Volume Integral Research Articles

Highly active CRISPR-adaptation proteins revealed by a robust enrichment technology.

Natural prokaryotic defense via the CRISPR-Cas system requires spacer integration into the CRISPR array in a process called adaptation. To search for adaptation proteins with enhanced capabilities, we established a robust perpetual DNA packaging and transfer (PeDPaT) system that uses a strain of T7 phage to package plasmids and transfer them without killing the host, and then uses a different strain of T7 phage to repeat the cycle. We used PeDPaT to identify better adaptation proteins-Cas1 and Cas2-by enriching mutants that provide higher adaptation efficiency. We identified two mutant Cas1 proteins that show up to 10-fold enhanced adaptation in vivo. In vitro, one mutant has higher integration and DNA binding activities, and another has a higher disintegration activity compared to the wild-type Cas1. Lastly, we showed that their specificity for selecting a protospacer adjacent motif is decreased. The PeDPaT technology may be used for many robust screens requiring efficient and effortless DNA transduction.

Kernel free boundary integral method for 3D incompressible flow and linear elasticity equations on irregular domains

A second-order accurate kernel-free boundary integral method is presented for Stokes flow and linear elasticity boundary value problems on three-dimensional irregular domains. It solves equations in the framework of boundary integral equations, whose corresponding discrete forms are well-conditioned and solved by the GMRES method. A notable feature of this approach is that the boundary or volume integrals encountered in BIEs are indirectly evaluated by a Cartesian grid-based method, which includes discretizing corresponding simple interface problems with a MAC scheme, correcting discrete linear systems to reduce large local truncation errors near the interface, solving the modified system by a CG method together with an FFT-based Poisson solver. No extra work or special quadratures are required to deal with singular or hyper-singular boundary integrals and the dependence on the analytical expressions of Green’s functions for the integral kernels is completely eliminated. Numerical results are given to demonstrate the efficiency and accuracy of the Cartesian grid-based method.

A novel energetic approach for predicting fatigue crack growth in pseudoelastic NiTi alloys

A novel strain energy-based method for analyzing fatigue crack growth (FCG) in pseudoelastic Nickel-Titanium (NiTi) -based shape memory alloys (SMAs) is proposed. It uses the dissipated energy to predict the FCG. This parameter can be computed either by volume integration of near-crack-tip strain energy or by the force–displacement hysteresis measured at the loading pins of the sample. Eccentrically-loaded single Edge Crack tension samples (ESE(T)) were used for FCG tests. High resolution Digital Image Correlation (DIC) was used to capture near-crack-tip displacement and strain fields. DIC data were also used to estimate the effective stress intensity range by regressing the William’s expansion series. Furthermore, a constitutive model for SMAs was used for FE simulations of ESE(T) samples, and the evolution of the dissipated energy during FCG tests was computed. Experimental FCG rate, plotted against the cyclic dissipated energy, are well fitted by a power law equation (R2 = 0.99). This result would open new perspectives to develop predictive models for FCG in SMAs considering intricate thermomechanical coupling mechanisms and material non-linearities.

A [3]-catenane non-autonomous molecular motor model: Geometric phase, no-pumping theorem, and energy transduction.

We study a model of a synthetic molecular motor-a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one-subjected to time-dependent driving using stochastic thermodynamics. The model presents nontrivial features due to the two interacting small macrocycles but is simple enough to be treated analytically in limiting regimes. Among the results obtained, we find a mapping into an equivalent [2]-catenane that reveals the implications of the no-pumping theorem stating that to generate net motion of the small macrocycles, both energies and barriers need to change. In the adiabatic limit (slow driving), we fully characterize the motor's dynamics and show that the net motion of the small macrocycles is expressed as a surface integral in parameter space, which corrects previous erroneous results. We also analyze the performance of the motor subjected to step-wise driving protocols in the absence and presence of an applied load. Optimization strategies for generating large currents and maximizing free energy transduction are proposed. This simple model provides interesting clues into the working principles of non-autonomous molecular motors and their optimization.

Predesigned Cluster-Based Spacers for Versatile Luminescent Metallacages.

