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Co-citation analysis is a form of content analysis that can be applied in the context of scholarly publications with the purpose of identifying prominent articles, authors and journals being referenced to by the citing authors. It identifies co-cited references that occur in the reference list of two or more citing articles, with the resultant co-citation network providing insights into the constituents of a knowledge domain (e.g., significant authors and papers). The contribution of the paper is twofold; (a) the demonstration of the added value of using co-citation analysis, and for this purpose the underlying dataset that is chosen is the peer-reviewed publication of the Society for Modeling and Simulation International (SCS)—SIMULATION; (b) the year 2012 being the 60th anniversary of the SCS, the authors hope that this paper will lead to further acknowledgement and appreciation of the Society in charting the growth of Modeling and Simulation (M&S) as a discipline.

Structures with artificially engineered mechanical properties, often called mechanical metamaterials, are interesting for their tunable functionality. Various types of mechanical metamaterials have been proposed in the literature, designed to harness light or magnetic interactions, structural instabilities in slender or hollow structures, and contact friction. However, most of the designs are ideally engineered without any imperfections, in order to perform deterministically as programmed. Here, we study the mechanical performance of randomly stacked cylindrical shells, which act as a disordered mechanical metamaterial. Combining experiments and simulations, we demonstrate that the stacked shells can absorb and store mechanical energy upon compression by exploiting large deformation and relocation of shells, snap-fits, and friction. Although shells are oriented randomly, the system exhibits statistically robust mechanical performance controlled by friction and geometry. Our results demonstrate that the rearrangement of flexible components could yield versatile and predictive mechanical responses. Mechanical metamaterials are artificially designed structures with tunable behavior, typically obeying precisely programmed dynamics. Here, a metamaterial based on randomly stacked flexible cylindrical shells provides a disordered yet statistically robust and controllable structure for mechanical energy dissipation and storage.

This paper addresses the background and current state of the field of agent-based modelling and simulation (ABMS). It revisits the issue of ABMS represents as a new development, considering the extremes of being an overhyped fad, doomed to disappear, or a revolutionary development, shifting fundamental paradigms of how research is conducted. This paper identifies key ABMS resources, publications, and communities. It also proposes several complementary definitions for ABMS, based on practice, intended to establish a common vocabulary for understanding ABMS, which seems to be lacking. It concludes by suggesting research challenges for ABMS to advance and realize its potential in the coming years.

Demand-responsive transit systems are seen as a solution to improve the level of service and decrease the costs of providing transit to rural or low-demand areas. There are great expectations on the impact that driverless demand-responsive transit (DDRT) systems can have on a regional setting. Nevertheless, the application of DDRT in such type of setting has not been widely studied, in particular for scenarios where the system is an addition to the existing alternatives (as characteristic of the early diffusion stage of an innovation). This study provides an assessment of the early-stage operation of a regional DDRT system used by a small portion of the entire potential adopters. A methodological approach is built upon an agent-based model through which the daily operation of a DDRT system is simulated in detail. This approach is applied to a case study in Portugal considering scenarios varying in terms of several operational parameters, adoption rates (from 1 to 20%), and types of services (private versus shared rides). Results show that each vehicle in the DDRT system with shared rides could replace up to 13 private vehicles with a decrease in the vehicle-kilometers traveled of 1%. The DDRT system operation is profitable even with low adoption rates (starting from 2% for the system with shared rides). When considering the adoption rate of 5%, the system with shared rides is 54% more profitable than the one with private rides, but, from the perspective of travelers, shared rides lead to longer waiting times and detours.

A plausible definition of “ reasoning ” could be “ algebraically manipulating previously acquired knowledge in order to answer a new question ”. This definition covers first-order logical inference or probabilistic inference. It also includes much simpler manipulations commonly used to build large learning systems. For instance, we can build an optical character recognition system by first training a character segmenter, an isolated character recognizer, and a language model, using appropriate labelled training sets. Adequately concatenating these modules and fine tuning the resulting system can be viewed as an algebraic operation in a space of models. The resulting model answers a new question, that is, converting the image of a text page into a computer readable text. This observation suggests a conceptual continuity between algebraically rich inference systems, such as logical or probabilistic inference, and simple manipulations, such as the mere concatenation of trainable learning systems. Therefore, instead of trying to bridge the gap between machine learning systems and sophisticated “all-purpose” inference mechanisms, we can instead algebraically enrich the set of manipulations applicable to training systems, and build reasoning capabilities from the ground up.

