Mechanical property and deformation mechanism of gold nanowire with non-uniform distribution of twinned boundaries:A molecular dynamics simulation study

The mechanical property and deformation mechanism of twinned gold nanowire with non-uniform distribution of twinned boundaries(TBs)are studied by the molecular dynamics(MD)method.It is found that the twin boundary spacing(TBS)has a great effect on the strength and plasticity of the nanowires with uniform distribution of TBs.And the strength enhances with the decrease of TBS,while its plasticity declines.For the nanowires with non-uniform distribution of TBs,the differences in distribution among different TBSs have little effect on the Young's modulus or strength,and the compromise in strength appears.But the differences have a remarkable effect on the plasticity of twinned gold nanowire.The twinned gold nanowire with higher local symmetry ratio has better plasticity.The initial dislocations always form in the largest TBS and the fracture always appears at or near the twin boundaries adjacent to the smallest TBS.Some simulation results are consistent with the experimental results.

Numerical simulation on rotordynamic characteristics of annular seal under uniform and non-uniform flows

Currently, the flow field of annular seals disturbed by the circular whirl motion of rotors is usually solved using computational fluid dynamics(CFD) to evaluate the five rotordynamic coefficients. The simulations are based on the traditional quasi-steady method. In this work, an improved quasi-steady method along with the transient method was presented to compute the rotordynamic coefficients of a long seal. By comparisons with experimental data, the shortcomings of quasi-steady methods have been identified. Then, the effects of non-uniform incoming flow on seal dynamic coefficients were studied by transient simulations. Results indicate that the long seal has large cross stiffness k and direct mass M which are not good for rotor stability, while the transient method is more suitable for the long seal for its excellent performance in predicting M. When the incoming flow is non-uniform, the stiffness coefficients vary with the eccentric directions. Based on the rotordynamic coefficients under uniform incoming flow, the linearized fluid force formulas, which can consider the effects of non-uniform incoming flow, have been presented and can well explain the varying-stiffness phenomenon.

Numerical Calculation of Dynamic Response for Multi-Span Non-Uniform Beam Subjected to Moving Mass with Friction

In order to simulate the coupling vibration of a vehicle or train moves on a multi-span continuous bridge with non-uniform cross sections, a moving mass model is used according to the Finite Element Method, the effect of the inertial force, Coriolis force and centrifugal force are considered by means of the additive matrices. For a non-uniform rectangular section beam with both linear and parabolic variable heights in a plane, the stiffness and mass matrices of the beam elements are presented. For a non-uniform box girder, Romberg numerical integral scheme is adopted, each coefficient of the stiffness matrix is obtained by means of a normal numerical computation. By applying these elements to calculate the non-uniform beam, the computational accuracy and efficiency are improved. The finite element method program is worked out and an entire dynamic response process of the beam with non-uniform cross sections subjected to a moving mass is simulated numerically, the results are compared to those previously published for some simple examples. For some complex multi-span bridges subjected to some moving vehicles with changeable velocity and friction, the computational results, which can be regarded as a reference for engineering design and scientific research, are also given simultaneously.

The Introduction of Specific Water and Maximum Airborne Specific Water &the Improvement of Dynamic Equations on Non-Uniform Saturated Moist Atmosphere

To eliminate the irrational supposition that condensed liquid water always falls immediately, specific water m?and maximum airborne specific water mm are introduced into the dynamic framework on non-uniform saturated moist atmosphere (m?is the ratio of the airborne liquid water mass to the moist air mass in unit cubage moist air, mm is its maximum value with , , and are airborne coefficient, vertical velocity and saturated specific humidity respectively). The balance equation between water vapor and airborne liquid water is derived. From the balance equation, a new formula of precipitate rate is got. The analysis shows that in the air stream with some upward vertical velocity ( ), the condensed liquid water can precipitate under the condition with (q is specific humidity) and? only, otherwise it is detained in the air and becomes airborne liquid water. Not only does precipitating liquid water contain condensed liquid water, but also contains converged and existing airborne liquid water. Following above discussion, improved dynamic equations on non-uniform saturated moist atmosphere are provided.

