated by a stochastic cellular automaton (CA) of skin scales. We additionally suggested that the canonical continuous 2D reaction-diffusion (RD) process of colour pattern development is transformed into this discrete CA by reduced diffusion coefficients at the borders of scales (justified by the corresponding thinning of the skin). Here, we use RD numerical simulations in 3D on realistic lizard skin geometries and demonstrate that skin thickness variation on its own is sufficient to cause scale-by-scale coloration and CA dynamics during RD patterning. Read More

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Coupled flow and biomass-nutrient growth at pore-scale with permeable biofilm, adaptive singularity and multiple species.

Math Biosci Eng 2021 03;18(3):2097-2149

Department of Mathematics, Oregon State University, Corvallis, OR 97331, USA.

In this paper we describe a coupled model for flow and microbial growth as well as nutrient utilization. These processes occur within and outside the biofilm phase formed by the microbes. The primary challenge is to address the volume constraint of maximum cell density but also to allow some microbial presence outside the contiguous biofilm phase. Read More

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First-Principles Nonadiabatic Dynamics Simulation of Azobenzene Photodynamics in Solutions.

Ruibin Liang

J Chem Theory Comput 2021 Apr 21. Epub 2021 Apr 21.

Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States.

The photoisomerization of azobenzene is a prototypical reaction of various light-activated processes in material and biomedical sciences. However, its reaction mechanism has been under debate for decades, partly due to the challenges in computational simulations to accurately describe the molecule's photodynamics. A recent study (. Read More

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Estimating Employment Gains of the Proposed Infrastructure Stimulus Plan in Post-Covid-19 South Africa.

Eur J Dev Res 2021 Apr 16:1-28. Epub 2021 Apr 16.

Human Sciences Research Council, Merchant House, 116-118 Buitengracht Street, Cape Town, 8001 South Africa.

For the economic recovery in the wake of Covid-19 pandemic, South Africa announced the launch of an ambitious ZAR 2.3 trillion infrastructure investment plan. This paper uses a simplified yet reliable method to analyse the potential growth and employment effects of this stimulus plan. Read More

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A dynamic simulation framework for CT perfusion in stroke assessment built from first principles.

Med Phys 2021 Apr 20. Epub 2021 Apr 20.

Departments of Bioengineering and Radiology, Stanford University, Stanford, CA, 94305, USA.

Purpose: Physicians utilize cerebral perfusion maps (e.g., cerebral blood flow, cerebral blood volume, transit time) to prescribe the plan of care for stroke patients. Read More

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Size segregation of irregular granular materials captured by time-resolved 3D imaging.

Sci Rep 2021 Apr 19;11(1):8352. Epub 2021 Apr 19.

Henry Moseley X-ray Imaging Facility, Department of Materials Science, The University of Manchester, Manchester, M13 9PL, UK.

When opening a box of mixed nuts, a common experience is to find the largest nuts at the top. This well-known effect is the result of size-segregation where differently sized 'particles' sort themselves into distinct layers when shaken, vibrated or sheared. Colloquially this is known as the 'Brazil-nut effect'. Read More

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Microphysical Modeling of Carbonate Fault Friction at Slip Rates Spanning the Full Seismic Cycle.

J Geophys Res Solid Earth 2021 Mar 25;126(3):e2020JB021024. Epub 2021 Mar 25.

HPT Laboratory Department of Earth Sciences Utrecht University Utrecht The Netherlands.

Laboratory studies suggest that seismogenic rupture on faults in carbonate terrains can be explained by a transition from high friction, at low sliding velocities (), to low friction due to rapid dynamic weakening as seismic slip velocities are approached. However, consensus on the controlling physical processes is lacking. We previously proposed a microphysically based model (the "Chen-Niemeijer-Spiers" [CNS] model) that accounts for the (rate-and-state) frictional behavior of carbonate fault gouges seen at low velocities characteristic of rupture nucleation. Read More

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Derjaguin-Landau-Verwey-Overbeek energy landscape of a Janus particle with a nonuniform cap.

Phys Rev E 2021 Mar;103(3-1):032610

Department of Chemical and Biomolecular Engineering, Case School of Engineering, Case Western Reserve University, Cleveland, Ohio 44106, USA.

A colloidal particle is often termed "Janus" when some portion of its surface is coated by a second material which has distinct properties from the native particle. The anisotropy of Janus particles enables unique behavior at interfaces. However, rigorous methodologies to predict Janus particle dynamics at interfaces are required to implement these particles in complex fluid applications. Read More

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