Concept and simulation of a novel dual-layer linear ion trap mass analyzer for micro-electromechanical systems mass spectrometry

This paper proposed a dual-layer linear ion trap mass analyzer (dLIT) based on micro-electromechanical systems (MEMS) technology and stacked-layer structure for the development of MEMS mass spectrometry. Its basic performance and potential capabilities were explored by ion trajectory simulations. The theoretical formulas were modified by implementing multipole expansion. The simulation results were confirmed to be highly consistent with theoretical calculations in multiple aspects, including stability diagram, secular frequencies, and mass linearity, with only a deviation of 1-2%. In the boundary ejection mode, close to 100% ejection was achieved in a single dimension by applying extra quadrupole DC voltage. Preliminary simulation results showed that dLIT can achieve a peak width of ∼2 mass units (full width at half maximum, FWHM) for m/z 60 ions even at pressures as high as 50 Pa. Furthermore, the application of AC frequency scanning mode in dLIT was also evaluated, and preliminary simulation results yield a peak width of 0.3-0.4 mass units (FWHM). The dLIT offered several advantages, including high-precision fabrication at the sub-millimeter scale, excellent high-pressure performance, and a clear physical model. It preliminarily proved to be an ideal mass analyzer for MEMS mass spectrometry.

Spherical Fourier-Transform-Based Real-TimeNear-Field Shaping and Focusing in Beyond-5G Networks

For ultra-reliable high-data-rate communication, the beyond fifth generation (B5G) and the sixth generation (6G) wireless networks will heavily rely on beamforming, with mobile users often located in the radiative near-field of large antenna systems. Therefore, a novel approach to shape both the amplitude and phase of the electric near-field of any general antenna array topology is presented. Leveraging on the active element patterns generated by each antenna port, the beam synthesis capabilities of the array are exploited through Fourier analysis and spherical mode expansions. As a proof-of-concept, two different arrays are synthesized from the same active antenna element. These arrays are used to obtain 2D near-field patterns with sharp edges and a 30 dB difference between the fields' magnitudes inside and outside the target regions. Various validation and application examples demonstrate the full control of the radiation in every direction, yielding optimal performance for the users in the focal zones, while significantly improving the management of the power density outside of them. Moreover, the advocated algorithm is very efficient, allowing for a fast, real-time modification and shaping of the array's radiative near-field.

Meta-Atoms with Toroidal Topology for Strongly Resonant Responses

A conductive meta-atom of toroidal topology is studied both theoretically and experimentally, demonstrating a sharp and highly controllable resonant response. Simulations are performed both for a free-space periodic metasurface and a pair of meta-atoms inserted within a rectangular metallic waveguide. A quasi-dark state with controllable radiative coupling is supported, allowing to tune the linewidth (quality factor) and lineshape of the supported resonance via the appropriate geometric parameters. By conducting a rigorous multipole analysis, we find that despite the strong toroidal dipole moment, it is the residual electric dipole moment that dictates the electromagnetic response. Subsequently, the structure is fabricated with 3D printing and coated with silver paste. Importantly, the structure is planar, consists of a single metallization layer and does not require a substrate when neighboring meta-atoms are touching, resulting in a practical, thin and potentially low-loss system. Measurements are performed in the 5 GHz regime with a vector network analyzer and a good agreement with simulations is demonstrated.

Near-exact non-relativistic ionization energies for many-electron atoms

Electron-electron interactions and correlations form the basis of difficulties encountered in the theoretical solution of problems dealing with multi-electron systems. Accurate treatment of the electron-electron problem is likely to unravel some nice physical properties of matter embedded in the interaction. In an effort to tackle this many-body problem, a symmetry-dependent all-electron potential generalized for an n-electron atom is suggested in this study. The symmetry dependence in the proposed potential hinges on an empirically determined angular momentum-dependent partitioning fraction for the electron-electron interaction. With the potential, all atoms are treated in the same way regardless of whether they are open or closed shell using their system specific information. The non-relativistic ground-state ionization potentials for atoms with up to 103 electrons generated using the all-electron potential are in reasonable agreement with the existing experimental and theoretical data. The effects of higher-order non-relativistic interactions as well as the finite nuclear mass of the atoms are also analysed.

