scholarly journals Efficient approximations for stationary single-channel Ca2+ nanodomains across length scales

2020 ◽  
Author(s):  
Y Chen ◽  
C Muratov ◽  
V Matveev
Keyword(s):  
Parameter Space ◽  
Single Channel ◽  
Asymptotic Series ◽  
Rational Functions ◽  
Great Accuracy ◽  
Model Parameters ◽  
Relevant Parameter ◽  
Buffer Concentration ◽  
Computationally Efficient ◽  
Wide Range

ABSTRACTWe consider the stationary solution for the Ca2+ concentration near a point Ca2+ source describing a single-channel Ca2+ nanodomain, in the presence of a single mobile Ca2+ buffer with one-to-one Ca2+ binding. We present computationally efficient approximants that estimate stationary single-channel Ca2+ nanodomains with great accuracy in broad regions of parameter space. The presented approximants have a functional form that combines rational and exponential functions, which is similar to that of the well-known Excess Buffer Approximation and the linear approximation, but with parameters estimated using two novel (to our knowledge) methods. One of the methods involves interpolation between the short-range Taylor series of the buffer concentration and its long-range asymptotic series in inverse powers of distance from the channel. Although this method has already been used to find Padé (rational-function) approximants to single-channel Ca2+ and buffer concentration, extending this method to interpolants combining exponential and rational functions improves accuracy in a significant fraction of the relevant parameter space. A second method is based on the variational approach, and involves a global minimization of an appropriate functional with respect to parameters of the chosen approximations. Extensive parameter sensitivity analysis is presented, comparing these two methods with previously developed approximants. Apart from increased accuracy, the strength of these approximants is that they can be extended to more realistic buffers with multiple binding sites characterized by cooperative Ca2+ binding, such as calmodulin and calretinin.STATEMENT OF SIGNIFICANCEMathematical and computational modeling plays an important role in the study of local Ca2+ signals underlying vesicle exocysosis, muscle contraction and other fundamental physiological processes. Closed-form approximations describing steady-state distribution of Ca2+ in the vicinity of an open Ca2+ channel have proved particularly useful for the qualitative modeling of local Ca2+ signals. We present simple and efficient approximants for the Ca2+ concentration in the presence of a mobile Ca2+ buffer, which achieve great accuracy over a wide range of model parameters. Such approximations provide an efficient method for estimating Ca2+ and buffer concentrations without resorting to numerical simulations, and allow to study the qualitative dependence of nanodomain Ca2+ distribution on the buffer’s Ca2+ binding properties and its diffusivity.

The prediction of solute transport in surcharged manholes using CFD

2007 ◽  
Vol 55 (4) ◽  
pp. 57-64 ◽  
Author(s):  
S.D. Lau ◽  
V.R. Stovin ◽  
I. Guymer
Keyword(s):  
Solute Transport ◽  
Laboratory Data ◽  
Transport Processes ◽  
Relevant Parameter ◽  
Computationally Efficient ◽  
Engineering Structures ◽  
Advection Dispersion ◽  
Hydraulic Regime ◽  
Wide Range ◽  
Discrete Phase

Solute transport processes occur within a wide range of water engineering structures, and urban drainage engineers increasingly rely on modelling tools to represent the transport of dissolved materials. The models take as input representative travel time and dispersion characteristics for key system components, and these generally have to be identified via field or laboratory measurements. Computational Fluid Dynamics (CFD) has the potential to reveal the underlying hydraulic processes that control solute transport, and to provide a generic means of identifying relevant parameter values. This paper reports on a study that has been undertaken to evaluate the feasibility of utilising a CFD-based approach to modelling solute transport. Discrete phase modelling has been adopted, as this is computationally efficient and robust when compared with the time-dependent solution of the advection–dispersion equation. Simulation results are compared with published laboratory data characterising the dispersion effects of surcharged manholes, focusing specifically on an 800 mm diameter laboratory manhole for a flowrate of 0.002 m3/s and a range of surcharge depths. Preliminary indications are that the CFD results adequately replicate the measured downstream temporal concentration profiles, and that a threshold surcharge depth, corresponding to a change in hydraulic regime within the manhole, can also be identified.

scholarly journals Stationary Ca2+ nanodomains in the presence of buffers with two binding sites