Luminescent metal-organic cages are of great interest in contemporary research; however, their designed synthesis remains challenging. Here, we created metal-cluster-derived spacers, where emissive C3-symmetric Cu4 clusters have three arms modified by benzene alkynyl ligands, which are terminally functionalized by extensile -COOH and 15-crown-5-ether groups with directional coordination ability. Through vertex orientation, -COOH-functionalized cluster-based spacers coassembled with paddle-wheel Cu(I)xZn(II)2-x(COO)3 nodes in 3+3 mode, generating an emissive cubic cage, which subsequently gave another distorted cubic cage by synthetic modification on the nodes. Through face orientation, 15-crown-5-ether-containing cluster-based spacers capturing K+ ions in 3+2 mode produced an octahedral cage whose empty phase showed dual emission peaks, leading to diverse stimuli-responsive photoluminescence. This work provides new design and synthesis strategies for the integration of nodes and spacers based on metal clusters for cage materials as well as prototypes of luminescent metal-cluster cages for important sensing applications.

Transmissive Mode Laser Micro-Ablation Performance of Ammonium Dinitramide-Based Liquid Propellant for Laser Micro-Thruster.

The transmissive mode laser micro-ablation performance of near-infrared (NIR) dye-optimized ammonium dinitramide (ADN)-based liquid propellant was investigated in laser plasma propulsion using a pulse YAG laser with 5 ns pulse width and 1064 nm wavelength. Miniature fiber optic near-infrared spectrometer, differential scanning calorimeter (DSC) and high-speed camera were used to study laser energy deposition, thermal analysis of ADN-based liquid propellants and the flow field evolution process, respectively. Experimental results indicate that two important factors, laser energy deposition efficiency and heat release from energetic liquid propellants, obviously affect the ablation performance. The results showed that the best ablation effect of 0.4 mL ADN solution dissolved in 0.6 mL dye solution (40%-AAD) liquid propellant was obtained with the ADN liquid propellant content increasing in the combustion chamber. Furthermore, adding 2% ammonium perchlorate (AP) solid powder gave rise to variations in the ablation volume and energetic properties of propellants, which enhanced the propellant enthalpy variable and burn rate. Based on the AP optimized laser ablation, the optimal single-pulse impulse (I)~9.8 μN·s, specific impulse (Isp)~234.9 s, impulse coupling coefficient (Cm)~62.43 dyne/W and energy factor (η)~71.2% were obtained in 200 µm scale combustion chamber. This work would enable further improvements in the small volume and high integration of liquid propellant laser micro-thruster.

Sensing Performance of Ethanol Microfiber Probe Augmented by ZnO Nanosheet and UV Glue Film

A microfiber reflective ethanol gas sensing probe was designed and fabricated. The single-mode fiber was heated and stretched to prepare a microfiber taper, on which a mixed material of ZnO nanosheets and UV glue was built by the dip-coating method. The influencing factors on its sensing performance for ethanol have been discussed, including the dozen ratio of ZnO nanosheets, UV glue materials, and end-face morphology. As the concentration of ethanol gas increased, the intensity of the reflection spectrum increased with the responding sensitivity of 7.28 × 10−4 dBm/ppm. The exchanging efficiency of the optical signal is enhanced by the strong evanescent field of the microfiber taper. This sensing probe is convenient for high-density integration and working in a small space and is capable of high-performance monitoring for ethanol at room temperature.

The Fox–Hatcher cycle and a Vassiliev invariant of order three

We show that the integration of a 1-cocycle I(X) of the space of long knots in R^3 over the Fox-Hatcher 1-cycles gives rise to a Vassiliev invariant of order exactly three. This result can be seen as a continuation of the previous work of the second named author, proving that the integration of I(X) over the Gramain 1-cycles is the Casson invariant, the unique nontrivial Vassiliev invariant of order two (up to scalar multiplications). The result in the present paper is also analogous to part of Mortier's result. Our result differs from, but is motivated by, Mortier's one in that the 1-cocycle I(X) is given by the configuration space integrals associated with graphs while Mortier's cocycle is obtained in a combinatorial way.

