A SARS-CoV-2 neutralizing antibody discovery by single cell sequencing and molecular modeling

Although vaccines have been developed,mutations of SARS-CoV-2,especially the dominant B.1.617.2(delta)and B.1.529(omicron)strains with more than 30 mutations on their spike protein,have caused a significant decline in prophylaxis,calling for the need for drug improvement.Antibodies are drugs preferentially used in infectious diseases and are easy to get from immunized organisms.The current study combined molecular modeling and single memory B cell sequencing to assess candidate sequences before experiments,providing a strategy for the fabrication of SARS-CoV-2 neutralizing antibodies.A total of 128 sequences were obtained after sequencing 196 memory B cells,and 42 sequences were left after merging extremely similar ones and discarding incomplete ones,followed by homology modeling of the antibody variable region.Thirteen candidate sequences were expressed,of which three were tested positive for receptor binding domain recognition but only one was confirmed as having broad neutralization against several SARS-CoV-2 variants.The current study successfully obtained a SARS-CoV-2 antibody with broad neutralizing abilities and provided a strategy for antibody development in emerging infectious diseases using single memory B cell BCR sequencing and computer assistance in antibody fabrication.

Lower Bounds of Decay Rates for Solution to the Single-Layer Quasi-Geostrophic Model

In this paper, we study the long-time behavior of solutions of the single-layer quasi-geostrophic model arising from geophysical fluid dynamics. We obtain the lower bound of the decay estimate of the solution. Utilizing the Fourier splitting method, under suitable assumptions on the initial data, for any multi-index α, we show that the solution Ψ satisfies .

Examining the effect of adverse geological conditions on jamming of a single shielded TBM in Uluabat tunnel using numerical modeling

Severe shield jamming events have been reported during excavation of Uluabat tunnel through adverse geological conditions, which resulted in several stoppages at advancing a single shielded tunnel boring machine(TBM). To study the jamming mechanism, three-dimensional(3D) simulation of the machine and surrounding ground was implemented using the finite difference code FLAC3D. Numerical analyses were performed for three sections along the tunnel with a higher risk for entrapment due to the combination of overburden and geological conditions. The computational results including longitudinal displacement contours and ground pressure profiles around the shield allow a better understanding of ground behavior within the excavation. Furthermore, they allow realistically assessing the impact of adverse geological conditions on shield jamming. The calculated thrust forces, which are required to move the machine forward, are in good agreement with field observations and measurements. It also proves that the numerical analysis can effectively be used for evaluating the effect of adverse geological environment on TBM entrapments and can be applied to prediction of loads on the shield and preestimating of the required thrust force during excavation through adverse ground conditions.

Evaluation of NASA GISS Post-CMIP5 Single Column Model Simulated Clouds and Precipitation Using ARM Southern Great Plains Observations

The planetary boundary layer turbulence and moist convection parameterizations have been modified recently in the NASA Goddard Institute for Space Studies （GISS） Model E2 atmospheric general circulation model （GCM; post-CMIP5, hereafter P5）. In this study, single column model （SCM_P5） simulated cloud fractions （CFs）, cloud liquid water paths （LWPs） and precipitation were compared with Atmospheric Radiation Measurement （ARM） Southern Great Plains （SGP） groundbased observations made during the period 2002-08. CMIP5 SCM simulations and GCM outputs over the ARM SGP region were also used in the comparison to identify whether the causes of cloud and precipitation biases resulted from either the physical parameterization or the dynamic scheme. The comparison showed that the CMIP5 SCM has difficulties in simulating the vertical structure and seasonal variation of low-level clouds. The new scheme implemented in the turbulence parameterization led to significantly improved cloud simulations in P5. It was found that the SCM is sensitive to the relaxation time scale. When the relaxation time increased from 3 to 24 h, SCM_P5-simulated CFs and LWPs showed a moderate increase （10%-20%） but precipitation increased significantly （56%）, which agreed better with observations despite the less accurate atmospheric state. Annual averages among the GCM and SCM simulations were almost the same, but their respective seasonal variations were out of phase. This suggests that the same physical cloud parameterization can generate similar statistical results over a long time period, but different dynamics drive the differences in seasonal variations. This study can potentially provide guidance for the further development of the GISS model.