2020 ◽  
Author(s):  
Y. Chen ◽  
V. Matveev
Keyword(s):  
Closed Form ◽  
Binding Sites ◽  
Interpolation Method ◽  
Secretory Vesicle ◽  
Model Parameters ◽  
Relevant Parameter ◽  
Wide Range ◽  
Vesicle Exocytosis ◽  
Cell Processes ◽  
The Impact

ABSTRACTWe examine closed-form approximations for the equilibrium Ca2+ concentration near a point Ca2+ source representing a Ca2+ channel, in the presence of a mobile Ca2+ buffer with 2:1 Ca2+ binding stoichiometry. We consider buffers with two Ca2+ binding sites activated in tandem and possessing distinct binding affinities and kinetics. This allows to model the impact on Ca2+ nanodomains of realistic endogenous Ca2+ buffers characterized by cooperative Ca2+ binding, such as calretinin. The approximations we present involve a combination or rational and exponential functions, whose parameters are constrained using the series interpolation method that we recently introduced for the case of 1:1 Ca2+ buffers. We conduct extensive parameter sensitivity analysis and show that the obtained closed-form approximations achieve reasonable qualitative accuracy for a wide range of buffer’s Ca2+ binding properties and other relevant model parameters. In particular, the accuracy of the newly derived approximants exceeds that of the rapid buffering approximation in large portions of the relevant parameter space.STATEMENT OF SIGNIFICANCEClosed-form approximations describing equilibrium distribution of Ca2+ in the vicinity of an open Ca2+ channel proved useful for the modeling of local Ca2+ signals underlying secretory vesicle exocytosis, muscle contraction and other cell processes. Such approximations provide an efficient method for estimating Ca2+ and buffer concentrations without computationally expensive numerical simulations. However, while most biological buffers have multiple Ca2+ binding sites, much of prior modeling work considered Ca2+ dynamics in the presence of Ca2+ buffers with a single Ca2+ binding site. Here we extend modeling work on equilibrium Ca2+ nanodomains to the case of Ca2+ buffers with two binding sites, allowing to gain deeper insight into the impact of more realistic Ca2+ buffers, including cooperative buffers, on cell Ca2+ dynamics.

scholarly journals A Multiscale Model of Terrain Dynamics for Real-Time Earthmoving Simulation

2020 ◽  
Author(s):  
Martin Servin ◽  
Tomas Berglund ◽  
Samuel Nystedt
Keyword(s):  
Real Time ◽  
Multibody Dynamics ◽  
Reference Model ◽  
Multiscale Model ◽  
Particle Model ◽  
Model Parameters ◽  
Computationally Efficient ◽  
Computational Performance ◽  
Wide Range ◽  
Dynamics Simulations

Abstract A multiscale model for real-time simulation of terrain dynamics is explored. To represent the dynamics on different scales the model combines the description of soil as a continuous solid, as distinct particles and as rigid multibodies. The models are dynamically coupled to each other and to the earthmoving equipment. Agitated soil is represented by a hybrid of contacting particles and continuum solid, with the moving equipment and resting soil as geometric boundaries. Each zone of active soil is aggregated into distinct bodies, with the proper mass, momentum and frictional-cohesive properties, which constrain the equipment's multibody dynamics. The particle model parameters are pre-calibrated to the bulk mechanical parameters for a wide range of different soils. The result is a computationally efficient model for earthmoving operations that resolve the motion of the soil, using a fast iterative solver, and provide realistic forces and dynamic for the equipment, using a direct solver for high numerical precision. Numerical simulations of excavation and bulldozing operations are performed to validate model and measure the computational performance. Reference data is produced using coupled discrete element and multibody dynamics simulations at relatively high resolution. The digging resistance and soil displacements with the real-time multiscale model agree with the reference model up to 10-25%, and run more than three orders in magnitude faster.

scholarly journals A multiscale model of terrain dynamics for real-time earthmoving simulation

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Martin Servin ◽  
Tomas Berglund ◽  
Samuel Nystedt
Keyword(s):  
Real Time ◽  
Multibody Dynamics ◽  
Reference Model ◽  
Multiscale Model ◽  
Particle Model ◽  
Model Parameters ◽  
Computationally Efficient ◽  
Computational Performance ◽  
Wide Range ◽  
Dynamics Simulations