Face Editing Based on Facial Recognition Features

Face editing generates a face image with the target attributes without changing the identity or other information. Current methods have achieved considerable performance; however, they cannot effectively retain the face’s identity and semantic information while controlling the attribute intensity. Inspired by two human cognitive characteristics, namely, the principle of global precedence and the principle of homology continuity, we propose a novel face editing approach called the information retention and intensity control generative adversarial network (IricGAN). It includes a learnable hierarchical feature combination (HFC) function, which can construct a sample’s source space through multiscale feature mixing; it can guarantee the integrity of the source space while significantly compressing the network. Additionally, the attribute regression module (ARM) can decouple different attribute paradigms in the source space to ensure the correct modification of the required attributes and preserve the other areas. The gradual process of modifying the face attributes can be simulated by applying different control strengths in the source space. In face editing experiments, both qualitative and quantitative results demonstrate that IricGAN achieves the best overall results among state-of-the-art alternatives. Target attributes can be continuously modified by re-feeding the relationship of the source space and the image, and the independence of each attribute can be retained to the greatest extent. IricGAN:https://github.com/nanfangzhe/IricGAN

Digitisation and renaissance of the manufacturing industry in major cities : The case of Berlin

The rise of digitisation will cause a major upheaval in the manufacturing industries, bringing changes to traditional industrial location patterns as well. In order to understand the direction these structural changes are taking, this paper analyses the start-up activity in the industrial sector. The frontrunners are metropolitan regions and in particular major cities such as Berlin or Munich. Furthermore, detailed analysis of the city of Berlin shows higher and stable concentrations of new industrial companies in inner city locations. This spatial pattern requires the proactive application of legal planning instruments for mixed land use, which contributes to the integration of hybrid spaces and clean and green factories in the inner city.

Wigner–Smith Time Delay Matrix for Electromagnetics: Systems With Material Dispersion and Losses

The Wigner-Smith (WS) time delay matrix relates a system’s scattering matrix to its frequency derivative and gives rise to so-called WS modes that experience well-defined group delays when interacting with the system. For systems composed of nondispersive and lossless materials, the WS time delay matrix previously was shown to consist of volume integrals of energy-like densities plus correction terms that account for the guiding, scattering, or radiating characteristics of the system. This study extends the use of the WS time delay matrix to systems composed of dispersive and lossy materials. Specifically, it shows that such systems’ WS time delay matrix can be expressed by augmenting the previously derived expressions with terms that account for the dispersive and lossy nature of the system, followed by a transformation that disentangles effects of losses from time delays. Analytical and numerical examples demonstrate the new formulation once again allows for the construction of frequency stable WS modes that experience well-defined group delays upon interacting with a system.

Constructing the general partial wave and renormalization in effective field theory

We construct the general partial wave amplitude basis for the $N\ensuremath{\rightarrow}M$ scattering, which consists of Poincar\'e Clebsch-Gordan coefficients, in a Lorentz invariant form given in terms of the spinor-helicity variables. The inner product of the Clebsch-Gordan coefficients is defined, which converts on-shell phase space integration into an algebraic problem. We also develop the technique of partial wave expansions of arbitrary amplitudes, including those with infrared divergence. These are applied to the computation of anomalous dimension matrix for general effective operators, where unitarity cuts for the loop amplitudes, with an arbitrary number of external particles, are obtained via partial wave expansion.

Polynomial tractability for integration in an unweighted function space with absolutely convergent Fourier series

In this note, we prove that the following function space with absolutely convergent Fourier series \[ F d ≔ { f ∈ L 2 ( [ 0 , 1 ) d ) | ‖ f ‖ ≔ ∑ k ∈ Z d | f ^ ( k ) | max ( 1 , min j ∈ supp ⁡ ( k ) log ⁡ | k j | ) > ∞ } F_d≔\left \{ f\in L^2([0,1)^d)\middle | \|f\|≔\sum _{\boldsymbol {k}\in {\mathbb {Z}}^d}|\hat {f}({\boldsymbol {k}}) |\max \left (1,\min _{j\in \operatorname {supp}({\boldsymbol {k}})}\log |k_j|\right )>\infty \right \} \] with f ^ ( k ) \hat {f}({\boldsymbol {k}}) being the k {\boldsymbol {k}} -th Fourier coefficient of f f and supp ⁡ ( k ) ≔ { j ∈ { 1 , … , d } ∣ k j ≠ 0 } \operatorname {supp}({\boldsymbol {k}}) ≔\{j\!\in \!\{1,\ldots ,d\}\mid k_j\neq 0\} is polynomially tractable for multivariate integration in the worst-case setting. Here polynomial tractability means that the minimum number of function evaluations required to make the worst-case error less than or equal to a tolerance ε \varepsilon grows only polynomially with respect to ε − 1 \varepsilon ^{-1} and d d . It is important to remark that the function space F d F_d is unweighted, that is, all variables contribute equally to the norm of functions. Our tractability result is in contrast to those for most of the unweighted integration problems studied in the literature, in which polynomial tractability does not hold and the problem suffers from the curse of dimensionality. Our proof is constructive in the sense that we provide an explicit quasi-Monte Carlo rule that attains a desired worst-case error bound.

