scholarly journals Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1638 ◽  
Author(s):  
Leng-Feng Lee ◽  
Brian R. Umberger
Keyword(s):  
Optimal Control ◽  
Open Source ◽  
Human Mobility ◽  
Human Movement ◽  
Great Promise ◽  
Shooting Methods ◽  
Simulation And Optimization ◽  
Direct Collocation ◽  
Data Tracking ◽  
Predictive Simulations

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1–2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility.

scholarly journals Rapid predictive simulations with complex musculoskeletal models suggest that diverse healthy and pathological human gaits can emerge from similar control strategies

2019 ◽  
Vol 16 (157) ◽  
pp. 20190402 ◽  
Author(s):  
Antoine Falisse ◽  
Gil Serrancolí ◽  
Christopher L. Dembia ◽  
Joris Gillis ◽  
Ilse Jonkers ◽  
...  
Keyword(s):  
Control Strategies ◽  
Three Dimensional ◽  
Human Movement ◽  
Performance Criterion ◽  
Computationally Efficient ◽  
Algorithmic Differentiation ◽  
Direct Collocation ◽  
Musculoskeletal Models ◽  
Model Control ◽  
Predictive Simulations

Physics-based predictive simulations of human movement have the potential to support personalized medicine, but large computational costs and difficulties to model control strategies have limited their use. We have developed a computationally efficient optimal control framework to predict human gaits based on optimization of a performance criterion without relying on experimental data. The framework generates three-dimensional muscle-driven simulations in 36 min on average—more than 20 times faster than existing simulations—by using direct collocation, implicit differential equations and algorithmic differentiation. Using this framework, we identified a multi-objective performance criterion combining energy and effort considerations that produces physiologically realistic walking gaits. The same criterion also predicted the walk-to-run transition and clinical gait deficiencies caused by muscle weakness and prosthesis use, suggesting that diverse healthy and pathological gaits can emerge from the same control strategy. The ability to predict the mechanics and energetics of a broad range of gaits with complex three-dimensional musculoskeletal models will allow testing novel hypotheses about gait control and hasten the development of optimal treatments for neuro-musculoskeletal disorders.

scholarly journals Predictive simulations of musculoskeletal function and jumping performance in a generalized bird

2021 ◽  
Author(s):  
P J Bishop ◽  
A Falisse ◽  
F De Groote ◽  
J R Hutchinson
Keyword(s):  
Optimal Control ◽  
Three Dimensional ◽  
Muscle Performance ◽  
Whole Body ◽  
Distal Limb ◽  
Jump Performance ◽  
Everyday Activity ◽  
Direct Collocation ◽  
Musculoskeletal Function ◽  
Predictive Simulations

Abstract Jumping is a common, but demanding, behaviour that many animals employ during everyday activity. In contrast to jump-specialists such as anurans and some primates, jumping biomechanics and the factors that influence performance remains little studied for generalized species that lack marked adaptations for jumping. Computational biomechanical modelling approaches offer a way of addressing this in a rigorous, mechanistic fashion. Here, optimal control theory and musculoskeletal modelling are integrated to generate predictive simulations of maximal height jumping in a small ground-dwelling bird, a tinamou. A three-dimensional musculoskeletal model with 36 actuators per leg is used, and direct collocation is employed to formulate a rapidly solvable optimal control problem involving both liftoff and landing phases. The resulting simulation raises the whole-body centre of mass to over double its standing height, and key aspects of the simulated behaviour qualitatively replicate empirical observations for other jumping birds. However, quantitative performance is lower, with reduced ground forces, jump heights and muscle–tendon power. A pronounced countermovement manoeuvre is used during launch. The use of a countermovement is demonstrated to be critical to the achievement of greater jump heights, and this phenomenon may only need to exploit physical principles alone to be successful; amplification of muscle performance may not necessarily be a proximate reason for the use of this manoeuvre. Increasing muscle strength or contractile velocity above nominal values greatly improves jump performance, and interestingly has the greatest effect at more distal limb extensor muscles (i.e., those of the ankle), suggesting that the distal limb may be a critical link for jumping behaviour. These results warrant a re-evaluation of previous inferences of jumping ability in some extinct species with foreshortened distal limb segments, such as dromaeosaurid dinosaurs.

scholarly journals Variation in human mobility and its impact on the risk of future COVID-19 outbreaks in Taiwan

