Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport

The interior of a eukaryotic cell is a highly complex composite material which consists of water, structural scaffoldings, organelles, and various biomolecular solutes. All these components serve as obstacles that impede the motion of vesicles. Hence, it is hypothesized that any alteration of the cytoskeletal network may directly impact or even disrupt the vesicle transport. A disruption of the vesicle-mediate cell transport is thought to contribute to several severe diseases and disorders, such as diabetes, Parkinson’s and Alzheimer’s disease, emphasizing the clinical relevance. To address the outlined objective, a multiscale finite element model of the diffusive vesicle transport is proposed on the basis of the concept of homogenization, owed to the complexity of the cytoskeletal network. In order to study the microscopic effects of specific nanoscopic actin filament network alterations onto the vesicle transport, a parametrized three-dimensional geometrical model of the actin filament network was generated on the basis of experimentally observed filament densities and network geometries in an adenocarcinomic human alveolar basal epithelial cell. Numerical analyzes of the obtained effective diffusion properties within two-dimensional sampling domains of the whole cell model revealed that the computed homogenized diffusion coefficients can be predicted statistically accurate by a simple two-parameter power law as soon as the inaccessible area fraction, due to the obstacle geometries and the finite size of the vesicles, is known. This relationship, in turn, leads to a massive reduction in computation time and allows to study the impact of a variety of different cytoskeletal alterations onto the vesicle transport. Hence, the numerical simulations predicted a 35% increase in transport time due to a uniformly distributed four-fold increase of the total filament amount. On the other hand, a hypothetically reduced expression of filament cross-linking proteins led to sparser filament networks and, thus, a speed up of the vesicle transport.

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Methods for Restricting Maximum Exposure Rate in Computerized Adaptative Testing

Methodology ◽

10.1027/1614-2241.3.1.14 ◽

2007 ◽

Vol 3 (1) ◽

pp. 14-23 ◽

Cited By ~ 9

Author(s):

Juan Ramon Barrada ◽

Julio Olea ◽

Vicente Ponsoda

Keyword(s):

Measurement Accuracy ◽

Computerized Adaptive Testing ◽

Computation Time ◽

Adaptive Testing ◽

Exposure Rate ◽

Control Parameters ◽

The Impact ◽

Two Alternatives ◽

Selection Of ◽

Maximum Exposure

Abstract. The Sympson-Hetter (1985) method provides a means of controlling maximum exposure rate of items in Computerized Adaptive Testing. Through a series of simulations, control parameters are set that mark the probability of administration of an item on being selected. This method presents two main problems: it requires a long computation time for calculating the parameters and the maximum exposure rate is slightly above the fixed limit. Van der Linden (2003) presented two alternatives which appear to solve both of the problems. The impact of these methods in the measurement accuracy has not been tested yet. We show how these methods over-restrict the exposure of some highly discriminating items and, thus, the accuracy is decreased. It also shown that, when the desired maximum exposure rate is near the minimum possible value, these methods offer an empirical maximum exposure rate clearly above the goal. A new method, based on the initial estimation of the probability of administration and the probability of selection of the items with the restricted method ( Revuelta & Ponsoda, 1998 ), is presented in this paper. It can be used with the Sympson-Hetter method and with the two van der Linden's methods. This option, when used with Sympson-Hetter, speeds the convergence of the control parameters without decreasing the accuracy.

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Nonlocal and Size-Dependent Dielectric Function for Plasmonic Nanoparticles

Applied Sciences ◽

10.3390/app9153083 ◽

2019 ◽

Vol 9 (15) ◽

pp. 3083

Author(s):

Kai-Jian Huang ◽

Shui-Jie Qin ◽

Zheng-Ping Zhang ◽

Zhao Ding ◽

Zhong-Chen Bai

Keyword(s):

Metallic Nanoparticles ◽

High Efficiency ◽

Finite Size ◽

Plasmonic Nanostructures ◽

Accurate Analysis ◽

Finite Size Effects ◽

Size Dependent ◽

Quantum Size ◽

The Impact ◽

Electron Energy Loss

We develop a theoretical approach to investigate the impact that nonlocal and finite-size effects have on the dielectric response of plasmonic nanostructures. Through simulations, comprehensive comparisons of the electron energy loss spectroscopy (EELS) and the optical performance are discussed for a gold spherical dimer system in terms of different dielectric models. Our study offers a paradigm of high efficiency compatible dielectric theoretical framework for accounting the metallic nanoparticles behavior combining local, nonlocal and size-dependent effects in broader energy and size ranges. The results of accurate analysis and simulation for these effects unveil the weight and the evolution of both surface and bulk plasmons vibrational mechanisms, which are important for further understanding the electrodynamics properties of structures at the nanoscale. Particularly, our method can be extended to other plasmonic nanostructures where quantum-size or strongly interacting effects are likely to play an important role.