Optimal Management Strategy for the Deviation of Urban Metro Public Space Development Tendency—Case Study Guangzhou City, China

Based on the existing literature and field observation, the research takes Guangzhou as representative city and its deviation in the development of urban metro public space represented as the research object. It is believed that the deviation is mainly manifested in six dimensions: variables of social demography, details of taking metro, daily stress perception of passengers, perception on humanized design level of metro, perception on integration and intelligent level of metro space, perception on characteristic design and humanistic design level of metro space, and their correlation will be verified through data collection and analysis. The results found that: 1) Stress perception of passengers will lead to a negative predictive effect on passengers’ perception on metro public space development trend. 2) Passengers’ perception on humanized design level of metro will have positive and active effect on their perception on metro public space development trend. 3) Characteristic design and humanistic design level of metro space will lead to a positive predictive effect on passengers’ perception on metro public space development trend. 4) In the process that humanized design level of metro affects passengers’ perception on metro public space development trend, characteristic design and humanistic design level of metro space play a mediating role. 5) Passengers’ stress perception have moderating effect in the process that humanized design level of metro indirectly affects the passengers’ perception on metro public space development trend.

Boundedness of Fourier integral operators on classical function spaces

We investigate the global boundedness of Fourier integral operators with amplitudes in the general Hörmander classes Sρ,δm(Rn), ρ,δ∈[0,1] and non-degenerate phase functions of arbitrary rank κ∈{0,1,…,n−1} on Besov-Lipschitz Bp,qs(Rn) and Triebel-Lizorkin Fp,qs(Rn) of order s and 0<p≤∞, 0<q≤∞. The results that are obtained are all up to the end-point and sharp and are also applied to the regularity of Klein-Gordon-type oscillatory integrals in the aforementioned function spaces.

Horizontal gravity disturbance vector in atmospheric dynamics

All meteorological and oceanographic textbooks unintentionally define the Earth gravitation outside the solid Earth through treating the Earth as a point-mass located at the Earth center containing the entire Earth mass or assuming the Earth with uniform mass density. Combination of such simplified gravitational and centrifugal accelerations leads to the effective gravity geff. The geopotential surface corresponding to geff (called the effective geopotential surface) is the ellipsoidal surface. The true Earth gravitation outside the solid Earth is the volume integration of gravitation of all point-masses inside the Earth. Combination of true gravitational and centrifugal accelerations leads to the true gravity g. The geopotential surface corresponding to g (called the true geopotential surface) and respect to the Earth ellipsoidal reference surface is the geoid, which varies approximately from -106 m to 86 m worldwide. The true gravity g minus the effective gravity geff is the gravity disturbance vector, δg = g – geff, which is a major variable in geodesy and solid Earth dynamics. Contrarily, δg is neglected completely in dynamics of atmosphere and ocean. In this study, the true gravity g replaces the effective gravity geff in atmospheric dynamic equations. Seven non-dimensional numbers are proposed to identify the magnitude of horizontal gravity disturbance vector (δg)⊥versus traditional horizontal forcing terms such as pressure gradient force and Coriolis force. These non-dimensional numbers are calculated from two publicly available and independent datasets with the geoid undulation (N) from the static gravity field model EIGEN-6C4 and long-term mean geopotential height (Z), wind velocity (u, v), and temperature (T) at 12 pressure levels in troposphere from the NCEP/NCAR reanalyzed climatology. The results demonstrate (δg)⊥ nonnegligible in hydrostatic equilibrium, geostrophic wind, geostrophic vorticity, Q vector, and Omega equation.

