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Table of Contents

July 2018

Movement is fundamental to human and animal life, emerging through interaction of complex neural, muscular, and skeletal systems. OpenSim is open-source software that unites state-of-the-art models and methods from biology, neuroscience, mechanics, robotics, and computer science to create fast and accurate physics-based simulations of movement. OpenSim complements experiments by computing muscle forces and other quantities that are difficult to measure, and enables prediction of movements such as bipedal locomotion in human ancestors and neuromuscular adaptations to exoskeletons or orthopaedic surgeries. Seth et al.

Image Credit: Human model and simulation from Rajagopal et al. [1]; chimpanzee model from O'Neill et al. [2] and unpublished simulation results provided by M.C. O'Neill and B.R. Umberger.

1. Rajagopal A, Dembia CL, DeMers MS, Delp DD, Hicks JL, Delp SL. Full-body musculoskeletal model for muscle-driven simulation of human gait. IEEE Trans Biomed Eng. 2016; 63(10):2068-2079

2. O'Neill MC, Lee LF, Larson SG, Demes B, Stern JT Jr, Umberger BR. A three-dimensional musculoskeletal model of the chimpanzee (Pan troglodytes) pelvis and hind limb. J Exp Biol. 2013; 216(19):3709-3723.

Research Articles

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Inter-trial effects in visual pop-out search: Factorial comparison of Bayesian updating models

Fredrik Allenmark, Hermann J. Müller, Zhuanghua Shi

Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion

Ida Friis, Ilia A. Solov’yov

Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception

Luigi Acerbi, Kalpana Dokka, Dora E. Angelaki, Wei Ji Ma

PyPhi: A toolbox for integrated information theory

William G. P. Mayner, William Marshall, Larissa Albantakis, Graham Findlay, Robert Marchman, Giulio Tononi

A model for hydrophobic protrusions on peripheral membrane proteins

Edvin Fuglebakk, Nathalie Reuter

OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement

Ajay Seth, Jennifer L. Hicks, Thomas K. Uchida, Ayman Habib, Christopher L. Dembia, James J. Dunne, Carmichael F. Ong, Matthew S. DeMers, Apoorva Rajagopal, Matthew Millard, Samuel R. Hamner, Edith M. Arnold, Jennifer R. Yong, Shrinidhi K. Lakshmikanth, Michael A. Sherman, Joy P. Ku, Scott L. Delp

FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer

Chia-Chin Wu, Hannah C. Beird, Jianhua Zhang, P. Andrew Futreal

Real-time decision-making during emergency disease outbreaks

William J. M. Probert, Chris P. Jewell, Marleen Werkman, Christopher J. Fonnesbeck, Yoshitaka Goto, Michael C. Runge, Satoshi Sekiguchi, Katriona Shea, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley

A marginalized two-part Beta regression model for microbiome compositional data

Haitao Chai, Hongmei Jiang, Lu Lin, Lei Liu

Punishment and inspection for governing the commons in a feedback-evolving game

Xiaojie Chen, Attila Szolnoki

Exploration and stabilization of Ras1 mating zone: A mechanism with positive and negative feedbacks

Bita Khalili, Laura Merlini, Vincent Vincenzetti, Sophie G. Martin, Dimitrios Vavylonis

The evolutionary dynamics of metabolic protocells

Ximo Pechuan, Raymond Puzio, Aviv Bergman

Correction of copy number induced false positives in CRISPR screens

Antoine de Weck, Javad Golji, Michael D. Jones, Joshua M. Korn, Eric Billy, E. Robert McDonald III, Tobias Schmelzle, Hans Bitter, Audrey Kauffmann

Stochastic resonance enhances the rate of evidence accumulation during combined brain stimulation and perceptual decision-making

Onno van der Groen, Matthew F. Tang, Nicole Wenderoth, Jason B. Mattingley

A quantitative physical model of the TMS-induced discharge artifacts in EEG

Dominik Freche, Jodie Naim-Feil, Avi Peled, Nava Levit-Binnun, Elisha Moses

Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study

Tanmay A. Gokhale, Huda Asfour, Shravan Verma, Nenad Bursac, Craig S. Henriquez

Modelling how responsiveness to interferon improves interferon-free treatment of hepatitis C virus infection

Vishnu Venugopal, Pranesh Padmanabhan, Rubesh Raja, Narendra M. Dixit

Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?

Sebastian D. Boie, Erin G. Connor, Margaret McHugh, Katherine I. Nagel, G. Bard Ermentrout, John P. Crimaldi, Jonathan D. Victor

Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis

Spase Petkoski, J. Matias Palva, Viktor K. Jirsa

Differential roles of sleep spindles and sleep slow oscillations in memory consolidation

Yina Wei, Giri P. Krishnan, Maxim Komarov, Maxim Bazhenov

Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition

Joshua H. Goldwyn, Bradley R. Slabe, Joseph B. Travers, David Terman

Age-dependent Pavlovian biases influence motor decision-making

Xiuli Chen, Robb B. Rutledge, Harriet R. Brown, Raymond J. Dolan, Sven Bestmann, Joseph M. Galea

Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure

Lukas Grossberger, Francesco P. Battaglia, Martin Vinck

A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants

Sonja E. M. Boas, Joao Carvalho, Marloes van den Broek, Ester M. Weijers, Marie-José Goumans, Pieter Koolwijk, Roeland M. H. Merks

Subgraphs of functional brain networks identify dynamical constraints of cognitive control

Ankit N. Khambhati, John D. Medaglia, Elisabeth A. Karuza, Sharon L. Thompson-Schill, Danielle S. Bassett

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