The Interface Between Empirical and Simulation-Based Ground-Motion Models.
Ontology highlight
ABSTRACT:
SUBMITTER: Atkinson GM
PROVIDER: S-EPMC7327539 | biostudies-literature | 2020
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Direct time-domain simulation of continuous-wave (CW) electron paramagnetic resonance (EPR) spectra from molecular dynamics (MD) trajectories has become increasingly popular, especially for proteins labeled with nitroxide spin labels. Due to the time-consuming nature of simulating adequately long MD trajectories, two approximate methods have been developed to reduce the MD-trajectory length required for modeling EPR spectra: hindered Brownian diffusion (HBD) and hidden Markov models (HMMs). Here, we assess the accuracy of these two approximate methods relative to direct simulations from MD trajectories for three spin-labeled protein systems (a simple helical peptide, a soluble protein, and a membrane protein) and two nitroxide spin labels with differing mobilities (R1 and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC)). We find that the HMMs generally outperform HBD. Although R1 dynamics partially resembles hindered Brownian diffusion, HMMs accommodate the multiple dynamic time scales for the transitions between rotameric states of R1 that cannot be captured accurately by a HBD model. The MD trajectories of the TOAC-labeled proteins show that its dynamics closely resembles slow multisite exchange between twist-boat and chair ring puckering states. This motion is modeled well by HMM but not by HBD. All MD-trajectory data processing, stochastic trajectory simulations, and CW EPR spectral simulations are implemented in EasySpin, a free software package for MATLAB.
| S-EPMC6941481 | biostudies-literature
Project description:Shear-waves are the most energetic body-waves radiated from an earthquake, and are responsible for the destruction of engineered structures. In both short-term emergency response and long-term risk forecasting of disaster-resilient built environment, it is critical to predict spatially accurate distribution of shear-wave amplitudes. Although decades' old theory proposes a deterministic, highly anisotropic, four-lobed shear-wave radiation pattern, from lack of convincing evidence, most empirical ground-shaking prediction models settled for an oversimplified stochastic radiation pattern that is isotropic on average. Today, using the large datasets of uniformly processed seismograms from several strike, normal, reverse, and oblique-slip earthquakes across the globe, compiled specifically for engineering applications, we could reveal, quantify, and calibrate the frequency-, distance-, and style-of-faulting dependent transition of shear-wave radiation between a stochastic-isotropic and a deterministic-anisotropic phenomenon. Consequent recalibration of empirical ground-shaking models dramatically improved their predictions: with isodistant anisotropic variations of ±40%, and 8% reduction in uncertainty. The outcomes presented here can potentially trigger a reappraisal of several practical issues in engineering seismology, particularly in seismic ground-shaking studies and seismic hazard and risk assessment.
| S-EPMC6353911 | biostudies-literature
Project description:Computer simulation can be used to predict human walking motions as a tool of basic science, device design, and for surgical planning. One the challenges of predicting human walking is accurately synthesizing both the movements and ground forces of the stance foot. Though the foot is commonly modeled as a viscoelastic element, rigid foot-ground contact models offer some advantages: fitting is reduced to a geometric problem, and the numerical stiffness of the equations of motion is similar in both swing and stance. In this work, we evaluate two rigid-foot ground contact models: the ellipse-foot (a single-segment foot), and the double-circle foot (a two-segment foot). To evaluate the foot models we use three different comparisons to experimental data: first we compare how accurately the kinematics of the ankle frame fit those of the model when it is forced to track the measured center-of-pressure (CoP) kinematics; second, we compare how each foot affects how accuracy of a sagittal plane gait model that tracks a subjects walking motion; and third, we assess how each model affects a walking motion prediction. For the prediction problem we consider a unique cost function that includes terms related to both muscular effort and foot-ground impacts. Although the ellipse-foot is superior to the double-circle foot in terms of fit and the accuracy of the tracking OCP solution, the predictive simulation reveals that the ellipse-foot is capable of producing large force transients due to its geometry: when the ankle quickly traverses its u-shaped trajectory, the body is accelerated the body upwards, and large ground forces result. In contrast, the two-segment double-circle foot produces ground forces that are of a similar magnitude to the experimental subject because the additional forefoot segment plastically contacts the ground, arresting its motion, similar to a human foot.