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The Impact of Microstructure Geometry on the Mass Transport in Artificial Pores: A Numerical Approach

Modelling and Simulation in Engineering ◽

10.1155/2014/109036 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 5

Author(s):

Matthias Galinsky ◽

Ulf Sénéchal ◽

Cornelia Breitkopf

Keyword(s):

Mass Transport ◽

Porous Materials ◽

Effective Diffusion ◽

Direct Simulation Monte Carlo ◽

Numerical Approach ◽

Porous System ◽

Length Scales ◽

General Evaluation ◽

Pulse Experiment ◽

The Impact

The microstructure of porous materials used in heterogeneous catalysis determines the mass transport inside networks, which may vary over many length scales. The theoretical prediction of mass transport phenomena in porous materials, however, is incomplete and is still not completely understood. Therefore, experimental data for every specific porous system is needed. One possible experimental technique for characterizing the mass transport in such pore networks is pulse experiments. The general evaluation of experimental outcomes of these techniques follows the solution of Fick’s second law where an integral and effective diffusion coefficient is recognized. However, a detailed local understanding of diffusion and sorption processes remains a challenge. As there is lack of proved models covering different length scales, existing classical concepts need to be evaluated with respect to their ability to reflect local geometries on the nanometer level. In this study, DSMC (Direct Simulation Monte Carlo) models were used to investigate the impact of pore microstructures on the diffusion behaviour of gases. It can be understood as a virtual pulse experiment within a single pore or a combination of different pore geometries.

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Protective Effect of Butylphthalide on Neuronal Apoptosis in Parkinson Rats and Its Effect on miR-146a-5p Expression and Phosphatidylinositide 3-Kinases/Protein Kinase B Pathway

Journal of Biomaterials and Tissue Engineering ◽

10.1166/jbt.2021.2766 ◽

2021 ◽

Vol 11 (10) ◽

pp. 1908-1917

Author(s):

Rongkang Mai ◽

Yiyao Cao ◽

Huitian Yu ◽

Yong Zheng ◽

Juke Huang

Keyword(s):

Cell Model ◽

Morphological Changes ◽

Neuroblastoma Cell ◽

Neuroblastoma Cell Line ◽

Vehicle Group ◽

Human Neuroblastoma Cell ◽

Human Neuroblastoma ◽

Oil Emulsion ◽

The Impact

80 male Wistar rats were stochastically assigned to Sham + Vehicle group, Sham + BUT group, PD + Vehicle group and PD + BUT group. Rotenone PD model rats were prepared by subcutaneous injection of rotenone sunflower oil emulsion 2 mg/(kg · d) for 5 consecutive weeks. Butylphthalide 80 mg/(kg · d) were given to the rats in Sham + BUT group and PD + BUT group by gavage from the first day of rotenone injection for 5 weeks. Subsequently, the motor retardation ability and the morphological changes of the substantia nigra (SN) of each group were evaluated. Meanwhile, the levels of neuronal injury, apoptosis, inflammation and oxidative stress in each group of rats were assayed. The impact of BUT treatment on miR-146a-5p expression and PI3K/AKT signal pathway in rat brain tissue was assayed. Finally, by constructing a PD cell model of the neurotoxin 6-hydroxydopamine (6-OHDA)-treated human neuroblastoma cell line SH-SY5Y, the in vitro anti-PD pharmacological effect of BUT was further verified.

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Forecasts covering one month using a cut-cell model

Geoscientific Model Development ◽

10.5194/gmd-6-875-2013 ◽

2013 ◽

Vol 6 (4) ◽

pp. 875-882 ◽

Cited By ~ 13

Author(s):

J. Steppeler ◽

S.-H. Park ◽

A. Dobler

Keyword(s):

