Sensitivity of a Hill-based muscle model to perturbations in model parameters

Musculoskeletal simulations of human movement commonly use Hill muscle models to predict muscle forces, but their sensitivity to model parameter values is not well understood. The purpose of this study was to evaluate muscle model sensitivity to perturbations in 14 Hill muscle model parameters in forward dynamic simulations of running and walking by varying each by +/-50%. Three evaluations of the muscle model were performed based on: (1) calculating the sensitivity of the muscle model only, (2) determining the continuous partial derivatives of the muscle equations with respect to each parameter, and (3) evaluating the effects on the running and walking simulations. Model evaluations were found to be very sensitive (percent change in outputs greater than parameter perturbation) to parameters defining the series elastic component (tendon), force-length curve of the contractile element and maximum isometric force. For some parameters, the range of literature values was larger than the model sensitivity. Model evaluations were insensitive to parameters defining the parallel elastic element, force-velocity curve of the contractile element and muscle activation time constants. The derivative method provided similar results, but also provided a generic, continuous equation that can easily be applied to other motions. The sensitivities of the running and walking simulations were reduced compared to the sensitivity of the muscle model alone. Results demonstrate the importance of evaluating sensitivity of a musculoskeletal simulation in a controlled manner and provide an indication of which parameters must be selected most carefully based on the sensitivity of a given movement.     

Deactivation of Src family kinases: hypothesis testing using a Monte Carlo sensitivity analysis of systems-level properties.

Src family tyrosine kinases play a key role in many cellular signalling networks, but due to the high complexity of these networks their precise function remains elusive. Many factors involved in Src regulation, such as specific kinases and phosphatases, are still unknown. Mathematical models have been constructed to improve the understanding of the system and its dynamic behavior. Using a computational random parameter search, we characterized and compared the dynamics of three alternative models in order to assess their likelihoods. For this, we investigated how systems-level properties such as bistability and excitable behavior relate to kinetic and physiological parameters and how robust these properties were. Our results suggest the existence of a putative negative feedback loop in the Src system. A previously suggested role for PTPalpha in the deactivation of Src was not supported by the model.     

Sensitivity of model predictions of muscle function to changes in moment arms and muscle-tendon properties: a Monte-Carlo analysis

Hill-type muscle models are commonly used in musculoskeletal models to estimate muscle forces during human movement. However, the sensitivity of model predictions of muscle function to changes in muscle moment arms and muscle-tendon properties is not well understood. In the present study, a three-dimensional muscle-actuated model of the body was used to evaluate the sensitivity of the function of the major lower limb muscles in accelerating the whole-body center of mass during gait. Monte-Carlo analyses were used to quantify the effects of entire distributions of perturbations in the moment arms and architectural properties of muscles. In most cases, varying the moment arm and architectural properties of a muscle affected the torque generated by that muscle about the joint(s) it spanned as well as the torques generated by adjacent muscles. Muscle function was most sensitive to changes in tendon slack length and least sensitive to changes in muscle moment arm. However, the sensitivity of muscle function to changes in moment arms and architectural properties was highly muscle-specific; muscle function was most sensitive in the cases of gastrocnemius and rectus femoris and insensitive in the cases of hamstrings and the medial sub-region of gluteus maximus. The sensitivity of a muscle's function was influenced by the magnitude of the muscle's force as well as the operating region of the muscle on its force-length curve. These findings have implications for the development of subject-specific models of the human musculoskeletal system.     

Optimising muscle parameters in musculoskeletal models using Monte Carlo simulation

The use of musculoskeletal simulation software has become a useful tool for modelling joint and muscle forces during human activity, including in reduced gravity because direct experimentation is difficult. Knowledge of muscle and joint loads can better inform the design of exercise protocols and exercise countermeasure equipment. In this study, the LifeModeler? (San Clemente, CA, USA) biomechanics simulation software was used to model a squat exercise. The initial model using default parameters yielded physiologically reasonable hip-joint forces but no activation was predicted in some large muscles such as rectus femoris, which have been shown to be active in 1-g performance of the activity. Parametric testing was conducted using Monte Carlo methods and combinatorial reduction to find a muscle parameter set that more closely matched physiologically observed activation patterns during the squat exercise. The rectus femoris was predicted to peak at 60.1% activation in the same test case compared to 19.2% activation using default parameters. These results indicate the critical role that muscle parameters play in joint force estimation and the need for exploration of the solution space to achieve physiologically realistic muscle activation.     