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Meng-Chun Chang ◽  
Rebecca Kahn ◽  
Yu-An Li ◽  
Cheng-Sheng Lee ◽  
Caroline O. Buckee ◽  
...  
Keyword(s):  
Disease Surveillance ◽  
Initial Conditions ◽  
Human Mobility ◽  
Human Movement ◽  
Disease Spread ◽  
Spatial Spread ◽  
Movement Data ◽  
Intercity Travel ◽  
Travel Restrictions ◽  
The Impact

Abstract Background As COVID-19 continues to spread around the world, understanding how patterns of human mobility and connectivity affect outbreak dynamics, especially before outbreaks establish locally, is critical for informing response efforts. In Taiwan, most cases to date were imported or linked to imported cases. Methods In collaboration with Facebook Data for Good, we characterized changes in movement patterns in Taiwan since February 2020, and built metapopulation models that incorporate human movement data to identify the high risk areas of disease spread and assess the potential effects of local travel restrictions in Taiwan. Results We found that mobility changed with the number of local cases in Taiwan in the past few months. For each city, we identified the most highly connected areas that may serve as sources of importation during an outbreak. We showed that the risk of an outbreak in Taiwan is enhanced if initial infections occur around holidays. Intracity travel reductions have a higher impact on the risk of an outbreak than intercity travel reductions, while intercity travel reductions can narrow the scope of the outbreak and help target resources. The timing, duration, and level of travel reduction together determine the impact of travel reductions on the number of infections, and multiple combinations of these can result in similar impact. Conclusions To prepare for the potential spread within Taiwan, we utilized Facebook’s aggregated and anonymized movement and colocation data to identify cities with higher risk of infection and regional importation. We developed an interactive application that allows users to vary inputs and assumptions and shows the spatial spread of the disease and the impact of intercity and intracity travel reduction under different initial conditions. Our results can be used readily if local transmission occurs in Taiwan after relaxation of border control, providing important insights into future disease surveillance and policies for travel restrictions.

scholarly journals SynBiopython: an open-source software library for Synthetic Biology

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Jing Wui Yeoh ◽  
Neil Swainston ◽  
Peter Vegh ◽  
Valentin Zulkower ◽  
Pablo Carbonell ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Open Source ◽  
Open Source Software ◽  
Development Projects ◽  
Software Library ◽  
Current State ◽  
Starting Point ◽  
Common Problems ◽  
Data Tracking ◽  
Python Package

Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.

scholarly journals Numerical Simulation and Optimization of CO2 Sequestration in Saline Aquifers

2012 ◽  
Author(s):  
Zheming Zhang ◽  
Ramesh Agarwal
Keyword(s):  
Numerical Simulation ◽  
Co2 Sequestration ◽  
Storage Capacity ◽  
Co2 Storage ◽  
Injection Well ◽  
Co2 Injection ◽  
Great Promise ◽  
Saline Aquifer ◽  
Simulation And Optimization ◽  
Co2 Plume

With recent concerns on CO2 emissions from coal fired electricity generation plants; there has been major emphasis on the development of safe and economical Carbon Dioxide Capture and Sequestration (CCS) technology worldwide. Saline reservoirs are attractive geological sites for CO2 sequestration because of their huge capacity for sequestration. Over the last decade, numerical simulation codes have been developed in U.S, Europe and Japan to determine a priori the CO2 storage capacity of a saline aquifer and provide risk assessment with reasonable confidence before the actual deployment of CO2 sequestration can proceed with enormous investment. In U.S, TOUGH2 numerical simulator has been widely used for this purpose. However at present it does not have the capability to determine optimal parameters such as injection rate, injection pressure, injection depth for vertical and horizontal wells etc. for optimization of the CO2 storage capacity and for minimizing the leakage potential by confining the plume migration. This paper describes the development of a “Genetic Algorithm (GA)” based optimizer for TOUGH2 that can be used by the industry with good confidence to optimize the CO2 storage capacity in a saline aquifer of interest. This new code including the TOUGH2 and the GA optimizer is designated as “GATOUGH2”. It has been validated by conducting simulations of three widely used benchmark problems by the CCS researchers worldwide: (a) Study of CO2 plume evolution and leakage through an abandoned well, (b) Study of enhanced CH4 recovery in combination with CO2 storage in depleted gas reservoirs, and (c) Study of CO2 injection into a heterogeneous geological formation. Our results of these simulations are in excellent agreement with those of other researchers obtained with different codes. The validated code has been employed to optimize the proposed water-alternating-gas (WAG) injection scheme for (a) a vertical CO2 injection well and (b) a horizontal CO2 injection well, for optimizing the CO2 sequestration capacity of an aquifer. These optimized calculations are compared with the brute force nearly optimized results obtained by performing a large number of calculations. These comparisons demonstrate the significant efficiency and accuracy of GATOUGH2 as an optimizer for TOUGH2. This capability holds a great promise in studying a host of other problems in CO2 sequestration such as how to optimally accelerate the capillary trapping, accelerate the dissolution of CO2 in water or brine, and immobilize the CO2 plume.