Solving chemical dynamic optimization problems with ranking-based differential evolution algorithms

Dynamic optimization problems(DOPs) described by differential equations are often encountered in chemical engineering. Deterministic techniques based on mathematic programming become invalid when the models are non-differentiable or explicit mathematical descriptions do not exist. Recently, evolutionary algorithms are gaining popularity for DOPs as they can be used as robust alternatives when the deterministic techniques are invalid. In this article, a technology named ranking-based mutation operator(RMO) is presented to enhance the previous differential evolution(DE) algorithms to solve DOPs using control vector parameterization. In the RMO, better individuals have higher probabilities to produce offspring, which is helpful for the performance enhancement of DE algorithms. Three DE-RMO algorithms are designed by incorporating the RMO. The three DE-RMO algorithms and their three original DE algorithms are applied to solve four constrained DOPs from the literature. Our simulation results indicate that DE-RMO algorithms exhibit better performance than previous non-ranking DE algorithms and other four evolutionary algorithms.

SYSTEM IDENTIFICATION USING DYNAMIC GA BASED ON NUMERIC ENCODING

A dynamic genetic algorithms based on numeric encoding is proposed and its application in system identification is discussed. Simulation shows that the introduction of both numeric encoding and dynamic mutation can effectively improve the accuracy and speed of searching for the optimum. It also show that the improved Genetic algorithm can identify time delay and parameters of the plant at the same time and converge to globle optimization.

Unraveling the molecular mechanism of prion disease:Insights fromα2 area mutations in human prion protein

Prion diseases are a class of fatal neurodegenerative diseases caused by misfolded prion proteins.The main reason is that pathogenic prion protein has a strong tendency to aggregate,which easily induces the damage to the central nervous system.Point mutations in the human prion protein gene can cause prion diseases such as Creutzfeldt-Jakob and Gerstmann's syndrome.To understand the mechanism of mutation-induced prion protein aggregation,the mutants in an aqueous solution are studied by molecular dynamics simulations,including the wild type,V180I,H187R and a double point mutation which is associated with CJD and GSS.After running simulations for 500 ns,the results show that these three mutations have different effects on the kinetic properties of PrP.The high fluctuations around the N-terminal residues of helix 2 in the V180I variant lead to a decrease in hydrogen bonding on helix 2,while an increase in the number of hydrogen bonds between the folded regions promotes the generation ofβ-sheet.Meanwhile,partial deletion of salt bridges in the H187R and double mutants allows the sub-structural domains of the prion protein to separate,which would accelerate the conversion from PrPC to PrPSc.A similar trend is observed in both SASA and Rg for all three mutations,indicating that the conformational space is reduced and the structure is compact.

MD Simulations of the P53 oncoprotein structure: the effect of the Arg273→His mutation on the DNA binding domain

A comparative molecular dynamics (MD) simulation study was performed on the p53 oncoprotein to investigate the effect of the Arg273His (R273H) mutation on the p53→DNA Binding Domain (DBD). The two p53 dimer structures of the wild-type and mutant Arg273His (R273H) were simulated with the same thermodynamic and environmental parameters. The obtained results demonstrate that the induced Arg273His mutation has a considerable effect on the p53→DNA close contact interaction and changes the picture of hydrogen formation. The Arg273His mutation, in some cases, destroys the existing native hydrogen bond, but, in other cases, forms a strong p53→DNA hydrogen bond, which is not proper for the native protein. The MD simulation results illustrate some molecular mechanism of the conformational changes of the Arg273His key amino acid residue in the p53→DNA binding domain, which might be important for the understanding of the physiological functioning of the p53 protein and the origin of cancer.

DYNAMICAL FORMATION OF CAVITY FOR COMPOSED THERMAL HYPERELASTIC SPHERES IN NONUNIFORM TEMPERATURE FIELDS

Dynamical formation and growth of compressible thermal-hyperelastic Gent-Thomas cavity in a sphere composed of two inmaterials were discussed under the case of a non-uniform temperature field and the surface dead loading. The mathematical model was first presented based on the dynamical theory of finite deformations. An exact differential relation between the void radius and surface load was obtained by using the variable transformation method. By numerical computation, critical loads and cavitation growth curves were obtained for different temperatures. The influence of the temperature and material parameters of the composed sphere on the void formation and growth was considered and compared with those for static analysis. The results show that the cavity occurs stiddenly with a finite radius and its evolvement with time displays a non-linear periodic vibration and that the critical load decreases with the increase of temperature and also the dynamical critical load is lower than the static critical load under the same conditions.