Monte Carlo sensitivity analysis for unmeasured confounding in dynamic treatment regimes

Data-driven methods for personalizing treatment assignment have garnered much attention from clinicians and researchers. Dynamic treatment regimes formalize this through a sequence of decision rules that map individual patient characteristics to a recommended treatment. Observational studies are commonly used for estimating dynamic treatment regimes due to the potentially prohibitive costs of conducting sequential multiple assignment randomized trials. However, estimating a dynamic treatment regime from observational data can lead to bias in the estimated regime due to unmeasured confounding. Sensitivity analyses are useful for assessing how robust the conclusions of the study are to a potential unmeasured confounder. A Monte Carlo sensitivity analysis is a probabilistic approach that involves positing and sampling from distributions for the parameters governing the bias. We propose a method for performing a Monte Carlo sensitivity analysis of the bias due to unmeasured confounding in the estimation of dynamic treatment regimes. We demonstrate the performance of the proposed procedure with a simulation study and apply it to an observational study examining tailoring the use of antidepressant medication for reducing symptoms of depression using data from Kaiser Permanente Washington.     

A study of the muscle force waveform using a population stochastic model of skeletal muscle

A population stochastic model based on the differing properties and the independent activation of motor units is used to describe the production of force in the contracting skeletal muscle. Detailed force predictions of the model concerning a hand muscle are obtained by computer simulation. General features of the force signal are established analyticaly on the basis of the general properties of the neuromuscular system which the population model takes into account. The results show that the asynchronous activity of motor units and the distribution of their filtering and firing properties at various levels of muscle contraction are esponsible, at least partially, for the main features of the muscle force waveform, including tremor.     

Studies on evolutionary and selective properties of hypercycles using a Monte Carlo method

Summary The most relevant properties of hypercycles were previously studied mainly from a theoretical point of view. We have developed a Monte Carlo method simulating hypercyclic organization to obtain information about the dynamics of this prebiotic organization. Nucleation, growth, and selective properties have been tested and the results obtained are in good agreement with those of the theoretical predictions. The influence of hypercyclic organization of the error threshold has also been studied. As a consequence of the emergence of a hypercycle, the value of this threshold decreases. The amount of this decrease depends on the population size. Moreover, for some interval of quality factor values, either the hypercycle organization or an error catastrophe can be produced, depending on the initial conditions. The influence of these phenomena on both the dynamic behavior and evolutionary advantages of the hypercycle, as well as their decisive roles on genome size, are discussed.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Monte Carlo studies of a model for lipid-gramicidin A bilayers.

This paper presents results of Monte Carlo simulations of a full bilayer of 200 lipid chains and one gramicidin A dimer. Simulations are described for systems with lipid chains of 14, 16, and 18 carbons, respectively. Using accepted potential functions to calculate interactions between all non-hydrogen atoms a Monte Carlo configuration sampling is generated from which order parameter profiles are calculated and specific configurations are displayed. Results are compared with experimental data for lipid-gramicidin bilayers.     

Monte Carlo model framework to simulate settlement dynamics

We developed an open source Monte Carlo based model to simulate Settlement Dynamics in Drylands (SeDD). The model assigns partial probabilities to each pixel within a grid region, based on several factors that can influence the establishment and subsistence of settlements: groundwater depth, vegetation type, proximity to rivers, paved roads, old river beds, and existing settlements. Partial probabilities are considered to be independent from each other, and therefore multiplied to calculate an overall probability for each pixel. Settlements are assigned by maximum probabilities or randomly, according to pre-established threshold probability values. We also modeled the gradual reduction of vegetation caused by a new settlement in neighboring pixels, decreasing the probabilities related to vegetation type. The final distribution of settlements is given by an average over multiple Monte Carlo simulations. The model is computationally efficient and could be used to rapidly explore different scenarios of settlement dynamics and vegetation degradation in arid environments, and other environmental factors that can be added to the framework without performing changes in the source code.     

A comparative study of muscle force estimates using Huxley's and Hill's muscle model

Determination of muscle forces in individual muscles is often essential to assess optimal performance of human motion. Inverse dynamic methods based on the kinematics of the given motion and on the use of optimisation approach are the most widely used for muscle force estimation. The aim of this study was to estimate how the choice of muscle model influences predicted muscle forces. Huxley's (1957, Prog Biophys Biop Chem. 7: 255–318) and Hill's (1938, Proc R Soc B. 126: 136–195) muscle models were used for determination of muscle forces of two antagonistic muscles of the lower extremity during cycling. Huxley's model is a complex model that couples biochemical and physical processes with the microstructure of the muscle whereas the Hill's model is a phenomenological model. Muscle forces predicted by both models are within the same range. Huxley's model predicts more realistic patterns of muscle activation but it is computationally more demanding. Therefore, if the overall muscle forces are to be assessed, it is reasonable to use a simpler implementation based on Hill's model.     