Migration, Displacement, and Dispossession

2021 ◽  
Author(s):  
Nina Glick Schiller
Keyword(s):  
Human Life ◽  
Human Mobility ◽  
Human Movement ◽  
Human Migration ◽  
Social Boundaries ◽  
Population Mobility ◽  
Political Climate ◽  
Political Transformations ◽  
Political Boundaries ◽  
Migration Regimes

Debates about migration, whether led by politicians or scholars, often approach migration as a relatively new challenge and categorize it as a “destabilizing force,” ignoring the fact that the world’s past and present has been built by human movement. Humans have always migrated. Individual and population mobility as well as settlement are part of humans’ shared history. To integrate migration into an understanding of humans’ shared past, present, and emerging possible futures, several concepts prove useful including migration regime, displacement, dispossession, conjuncture, colonization, border-making, nationalism, and racialization. Deployed together, these concepts identify moments in human history in which migration has been understood to be part of the human experience and when, where, and how migrants have been stigmatized, and those who move defined as culturally or biologically inferior. By coupling the concept of migration regimes with an analysis of changing modes of dispossession and displacement over millennia, scholars can illuminate the intersection of the economic and political transformations of governance structures as well as the varying concepts of “the migrant” and “nonmigrant,” and “native” and “foreigner.” Anti-immigrant ideologies preclude discussion of the broader economic and political restructurings that underlie both increased human movement and anti-migrant sentiments. They also deflect attention from a set of questions that are at the heart of the anthropology of migration: Why do people leave familiar terrains, family, and friends? How do they manage to move and settle elsewhere? How do they relate to the life they left behind? These are questions that can equally be asked of people who move to another region of a country or travel across political boundaries. To answer these questions migration scholars have explored the linkages between forms of human mobility and processes of dispossession, displacement, and resettlement. In these investigations, social networks prove to be central to mobility and settlement. Since the 15th century, changing Western theories about human migration and the origins of political and social boundaries reflected transformations in political economy. Globe-spanning migration regimes used violent force, border formation and dissolution, documents, surveillance, and criminalization to allow the migration of some and disallow the movement or settlement of others. During that period, marked initially by colonialism and slavery, and then by nation state building and anticolonial struggles, migration scholars including the anthropologists took varying positions on the significance of mobility and stasis in human life. By the beginning of the 21st century, the accumulation of capital by dispossession emerged as a process increasingly central to a historical conjuncture marked by both heightened migration and anti-immigrant nationalism. Political struggles for social and environmental justice began to merge with movements in support of migration. This political climate shaped a new engaged anthropology of migration.

scholarly journals Estimating infection-related human mobility networks based on time series data of COVID-19 infection in Japan

2021 ◽  
Author(s):  
Tetsuya Yamada ◽  
Shoi Shi
Keyword(s):  
Time Series ◽  
Infectious Diseases ◽  
Time Series Data ◽  
Human Mobility ◽  
Emerging Infectious Diseases ◽  
Human Movement ◽  
Data Driven ◽  
Disease Spread ◽  
Series Data ◽  
Data Infrastructure

Comprehensive and evidence-based countermeasures against emerging infectious diseases have become increasingly important in recent years. COVID-19 and many other infectious diseases are spread by human movement and contact, but complex transportation networks in 21 century make it difficult to predict disease spread in rapidly changing situations. It is especially challenging to estimate the network of infection transmission in the countries that the traffic and human movement data infrastructure is not yet developed. In this study, we devised a method to estimate the network of transmission of COVID-19 from the time series data of its infection and applied it to determine its spread across areas in Japan. We incorporated the effects of soft lockdowns, such as the declaration of a state of emergency, and changes in the infection network due to government-sponsored travel promotion, and predicted the spread of infection using the Tokyo Olympics as a model. The models used in this study are available online, and our data-driven infection network models are scalable, whether it be at the level of a city, town, country, or continent, and applicable anywhere in the world, as long as the time-series data of infections per region is available. These estimations of effective distance and the depiction of infectious disease networks based on actual infection data are expected to be useful in devising data-driven countermeasures against emerging infectious diseases worldwide.

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