| S-EPMC6693511 | biostudies-literature
Project description:Interactions of molecules, such as signaling proteins, with multiple binding sites and/or multiple sites of post-translational covalent modification can be modeled using reaction rules. Rules comprehensively, but implicitly, define the individual chemical species and reactions that molecular interactions can potentially generate. Although rules can be automatically processed to define a biochemical reaction network, the network implied by a set of rules is often too large to generate completely or to simulate using conventional procedures. To address this problem, we present DYNSTOC, a general-purpose tool for simulating rule-based models.DYNSTOC implements a null-event algorithm for simulating chemical reactions in a homogenous reaction compartment. The simulation method does not require that a reaction network be specified explicitly in advance, but rather takes advantage of the availability of the reaction rules in a rule-based specification of a network to determine if a randomly selected set of molecular components participates in a reaction during a time step. DYNSTOC reads reaction rules written in the BioNetGen language which is useful for modeling protein-protein interactions involved in signal transduction. The method of DYNSTOC is closely related to that of StochSim. DYNSTOC differs from StochSim by allowing for model specification in terms of BNGL, which extends the range of protein complexes that can be considered in a model. DYNSTOC enables the simulation of rule-based models that cannot be simulated by conventional methods. We demonstrate the ability of DYNSTOC to simulate models accounting for multisite phosphorylation and multivalent binding processes that are characterized by large numbers of reactions.DYNSTOC is free for non-commercial use. The C source code, supporting documentation and example input files are available at http://public.tgen.org/dynstoc/.Supplementary data are available at Bioinformatics online.
| S-EPMC2660871 | biostudies-other
Project description:Grasslands contribute to global biogeochemical cycles and can host a high number of plant species. Both-species dynamics and biogeochemical fluxes-are influenced by abiotic and biotic environmental factors, management and natural disturbances. In order to understand and project grassland dynamics under global change, vegetation models which explicitly capture all relevant processes and drivers are required. However, the parameterization of such models is often challenging. Here, we report on testing an individual- and process-based model for simulating the dynamics and structure of a grassland experiment in temperate Europe. We parameterized the model for three species and confront simulated grassland dynamics with empirical observations of their monocultures and one two-species mixture. The model reproduces general trends of vegetation patterns (vegetation cover and height, aboveground biomass and leaf area index) for the monocultures and two-species community. For example, the model simulates well an average annual grassland cover of 70% in the species mixture (observed cover of 77%), but also shows mismatches with specific observation values (e.g. for aboveground biomass). By a sensitivity analysis of the applied inverse model parameterization method, we demonstrate that multiple vegetation attributes are important for a successful parameterization while leaf area index revealed to be of highest relevance. Results of our study pinpoint to the need of improved grassland measurements (esp. of temporally higher resolution) in close combination with advanced modelling approaches.
| S-EPMC7386574 | biostudies-literature
Project description:Within this work we present AMiCUS, a Human-Robot Interface that enables tetraplegics to control a multi-degree of freedom robot arm in real-time using solely head motion, empowering them to perform simple manipulation tasks independently. The article describes the hardware, software and signal processing of AMiCUS and presents the results of a volunteer study with 13 able-bodied subjects and 6 tetraplegics with severe head motion limitations. As part of the study, the subjects performed two different pick-and-place tasks. The usability was assessed with a questionnaire. The overall performance and the main control elements were evaluated with objective measures such as completion rate and interaction time. The results show that the mapping of head motion onto robot motion is intuitive and the given feedback is useful, enabling smooth, precise and efficient robot control and resulting in high user-acceptance. Furthermore, it could be demonstrated that the robot did not move unintendedly, giving a positive prognosis for safety requirements in the framework of a certification of a product prototype. On top of that, AMiCUS enabled every subject to control the robot arm, independent of prior experience and degree of head motion limitation, making the system available for a wide range of motion impaired users.
