Influence of model selection and data structure on the estimation of genetic parameters in honeybee populations

Estimating genetic parameters of quantitative traits is a prerequisite for animal breeding. In honeybees, the genetic variance separates into queen and worker effects. However, under data paucity, parameter estimations that account for this peculiarity often yield implausible results. Consequently, simplified models which attribute all genetic contributions to either the queen (queen model) or the workers (worker model) are often used to estimate variance components in honeybees. However, the causes for estimations with the complete model (colony model) to fail and the consequences of simplified models for variance estimates are little understood. We newly developed the necessary theory to compare parameter estimates that were achieved by the colony model with those of the queen and worker models. Furthermore, we performed computer simulations to quantify the influence of model choice, estimation algorithm, true genetic parameters, rates of controlled mating, apiary sizes, and phenotype data completeness on the success of genetic parameter estimations. We found that successful estimations with the colony model were only possible if at least some of the queens mated controlledly on mating stations. In that case, estimates were largely unbiased if more than 20% of the colonies had phenotype records. The simplified queen and worker models proved more stable and yielded plausible parameter estimates for almost all settings. Results obtained from these models were unbiased when mating was uncontrolled, but with controlled mating, the simplified models consistently overestimated heritabilities. This work elucidates the requirements for variance component estimation in honeybees and provides the theoretical groundwork for simplified honeybee models.

Rheology of crossbridge ensembles

Muscle rheology, or the characterization of a muscle's response to external mechanical perturbations, is crucial to an animal's motor control and locomotive abilities. How the rheology emerges from the ensemble dynamics of microscopic actomyosin crossbridges known to underlie muscle forces is however a longstanding question. Classical descriptions in terms of force-length and force-velocity relationships capture only part of the rheology, namely under steady but not dynamical conditions. Although much is known about the actomyosin machinery, current mathematical models that describe the behavior of a population or an ensemble of crossbridges are plagued by an excess of parameters and computational complexity that limits their usage in large-scale musculoskeletal simulations. In this paper, we examine models of crossbridge dynamics of varying complexity and show that the emergent rheology of an ensemble of crossbridges can be simplified to a few dominant time-constants associated with intrinsic dynamical processes. For Huxley's classical two-state crossbridge model, we derive exact analytical expressions for the emergent ensemble rheology and find that it is characterized by a single time-constant. For more complex models with up to five crossbridge states, we show that at most three time-constants are needed to capture the ensemble rheology. Our results thus yield simplified models comprising of a few time-constants for muscle's bulk rheological response that can be readily used in large-scale simulations without sacrificing the model's interpretability in terms of the underlying actomyosin crossbridge dynamics.

A Simplified FE Modeling Strategy for the Drop Process Simulation Analysis of Light and Small Drone

The numerical accuracy of drop process simulation and collision response for drones is primarily determined by the finite element modeling method and simplified method of drone airframe structure. For light and small drones exhibiting diverse shapes and configurations, mixed materials and structures, deformation and complex destruction behaviors, the way of developing a reasonable and easily achieved high-precision simplified modeling method by ensuring the calculation accuracy and saving the calculation cost has aroused increasing concern in impact dynamics simulation. In the present study, the full-size modeling and simplified modeling methods that are specific to different components of a relatively popular light and small drone were analyzed in an LS-DYNA software environment. First, a full-size high-precision model of the drone was built, and the model accuracy was verified by performing the drop tests at the component level as well as the whole machine level. Subsequently, based on the full-size high-precision model, the property characteristics of the main components of the light and small drone and their common simplification methods were classified, a series of simplified modeling methods for different components were developed, several single simplified models and combined simplified models were built, and a method to assess the calculation error of the peak impact load in the simplified models was proposed. Lastly, by comparing and analyzing the calculation accuracy of various simplified models, the high-precision simplified modeling strategy was formulated, and the suggestions were proposed for the impact dynamics simulation of the light and small drone falling. Given the analysis of the calculation scale and solution time of the simplified model, the high-precision simplified modeling method developed here is capable of noticeably reducing the modeling difficulty, the solution scale and the calculation time while ensuring the calculation accuracy. Moreover, it shows promising applications in several fields (e.g., structure design, strength analysis and impact process simulation of drone).

Determining the Influence of Casing Vibrational Behaviour On Rotordynamics

Casings of machinery and support structures have an influence on the rotordynamic behaviour which is commonly considered by simplified models (e.g. one degree of freedom models). These are in many cases insufficient. Hence, more accurate modelling approaches are required which can be used in the design process or the rotordynamic calculation to achieve a better representation of the overall vibrational behaviour. To study the effects of casing and supporting structures on rotordynamics, the casing modal parameters of an axial compressor are determined by an experimental modal analysis. In parallel, a numerical model is established. As experimental data are rarely found in the literature, this work focuses on the parameter identification of the casing structure. The results are subsequently incorporated into a model updating strategy, in order to tune and improve the numerical model. Experimental and numerical data are compared to assess the quality of the data and the results gained. The ultimate objective is a reduced order model, which can be integrated in existing rotordynamic tools via an interface while keeping the calculation time low.