Energy principle of ferroelectric ceramics and single domain mechanical model

Many physical experiments have shown that the domain switching in a ferroelectric material is a complicated evolution process of the domain wall with the variation of stress and electric field. According to this mechanism, the volume fraction of the domain switching is introduced in the constitutive law of ferroelectric ceramic and used to study the nonlinear constitutive behavior of ferroelectric body in this paper. The principle of stationary total energy is put forward in which the basic unknown quantities are the displacement ui, electric displacement Di and volume fraction pI of the domain switching for the variant I. Mechanical field equation and a new domain switching criterion are obtained from the principle of stationary total energy. The domain switching criterion proposed in this paper is an expansion and development of the energy criterion. On the basis of the domain switching criterion, a set of linear algebraic equations for the volume fraction PI of domain switching is obtained, in which the coefficients of the linear algebraic equations only contain the unknown strain and electric fields. Then a single domain mechanical model is proposed in this paper. The poled ferroelectric specimen is considered as a transversely isotropic single domain. By using the partial experimental results, the hardening relation between the driving force of domain switching and the volume fraction of domain switching can be calibrated. Then the electromechanical response can be calculated on the basis of the calibrated hardening relation. The results involve the electric butterfly shaped curves of axial strain versus axial electric field, the hysteresis loops of electric displacement versus electric filed and the evo- lution process of the domain switching in the ferroelectric specimens under uniaxial coupled stress and electric field loading. The present theoretic prediction agrees reasonably with the experimental results given by Lynch.

Implementation of positive-operator-value measurements for single spin qubit via Heisenberg model

This paper shows that a proposal for implementing all possible two-operator positive-operator-value measurements of single spin qubit can be obtained via introducing another spin qubit as ancilla. The realization process is accomplished from the free evolution of the Heisenberg XX model by considering nearest-neighbour spin interaction. A controlled- NOT gate, which is a significant operator for this scheme is also constructed and the generalisation to multiple-operator is considered finally.

Multiscale modelling and simulation of single crystal superalloy turbine blade casting during directional solidification process

As the key parts of an aero-engine,single crystal(SX)superalloy turbine blades have been the focus of much attention.However,casting defects often occur during the manufacturing process of the SX turbine blades.Modeling and simulation technology can help to optimize the manufacturing process of SX blades.Multiscale coupled models were proposed and used to simulate the physical phenomena occurring during the directional solidification(DS)process.Coupled with heat transfer(macroscale)and grain growth(meso-scale),3D dendritic grain growth was calculated to show the competitive grain growth at micro-scale.SX grain selection behavior was studied by the simulation and experiments.The results show that the geometrical structure and technical parameters had strong influences on the grain selection effectiveness.Based on the coupled models,heat transfer,grain growth and microstructure evolution of a complex hollow SX blade were simulated.Both the simulated and experimental results show that the stray grain occurred at the platform of the SX blade when a constant withdrawal rate was used in manufacturing process.In order to avoid the formation of the stray crystal,the multi-scale coupled models and the withdrawal rate optimized technique were applied to the same SX turbine blade.The modeling results indicated that the optimized variable withdrawal rate can achieve SX blade castings with no stray grains,which was also proved by the experiments.

Model tests and numerical analyses on horizontal impedance functions of inclined single piles embedded in cohesionless soil

Horizontal impedance functions of inclined single piles are measured experimentally for model soil-pile systems with both the effects of local soil nonlinearity and resonant characteristics.Two practical pile inclinations of 5掳 and 10掳 in addition to a vertical pile embedded in cohesionless soil and subjected to lateral harmonic pile head loadings for a wide range of frequencies are considered.Results obtained with low-to-high amplitude of lateral loadings on model soil-pile systems encased in a laminar shear box show that the local nonlinearities have a profound impact on the horizontal impedance functions of piles.Horizontal impedance functions of inclined piles are found to be smaller than the vertical pile and the values decrease as the angle of pile inclination increases.Distinct values of horizontal impedance functions are obtained for the ＇positive＇ and ＇negative＇ cycles of harmonic loadings,leading to asymmetric force-displacement relationships for the inclined piles.Validation of these experimental results is carried out through three-dimensional nonlinear finite element analyses,and the results from the numerical models are in good agreement with the experimental data.Sensitivity analyses conducted on the numerical models suggest that the consideration of local nonlinearity at the vicinity of the soil-pile interface influence the response of the soil-pile systems.

