REVIEW: The evolution of polyembryony in parasitoid wasps

Polyembryony has evolved independently in four families of parasitoid wasps. We review three main hypotheses for the selective forces favouring this developmental mode in parasitoids: polyembryony (i) reduces the costs of egg limitation; (ii) reduces the genetic conflict among offspring; and (iii) allows offspring to adjust their numbers to the quality of the host. Using comparative data and verbal and mathematical arguments, we evaluate the relative importance of the different selective forces through different evolutionary stages and in the different groups of polyembryonic wasps. We conclude that reducing the cost of egg limitation is especially important when large broods are favoured. Reducing genetic conflict may be most important when broods are small, thus might have been important during, or immediately following, the initial transition from monoembryony to polyembryony. Empirical data provide little support for the brood‐size adjustment hypothesis, although it is likely to interact with other selective forces favouring polyembryony.     

Patch leaving decision rules and the Marginal Value Theorem: an experimental analysis and a simulation model

The patch exploitation strategy of females of the insect parasitoid Trichogramma brassicae was studied on patches containing different proportions of hosts that were previously attacked by conspecificfemales. On average, T. brassicae females spent more time onpatches of higher quality, and all patches were reduced tothe same level of profitability before being left. This appearedto be in accordance to the optimal predictions of the CharnovMarginal Value Theorem. The proximate leaving mechanisms involvedwere analyzed by means of a Cox proportional hazards model.Each oviposition in a healthy host appeared to have an incremental influence on the patch residence time, whereas each rejectionof a healthy host or of a host that was previously attackedby the same female (i.e., self-superparasitism) had a decrementaleffect. These patch leaving mechanisms did not change accordingto the quality of the patch the females were exploiting. AMonte Carlo simulation was developed around the results of the Cox regression model. The results suggest that this set of patchleaving rules seems to provide the females with a sufficientway to reach the predictions of the Charnov model. Among thedifferent mechanisms involved, the incremental effect associatedwith each oviposition in a healthy host appeared to play the most important role. The relationship between the proximatemechanistic rules adopted by the females and the ultimate predictionof the Charnov model is discussed.     

The ‘paradox’ of polyembryony: A review of the cases and a hypothesis for its evolution

Animal polyembryony appears to be paradoxical because it clones an unproven genotype at the expense of genetic diversity in a clutch. However, it is employed by at least 18 taxa in six phyla (excluding instances of occasional twinning). Most polyembryony occurs in parasitic stages or in other environments whose quality is not predictable by the mother; in some instances, it compensates for a constraint on zygote number. We predict that polyembryony is likely to evolve when the offspring has more information regarding optimal clutch size than the parents.     

Host kairomone learning and foraging success in an egg parasitoid: a simulation model

Abstract 1. Trissolcus basalis (Wollaston) (Hymenoptera: Scelionidae) is an egg parasitoid that recognises chemical residues left by its host the green stink bug Nezara viridula (L.) (Heteroptera: Pentatomidae) as kairomone signals, enabling it to find egg masses in which to lay eggs. 2. Kairomones are usually present as patches deposited by N. viridula females, and recent results (Peri et al., Journal of Experimental Biology, 209 , 3629–3635, 2006) indicated that females of T. basalis are able to learn the features of their foraging environment and to adjust accordingly the amount of time spent on the patches of kairomones they are visiting, depending on whether or not host eggs are found. 3. In order to assess the impact of this learning ability, a Monte Carlo, spatially explicit and individual‐based simulation model was built to quantify the foraging efficiency of T. basalis females in environments with different levels of host abundance and distribution. In all cases, the present study compared the foraging efficiency of simulated T. basalis females having the ability to learn with those lacking this ability. 4. Learning females always visited a higher number of kairomone patches and attacked a higher number of hosts than non‐learning females, especially when there was a high density of kairomone patches in the environment. 5. Learning ability globally appears to allow the maintenance of efficient foraging success, especially when there is a low probability for the kairomone patches to contain discoverable hosts. 6. The increase in foraging efficiency for learning females appears to depend on the characteristics of the habitat in which they are foraging. Results thus suggest that significant variation in learning ability is likely to occur in natural wasp populations facing different environments with different host spatial distributions.     