Impact of Mutations on K-Ras-p120GAP Interaction

The K-Ras protein plays a key role in the signal transduction cascade. Certain mutations in K-Ras lead to a permanent “on” state which results in tumorigenesis due to failed interaction with the GTPase activating protein (GAP). In this study, we examined the mutations E31N, D33N and D38N of K-Ras coupled and decoupled to wildtype GAP-334 and mutation K935N of GAP-334 coupled and decoupled to wildtype K-Ras, to illustrate the potential mechanism by which these mutants affect the interaction between the two proteins. We identify Tyr32 in the Ras Switch I region as a critical residue that acts as a gate to the GTP binding site and which needs to be “open” during Ras coupling with GAP to allow for insertion of GAP residue Arg789. This residue plays a vital role in stabilizing the transition state during GTP hydrolysis. The different mutations studied herein caused a reduced binding affinity, and the fluctuation of the Tyr32 side chain might hinder the insertion of Arg789. This may in turn be the cause of decreased GTP hydrolysis, and permanent “on” state of K-Ras, observed for these mutants.

Abnormality diagnosis of cracks in the concrete dam based on dynamical structure mutation

A method of the fuzzy cross-correlation factor exponent in dynamics is researched and proposed to diagnose abnormality of cracks in the concrete dam. Moreover, the Logistic time series changing from period-doubling bifurcation to chaos is tested first using this method. Results indicate that it can distinguish inherent dynamics of time series and can detect mutations. Considering that cracks in the concrete dam constitute an open, dissipative and complex nonlinear dynamical system, a typical crack on the downstream face of a concrete gravity arch dam is analyzed with the proposed method. Two distinct mutations are discovered to indicate that the abnormality diagnosis of cracks in the concrete dam is achieved dynamically through this method. Furthermore, because it can be directly utilized in the measured crack opening displacement series to complete abnormality diagnosis, it has a good prospect for practical applications.

Analytic model of non-uniform corrosion induced cracking of reinforced concrete structure

In order to perfectly reflect the dynamic corrosion of reinforced concrete (RC) cover in practical engineering,an analytic model of non-uniform corrosion induced cracking was presented based on the elastic-plastic fracture mechanics theory.Comparisons with the published experimental data show that the predictions given by the present model are in good agreement with the results both for natural exposed experiments and short-time indoor tests (the best difference is about 2.7%).Also it obviously provides much better precision than those models under the assumption of uniform corrosion (the maximal improved precision is about 48%).Therefore,it is pointed out that the so-called uniform corrosion models to describe the cover cracking of RC should be adopted cautiously.Finally,the influences of thickness of local rusty layer around the reinforcing steel bar on the critical corrosion-induced crack indexes were investigated.It is found that the thickness of local rusty layer has great effect on the critical mass loss of reinforcing steel,threshold expansion pressure,and time to cover cracking.For local rusty layer thickness with a size of a=0.5 mm,the time to cover cracking will increase by about one times when a/b (a,semi-minor axis;b,semi-major axis) changes from 0.1 to 1 mm.

Dynamics of a stochastic delayed avian influenza model with mutation and temporary immunity

In this paper,the dynamic behaviors are studied for a stochastic delayed avian influenza model with mutation and temporary immunity.First,we prove the existence and uniqueness of the global positive solution for the stochastic model.Second,we give two different thresholds R_(01)^(s) and,R_(02)^(s) and further establish the sufficient conditions of extinction and persistence in the mean for the avian-only subsystem and avian-human system,respectively.Compared with the corresponding deterministic model,the thresholds affected by the white noises are smaller than the ones of the deterministic system.Finally,numerical simulations are carried out to support our theoretical results.It is concluded that the vaccination immunity period can suppress the spread of avian influenza during poultry and human populations,while prompt the spread of mutant avian influenza in human population.

Non-Uniform FFT and Its Applications in Particle Simulations

Ewald summation method, based on Non-Uniform FFTs (ENUF) to compute the electrostatic interactions and forces, is implemented in two different particle simulation schemes to model molecular and soft matter, in classical all-atom Molecular Dynamics and in Dissipative Particle Dynamics for coarse-grained particles. The method combines the traditional Ewald method with a non-uniform fast Fourier transform library (NFFT), making it highly efficient. It scales linearly with the number of particles as , while being both robust and accurate. It conserves both energy and the momentum to float point accuracy. As demonstrated here, it is straight- forward to implement the method in existing computer simulation codes to treat the electrostatic interactions either between point-charges or charge distributions. It should be an attractive alternative to mesh-based Ewald methods.