Uncertainty analysis of penicillin V production using Monte Carlo simulation

Uncertainty and variability affect economic and environmental performance in the production of biotechnology and pharmaceutical products. However, commercial process simulation software typically provides analysis that assumes deterministic rather than stochastic process parameters and thus is not capable of dealing with the complexities created by variance that arise in the decision-making process. Using the production of penicillin V as a case study, this article shows how uncertainty can be quantified and evaluated. The first step is construction of a process model, as well as analysis of its cost structure and environmental impact. The second step is identification of uncertain variables and determination of their probability distributions based on available process and literature data. Finally, Monte Carlo simulations are run to see how these uncertainties propagate through the model and affect key economic and environmental outcomes. Thus, the overall variation of these objective functions are quantified, the technical, supply chain, and market parameters that contribute most to the existing variance are identified and the differences between economic and ecological evaluation are analyzed. In our case study analysis, we show that final penicillin and biomass concentrations in the fermenter have the highest contribution to variance for both unit production cost and environmental impact. The penicillin selling price dominates return on investment variance as well as the variance for other revenue-dependent parameters.     

A mathematical model for predicting relative muscle force with a perturbation analysis of selected muscle parameters

A mathematical model is presented that predicts relative muscle forces using a minimum of experimentally derived input data. Tests of this model against literature values for maximum muscle force of four cat hindlimb muscles show a maximum error of only 5%. A perturbation analysis using this model demonstrates its sensitivity and applicability, as well as the congruence between this model and previous theoretical discussions of muscle function.     

Dynamical estimation of neuron and network properties II: path integral Monte Carlo methods

Hodgkin–Huxley (HH) models of neuronal membrane dynamics consist of a set of nonlinear differential equations that describe the time-varying conductance of various ion channels. Using observations of voltage alone we show how to estimate the unknown parameters and unobserved state variables of an HH model in the expected circumstance that the measurements are noisy, the model has errors, and the state of the neuron is not known when observations commence. The joint probability distribution of the observed membrane voltage and the unobserved state variables and parameters of these models is a path integral through the model state space. The solution to this integral allows estimation of the parameters and thus a characterization of many biological properties of interest, including channel complement and density, that give rise to a neuron’s electrophysiological behavior. This paper describes a method for directly evaluating the path integral using a Monte Carlo numerical approach. This provides estimates not only of the expected values of model parameters but also of their posterior uncertainty. Using test data simulated from neuronal models comprising several common channels, we show that short (<50 ms) intracellular recordings from neurons stimulated with a complex time-varying current yield accurate and precise estimates of the model parameters as well as accurate predictions of the future behavior of the neuron. We also show that this method is robust to errors in model specification, supporting model development for biological preparations in which the channel expression and other biophysical properties of the neurons are not fully known.     

Individual-specific muscle maximum force estimation using ultrasound for ankle joint torque prediction using an EMG-driven Hill-type model

EMG-driven models can be used to estimate muscle force in biomechanical systems. Collected and processed EMG readings are used as the input of a dynamic system, which is integrated numerically. This approach requires the definition of a reasonably large set of parameters. Some of these vary widely among subjects, and slight inaccuracies in such parameters can lead to large model output errors. One of these parameters is the maximum voluntary contraction force (F^om). This paper proposes an approach to find F^om by estimating muscle physiological cross-sectional area (PCSA) using ultrasound (US), which is multiplied by a realistic value of maximum muscle specific tension. Ultrasound is used to measure muscle thickness, which allows for the determination of muscle volume through regression equations. Soleus, gastrocnemius medialis and gastrocnemius lateralis PCSAs are estimated using published volume proportions among leg muscles, which also requires measurements of muscle fiber length and pennation angle by US. F^om obtained by this approach and from data widely cited in the literature was used to comparatively test a Hill-type EMG-driven model of the ankle joint. The model uses 3 EMGs (Soleus, gastrocnemius medialis and gastrocnemius lateralis) as inputs with joint torque as the output. The EMG signals were obtained in a series of experiments carried out with 8 adult male subjects, who performed an isometric contraction protocol consisting of 10 s step contractions at 20% and 60% of the maximum voluntary contraction level. Isometric torque was simultaneously collected using a dynamometer. A statistically significant reduction in the root mean square error was observed when US-obtained F^om was used, as compared to F^om from the literature.     