Theoretical analysis of RNA polymerase fidelity: a steady-state copolymerization approach

The fidelity of DNA transcription catalyzed by RNA polymerase (RNAP) has long been an important issue in biology. Experiments have revealed that RNAP can incorporate matched nucleotides selectively and proofread the incorporated mismatched nucleotides. However, systematic theoretical researches on RNAP fidelity are still lacking. In the last decade, several theories on RNA transcription have been proposed, but they only handled highly simplified models without considering the high-order neighbor effects and the oligonucleotides cleavage both of which are critical for the overall fidelity. In this paper, we regard RNA transcription as a binary copolymerization process and calculate the transcription fidelity by the steady-state copolymerization theory recently proposed by us for DNA replication. With this theory, the more realistic models considering higher-order neighbor effects, oligonucleotides cleavage, multi-step incorporation and multi-step cleavage can be rigorously handled.

Damage risk assessment of building materials with moisture hysteresis

Heat and Moisture Transfer (HMT) simulations are used to evaluate moisture related damage risks in building envelopes. HMT simulations are commonly performed accepting the hypothesis of not considering the moisture hysteresis of materials. The results of HMT simulation of a timber wall with hysteresis are presented, and compared to the results of three simplified models, showing the effects of hysteresis on the simulation results and on the assessment of the risk of decay. Moisture content is the most influenced variable, while temperature and relative humidity are slightly affected. The wood decay risk analysis is performed using the simplified 20% moisture content rule. Similar temperature values and relative humidity values are calculated as simplified models, while the moisture content annual average values have differences up to 2.3%. The wood decay risk obtained with the simplified models could be overestimated if the simulation is performed using the desorption curve, while it could be underestimated with the adsorption curve. The best approximation is obtained with the mean sorption curve, while the desorption curve and the adsorption curve could be used to calculate the upper and lower boundary of the moisture contents respectively.

How to Improve Accuracy of a Kick Tolerance Model by Considering the Effects of Kick Classification, Frictional Losses, Pore Pressure Profile, and Influx Temperature

Summary Kick tolerance (KT) calculation is essential for a cost-effective well design and safe drilling operations. While most exploration and production operators have a similar definition of KT, the calculation is not consistent because of different assumptions that are made and the computational power of KT calculators. Dynamic multiphase drilling simulators usually provide KT estimates with a minimum number of assumptions. They are much more accessible nowadays for use in predicting the behavior of multiphase flow in drilling and well control operations. However, as far as we observed, the simulation services are mainly used for complex and marginal wells in which low KT may impose additional casing strings, unconventional costly drilling practices, or a high risk of major well control events. Thus, companies often use simplified steady-state models for relatively uncomplicated wells through their own KT calculation worksheets. This practice is usually justified by the misconception that simplified models are always conservative and give less KT than actual conditions. In contrast, some simplifications may lead to higher operational risks due to an overestimated KT, depending on well conditions and parameters. The primary objective of this work was to perform a quality assurance/quality control on KT calculation practices in Company P. Later on, based on our findings, we determined some solutions to improve accuracy in the simplified KT worksheets commonly used by engineers across the company. This became a driver for generating a new KT worksheet (Company Model), in particular for situations in which engineers do not have access to a kick simulator. However, it should not mislead readers about the requirements of the simulator for complex and low-KTwells. Quality assurance/quality control and subsequent investigations found that there are some important criteria and parameters that affect KT calculations, but they are missing in many simplified models or ignored by engineers because they are unaware of or lack adequate references. After reviewing relevant academic literature, common practices and assessing several off-the-shelf software programs, we generated a computer program using Visual Basic for applications to address KT sensitivity to different parameters in steady-state conditions. The newly developed program is based on a single gas bubble model that applies the effect of annular frictional losses, influx temperature, gas compressibility factor, well trajectory, and bottomhole assembly (BHA). Moreover, the program differentiates between swabbing and underbalanced conditions. A logical test is applied to determine the type of kick before computing the relevant influx volume. This kick classification concept is ignored in many KT models; this is a common mistake that leads to misleading results. The annular pressure loss (APL) parameter is sometimes assumed to be zero in KT spreadsheets, while as an additional stress load on the wellbore, it affects the kick budget and must be considered.