Sexual cannibalism in the fishing spider and a model for the evolution of sexual cannibalism based on genetic constraints

Several hypotheses have been proposed for the evolution of sexual cannibalism by females. Newman and Elgar (1991) suggested that sexual cannibalism prior to mating by virgin female spiders may have evolved as a result of female foraging considerations. According to this model, an adult female's decision to mate or cannibalize a courting male should be based on an assessment of the male's value as a meal versus his value as a mate. The current study provides an empirical test of the assumptions and predictions of this model in the sexually cannibalistic fishing spider. Adult females were subjected to different food treatments, and exposed to adult males in the laboratory. However, only one of the assumptions of the model and none of its five predictions were upheld. We failed to find any effects of female foraging, female mating status, female size, male size or time of the season on females' behaviour towards courting males. Females behaved stereotypically, and many females were left unmated despite numerous mating opportunities. We also demonstrate costs of sexual cannibalism in a natural population. We propose that the act of sexual cannibalism in the fishing spider is non-adaptive, and develop a model for the evolution of premating sexual cannibalism in spiders based on genetic constraints. According to this hypothesis, sexual cannibalism by adult females may have evolved as an indirect result of selection for high and non-discriminate aggression during previous ontogenetic stages. Genetic covariance between different components of aggressive behaviour may constrain the degree to which (1) juvenile and adult aggression and/or (2) aggression towards conspecifics and heterospecifics can vary independently. We briefly review the support for our model, and suggest several critical tests that may be used to assess the assumptions and predictions of the model.     

海洋牧场生态安全监管的演化博弈模型及仿真

海洋牧场生态安全监管是由政府部门对海洋牧场企业的资源开发利用、环境治理保护等行为进行监督和管理,保证海洋牧场海域的资源与环境符合生态安全需要,其对实现海洋牧场的环境保护、资源养护和渔业持续产出功能具有重要作用。首先分析了海洋牧场生态安全监管中的参与主体为政府部门和海洋牧场企业,然后从监管与不监管、重视与不重视两个维度构建了海洋牧场生态安全监管博弈参与主体的策略集合及收益矩阵,在此基础上结合复制动态方程和雅可比矩阵求解了海洋牧场生态安全监管博弈中演化稳定策略并进行了稳定性分析和模拟仿真,最后提出了海洋牧场生态安全监管的对策建议。研究结果表明,对海洋牧场企业不重视生态安全行为的惩罚力度、政府部门从发现企业不重视生态安全中获取的收益、外界监督力量监督成功的概率是影响演化博弈结果的重要因素。据此提出"加大对海洋牧场企业不重视海洋牧场生态安全行为的处罚力度、提高政府部门发现海洋牧场企业不重视海洋牧场生态安全时的收益、建立健全海洋牧场生态安全监管机制、发挥外界监督力量的作用"等政策建议,以维护我国海洋牧场生态安全。     

Evaluation of three scatter correction methods based on estimation of photopeak scatter spectrum in SPECT imaging: A simulation study

Three practical methods for scatter correction of Tc-99m SPECT images are evaluated. Among these, two methods, three-energy window (TEW) methods using the trapezoidal and triangular approximations, have been described previously by investigators, and a new approximation is offered in this work. The SIMIND (SIMulation of Imaging Nuclear Detectors) Monte Carlo program is used to simulate a line source placed at on-axis and 5 cm off-axis locations, a cold-sphere/hot-background phantom, a hot-sphere/cold-background phantom, and a more clinically realistic NCAT (Nonuniform Rational B-spline-based CArdiac-Torso) phantom. For evaluation of these methods, the scatter line-spread functions and scatter fractions for the on- and off-axis line source, image contrast, signal-to-noise ratio and relative noise for the cold spheres, and recovery coefficient for the hot spheres of different diameters are compared. For the NCAT phantom, a line profile through a slice of the reconstructed image is considered before and after scatter correction, and also image contrast defined by this profile is used to compare the correction methods. The results of this study indicate that for the line source simulation the scatter fractions obtained from the proposed method are a better estimation of true scatter fractions. Also, for both the sphere simulation and NCAT simulation, the proposed method improves the image contrast as compared to the two other methods.     

