scholarly journals The Mechanical Origin of the Radial Shape in Distichous Phyllotaxy Grass Plants

2021 ◽  
Author(s):  
Yoshiki Tokuyama ◽  
Yohei Koide ◽  
Kazumitsu Onishi ◽  
Kiwamu Hikichi ◽  
Miku Omachi ◽  
...  
Keyword(s):  
Time Course ◽  
Computational Models ◽  
Shape Change ◽  
Kinematic Model ◽  
Elevation Angle ◽  
Three Dimensional ◽  
Oryza Rufipogon ◽  
Model Parameters ◽  
Isogenic Line ◽  
Wild Rice Species

Abstract Three-dimensional plant shapes are influenced by their phyllotaxy, which plays a significant role in their environmental adaptation. Grasses with distichous phyllotaxy have linearly aligned culms and usually have vertical fan-like shapes. Counterintuitively, some distichous phyllotaxy grasses have radial shapes. Here, we investigate the organ-level mechanism underlying radial shape development in the distichous phyllotactic wild rice species (Oryza rufipogon). Detailed time-course phenotyping and three-dimensional micro-computed tomography showed that changes in the elevation angle in the main culm and azimuth angle in the primary tillers contribute to radial shape development. To infer the mechanical basis of the shape change, we simulated the movements of culms controlled by different kinematic factors. The computational models predicted that the combination of movements, including that controlled by negative gravitropism, produces the overall radial shape. This prediction was experimentally assessed. The analysis using a near-isogenic line of the gene, PROG1 for prostrate growth and the gravitropic mutant (lazy1) showed an association between genes and our model parameters. Our findings provide a simple, yet substantial, kinematic model for how the shape in distichous phyllotaxy plants changes as part of their adaptation to the surrounding environment.

scholarly journals The Design of Compact Robotic-Assisted Needle Position System with MPC-Based Remote Control

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Jing Guo ◽  
Yi Liu ◽  
Jin Wang ◽  
Chao Zeng ◽  
Jie Huang ◽  
...  
Keyword(s):  
Control Method ◽  
Kinematic Model ◽  
Three Dimensional ◽  
Percutaneous Biopsy ◽  
Target Point ◽  
Model Parameters ◽  
Control Input ◽  
Control Performance ◽  
Robot System ◽  
Needle Position

This article introduces the design and control performance of a lightweight, flexible, 4-degree-of-freedom (DOF) parallel robot for percutaneous biopsy guided by computed tomography (CT). At present, the CT guidance method allows surgeons to quickly locate the lesion area; however, it is necessary to manually adjust the position of the puncture needle for insertion. In this paper, a three-dimensional assisted method is used to infer the control input required to reach the target point through the kinematic model of the robot. A Kalman filter is designed to estimate model parameters and obtain a more accurate model. To further improve the control performance of the robot system, a model-based control method—the model predictive control (MPC) controller—is used to increase the accuracy of the needle position in the developed robot system. In this way, medical efficiency is improved while reducing the burden on the surgeon.

Parameter Estimation of Nonlinear Biomedical Systems Using Extended Kalman Filter Algorithm

2017 ◽  
pp. 76-99 ◽  
Author(s):  
Kamalanand Krishnamurthy
Keyword(s):  
Parameter Estimation ◽  
Kalman Filter ◽  
Extended Kalman Filter ◽  
Computational Models ◽  
Three Dimensional ◽  
Model Parameters ◽  
State Variables ◽  
Three Dimensional Model ◽  
Biomedical Systems ◽  
Estimation Of Model Parameters

Parameter estimation is a central issue in mathematical modelling of biomedical systems and for the development of patient specific models. The technique of estimating parameters helps in obtaining diagnostic information from computational models of biological systems. However, in most of the biomedical systems, the estimation of model parameters is a challenging task due to the nonlinearity of mathematical models. In this chapter, the method of estimation of nonlinear model parameters from measurements of state variables, using the extended Kalman filter, is extensively explained using an example of the three-dimensional model of the HIV/AIDS system.

scholarly journals Manufactured solutions and the numerical verification of isothermal, nonlinear, three-dimensional Stokes ice-sheet models

2012 ◽  
Vol 6 (4) ◽  
pp. 2689-2714 ◽  
Author(s):  
W. Leng ◽  
L. Ju ◽  
M. Gunzburger ◽  
S. Price
Keyword(s):  
Computational Models ◽  
Initial Conditions ◽  
Three Dimensional ◽  
Ice Sheet ◽  
Analytic Solutions ◽  
Model Parameters ◽  
Numerical Verification ◽  
Order Partial Differential Equation ◽  
Manufactured Solutions ◽  
Manufactured Solution