Comparative Analysis between Single Diode and Double Diode Model of PV Cell: Concentrate Different Parameters Effect on Its Efficiency

This research appraises comparative analysis between single diode and double diode model of photovoltaic (PV) solar cells to enhance the conversion efficiency of power engendering PV solar systems. Single diode model is simple and easy to implement, whereas double diode model has better accuracy which acquiesces for more precise forecast of PV systems performance. Exploration is done on the basis of simulation results and MATLAB tool is used to serve this purpose. Simulations are performed by varying distinct model parameters such as solar irradiance, temperature, value of parasitic resistances, ideality factor of diode and number of series and parallel connected solar cells used to assemble PV array. Conspicuous demonstration is executed to analyze effects of these specifications on the efficiency curve and power vs. voltage output characteristics of PV cell for specified models.

Correctness and accuracy of template-based modeled single chain fragment variable (scFv) protein anti-breast cancer cell line (MCF-7)

Multiple sequence alignments can be used in the template-based modelling of protein structures to build fragment-based assembly models. Therefore, useful functional information on the 3D structure of the anti-MCF-7 scFv protein can be obtained using available bioinformatics tools. This paper utilises several commonly-used bioinformatics tools and databases, including BLAST (Basic Local Alignment Search Tool), GenBank, PDB (Protein Data Bank), KABAT numbering and SWISS-MODEL, to gain specific functional insights into the anti-MCF-7 scFv protein and the assembly of single-chain fragment variable (scFv) antibodies, which consist of a variable heavy chain (VH) and a variable light chain (VL) connected by the linker (Gly4-Ser)3. The linker has been built as a loop structure using the Insight II software. The accuracy of the loop structure has been evaluated using Root Mean Square Deviation (RMSD). The accuracies of the VL and VH template-based structures are enhanced by using the evaluation methods Verify3D, ERRAT and Ramchandran plotting, which measure the error in the residues. In the results, 100% of the light-chain residues scored above 0.2, whereas 88.5% of the heavy-chain residues’ scored above 0.15 in the Verify3D evaluation method. Meanwhile, using ERRAT, the alignments of both chains scored more than 70% in space. Additionally, the Ramchandran plot evaluation method showed large numbers of residues in the favoured areas in both chains;these findings demonstrated that all of the chosen templates were the best candidates.

Three-dimensional constitutive model for magneto-mechanical deformation of NiMnGa ferromagnetic shape memory alloy single crystals

Existing experimental results have shown that four types of physical mechanisms, namely, martensite transformation, martensite reorientation, magnetic domain wall motion and magnetization vector rotation, can be activated during the magneto-mechanical deformation of NiMnGa ferromagnetic shape memory alloy (FSMA) single crystals. In this work, based on irreversible thermodynamics, a three-dimensional (3D) single crystal constitutive model is constructed by considering the aforementioned four mechanisms simultaneously. Three types of internal variables, i.e., the volume fraction of each martensite variant, the volume fraction of magnetic domain in each variant and the deviation angle between the magnetization vector, and easy axis are introduced to characterize the magneto-mechanical state of the single crystals. The thermodynamic driving force of each mechanism and the thermodynamic constraints on the constitutive model are obtained from Clausius's dissipative inequality and constructed Gibbs free energy. Then, thermodynamically consistent kinetic equations for the four mechanisms are proposed, respectively. Finally, the ability of the proposed model to describe the magneto-mechanical deformation of NiMnGa FSMA single crystals is verified by comparing the predictions with corresponding experimental results. It is shown that the proposed model can quantitatively capture the main experimental phenomena. Further, the proposed model is used to predict the deformations of the single crystals under the non-proportional mechanical loading conditions.