Construction of an intermediate-resolution lattice model and re-examination of the helix-coil transition: a dynamic Monte Carlo simulation

In protein modeling, spatial resolution and computational efficiency are always incompatible. As a compromise, an intermediate-resolution lattice model has been constructed in the present work. Each residue is decomposed into four basic units, i.e. the α-carbon group, the carboxyl group, the imino group, and the side-chain group, and each basic coarse-grained unit is represented by a minimum cubic box with eight lattice sites. The spacing of the lattice is about 0.56?Å, holding the highest spatial resolution for the present lattice protein models. As the first report of this new model, the helix-coil transition of a polyalanine chain was examined via dynamic Monte Carlo simulation. The period of formed α-helix was about 3.68 residues, close to that of a natural α-helix. The resultant backbone motion was found to be in the realistic regions of the conformational space in the Ramachandran plot. Helix propagation constant and nucleation constant were further determined through the dynamic hydrogen bonding process and torsional angle variation, and the results were used to make comparison between classical Zimm-Bragg theory and Lifson-Roig theory based on the Qian-Schellman relationship. The simulation results confirmed that our lattice model can reproduce the helix-coil transition of polypeptide and construct a moderately fine α-helix conformation without significantly weakening the priority in efficiency for a lattice model.     

像元尺度上不确定性对空间景观直观模型模拟的影响

LANDIS模型是模拟自然和人为干扰下森林景观变化的空间直观景观模型。模型把景观概念化为由相同大小的像元或样地组成的格网。在每一个像元上,模型要求输入物种和年龄组信息。但是,由于研究区一般由成千上百万个像元构成,不可能通过实际调查获取每一个像元上的物种和年龄组信息。因此,采用了一种基于小班的随机赋值法从森林调查数据中获取每一个像元的物种和年龄组信息。该方法是一种基于概率的方法,会在LANDIS模型模拟的物种和年龄组信息的输入中引入不确定性。为了评价由基于小班的随机赋值法所引入像元尺度上的不确定性对模型模拟结果的影响,用蒙特卡罗模拟法进行不确定性分析。对LANDIS模型模拟的每一个物种,用众数年龄组发生频率来定量化单个像元上年龄组信息的不确定性,用所有像元上的众数年龄组平均发生频率来定量化年龄组信息在像元尺度上总的不确定性。平均发生频率越高,不确定性越低。为了评价基于小班的随机赋值法对景观尺度上模型模拟结果的影响,计算了每一个物种在整个研究区内的面积百分比和聚集度指数。变异系数越大,不确定性越高。对所有物种,年龄组信息不确定性在模型模拟的初期是比较低的(平均发生频率大于10)。种子传播、建群、死亡和火干扰使模型结果的不确定性随模拟时间增加而增加。最后,不确定性达到稳定状态,达到平衡状态的时间与物种寿命接近。此时,初始的物种和年龄组信息不再对模型结果有影响。在景观尺度上,物种分布面积百分比和由聚集度指数所定量化的空间格局并未受像元尺度上不确定性增加的影响。因为LANDIS模型模拟研究的目的在于预测总的景观格局变化,而不是单一的事件,所以,基于小班的随机赋值法可用于LANDIS模型的参数化。     

The effects of structural parameters of zeolite on the adsorption of hydrogen: a molecular simulation study

The adsorption isotherm of hydrogen in zeolites FAU, LTA, KFI, RWY, RHO and TSC has been simulated employing grand canonical Monte Carlo procedure for a temperature range of 77 to 95 K and different pressures. The effects of structural composition, unit cell volume, framework density and specific surface area of zeolite on hydrogen adsorption in zeolites were investigated. The results clearly show that the adsorption of hydrogen in zeolites with the same silica density is a function of oxygen density at low pressures, and it is approximately the same at intermediate pressures. Nevertheless, at high pressures, the adsorption of hydrogen is a function of pore diameter for zeolites with same silica density. The effect of specific surface area on the adsorption isotherm of hydrogen on zeolites with approximately the same specific surface area is significant at low and high pressures. The results clearly indicate that the adsorption of hydrogen in RWY zeolite has maximum value at 77 K and at high pressures. The optimum condition of pressure for hydrogen adsorption isotherm in RWY zeolite is determined to be 600 bar. At a temperature of 77 K and a pressure of 600 bar, the adsorption of hydrogen in RWY zeolite is 6.93 wt %.     

