scholarly journals Hodgkin and Huxley Opsin Model for Computationally Efficient Optogenetic Neurostimulation in Cells and Networks

2020 ◽  
Author(s):  
Ruben Schoeters ◽  
Thomas Tarnaud ◽  
Luc Martens ◽  
Wout Joseph ◽  
Robrecht Raedt ◽  
...  
Keyword(s):  
Differential Equations ◽  
Markov Models ◽  
Neuronal Response ◽  
Computational Cost ◽  
Model Fitting ◽  
Time Frame ◽  
Great Accuracy ◽  
Computationally Efficient ◽  
Fitting Procedure ◽  
Proposed Model

AbstractOptogenetics has a lot of potential to become an effective neuromodulative therapy for clinical application. Selecting the correct opsin is crucial to have an optimal optogenetic tool. With computational modeling, the neuronal response to the current dynamics of an opsin can be extensively and systematically tested. Unlike electrical stimulation where the effect is directly defined by the applied field, the stimulation in optogenetics is indirect, depending on the selected opsin’s non-linear kinetics. With the continuous expansion of opsin possibilities, computational studies are difficult due to the need for an accurate model of the selected opsin first. To this end, we propose a Hodgkin-and-Huxley based model (22HH) as alternative to the conventional three and four state Markov models used for opsin modeling. Furthermore, we provide a fitting procedure, which allows for nearly automatic model fitting starting from a vast parameter space. With this procedure, we successfully fitted two distinctive opsins ChR2(H134R) and MerMAID. Both models are able to represent the experimental data with great accuracy and were obtained within an acceptable time frame. This is due to the absence of differential equations in the fitting procedure, with an enormous reduction in computational cost as result. The performance of the proposed model with a fit to ChR2(H134R) was tested, by comparing the neural response in a regular spiking neuron to the response obtained with the non-instantaneous, four state Markov model (4SB), derived by Williams et al. (2013) [1]. Finally, a computational speed gain was observed with the 22HH model in a regular spiking and sparse Pyramidal-Interneuron-Network-Gamma (sPING) network simulation with respect to the 4SB-model, due to the former having two differential equations less. Consequently, the proposed model allows for computationally efficient optogenetic neurostimulation and with the proposed fitting procedure will be valuable for further research in the field of optogenetics.

scholarly journals Double Two-State Opsin Model With Autonomous Parameter Inference

2021 ◽  
Vol 15 ◽  
Author(s):  
Ruben Schoeters ◽  
Thomas Tarnaud ◽  
Luc Martens ◽  
Wout Joseph ◽  
Robrecht Raedt ◽  
...  
Keyword(s):  
Differential Equations ◽  
Markov Models ◽  
Neuronal Response ◽  
Computational Cost ◽  
Model Fitting ◽  
Time Frame ◽  
Great Accuracy ◽  
Computationally Efficient ◽  
Fitting Procedure ◽  
Proposed Model

Optogenetics has a lot of potential to become an effective neuromodulative therapy for clinical applications. Selecting the correct opsin is crucial to have an optimal optogenetic tool. With computational modeling, the neuronal response to the current dynamics of an opsin can be extensively and systematically tested. Unlike electrical stimulation where the effect is directly defined by the applied field, the stimulation in optogenetics is indirect, depending on the selected opsin's non-linear kinetics. With the continuous expansion of opsin possibilities, computational studies are difficult due to the need for an accurate model of the selected opsin first. To this end, we propose a double two-state opsin model as alternative to the conventional three and four state Markov models used for opsin modeling. Furthermore, we provide a fitting procedure, which allows for autonomous model fitting starting from a vast parameter space. With this procedure, we successfully fitted two distinctive opsins (ChR2(H134R) and MerMAID). Both models are able to represent the experimental data with great accuracy and were obtained within an acceptable time frame. This is due to the absence of differential equations in the fitting procedure, with an enormous reduction in computational cost as result. The performance of the proposed model with a fit to ChR2(H134R) was tested, by comparing the neural response in a regular spiking neuron to the response obtained with the non-instantaneous, four state Markov model (4SB), derived by Williams et al. (2013). Finally, a computational speed gain was observed with the proposed model in a regular spiking and sparse Pyramidal-Interneuron-Network-Gamma (sPING) network simulation with respect to the 4SB-model, due to the former having two differential equations less. Consequently, the proposed model allows for computationally efficient optogenetic neurostimulation and with the proposed fitting procedure will be valuable for further research in the field of optogenetics.