The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro

Since its outbreak in 2019,Severe Acute Respiratory Syndrome Coronavirus 2(SARS-Co V-2)keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective manner.To gain deeper insight into mutation frequency and dynamics,we isolated ten ancestral strains of SARS-Co V-2 and performed consecutive serial incubation in ten replications in a suitable and common cell line and subsequently analysed them using RT-q PCR and whole genome sequencing.Along those lines we hoped to gain fundamental insights into the evolutionary capacity of SARS-Co V-2 in vitro.Our results identified a series of adaptive genetic changes,ranging from unique convergent substitutional mutations and hitherto undescribed insertions.The region coding for spike proved to be a mutational hotspot,evolving a number of mutational changes including the already known substitutions at positions S:484 and S:501.We discussed the evolution of all specific adaptations as well as possible reasons for the seemingly inhomogeneous potential of SARS-Co V-2 in the adaptation to cell culture.The combination of serial passage in vitro with whole genome sequencing uncovers the immense mutational potential of some SARS-Co V-2 strains.The observed genetic changes of SARS-Co V-2 in vitro could not be explained solely by selectively neutral mutations but possibly resulted from the action of directional selection accumulating favourable genetic changes in the evolving variants,along the path of increasing potency of the strain.Competition among a high number of quasi-species in the SARS-Co V-2 in vitro population gene pool may reinforce directional selection and boost the speed of evolutionary change.

Pyrotinib in HER2 heterogeneously mutated or amplified advanced non-small cell lung cancer patients:a retrospective real-world study(PEARL)

Human epidermal growth factor receptor 2(HER2)amplification or activating mutations are found in 1.6%–4%of non-small cell lung cancer(NSCLC).Pyrotinib has been reported to have better potency in NSCLC patients with HER2 exon 20 insertion(ex20ins)mutations;however,more clinical evidence is urgently needed to guide pyrotinib-based therapy in NSCLC with HER2 amplification or heterogeneous mutations.We retrospectively analyzed advanced NSCLC patients with HER2 amplification or mutations who were treated with pyrotinib-based therapy between September 25,2018 and October 30,2020 in our hospital.Molecular dynamics simulation was used to explore the bioactive conformation and binding mechanisms of pan-ErbB tyrosine kinase inhibitors(TKIs)including pyrotinib for different HER2 ex20ins variants.In this study,79 eligible patients were included with 70 ex20ins variants,6 missense mutations and 3 primary HER2 amplifications identified.A775_G776insYVMA insertion was the most common observed subtype.The median progression-free survival(mPFS)was 5.8(95%CI:4.1–7.4)months.Use of pyrotinib-based therapy in first-/second-line settings showed a significantly better prognosis than that observed in third-line settings or above(mPFS:9.1 vs.4.4 months;P=0.0003).Compared with HER2 amplification and exon 20 non-YVMA insertion variants,patients with HER2 missense mutations had a visible mPFS benefit(12.2 vs.6.8 vs.5.2 months).Computational docking simulations revealed that pyrotinib failed to interact with the specific insertion variant P780_Y781insGSP.These results indicated that pyrotinib-based therapy exhibited good anti-tumor activity and acceptable safety profile in HER2-altered advanced NSCLC.

基于突变理论的隔水岩体失稳分析及安全厚度计算

为了保障岩溶突水隧道施工和运营安全,基于弹性梁模型,应用突变理论建立岩溶突水顶板在动力扰动下失稳的双尖点突变模型;综合考虑围岩性质、静水压力、动力扰动等因素,分析岩溶突水隧道顶板的失稳机制和破坏条件,建立其失稳突变的判别方程,并采用Matlab软件编程,求解顶板的最小安全厚度;同时,为了避免当静水压力过大时,突变理论公式的不合理性,单独计算仅在静水压力的情况下的最小安全厚度,并取两者计算值中的更大值。结果表明:隔水岩体是否保持稳定是由岩体内外因素共同决定的;岩体跨度越长,岩体最小安全厚度越大;岩体弹性模量越大,岩体最小安全厚度越小。在振动频率一定时,爆破荷载越大,岩体最小安全厚度越大;在爆破荷载的大小一定时,爆破振动的频率越大,岩体最小安全厚度越小;静水压力越大,岩体最小安全厚度越大。该岩溶突水隧道顶板安全厚度计算方法具有可行性与较高的准确性。