Zooplankton plays a major role in ocean food webs and biogeochemical cycles, and provides major ecosystem services as a main driver of the biological carbon pump and in sustaining fish communities. Zooplankton is also sensitive to its environment and reacts to its changes. To better understand the importance of zooplankton, and to inform prognostic models that try to represent them, spatially-resolved biomass estimates of key plankton taxa are desirable. In this study we predict, for the first time, the global biomass distribution of 19 zooplankton taxa (1-50 mm Equivalent Spherical Diameter) using observations with the Underwater Vision Profiler 5, a quantitative in situ imaging instrument. After classification of 466,872 organisms from more than 3,549 profiles (0-500 m) obtained between 2008 and 2019 throughout the globe, we estimated their individual biovolumes and converted them to biomass using taxa-specific conversion factors. We then associated these biomass estimates with climatologies of environmental variables (temperature, salinity, oxygen, etc.), to build habitat models using boosted regression trees. The results reveal maximal zooplankton biomass values around 60°N and 55°S as well as minimal values around the oceanic gyres. An increased zooplankton biomass is also predicted for the equator. Global integrated biomass (0-500 m) was estimated at 0.403 PgC. It was largely dominated by Copepoda (35.7%, mostly in polar regions), followed by Eumalacostraca (26.6%) Rhizaria (16.4%, mostly in the intertropical convergence zone). The machine learning approach used here is sensitive to the size of the training set and generates reliable predictions for abundant groups such as Copepoda (R2 ≈ 20-66%) but not for rare ones (Ctenophora, Cnidaria, R2 < 5%). Still, this study offers a first protocol to estimate global, spatially resolved zooplankton biomass and community composition from in situ imaging observations of individual organisms. The underlying dataset covers a period of 10 years while approaches that rely on net samples utilized datasets gathered since the 1960s. Increased use of digital imaging approaches should enable us to obtain zooplankton biomass distribution estimates at basin to global scales in shorter time frames in the future.

Neuromechanical studies investigate how the nervous system interacts with the musculoskeletal (MSK) system to generate volitional movements. Such studies have been supported by simulation models that provide insights into variables that cannot be measured experimentally and allow a large number of conditions to be tested before the experimental analysis. However, current simulation models of electromyography (EMG), a core physiological signal in neuromechanical analyses, are mainly limited to static contractions and cannot fully represent the dynamic modulation of EMG signals during volitional movements. Here, we overcome these limitations by presenting NeuroMotion, an open-source simulator that provides a full-spectrum synthesis of EMG signals during voluntary movements. NeuroMotion is comprised of three modules. The first module is an upper-limb MSK model with OpenSim API to estimate the muscle fibre lengths and muscle activations during movements. The second module is BioMime, a deep neural network-based EMG generator that receives nonstationary physiological parameter inputs, such as muscle fibre lengths, and efficiently outputs motor unit action potentials (MUAPs). The third module is a motor unit pool model that transforms the muscle activations into discharge timings of motor units. The discharge timings are convolved with the output of BioMime to simulate EMG signals during the movement. Here we also provide representative applications of NeuroMotion. We first show how simulated MUAP waveforms change during different levels of physiological parameter variations and different movements. We then show that the synthetic EMG signals during two-degree-of-freedom hand and wrist movements can be used to augment experimental data for regression. Ridge regressors trained on the synthetic dataset were directly used to predict joint angles from experimental data. NeuroMotion is the first full-spectrum EMG generative model to simulate human forearm electrophysiology during voluntary hand, wrist, and forearm movements. All intermediate variables are available, which allows the user to study cause-effect relationships in the complex neuromechanical system, fast iterate algorithms before collecting experimental data, and validate algorithms that estimate non-measurable parameters in experiments. We expect this full-spectrum model will complement experimental approaches and facilitate neuromechanical research.

Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Nowak et al. argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.

Resistant cultivars are of value for protecting crops from disease, but can be rapidly overcome by pathogens. Several strategies have been proposed to delay pathogen adaptation (evolutionary control), while maintaining effective protection (epidemiological control). Resistance genes can be (i) combined in the same cultivar (pyramiding), (ii) deployed in different cultivars sown in the same field (mixtures) or in different fields (mosaics), or (iii) alternated over time (rotations). The outcomes of these strategies have been investigated principally in pathogens displaying pure clonal reproduction, but many pathogens have at least one sexual event in their annual life cycles. Sexual reproduction may promote the emergence of superpathogens adapted to all the resistance genes deployed. Here, we improved the spatially explicit stochastic model landsepi to include pathogen sexual reproduction, and we used the improved model to investigate the effect of sexual reproduction on evolutionary and epidemiological outcomes across deployment strategies for two major resistance genes. Sexual reproduction favours the establishment of a superpathogen when single mutant pathogens are present together at a sufficiently high frequency, as in mosaic and mixture strategies. However, sexual reproduction did not affect the strategy recommendations for a wide range of mutation probabilities, associated fitness costs, and landscape organisations.

Size, shape, overall composition, and surface functionality largely determine the properties and applications of metal nanoparticles. Aside from well-defined metal clusters, their composition is often estimated assuming a quasi-spherical shape of the nanoparticle core. With decreasing diameter of the assumed circumscribed sphere, particularly in the range of only a few nanometers, the estimated nanoparticle composition increasingly deviates from the real composition, leading to significant discrepancies between anticipated and experimentally observed composition, properties, and characteristics. We here assembled a compendium of tables, models, and equations for thiol-protected gold nanoparticles that will allow experimental scientists to more accurately estimate the composition of their gold nanoparticles using TEM image analysis data. The estimates obtained from following the routines described here will then serve as a guide for further analytical characterization of as-synthesized gold nanoparticles by other bulk (thermal, structural, chemical, and compositional) and surface characterization techniques. While the tables, models, and equations are dedicated to gold nanoparticles, the composition of other metal nanoparticle cores with face-centered cubic lattices can easily be estimated simply by substituting the value for the radius of the metal atom of interest. Graphical abstract