Abstract. The technique of manufactured solutions is used for verification of computational models in many fields. In this paper we construct manufactured solutions for models of three-dimensional, isothermal, nonlinear Stokes flow in glaciers and ice sheets. The solution construction procedure starts with kinematic boundary conditions and is mainly based on the solution of a first-order partial differential equation for the ice velocity that satisfies the incompressibility condition. The manufactured solutions depend on the geometry of the ice sheet and other model parameters. Initial conditions are taken from the periodic geometry of a standard problem of the ISMIP-HOM benchmark tests and altered through the manufactured solution procedure to generate an analytic solution for the time-dependent flow problem. We then use this manufactured solution to verify a parallel, high-order accurate, finite element Stokes ice-sheet model. Results from the computational model show excellent agreement with the manufactured analytic solutions.

Parameter Estimation of Nonlinear Biomedical Systems Using Extended Kalman Filter Algorithm

2018 ◽  
pp. 690-713
Author(s):  
Kamalanand Krishnamurthy
Keyword(s):  
Parameter Estimation ◽  
Kalman Filter ◽  
Extended Kalman Filter ◽  
Computational Models ◽  
Three Dimensional ◽  
Model Parameters ◽  
State Variables ◽  
Three Dimensional Model ◽  
Biomedical Systems ◽  
Estimation Of Model Parameters

Parameter estimation is a central issue in mathematical modelling of biomedical systems and for the development of patient specific models. The technique of estimating parameters helps in obtaining diagnostic information from computational models of biological systems. However, in most of the biomedical systems, the estimation of model parameters is a challenging task due to the nonlinearity of mathematical models. In this chapter, the method of estimation of nonlinear model parameters from measurements of state variables, using the extended Kalman filter, is extensively explained using an example of the three-dimensional model of the HIV/AIDS system.

scholarly journals Subject-Specific Computational Modeling of Evoked Rabbit Phonation

2015 ◽  
Vol 138 (1) ◽  
Author(s):  
Siyuan Chang ◽  
Carolyn K. Novaleski ◽  
Tsuyoshi Kojima ◽  
Masanobu Mizuta ◽  
Haoxiang Luo ◽  
...  
Keyword(s):  
Vocal Fold ◽  
Computational Models ◽  
Three Dimensional ◽  
Model Parameters ◽  
Individual Subject ◽  
Vocal Fold Vibration ◽  
Subject Specific ◽  
Vocal Fold Dynamics ◽  
1D Model

When developing high-fidelity computational model of vocal fold vibration for voice production of individuals, one would run into typical issues of unknown model parameters and model validation of individual-specific characteristics of phonation. In the current study, the evoked rabbit phonation is adopted to explore some of these issues. In particular, the mechanical properties of the rabbit's vocal fold tissue are unknown for individual subjects. In the model, we couple a 3D vocal fold model that is based on the magnetic resonance (MR) scan of the rabbit larynx and a simple one-dimensional (1D) model for the glottal airflow to perform fast simulations of the vocal fold dynamics. This hybrid three-dimensional (3D)/1D model is then used along with the experimental measurement of each individual subject for determination of the vocal fold properties. The vibration frequency and deformation amplitude from the final model are matched reasonably well for individual subjects. The modeling and validation approaches adopted here could be useful for future development of subject-specific computational models of vocal fold vibration.

Time Series Analysis of Transmesothelial Invasion by Endometrial Stromal and Epithelial Cells Using Three-dimensional Confocal Microscopy

2001 ◽  
Vol 7 (S2) ◽  
pp. 580-581
Author(s):  
CA Witz ◽  
S Cho ◽  
VE Centonze ◽  
IA Montoya-Rodriguez ◽  
RS Schenken
Keyword(s):  
Epithelial Cells ◽  
Stromal Cells ◽  
Time Course ◽  
Three Dimensional ◽  
Collagen Iv ◽  
Mesothelial Cells ◽  
Endometrial Stromal Cells ◽  
Human Collagen ◽  
Endometrial Epithelial Cells