Effect of mutation on helper T-cells and viral population: A computer simulation model for HIV

Summary A Monte Carlo simulation is proposed to study the dynamics of helper T-cells (N _H) and viral (N _V) populations in an immune response model relevant to HIV. Cellular states are binary variables and the interactions are described by logical expressions. Viral population shows a nonmonotonic growth before reaching a constant value while helper T-cells grow to a constant after a relaxation/reaction time. Initially, the population of helper cells grows with time with a power-law, N _H ∼t ^β, before reaching the steady-state; the growth exponent β increases systematically (β ≈ 1 – 2) with the mutation rate (P _mut≈0.1–0.4). The critical recovery time (t _c) increases exponentially with the viral mutation, t _c≈Ae ^αP _mut , with α=4.52±0.29 in low mutation regime and α=15.21±1.41 in high mutation regime. The equilibrium population of helper T-cell declines slowly with P _mut and collapses at ∼ 0.40; the viral population exhibits a reverse trend, i.e., a slow increase before the burst around the same mutation regime.     

FLUKA simulation of target fragmentation in proton therapy

In proton therapy, secondary fragments are created in nuclear interactions of the beam with the target nuclei. The secondary fragments have low kinetic energies and high atomic numbers as compared to primary protons. Fragments have a high LET and deposit all their energy close to the generation point. For their characteristics, secondary fragments can alter the dose distribution and lead to an increase of RBE for the same delivered physical dose. Moreover, the radiobiological impact of target fragmentation is significant mostly in the region before the Bragg peak, where generally healthy tissues are present, and immediately after Bragg peak. Considering the high biological impact of those particles, especially in the case of healthy tissues or organs at risk, the inclusion of target fragmentation processes in the dose calculation of a treatment planning system can be relevant to improve the treatment accuracy and for this reason it is one of the major tasks of the MoVe IT project.In this study, Monte Carlo simulations were employed to fully characterize the mixed radiation field generated by target fragmentation in proton therapy. The dose averaged LET has been evaluated in case of a Spread Out Bragg Peak (SOBP). Starting from LET distribution, RBE has been evaluated with two different phenomenological models. In order to characterize the mixed radiation field, the production cross section has been evaluated by means of the FLUKA code. The future development of present work is to generate a MC database of fragments fluence to be included in TPS.     

An approach to generate noncontact ACL-injury prone situations on a computer using kinematic data of non-injury situations and Monte Carlo simulation

ACL-injuries are one of the most common knee injuries in noncontact sports. Kinematic data of injury prone situations provide important information to study the underlying ACL-injury mechanisms. However, these data are rare. In this work an approach is presented to generate injury prone situations for noncontact ACL-injuries on a computer. The injury prone situations are generated by a musculoskeletal simulation model using kinematic data of a non-injury situation and the method of Monte Carlo simulation. The approach is successfully applied to generate injury prone landings in downhill ski racing. The characteristics of the obtained injury prone landings are consistent with video recordings of injury cases.     

BioMOCA—a Boltzmann transport Monte Carlo model for ion channel simulation

With the recent availability of high-resolution structural information for several key ion channel proteins and large-scale computational resources, Molecular Dynamics has become an increasingly popular tool for ion channel simulation. However, the CPU requirements for simulating ion transport on time scales relevant to conduction still exceed the resources presently available. To address this problem, we have developed Biology Monte Carlo (BioMOCA), a three-dimensional (3D) coarse-grained particle ion channel simulator based on the Boltzmann Transport Monte Carlo (BTMC) methodology. Although this approach is widely employed in the engineering community to study charge transport in electron devices, its application to molecular biology and electrolytes in general is new and hence must be validated. The pair correlation function, which is a measure of the microscopic structure of matter, provides a suitable benchmark to compare the BTMC method against the well-established Equilibrium Monte Carlo (EMC) approach. For validation purposes BioMOCA is used to simulate several simple homogeneous equilibrium electrolytes at concentrations of physiological interest. The ion–ion pair correlation functions computed from these simulations compare very well with those obtained from EMC simulations. We also demonstrate several performance-improving techniques that result in a several-fold speed-up without compromising the pair correlation function. BioMOCA is then used to perform full 3D simulations of ion transport in the gramicidin A channel in situ in a membrane environment, as well as to study the link between the electrostatic and dielectric properties of the protein and the channel's selectivity.     