AbstractA multiscale model for real-time simulation of terrain dynamics is explored. To represent the dynamics on different scales the model combines the description of soil as a continuous solid, as distinct particles and as rigid multibodies. The models are dynamically coupled to each other and to the earthmoving equipment. Agitated soil is represented by a hybrid of contacting particles and continuum solid, with the moving equipment and resting soil as geometric boundaries. Each zone of active soil is aggregated into distinct bodies, with the proper mass, momentum and frictional-cohesive properties, which constrain the equipment’s multibody dynamics. The particle model parameters are pre-calibrated to the bulk mechanical parameters for a wide range of different soils. The result is a computationally efficient model for earthmoving operations that resolve the motion of the soil, using a fast iterative solver, and provide realistic forces and dynamic for the equipment, using a direct solver for high numerical precision. Numerical simulations of excavation and bulldozing operations are performed to test the model and measure the computational performance. Reference data is produced using coupled discrete element and multibody dynamics simulations at relatively high resolution. The digging resistance and soil displacements with the real-time multiscale model agree with the reference model up to 10–25%, and run more than three orders of magnitude faster.

An Investigation on the Performance of an Oxidation Catalyst Using Two-dimensional Simulation with Detailed Reaction Mechanism

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Sreeharsh Nair ◽  
Mayank Mittal
Keyword(s):  
Single Channel ◽  
Catalytic Converter ◽  
Oxidation Catalyst ◽  
Low Temperature Combustion ◽  
Wide Range ◽  
Detailed Reaction Mechanism ◽  
Temperature Combustion ◽  
High Concentrations ◽  
Dimensional Simulation ◽  
Surface Reaction Kinetics

AbstractThe advent of stricter emission standards has increased the importance of aftertreatment devices and the role of numerical simulations in the evolution of better catalytic converters in order to satisfy these emission regulations. In this paper, a 2-D numerical simulation of a single channel of the monolith catalytic converter is presented by using detailed surface reaction kinetics aiming to investigate the chemical behaviour inside the converter. The model has been developed to study the conversion of carbon monoxide (CO) in the presence of propene (C3H6) for low-temperature combustion (LTC) engine application. The inhibition effect of C3H6 over a wide range of CO inlet concentrations is investigated. Considering both low and high levels of CO concentration at the inlet, the 2-D model predicted better results than their corresponding 1-D counterparts when compared with the experimental data from literature. It was also observed that C3H6 inhibition at high temperatures was significant, particularly for high concentrations of CO compared to low concentrations of CO at the inlet.

Nearly Exact Bayesian Estimation of Non-linear No-Arbitrage Term-Structure Models*

2021 ◽  
Author(s):  
Marcello Pericoli ◽  
Marco Taboga
Keyword(s):  
Bayesian Estimation ◽  
Term Structure ◽  
Broad Class ◽  
Model Parameters ◽  
State Variables ◽  
Computationally Efficient ◽  
Macroeconomic Factors ◽  
No Arbitrage ◽  
Term Structure Models ◽  
Non Linear

Abstract We propose a general method for the Bayesian estimation of a very broad class of non-linear no-arbitrage term-structure models. The main innovation we introduce is a computationally efficient method, based on deep learning techniques, for approximating no-arbitrage model-implied bond yields to any desired degree of accuracy. Once the pricing function is approximated, the posterior distribution of model parameters and unobservable state variables can be estimated by standard Markov Chain Monte Carlo methods. As an illustrative example, we apply the proposed techniques to the estimation of a shadow-rate model with a time-varying lower bound and unspanned macroeconomic factors.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Antifungal Activity of Propyl Disulfide from Neem (Azadirachta indica) in Vapor and Agar Diffusion Assays against Anthracnose Pathogens (Colletotrichum gloeosporioides and Colletotrichum acutatum) in Mango Fruit

2021 ◽  
Vol 9 (4) ◽  
pp. 839
Author(s):  
Muhammad Rafiullah Khan ◽  
Vanee Chonhenchob ◽  
Chongxing Huang ◽  
Panitee Suwanamornlert
Keyword(s):  
Antifungal Activity ◽  
Mycelial Growth ◽  
Colletotrichum Gloeosporioides ◽  
Colletotrichum Acutatum ◽  
Model Parameters ◽  
Pathogenicity Test ◽  
Agar Diffusion ◽  
Wide Range ◽  
Significant Difference ◽  
Diffusion Assay