Using human peritoneal explants, we have previously demonstrated that endometrial stromal cells (ESCs) and endometrial epithelial cells (EECs) attach to intact mesothelium. Attachment occurs within one hour and mesothelial invasion occurs within 18 hours (Figure 1). We have also demonstrated that, in vivo, the mesothelium overlies a continuous layer of collagen IV (Col IV).More recently we have used CLSM, to study the mechanism and time course of ESC and EEC attachment and invasion through mesothelial monolayers. in these studies, CellTracker® dyes were used to label cells. Mesothelial cells were labeled with chloromethylbenzoylaminotetramethylrhodamine (CellTracker Orange). Mesothelial cells were then plated on human collagen IV coated, laser etched coverslips. Mesothelial cells were cultured to subconfluence. ESCs and EECs, labeled with chloromethylfluorscein diacetate (CellTracker Green) were plated on the mesothelial monolayers. Cultures were examined at 1, 6, 12 and 24 hours with simultaneous differential interference contrast and CLSM.

scholarly journals A flexible framework for sequential estimation of model parameters in computational hemodynamics

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Christopher J. Arthurs ◽  
Nan Xiao ◽  
Philippe Moireau ◽  
Tobias Schaeffter ◽  
C. Alberto Figueroa
Keyword(s):  
Unscented Kalman Filter ◽  
Three Dimensional ◽  
Synthetic Data ◽  
Sequential Estimation ◽  
Wall Material ◽  
Patient Specific ◽  
Model Parameters ◽  
Computational Framework ◽  
Lumped Parameter ◽  
Estimation Of Model Parameters

AbstractA major challenge in constructing three dimensional patient specific hemodynamic models is the calibration of model parameters to match patient data on flow, pressure, wall motion, etc. acquired in the clinic. Current workflows are manual and time-consuming. This work presents a flexible computational framework for model parameter estimation in cardiovascular flows that relies on the following fundamental contributions. (i) A Reduced-Order Unscented Kalman Filter (ROUKF) model for data assimilation for wall material and simple lumped parameter network (LPN) boundary condition model parameters. (ii) A constrained least squares augmentation (ROUKF-CLS) for more complex LPNs. (iii) A “Netlist” implementation, supporting easy filtering of parameters in such complex LPNs. The ROUKF algorithm is demonstrated using non-invasive patient-specific data on anatomy, flow and pressure from a healthy volunteer. The ROUKF-CLS algorithm is demonstrated using synthetic data on a coronary LPN. The methods described in this paper have been implemented as part of the CRIMSON hemodynamics software package.

Use of ionic currents to identify and estimate parameters in models of channel blockade

1990 ◽  
Vol 259 (2) ◽  
pp. H626-H634
Author(s):  
C. F. Starmer ◽  
V. V. Nesterenko ◽  
F. R. Gilliam ◽  
A. O. Grant
Keyword(s):  
Time Course ◽  
Experimental Studies ◽  
Ionic Currents ◽  
Blocking Agent ◽  
Model Parameters ◽  
Protein Conformations ◽  
Channel Blockade ◽  
Channel Blocking ◽  
Individual Contributions ◽  
Modulated Receptor

Models of ion channel blockade are frequently validated with observations of ionic currents resulting from electrical or chemical stimulation. Model parameters for some models (modulated receptor hypothesis) cannot be uniquely determined from ionic currents. The time course of ionic currents reflects the activation (fraction of available channels that conduct in the presence of excitation) and availability of channels (the ability of the protein to make a transition to a conducting conformation and where this conformation is not complexed with a drug). In the presence of a channel blocking agent, the voltage dependence of availability appears modified and has been interpreted as evidence that drug-complexed channels exhibit modified transition rates between channel protein conformations. Because blockade and availability both modify ionic currents, their individual contributions to macroscopic conductance cannot be resolved from ionic currents except when constant affinity binding to a bindable site is assumed. Experimental studies of nimodipine block of calcium channels and lidocaine block of sodium channels illustrate these concepts.

scholarly journals Computational Modeling of Music Cognition: A Case Study on Model Selection

2006 ◽  
Vol 23 (5) ◽  
pp. 365-376 ◽  
Author(s):  
Henkjan Honing
Keyword(s):  
Model Selection ◽  
Strong Evidence ◽  
Goodness Of Fit ◽  
Computational Models ◽  
Recent Literature ◽  
Music Cognition ◽  
Kinematic Model ◽  
Music Performance ◽  
Limited Range

While the most common way of evaluating a computational model is to see whether it shows a good fit with the empirical data, recent literature on theory testing and model selection criticizes the assumption that this is actually strong evidence for the validity of a model. This article presents a case study from music cognition (modeling the ritardandi in music performance) and compares two families of computational models (kinematic and perceptual) using three different model selection criteria: goodness-of-fit, model simplicity, and the degree of surprise in the predictions. In the light of what counts as strong evidence for a model’s validity—namely that it makes limited range, nonsmooth, and relatively surprising predictions—the perception-based model is preferred over the kinematic model.

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