Monte Carlo simulation of damascene electroplating: effects of additives

The influence of additives on the filling process of via holes in damascene electroplating is investigated with use of a kinetic Monte Carlo method. The basic system is the solid-by-solid model for crystal growth which includes the vacancy formation during the growth of thin film. Three kinds of additives are included in the model to control the local surface growth rate. Inhibitors and levelers have the effect of preventing the deposition, while accelerators increase the local growth rate. Levelers are modeled to stick to the tips of the surface. We performed a series of simulations by changing the parameters which characterize the additives to see their influence on the filling mechanism. It is shown that void-free filling is possible by the combination of the effects of the additives.     

Effects of viral mutation on cellular dynamics in a monte carlo simulation of HIV immune response model in three dimensions

Summary The cellular dynamics of HIV interaction with the immune system is explored in three-dimensions using a direct Monte Carlo simulation. Viral mutation with probability, Pmut, is considered with immobile and mobile cells. With immobile cells, the viral population becomes larger than that of the helper cells beyond a latency period Tcrit and above a mutation threshold Pcrit. That is at Pmut ≥ Pcrit, { }, with γ ⋍ 0.73 in three dimensions and γ ⋍ 0.88 in 2-D. Very little difference in Pcrit is observed between two and three dimensions. With mobile cells, no power-law is observed for the period of latency, but the difference in Pcrit between two and three dimensions is increased. The time-dependency of the density difference between Viral and Helper cell populations (ρV − ρH) is explored and follows the basic pattern of an immune response to infection. This is markedly more defined than in the 2-D case, where no clear pattern emerges.     

Carbon footprint of a scientific publication: A case study at Dalian University of Technology,China

Knowledge of the carbon footprint (CF) of a scientific publication can help to guide changes in behavior for mitigating global warming. A knowledge gap, however, still exists in academic circles. We quantified the CF of a publication by parameterizing searches, downloads, reading, and writing in the processes of publication with both direct and indirect emissions covered. We proposed a time-loaded conversion coefficient to transfer indirect emissions to final consumers. A questionnaire survey, certification database of Energy Star, fixed-asset databases specific to our campus, and reviewed life-cycle-assessment studies on both print media and electronic products were integrated with Monte Carlo simulations to quantify uncertainties. The average CF [(CI: 95%), SD] of a scientific publication was 5.44 kg CO₂-equiv. [(1.65, 14.78), 4.97], with 37.65 MJ [(0.00, 71.32), 30.40] of energy consumed. Reading the literature contributed the most, followed by writing and searching. A sensitivity analysis indicated that reading efficiency, the proportion of e-reading, and reference quantity were the most dominant of 52 parameters. Durable media generated a higher CF (4.24 kg CO₂-equiv.) than consumable media (1.35 kg CO₂-equiv.) due to both direct and indirect reasons. Campus policy makers should thus not promote the substitution of e-reading for print reading at the present stage, because their environmental advantages are highly dependent on time-loaded and behavioral factors. By comparison, replacing desktops with laptops is more attractive, by potentially reducing CFs by 50% and the disproportionate consumption of energy.     

An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments

We report on an advanced universal Monte Carlo simulation model of actin polymerization processes offering a broad application panel. The model integrates major actin-related reactions, such as assembly of actin nuclei, association/dissociation of monomers to filament ends, ATP-hydrolysis via ADP-Pi formation and ADP-ATP exchange, filament branching, fragmentation and annealing or the effects of regulatory proteins. Importantly, these reactions are linked to information on the nucleotide state of actin subunits in filaments (ATP hydrolysis) and the distribution of actin filament lengths. The developed stochastic simulation modelling schemes were validated on: i) synthetic theoretical data generated by a deterministic model and ii) sets of our and published experimental data obtained from fluorescence pyrene-actin experiments. Build on an open-architecture principle, the designed model can be extended for predictive evaluation of the activities of other actin-interacting proteins and can be applied for the analysis of experimental pyrene actin-based or fluorescence microscopy data. We provide a user-friendly, free software package ActinSimChem that integrates the implemented simulation algorithms and that is made available to the scientific community for modelling in silico any specific actin-polymerization system.