Microorganisms causing anthracnose diseases have a medium to a high level of resistance to the existing fungicides. This study aimed to investigate neem plant extract (propyl disulfide, PD) as an alternative to the current fungicides against mango’s anthracnose. Microorganisms were isolated from decayed mango and identified as Colletotrichum gloeosporioides and Colletotrichum acutatum. Next, a pathogenicity test was conducted and after fulfilling Koch’s postulates, fungi were reisolated from these symptomatic fruits and we thus obtained pure cultures. Then, different concentrations of PD were used against these fungi in vapor and agar diffusion assays. Ethanol and distilled water were served as control treatments. PD significantly (p ≤ 0.05) inhibited more of the mycelial growth of these fungi than both controls. The antifungal activity of PD increased with increasing concentrations. The vapor diffusion assay was more effective in inhibiting the mycelial growth of these fungi than the agar diffusion assay. A good fit (R2, 0.950) of the experimental data in the Gompertz growth model and a significant difference in the model parameters, i.e., lag phase (λ), stationary phase (A) and mycelial growth rate, further showed the antifungal efficacy of PD. Therefore, PD could be the best antimicrobial compound against a wide range of microorganisms.

scholarly journals A Reinforcement Learning Framework for Spiking Networks with Dynamic Synapses

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Karim El-Laithy ◽  
Martin Bogdan
Keyword(s):  
Reinforcement Learning ◽  
Spike Timing ◽  
Neural Representation ◽  
Model Parameters ◽  
Learning Framework ◽  
Reference Target ◽  
Wide Range ◽  
Spiking Network ◽  
Dynamic Synapses ◽  
Exclusive Or

An integration of both the Hebbian-based and reinforcement learning (RL) rules is presented for dynamic synapses. The proposed framework permits the Hebbian rule to update the hidden synaptic model parameters regulating the synaptic response rather than the synaptic weights. This is performed using both the value and the sign of the temporal difference in the reward signal after each trial. Applying this framework, a spiking network with spike-timing-dependent synapses is tested to learn the exclusive-OR computation on a temporally coded basis. Reward values are calculated with the distance between the output spike train of the network and a reference target one. Results show that the network is able to capture the required dynamics and that the proposed framework can reveal indeed an integrated version of Hebbian and RL. The proposed framework is tractable and less computationally expensive. The framework is applicable to a wide class of synaptic models and is not restricted to the used neural representation. This generality, along with the reported results, supports adopting the introduced approach to benefit from the biologically plausible synaptic models in a wide range of intuitive signal processing.

scholarly journals Modelling the Inflation and Elastic Instabilities of Rubber-Like Spherical and Cylindrical Shells Using a New Generalised Neo-Hookean Strain Energy Function

2021 ◽  
Author(s):  
Afshin Anssari-Benam ◽  
Andrea Bucchi ◽  
Giuseppe Saccomandi
Keyword(s):  
Experimental Data ◽  
Energy Function ◽  
Limit Point ◽  
Strain Energy ◽  
Cylindrical Shells ◽  
Strain Energy Function ◽  
Model Parameters ◽  
Wide Range ◽  
Cylindrical Tubes ◽  
Gent Model

AbstractThe application of a newly proposed generalised neo-Hookean strain energy function to the inflation of incompressible rubber-like spherical and cylindrical shells is demonstrated in this paper. The pressure ($P$ P ) – inflation ($\lambda $ λ or $v$ v ) relationships are derived and presented for four shells: thin- and thick-walled spherical balloons, and thin- and thick-walled cylindrical tubes. Characteristics of the inflation curves predicted by the model for the four considered shells are analysed and the critical values of the model parameters for exhibiting the limit-point instability are established. The application of the model to extant experimental datasets procured from studies across 19th to 21st century will be demonstrated, showing favourable agreement between the model and the experimental data. The capability of the model to capture the two characteristic instability phenomena in the inflation of rubber-like materials, namely the limit-point and inflation-jump instabilities, will be made evident from both the theoretical analysis and curve-fitting approaches presented in this study. A comparison with the predictions of the Gent model for the considered data is also demonstrated and is shown that our presented model provides improved fits. Given the simplicity of the model, its ability to fit a wide range of experimental data and capture both limit-point and inflation-jump instabilities, we propose the application of our model to the inflation of rubber-like materials.

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