scholarly journals Modeling the Conductivity Response to NO2 Gas of Films Based on MWCNT Networks

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4723
Author(s):  
Ada Fort ◽  
Marco Mugnaini ◽  
Enza Panzardi ◽  
Anna Lo Grasso ◽  
Ammar Al Hamry ◽  
...  
Keyword(s):  
Dynamic Behavior ◽  
Electronic Transport ◽  
Au Nanoparticles ◽  
Model Fitting ◽  
Time Variable ◽  
Fitting Procedure ◽  
Proposed Model ◽  
Disordered Networks ◽  
Physical Quantities

This work proposes a model describing the dynamic behavior of sensing films based on functionalized MWCNT networks in terms of conductivity when exposed to time-variable concentrations of NO2 and operating with variable working temperatures. To test the proposed model, disordered networks of MWCNTs functionalized with COOH and Au nanoparticles were exploited. The model is derived from theoretical descriptions of the electronic transport in the nanotube network, of the NO2 chemisorption reaction and of the interaction of these two phenomena. The model is numerically implemented and then identified by estimating all the chemical/physical quantities involved and acting as parameters, through a model fitting procedure. Satisfactory results were obtained in the fitting process, and the identified model was used to further the analysis of the MWCNT sensing in dynamical conditions.

scholarly journals Compressed pseudo-SLAM: pseudorange-integrated compressed simultaneous localisation and mapping for unmanned aerial vehicle navigation

2021 ◽  
pp. 1-13
Author(s):  
Jonghyuk Kim ◽  
Jose Guivant ◽  
Martin L. Sollie ◽  
Torleiv H. Bryne ◽  
Tor Arne Johansen
Keyword(s):  
Unmanned Aerial Vehicle ◽  
Computational Cost ◽  
Satellite System ◽  
Measurement Unit ◽  
Electronic Systems ◽  
Computationally Efficient ◽  
Global Correlation ◽  
Aerial Vehicle ◽  
Correlation Information ◽  
Global Navigation Satellite

Abstract This paper addresses the fusion of the pseudorange/pseudorange rate observations from the global navigation satellite system and the inertial–visual simultaneous localisation and mapping (SLAM) to achieve reliable navigation of unmanned aerial vehicles. This work extends the previous work on a simulation-based study [Kim et al. (2017). Compressed fusion of GNSS and inertial navigation with simultaneous localisation and mapping. IEEE Aerospace and Electronic Systems Magazine, 32(8), 22–36] to a real-flight dataset collected from a fixed-wing unmanned aerial vehicle platform. The dataset consists of measurements from visual landmarks, an inertial measurement unit, and pseudorange and pseudorange rates. We propose a novel all-source navigation filter, termed a compressed pseudo-SLAM, which can seamlessly integrate all available information in a computationally efficient way. In this framework, a local map is dynamically defined around the vehicle, updating the vehicle and local landmark states within the region. A global map includes the rest of the landmarks and is updated at a much lower rate by accumulating (or compressing) the local-to-global correlation information within the filter. It will show that the horizontal navigation error is effectively constrained with one satellite vehicle and one landmark observation. The computational cost will be analysed, demonstrating the efficiency of the method.

Analysis of a New Class of Impulsive Implicit Sequential Fractional Differential Equations

2020 ◽  
Vol 21 (6) ◽  
pp. 571-587 ◽  
Author(s):  
Akbar Zada ◽  
Sartaj Ali ◽  
Tongxing Li
Keyword(s):  
Differential Equations ◽  
Fractional Order ◽  
Fractional Differential Equations ◽  
Sufficient Conditions ◽  
Uniqueness Of Solutions ◽  
Integer Order ◽  
New Class ◽  
Proposed Model ◽  
Fractional Differential ◽  
Sequential Fractional Differential Equations

AbstractIn this paper, we study an implicit sequential fractional order differential equation with non-instantaneous impulses and multi-point boundary conditions. The article comprehensively elaborate four different types of Ulam’s stability in the lights of generalized Diaz Margolis’s fixed point theorem. Moreover, some sufficient conditions are constructed to observe the existence and uniqueness of solutions for the proposed model. The proposed model contains both the integer order and fractional order derivatives. Thus, the exponential function appearers in the solution of the proposed model which will lead researchers to study fractional differential equations with well known methods of integer order differential equations. In the last, few examples are provided to show the applicability of our main results.