Investigation of a Monte Carlo model for chemical reactions

Monte Carlo computer simulations are in use at a number of laboratories for calculating time-dependent yields, which can be compared with experiments in the radiolysis of water. We report here on calculations to investigate the validity and consistency of the procedures used for simulating chemical reactions in our code, RADLYS. Model calculations were performed of the rate constants themselves. The rates thus determined showed an expected rapid decline over the first few hundred ps and a very gradual decline thereafter out to the termination of the calculations at 4.5 ns. Results are reported for different initial concentrations and numbers of reactive species. Generally, the calculated rate constants are smallest when the initial concentrations of the reactants are largest. It is found that inhomogeneities that quickly develop in the initial random spatial distribution of reactants persist in time as a result of subsequent chemical reactions, and thus conditions may poorly approximate those assumed from diffusion theory. We also investigated the reaction of a single species of one type placed among a large number of randomly distributed species of another type with which it could react. The distribution of survival times of the single species was calculated by using three different combinations of the diffusion constants for the two species, as is sometimes discussed in diffusion theory. The three methods gave virtually identical results. Received: 6 May 1998 / Accepted in revised form: 5 July 1998     

Dual-energy contrast-enhanced digital mammography: Glandular dose estimation using a Monte Carlo code and voxel phantom

PurposeTo estimate the mean glandular dose of contrast enhanced digital mammography, using the EGSnrc Monte Carlo code and female adult voxel phantom.MethodsAutomatic exposure control of full field digital mammography system was used for the selection of the X-ray spectrum and the exposure settings for dual energy imaging. Measurements of the air-kerma and of the half value layers were performed and a Monte Carlo simulation of the digital mammography system was used to compute the mean glandular dose, for breast phantoms of various thicknesses, glandularities and for different X-ray spectra (low and high energy).ResultsFor breast phantoms of 2.0–8.0 cm thick and 0.1–100% glandular fraction, CC view acquisition, from AEC settings, can result in a mean glandular dose of 0.450 ± 0.022 mGy −2.575 ± 0.033 mGy for low energy images and 0.061 ± 0.021 mGy – 0.232 ± 0.033 mGy for high energy images. In MLO view acquisition mean glandular dose values ranged between 0.488 ± 0.007 mGy – 2.080 ± 0.021 mGy for low energy images and 0.065 ± 0.012 mGy – 0.215 ± 0.010 mGy for high energy images.ConclusionThe low kV part of contrast enhanced digital mammography is the main contributor to total mean glandular breast dose. The results of this study can be used to provide an estimated mean glandular dose for individual cases.     

Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo

A common problem in molecular phylogenetics is choosing a model of DNA substitution that does a good job of explaining the DNA sequence alignment without introducing superfluous parameters. A number of methods have been used to choose among a small set of candidate substitution models, such as the likelihood ratio test, the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC), and Bayes factors. Current implementations of any of these criteria suffer from the limitation that only a small set of models are examined, or that the test does not allow easy comparison of non-nested models. In this article, we expand the pool of candidate substitution models to include all possible time-reversible models. This set includes seven models that have already been described. We show how Bayes factors can be calculated for these models using reversible jump Markov chain Monte Carlo, and apply the method to 16 DNA sequence alignments. For each data set, we compare the model with the best Bayes factor to the best models chosen using AIC and BIC. We find that the best model under any of these criteria is not necessarily the most complicated one; models with an intermediate number of substitution types typically do best. Moreover, almost all of the models that are chosen as best do not constrain a transition rate to be the same as a transversion rate, suggesting that it is the transition/transversion rate bias that plays the largest role in determining which models are selected. Importantly, the reversible jump Markov chain Monte Carlo algorithm described here allows estimation of phylogeny (and other phylogenetic model parameters) to be performed while accounting for uncertainty in the model of DNA substitution.     

Biofilm model calibration and microbial diversity study using Monte Carlo simulations

Mathematical models are useful tools for studying and exploring biological conversion processes as well as microbial competition in biological treatment processes. A single‐species biofilm model was used to describe biofilm reactor operation at three different hydraulic retention times (HRT). The single‐species biofilm model was calibrated with sparse experimental data using the Monte Carlo filtering method. This calibrated single‐species biofilm model was then extended to a multi‐species model considering 10 different heterotrophic bacteria. The aim was to study microbial diversity in bulk phase biomass and biofilm, as well as the competition between suspended and attached biomass. At steady state and independently of the HRT, Monte Carlo simulations resulted only in one unique dominating bacterial species for suspended and attached biomass. The dominating bacterial species was determined by the highest specific substrate affinity (ratio of µ/K_S). At a short HRT of 20 min, the structure of the microbial community in the bulk liquid was determined by biomass detached from the biofilm. At a long HRT of 8 h, both biofilm detachment and microbial growth in the bulk liquid influenced the microbial community distribution. Biotechnol. Bioeng. 2013; 110: 1323–1332. © 2012 Wiley Periodicals, Inc.