| S-EPMC6630260 | biostudies-literature
Project description:BACKGROUND:Standard random-effects meta-analysis methods perform poorly when applied to few studies only. Such settings however are commonly encountered in practice. It is unclear, whether or to what extent small-sample-size behaviour can be improved by more sophisticated modeling. METHODS:We consider likelihood-based methods, the DerSimonian-Laird approach, Empirical Bayes, several adjustment methods and a fully Bayesian approach. Confidence intervals are based on a normal approximation, or on adjustments based on the Student-t-distribution. In addition, a linear mixed model and two generalized linear mixed models (GLMMs) assuming binomial or Poisson distributed numbers of events per study arm are considered for pairwise binary meta-analyses. We extract an empirical data set of 40 meta-analyses from recent reviews published by the German Institute for Quality and Efficiency in Health Care (IQWiG). Methods are then compared empirically as well as in a simulation study, based on few studies, imbalanced study sizes, and considering odds-ratio (OR) and risk ratio (RR) effect sizes. Coverage probabilities and interval widths for the combined effect estimate are evaluated to compare the different approaches. RESULTS:Empirically, a majority of the identified meta-analyses include only 2 studies. Variation of methods or effect measures affects the estimation results. In the simulation study, coverage probability is, in the presence of heterogeneity and few studies, mostly below the nominal level for all frequentist methods based on normal approximation, in particular when sizes in meta-analyses are not balanced, but improve when confidence intervals are adjusted. Bayesian methods result in better coverage than the frequentist methods with normal approximation in all scenarios, except for some cases of very large heterogeneity where the coverage is slightly lower. Credible intervals are empirically and in the simulation study wider than unadjusted confidence intervals, but considerably narrower than adjusted ones, with some exceptions when considering RRs and small numbers of patients per trial-arm. Confidence intervals based on the GLMMs are, in general, slightly narrower than those from other frequentist methods. Some methods turned out impractical due to frequent numerical problems. CONCLUSIONS:In the presence of between-study heterogeneity, especially with unbalanced study sizes, caution is needed in applying meta-analytical methods to few studies, as either coverage probabilities might be compromised, or intervals are inconclusively wide. Bayesian estimation with a sensibly chosen prior for between-trial heterogeneity may offer a promising compromise.
| S-EPMC6330405 | biostudies-literature
Project description:Recently the distributed fibre optic strain sensing (DFOSS) technique has been applied to monitor deformations of various earth structures. However, the reliability of soil deformation measurements remains unclear. Here we present an integrated DFOSS- and photogrammetry-based test study on the deformation behaviour of a soil foundation model to highlight the role of strain sensing fibre-soil interface in DFOSS-based geotechnical monitoring. Then we investigate how the fibre-soil interfacial behaviour is influenced by environmental changes, and how the strain distribution along the fibre evolves during progressive interface failure. We observe that the fibre-soil interfacial bond is tightened and the measurement range of the fibre is extended under high densities or low water contents of soil. The plastic zone gradually occupies the whole fibre length when the soil deformation accumulates. Consequently, we derive a theoretical model to simulate the fibre-soil interfacial behaviour throughout the progressive failure process, which accords well with the experimental results. On this basis, we further propose that the reliability of measured strain can be determined by estimating the stress state of the fibre-soil interface. These findings may have important implications for interpreting and evaluating fibre optic strain measurements, and implementing reliable DFOSS-based geotechnical instrumentation.
| S-EPMC5101507 | biostudies-literature
Project description:Animal groups frequently move in a highly organized manner, as represented by flocks of birds and schools of fish. Despite being an everyday occurrence, we do not fully understand how this works. In particular, what social interactions between animals give rise to the flock structures we observe? This question is often investigated using self-propelled particle models where particles represent the individual animals. These models differ in the social interactions used, individual particle properties, and various technical assumptions. One particular technical assumption relates to whether all particles update their headings and positions at exactly the same time (synchronous update) or not (asynchronous update). Here, we investigate the causal effects of this assumption in an attraction-only model and find that it has a dramatic impact. Polarized groups do not form when synchronous update is used, but are produced with asynchronous update, and this phenomenon is robust with respect to variation in particle displacements and inclusion of noise. Given that many important models have been implemented with synchronous update only, we speculate that our understanding of the social interactions on which they are based may be incomplete. Perhaps previously unobserved phenomena will emerge if other potentially more realistic update schemes are used.
| S-EPMC6502356 | biostudies-literature
Project description:Atmospheric humidity strongly influences the interactions between dry granular particles in process containers. To reduce the energy loss in industrial production processes caused by particle agglomeration, a basic understanding of the dependence of particle interactions on humidity is necessary. Hence, in this study, molecular dynamic simulations were carried out to calculate the adhesion between silica surfaces in the presence of adsorbed water. For a realistic description, the choice of force field is crucial. Because of their frequent use and transferability to biochemical systems, the Clay and CWCA force fields were investigated with respect to their ability to describe the water-silica interface in comparison to the more advanced Reax force field, ab initio calculations, and experiments.
| S-EPMC3558025 | biostudies-other