Multilevel Monte Carlo by using the Halton sequence

2020 ◽  
Vol 26 (3) ◽  
pp. 193-203
Author(s):  
Shady Ahmed Nagy ◽  
Mohamed A. El-Beltagy ◽  
Mohamed Wafa
Keyword(s):  
Monte Carlo ◽  
Differential Equations ◽  
Stochastic Differential Equations ◽  
Computational Cost ◽  
Random Numbers ◽  
Multilevel Monte Carlo ◽  
Halton Sequence ◽  
Random Generator ◽  
Mc Simulation ◽  
Multilevel Monte Carlo Method

AbstractMonte Carlo (MC) simulation depends on pseudo-random numbers. The generation of these numbers is examined in connection with the Brownian motion. We present the low discrepancy sequence known as Halton sequence that generates different stochastic samples in an equally distributed form. This will increase the convergence and accuracy using the generated different samples in the Multilevel Monte Carlo method (MLMC). We compare algorithms by using a pseudo-random generator and a random generator depending on a Halton sequence. The computational cost for different stochastic differential equations increases in a standard MC technique. It will be highly reduced using a Halton sequence, especially in multiplicative stochastic differential equations.

Hybrid LES Approach for Practical Turbomachinery Flows—Part I: Hierarchy and Example Simulations

2011 ◽  
Vol 134 (2) ◽  
Author(s):  
Paul Tucker ◽  
Simon Eastwood ◽  
Christian Klostermeier ◽  
Richard Jefferson-Loveday ◽  
James Tyacke ◽  
...  
Keyword(s):  
Convex Surface ◽  
Computational Cost ◽  
Companion Paper ◽  
Navier Stokes ◽  
Computationally Efficient ◽  
Turbulent Structures ◽  
Hybrid Strategy ◽  
Eddy Simulation ◽  
Related Approach ◽  
Les Model

Unlike Reynolds-averaged Navier–Stokes (RANS) models that need calibration for different flow classes, LES (where larger turbulent structures are resolved by the grid and smaller modeled in a fashion reminiscent of RANS) offers the opportunity to resolve geometry dependent turbulence as found in complex internal flows—albeit at substantially higher computational cost. Based on the results for a broad range of studies involving different numerical schemes, large eddy simulation (LES) models and grid topologies, an LES hierarchy and hybrid LES related approach is proposed. With the latter, away from walls, no LES model is used, giving what can be termed numerical LES (NLES). This is relatively computationally efficient and makes use of the dissipation present in practical industrial computational fluid dynamics (CFD) programs. Near walls, RANS modeling is used to cover over numerous small structures, the LES resolution of which is generally intractable with current computational power. The linking of the RANS and NLES zones through a Hamilton–Jacobi equation is advocated. The RANS-NLES hybridization makes further sense for compressible flow solvers, where, as the Mach number tends to zero at walls, excessive dissipation can occur. The hybrid strategy is used to predict flow over a rib roughened surface and a jet impinging on a convex surface. These cases are important for blade cooling and show encouraging results. Further results are presented in a companion paper.

scholarly journals Neural Decoding Using a Parallel Sequential Monte Carlo Method on Point Processes with Ensemble Effect

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Kai Xu ◽  
Yiwen Wang ◽  
Fang Wang ◽  
Yuxi Liao ◽  
Qiaosheng Zhang ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Point Process ◽  
Goodness Of Fit ◽  
Point Processes ◽  
Sequential Monte Carlo ◽  
Neuronal Response ◽  
Position Estimation ◽  
Monte Carlo Algorithm ◽  
Sequential Monte Carlo Method ◽  
Proposed Model

Sequential Monte Carlo estimation on point processes has been successfully applied to predict the movement from neural activity. However, there exist some issues along with this method such as the simplified tuning model and the high computational complexity, which may degenerate the decoding performance of motor brain machine interfaces. In this paper, we adopt a general tuning model which takes recent ensemble activity into account. The goodness-of-fit analysis demonstrates that the proposed model can predict the neuronal response more accurately than the one only depending on kinematics. A new sequential Monte Carlo algorithm based on the proposed model is constructed. The algorithm can significantly reduce the root mean square error of decoding results, which decreases 23.6% in position estimation. In addition, we accelerate the decoding speed by implementing the proposed algorithm in a massive parallel manner on GPU. The results demonstrate that the spike trains can be decoded as point process in real time even with 8000 particles or 300 neurons, which is over 10 times faster than the serial implementation. The main contribution of our work is to enable the sequential Monte Carlo algorithm with point process observation to output the movement estimation much faster and more accurately.