Cell Model ◽

Control Model ◽

Precipitation Forecast ◽

Target Area ◽

Strong Impact ◽

Monthly Precipitation ◽

Small Areas ◽

Cut Cell ◽

Terrain Following ◽

The Impact

Abstract. This paper investigates the impact and potential use of the cut-cell vertical discretisation for forecasts covering five days and climate simulations. A first indication of the usefulness of this new method is obtained by a set of five-day forecasts, covering January 1989 with six forecasts. The model area was chosen to include much of Asia, the Himalayas and Australia. The cut-cell model LMZ (Lokal Modell with z-coordinates) provides a much more accurate representation of mountains on model forecasts than the terrain-following coordinate used for comparison. Therefore we are in particular interested in potential forecast improvements in the target area downwind of the Himalayas, over southeastern China, Korea and Japan. The LMZ has previously been tested extensively for one-day forecasts on a European area. Following indications of a reduced temperature error for the short forecasts, this paper investigates the model error for five days in an area influenced by strong orography. The forecasts indicated a strong impact of the cut-cell discretisation on forecast quality. The cut-cell model is available only for an older (2003) version of the model LM (Lokal Modell). It was compared using a control model differing by the use of the terrain-following coordinate only. The cut-cell model improved the precipitation forecasts of this old control model everywhere by a large margin. An improved, more transferable version of the terrain-following model LM has been developed since then under the name CLM (Climate version of the Lokal Modell). The CLM has been used and tested in all climates, while the LM was used for small areas in higher latitudes. The precipitation forecasts of the cut-cell model were compared also to the CLM. As the cut-cell model LMZ did not incorporate the developments for CLM since 2003, the precipitation forecast of the CLM was not improved in all aspects. However, for the target area downstream of the Himalayas, the cut-cell model considerably improved the prediction of the monthly precipitation forecast even in comparison with the modern CLM version. The cut-cell discretisation seems to improve in particular the localisation of precipitation, while the improvements leading from LM to CLM had a positive effect mainly on amplitude.

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Extraction of Triterpenic Acids and Phytosterols from Apple Pomace with Supercritical Carbon Dioxide: Impact of Process Parameters, Modelling of Kinetics, and Scaling-Up Study

Molecules ◽

10.3390/molecules23112790 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2790 ◽

Cited By ~ 3

Author(s):

Łukasz Woźniak ◽

Anna Szakiel ◽

Cezary Pączkowski ◽

Krystian Marszałek ◽

Sylwia Skąpska ◽

...

Keyword(s):

Carbon Dioxide ◽

Process Parameters ◽

Binary Systems ◽

Cell Model ◽

Intact Cell ◽

Selective Extraction ◽

Apple Pomace ◽

Extraction Curve ◽

Hydrophobic Compounds ◽

The Impact

Apple pomace, a byproduct of juice production, is a rich source of bioactive compounds and nutrients. Supercritical fluid extraction was proposed as a method for a fast and selective extraction of hydrophobic compounds with a pharmaceutical potential from this matrix. Chromatographic analysis showed that the pomace contained significant amounts of such substances, the most abundant of them were ursolic acid, oleanolic acid, and β-sitosterol. The solubility was chosen as a primary factor for a selection of the extraction conditions; the best results were acquired for a temperature of 80 °C and a pressure of 30 MPa. The equation proposed by Chrastil was applied for the description of the impact of the process parameters on the solubility of the analytes; the obtained values of coefficients of determination were satisfactory, despite the fact that the equation was developed for binary systems. The extraction curves obtained during the experiments were used for the description of the process kinetics using the Broken plus Intact Cell model. The impact of the temperature, pressure, and flow rate of carbon dioxide on the mass transfer phenomena was investigated. The data obtained allowed the prediction of the extraction curve for the process conducted on the larger scale.

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The Cortical Actin Filament Network of Neutrophil Leucocytes During Phagocytosis and Chemotaxis

The Neutrophil: Cellular Biochemistry and Physiology ◽

10.1201/9781351077200-6 ◽

2018 ◽

pp. 141-165 ◽

Cited By ~ 1

Author(s):

Peter Sheterline ◽

Janet E. Rickard

Keyword(s):

Actin Filament ◽

Cortical Actin ◽

Filament Network

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Localisation determines the optimal noise rate for quantum transport

New Journal of Physics ◽

10.1088/1367-2630/ac3b2c ◽

2021 ◽

Author(s):

Alexandre Coates ◽

Brendon W Lovett ◽

Erik Gauger

Keyword(s):

Energy Transport ◽

Optimal Transport ◽

Detailed Balance ◽

Finite Size ◽

Temperature Limit ◽

Transport Efficiency ◽

Size Dependent ◽

Noise Rate ◽

Pure Dephasing ◽

The Impact

Abstract Environmental noise plays a key role in determining the efficiency of transport in quantum systems. However, disorder and localisation alter the impact of such noise on energy transport. To provide a deeper understanding of this relationship we perform a systematic study of the connection between eigenstate localisation and the optimal dephasing rate in 1D chains. The effects of energy gradients and disorder on chains of various lengths are evaluated and we demonstrate how optimal transport efficiency is determined by both size-independent, as well as size-dependent factors. By discussing how size-dependent influences emerge from finite size effects we establish when these effects are suppressed, and show that a simple power law captures the interplay between size-dependent and size-independent responses. Moving beyond phenomenological pure dephasing, we implement a finite temperature Bloch-Redfield model that captures detailed balance. We show that the relationship between localisation and optimal environmental coupling strength continues to apply at intermediate and high temperature but breaks down in the low temperature limit.

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