Models and analysis of stadium and commercial space integration: a case study from China

ABSTRACT Stadiums that are solely used for athletic competitions can lead to a desolate post-event environment and the waste of resources. However, China still lacks systematic research on the integration models of and paths between stadiums and commercial spaces. This study identified models of stadium and commercial space integration, analyzed the associated factors, and proposed a development framework. The research methods included literature review, case data collection, pattern induction and expert interviews. By analyzing 58 cases, this study summarized eight models for stadium–commercial space integration; analyzed the correlation between different models and development types, land use environments, and business configurations; and conducted in-depth analysis of two cases. The findings indicate that an open mindset during the development stage can promote the emergence of new models, utilizing the land environment during the design stage can improve stadium utilization rate, and a multi-business configuration during the operation stage can promote the formation of urban vitality. A development framework is proposed, which emphasizes the collaboration of all stakeholders to optimize every step of the decision-making, construction and operation processes. These findings contribute to identifying development directions for stadiums in China and provide practical methods for the transformation of stadiums into dynamic urban complexes.

GNN-assisted phase space integration with application to atomistics

Overcoming the time scale limitations of atomistics can be achieved by switching from the state-space representation of Molecular Dynamics (MD) to a statistical-mechanics-based representation in phase space, where approximations such as maximum-entropy or Gaussian phase packets (GPP) evolve the atomistic ensemble in a time-coarsened fashion. In practice, this requires the computation of expensive high-dimensional integrals over all of phase space of an atomistic ensemble. This, in turn, is commonly accomplished efficiently by low-order numerical quadrature. We show that numerical quadrature in this context, unfortunately, comes with a set of inherent problems, which corrupt the accuracy of simulations—especially when dealing with crystal lattices with imperfections. As a remedy, we demonstrate that Graph Neural Networks, trained on Monte-Carlo data, can serve as a replacement for commonly used numerical quadrature rules, overcoming their deficiencies and significantly improving the accuracy. This is showcased by three benchmarks: the thermal expansion of copper, the martensitic phase transition of iron, and the energy of grain boundaries. We illustrate the benefits of the proposed technique over classically used third- and fifth-order Gaussian quadrature, highlight the impact on time-coarsened atomistic predictions, and discuss the computational efficiency. The latter is of general importance when performing frequent evaluation of phase space or other high-dimensional integrals, which is why the proposed framework promises applications beyond the scope of atomistics.

Vortex-induced sound prediction of slat noise from time-resolved particle image velocimetry data

A data-driven method for predicting the vortex-induced sound from time-resolved velocimetry data is presented and applied to the sound generated by flow passing through the slat in a multi-element high-lift airfoil. The time-dependent velocity fields in the slat-cove region of the 30P30N multi-element airfoil are obtained from time-resolved particle image velocimetry measurements, and a low-order reconstruction is achieved by using the rank-one vbnm modes from spectral proper orthogonal decomposition. The pressure force and associated dipole sound are then computed via the application of the force and acoustic partitioning methods (Seo et al. in Phys Fluids 34(5):053607, 2002) which involve volume integrals of the product of the second invariant of the velocity gradient tensor and geometry-dependent influence fields. The method enables estimation of the dipole sound generated by local flow structures, and the results are shown to be consistent with theory of vortex sound. Comparison with the measured sound data suggests that while the shear layer modes are responsible for the tonal noise, the interactions between the shear layer modes and other parts of the wing also generate a substantial level of flow noise.

Assembly Solutions for Cost-Effective Heterogeneous Integration with Disparate Die Types

The semiconductor industry is driving to enable high volume integration of disparate die types via Heterogeneous Integration. These die can come from a range of wafer sizes fabricated in different technology nodes. This emerging package type creates new challenges regarding assembly efficiency and yield. Traditionally, flip-chip assembly process flows have utilized a single placement tool for the placement of the single die type onto the target substrate. For applications with multiple die types, a series of placement tools have been configured in a production line, with each tool dedicated to the placement of a specific die type. This paper and presentation explore the implications of this type of solution in the era of Heterogeneous Integration. Impacts on product yield, throughput, manufacturing efficiency, and overall cost of assembly will be explored for a broad range of Heterogeneous Integration die configurations. Based on a sensitivity analysis for the range of die types expected in these applications, a novel approach to optimization of overall assembly economics will be proposed. Appropriateness of this novel approach will be explored for a range of packaging solutions, including Flip-Chip, 2.5D, 3D, and Fan-Out.