Similar Single-Difference Model and Its Algorithm for Solving GPS Monitoring Deformation Directly at Single Epoch

A new similar single-difference mathematical model (SS-DM) and its corresponding algorithmare advanced to solve the deformationof monitoring point directly in singleepoch. The method for building theSSDM is introduced in detail, and themain error sources affecting the accu-racy of deformation measurement areanalyzed briefly, and the basic algo-rithm and steps of solving the deform-ation are discussed.In order to validate the correctnessand the accuracy of the similar single-difference model, the test with fivedual frequency receivers is carried outon a slideway which moved in plane inFeb. 2001. In the test,five sessions areobserved. The numerical results oftest data show that the advanced mod-el is correct.

Single Point Positioning with Sequential Least-Squares Filter and Estimated Real-Time Stochastic Model

获得更高精确的位置估计，随机的模型被估计由用观察的剩余，，因此随机的模型更写实地在大小描述噪音和偏爱。由使用 GPS 数据和广播位置推算历，在亚米水平显示精确位置估计的数字结果是可获得的。

An analytical model for pyrolysis of a single biomass particle

Decreasing in emissions of greenhouse gases to confront the global warming needs to replace fossil fuels as the main doer of the world climate changes by renewable and clean fuels produced from biomass like wood waste which is neutral on the amount of CO2. An analytical and engineering model for pyrolysis process of a single biomass particle has been presented. Using a two-stage semi global kinetic model which includes both primary and secondary reactions, the effects of parameters like shape and size of particle as well as porosity on the particle temperature profile and product yields have been investigated. Comparison of the obtained results with experimental data shows that our results are in a reasonable agreement with previous researchers' works. Finally, a sensitivity analysis is done to determine the importance of each parameter on pyrolysis of a single biomass particle which is affected by many constant parameters.

A new approach for time effect analysis of settlement for single pile based on virtual soil-pile model

A new approach is proposed to analyze the settlement behavior for single pile embedded in layered soils.Firstly,soil layers surrounding pile shaft are simulated by using distributed Voigt model,and finite soil layers under the pile end are assumed to be virtual soil-pile whose cross-section area is the same as that of the pile shaft.Then,by means of Laplace transform and impedance function transfer method to solve the static equilibrium equation of pile,the analytical solution of the displacement impedance function at the pile head is derived.Furthermore,the analytical solution of the settlement at the head of single pile is theoretically derived by virtue of convolution theorem.Based on these solutions,the influences of parameters of soil-pile system on the settlement behavior for single pile are analyzed.Also,comparison of the load-settlement response for two well-instrumented field tests in multilayered soils is given to demonstrate the effectiveness and accuracy of the proposed approach.It can be noted that the presented solution can be used to calculate the settlement of single pile for the preliminary design of pile foundation.

Identification of thermal front dynamics in the northern Malacca Strait using ROMS 3D-model

The thermal front in the oceanic system is believed to have a significant effect on biological activity.During an era of climate change,changes in heat regulation between the atmosphere and oceanic interior can alter the characteristics of this important feature.Using the simulation results of the 3D Regional Ocean Modelling System(ROMS),we identified the location of thermal fronts and determined their dynamic variability in the area between the southern Andaman Sea and northern Malacca Strait.The Single Image Edge Detection(SIED)algorithm was used to detect the thermal front from model-derived temperature.Results show that a thermal front occurred every year from 2002 to 2012 with the temperature gradient at the location of the front was 0.3°C/km.Compared to the years affected by El Ni?o and negative Indian Ocean Dipole(IOD),the normal years(e.g.,May 2003)show the presence of the thermal front at every selected depth(10,25,50,and 75 m),whereas El Ni?o and negative IOD during 2010 show the presence of the thermal front only at depth of 75 m due to greater warming,leading to the thermocline deepening and enhanced stratification.During May 2003,the thermal front was separated by cooler SST in the southern Andaman Sea and warmer SST in the northern Malacca Strait.The higher SST in the northern Malacca Strait was believed due to the besieged Malacca Strait,which trapped the heat and make it difficult to release while higher chlorophyll a in Malacca Strait is due to the freshwater conduit from nearby rivers(Klang,Langat,Perak,and Selangor).Furthermore,compared to the southern Andaman Sea,the chlorophyll a in the northern Malacca Strait is easier to reach the surface area due to the shallower thermocline,which allows nutrients in the area to reach the surface faster.