多策略融合改进的自适应蜉蝣算法

为改进蜉蝣算法全局搜索能力较差、种群多样性较小和自适应能力弱等问题,提出一种多策略融合改进的自适应蜉蝣算法(MIMA)。采用Sin混沌映射初始化蜉蝣种群,使种群能够均匀分布在解空间中,提高初始种群质量,增强全局搜索能力;引入Tent混沌映射和高斯变异对种群个体进行调节,增加种群多样性的同时调控种群密度,增强局部最优逃逸能力;引入不完全伽马函数,重构自适应动态调节的重力系数,建立全局搜索和局部开发能力之间更好的平衡,进而提升算法收敛精度,有利于提高全局搜索能力;采用随机反向学习(ROBL)策略,增强全局搜索能力,提高收敛速度并增强稳定性。利用经典测试函数集进行算法对比,并利用Wilcoxon秩和检验分析算法的优化效果,证明改进的有效性和可靠性。实验结果表明:所提算法与其他算法相比,寻优精度、收敛速度、稳定性都取得了较大提升。

动态对比增强磁共振成像及弥散加权成像参数与乳腺癌肿瘤突变负荷的相关性

目的探讨动态对比增强磁共振成像(DCE-MRI)及弥散加权成像(DWI)参数与乳腺癌肿瘤突变负荷(TMB)的相关性,评价DCE-MRI及DWI在乳腺癌免疫治疗中的潜在价值。方法回顾性分析山西医科大学附属运城医院暨第八临床医学院2019~2021年共100例乳腺癌患者的临床资料和术前MRI检查结果。根据TMB值的中位数(5.4/Mb),将100例患者分为TMB高表达组(TMB≥5.4/Mb,n=28)和TMB低表达组(TMB<5.4/Mb,n=72)。提取DCE-MRI及DWI的影像特征,计算表观扩散系数(ADC)和动态增强曲线类型等参数。采用高通量测序技术检测肿瘤组织中的基因突变情况,计算TMB值。分析DCE-MRI及DWI参数与TMB值之间的相关性,以及与乳腺癌病理指标[雌激素受体、孕激素受体、人表皮生长因子受体2、Ki67]之间的关系。采用单因素和多因素Logistic回归分析筛选影响TMB值的独立危险因素。结果DCE-MRI及DWI参数中,ADC值、动态增强曲线类型、峰值信号强度、时间-信号强度曲线斜率等与TMB值呈负相关关系(P<0.05),而峰时、时间-信号强度曲线下面积等与TMB值呈正相关关系(P<0.05)。乳腺癌病理指标中,雌激素受体、孕激素受体、人表皮生长因子受体2、Ki67的表达与TMB值均无相关性(P>0.05)。多因素Logistic回归分析显示,ADC值、动态增强曲线类型和峰时是影响TMB值的独立危险因素。结论DCEMRI及DWI参数与乳腺癌TMB值存在显著相关性,可作为评估乳腺癌免疫治疗效果的辅助手段。

面向动态公交的离散分层记忆粒子群优化算法

随着智慧城市、智慧交通的发展,移动互联网和公交智能基础设施以及相关数据的不断完善,通过用户手机预约公交服务的新型公交运营方式——动态公交,已经成为许多城市公交发展的重要探索方向。但目前,对动态公交问题的建模、算法研究不足。基于这一研究现状,提出动态公交问题模型和面向动态公交的离散分层记忆粒子群优化(PSO)算法。首先给出动态公交问题的目标函数和约束条件,给出动态公交问题的解的形式,并定义解的编辑距离;其次提出使用数据驱动的预计算路径集生成PSO算法的优质初始解的方法,给出基于解的编辑距离的PSO算法中粒子的变异概率和自适应收敛系数的计算方式;最后提出将粒子群分层求解的方法,其中低层粒子群可复用、可继承,从而减少单时间片内、时间片间复制和重初始化带来的性能损耗。基于重庆市北碚区蔡家岗街道的真实场景和亿级历史数据建立仿真环境进行实验,实验结果表明:相对于不分层PSO算法,分层PSO算法通过复用和继承能缩短超80%计算用时;自适应参数和变异机制能帮助算法更稳定地收敛到更优解;相对于传统公交系统,动态公交能在同等运力限制下,提高22%的乘客接单率,节省39.1%的乘客出行时间,所提算法能满足公交运营商在片区内进行动态公交调度的需求;相对于对比算法,所提算法平均缩短了85.3%的计算用时,并且在仅耗用80%里程的情况下提高了至少12%的接单率。