An Efficient Preconditioner for Linear System Solution in Multi-Domain Modeling of the Circulatory System

2013 ◽  
Author(s):  
Mahdi Esmaily Moghadam ◽  
Yuri Bazilevs ◽  
Tain-Yen Hsia ◽  
Alison Marsden
Keyword(s):  
Strong Coupling ◽  
Large Scale ◽  
Computational Cost ◽  
Circulatory System ◽  
Flow Simulation ◽  
Global Dynamics ◽  
Domain Modeling ◽  
Computationally Efficient ◽  
Lumped Parameter ◽  
System Solution

A closed-loop lumped parameter network (LPN) coupled to a 3D domain is a powerful tool that can be used to model the global dynamics of the circulatory system. Coupling a 0D LPN to a 3D CFD domain is a numerically challenging problem, often associated with instabilities, extra computational cost, and loss of modularity. A computationally efficient finite element framework has been recently proposed that achieves numerical stability without sacrificing modularity [1]. This type of coupling introduces new challenges in the linear algebraic equation solver (LS), producing an strong coupling between flow and pressure that leads to an ill-conditioned tangent matrix. In this paper we exploit this strong coupling to obtain a novel and efficient algorithm for the linear solver (LS). We illustrate the efficiency of this method on several large-scale cardiovascular blood flow simulation problems.

scholarly journals Computing Optimal Properties of Drugs Using Mathematical Models of Single Channel Dynamics

2018 ◽  
Vol 6 (1) ◽  
pp. 41-64 ◽  
Author(s):  
Aslak Tveito ◽  
Mary M. Maleckar ◽  
Glenn T. Lines
Keyword(s):  
Differential Equations ◽  
Markov Model ◽  
Stochastic Models ◽  
Markov Models ◽  
Single Channel ◽  
Probability Density Functions ◽  
Density Functions ◽  
Mathematical Framework ◽  
Wild Type ◽  
Channel Dynamics

AbstractSingle channel dynamics can be modeled using stochastic differential equations, and the dynamics of the state of the channel (e.g. open, closed, inactivated) can be represented using Markov models. Such models can also be used to represent the effect of mutations as well as the effect of drugs used to alleviate deleterious effects of mutations. Based on the Markov model and the stochastic models of the single channel, it is possible to derive deterministic partial differential equations (PDEs) giving the probability density functions (PDFs) of the states of the Markov model. In this study, we have analyzed PDEs modeling wild type (WT) channels, mutant channels (MT) and mutant channels for which a drug has been applied (MTD). Our aim is to show that it is possible to optimize the parameters of a given drug such that the solution of theMTD model is very close to that of the WT: the mutation’s effect is, theoretically, reduced significantly.We will present the mathematical framework underpinning this methodology and apply it to several examples. In particular, we will show that it is possible to use the method to, theoretically, improve the properties of some well-known existing drugs.

A Computationally Efficient Predictive Controller for Lane Keeping of Semi-Autonomous Vehicles

2014 ◽  
Author(s):  
Changchun Liu ◽  
Chankyu Lee ◽  
Andreas Hansen ◽  
J. Karl Hedrick ◽  
Jieyun Ding
Keyword(s):  
Autonomous Vehicles ◽  
Piecewise Linear ◽  
Computational Cost ◽  
Parametric Programming ◽  
Linear Feedback ◽  
Loop Model ◽  
Computationally Efficient ◽  
Feedback Function ◽  
Predictive Controller ◽  
Lane Keeping

Model predictive control (MPC) is a popular technique for the development of active safety systems. However, its high computational cost prevents it from being implemented on lower-cost hardware. This paper presents a computationally efficient predictive controller for lane keeping assistance systems. The controller shares control with the driver, and applies a correction steering when there is a potential lane departure. Using the explicit feedback MPC, a multi-parametric nonlinear programming problem with a human-in-the-loop model and safety constraints is formulated. The cost function is chosen as the difference between the linear state feedback function to be determined and the resultant optimal control sequence of the MPC problem solved off-line given the current state. The piecewise linear feedback function is obtained by solving the parametric programming with an approximation approach. The effectiveness of the controller is evaluated through numerical simulations.

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