Catalytic Cracking of Cycloparaffins Admixed with Olefins:1. Single-Event Microkinetic(SEMK) Modeling

Single-event microkinetic(SEMK) model of the catalytic cracking of methylcyclohexane admixed with 1-octene over REUSY zeolites at 693 K—753 K in the absence of coke formation is enhanced. To keep consistency with the wellknown carbenium ion chemistry, hydride transfer forming and consuming allylic carbenium ions in the aromatization of cycloparaffins are further investigated and differentiated. The reversibility of endocyclic β-scission and cyclization reactions is refined by accounting explicitly for the reacting olefins and resulting cycloparaffins in the corresponding thermodynamics. 24 activation energies for the reactions involved in the cracking of cycloparaffins are obtained by the regression of 15 sets of experimental data upon taking the resulting 37 main cracking products, i. e., responses into account. The enhanced SEMK model can adequately describe the catalytic behavior of 37 main products with conversion and temperature.

Model experiment of rock blasting with single borehole and double free-surface

In order to improve the quality of laneways and tunnel excavation by drilling and blasting and by making effective use of explosive energy, a model experiment of rock blasting with a single borehole and a double free-surface was performed with the objective of studying the effect of parameters such as charge structure, free-surface and rock compressive strength on rock blasting.The model experiments indicate that:1) the smaller the rock compressive strength and density, the more distinctive the cavity expanding action by blasting;2) the powder factor in an air-decoupling charge structure is larger than that in a coupling charge structure, i.e., the explosive energy in an air-decoupling charge structure transferred to the rocks is less than that in a coupling charge structure;3) a free-surface improves the utilizations of explosive energy;4) an air-decoupling charge structure helps to maintain the integrity and stability of wall rock in controlled perimeter blasting, such as in roadways and tunnel excavation by drilling and blasting.

Dynamic Analysis of the Seafloor Pilot Miner Based on Single-Body Vehicle Model and Discretized Track-Terrain Interaction Model

In order to achieve the complex dynamic analysis of the self-propelled seafloor pilot miner moving on the seafloor of extremely cohesive soft soil and further to make it possible to integrate the miner system with some subsystems to form the complete integrated deep ocean mining pilot system and perform dynamic analysis, a new method for the dynamic modeling and analysis of the miner is proposed and developed in this paper, resulting in a simplified 3D single-body vehicle model with three translational and three rotational degrees of freedom, while the track-terrain interaction model is built by partitioning the track-terrain interface into discrete elements with parameterized force dements built on the theory of terramechanics acting on each discrete dement. To evaluate and verify the correctness and effectiveness of this new modeling and analysis method, typical comparative studies with regard to computational efficiency and solution accuracy are carried out between the traditional modeling method of building the tracked vehicle as a multi-body model and the new modeling method. In full consideration of the particMar structure design of the pilot miner, the special characteristics of the seafioor soil and the hydrodynamic force of near-seafloor currnt, the dynamic simulation analysis of the miner is performed and discussed, which can provide useful guidance and reference for the practical miner system in design and operation. This new method can not only realize the rapid dynamic simulation analysis of the miner but also make possible the integration and rapid dynamic analysis of the complete integrated deep ocean mining pilot system in further researches.

Vertical two-dimensional non-hydrostatic pressure model with single layer

The vertical two-dimensional non-hydrostatic pressure models with multiple layers can make prediction more accurate than those obtained by the hydrostatic pres- sure assumption. However, they are time-consuming and unstable, which makes them unsuitable for wider application. In this study, an efficient model with a single layer is developed. Decomposing the pressure into the hydrostatic and dynamic components and integrating the x-momentum equation from the bottom to the free surface can yield a horizontal momentum equation, in which the terms relevant to the dynamic pressure are discretized semi-implicitly. The convective terms in the vertical momentum equation are ignored, and the rest of the equation is approximated with the Keller-box scheme. The velocities expressed as the unknown dynamic pressure are substituted into the continuity equation, resulting in a tri-diagonal linear system solved by the Thomas algorithm. The validation of solitary and sinusoidal waves indicates that the present model can provide comparable results to the models with multiple layers but at much lower computation cost.