On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model. II. Evaluation of the properties in an infinite crystal

The previously reported exact potential and multipole moment (EP/MM) method for fast and precise evaluation of the intermolecular electrostatic interaction energies in molecular crystals using the pseudoatom representation of the electron density [Nguyen, Macchi & Volkov (2020), Acta Cryst. A76, 630-651] has been extended to the calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) in an infinite crystal. The presented approach combines an efficient Ewald-type summation (ES) of atomic multipoles up to the hexadecapolar level in direct and reciprocal spaces with corrections for (i) the net polarization of the sample (the `surface term') due to a net dipole moment of the crystallographic unit cell (if present) and (ii) the short-range electron-density penetration effects. The rederived and reported closed-form expressions for all terms in the ES algorithm have been augmented by the expressions for the surface term available in the literature [Stenhammar, Trulsson & Linse (2011), J. Chem. Phys. 134, 224104] and the exact potential expressions reported in a previous study [Volkov, King, Coppens & Farrugia (2006), Acta Cryst. A62, 400-408]. The resulting algorithm, coded using Fortran in the XDPROP module of the software package XD, was tested on several small molecular crystal systems (formamide, benzene, L-dopa, paracetamol, amino acids etc.) and compared with a series of EP/MM-based direct-space summations (DS) performed within a certain number of unit cells generated along both the positive and negative crystallographic directions. The EP/MM-based ES technique allows for a noticeably more precise determination of the EF and EFG and significantly better precision of the evaluated ESP when compared with the DS calculations, even when the latter include contributions from an array of symmetry-equivalent atoms generated within four additional unit cells along each crystallographic direction. In terms of computational performance, the ES/EP/MM method is significantly faster than the DS calculations performed within the extended unit-cell limits but trails the DS calculations within the reduced summation ranges. Nonetheless, the described EP/MM-based ES algorithm is superior to the direct-space summations as it does not require the user to monitor continuously the convergence of the evaluated properties as a function of the summation limits and offers a better precision-performance balance.

Nearly Perfect Transmissive Subtractive Coloration through the Spectral Amplification of Mie Scattering and Lattice Resonance

Silicon has been utilized in metasurfaces to produce structural color filters due to its compatibility with mature and cost-effective methods for complementary metal oxide semiconductor devices. In this work, we propose and demonstrate efficiency- and scattering-enhanced structural color filters using all-dielectric metasurfaces made up of engineered hydrogenated amorphous silicon (a-Si:H) nanoblocks. Wavelength-dependent filtering is achieved by Mie scattering as each structure individually supports the electric dipole (ED) and magnetic dipole (MD) resonances. The ED and MD resonances are identified by observing the field profiles of the resonance calculated by finite element method (FEM) simulations. To enhance the efficiency and scattering response of the all-dielectric metasurfaces, the proposed structural color filters are designed with consideration of the lattice resonances and scattering directivity. The spectral positions of the transmission dips and peaks are rigorously analyzed in accordance with the Mie theory and multipole expansion. The transmission spectra exhibit 100% transmission where Kerker's first condition is satisfied, while the lattice resonances amplify the ED and MD scattering responses throughout the entire visible regime. Various colors are generated by varying the resonance peak, which is controlled by varying the geometric parameters of a-Si:H nanoblocks. The proposed structural color printing devices are expected to have applications in dynamic color displays, imaging devices, and photorealistic color printing.

Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170-175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536; Nguyen & Volkov (2019). Acta Cryst. A75, 448-464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283-4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10^-5 kJ mol^-1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28-64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.

Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

A new method called Pepsi-SAXS is presented that calculates small-angle X-ray scattering profiles from atomistic models. The method is based on the multipole expansion scheme and is significantly faster compared with other tested methods. In particular, using the Nyquist-Shannon-Kotelnikov sampling theorem, the multipole expansion order is adapted to the size of the model and the resolution of the experimental data. It is argued that by using the adaptive expansion order, this method has the same quadratic dependence on the number of atoms in the model as the Debye-based approach, but with a much smaller prefactor in the computational complexity. The method has been systematically validated on a large set of over 50 models collected from the BioIsis and SASBDB databases. Using a laptop, it was demonstrated that Pepsi-SAXS is about seven, 29 and 36 times faster compared with CRYSOL, FoXS and the three-dimensional Zernike method in SAStbx, respectively, when tested on data from the BioIsis database, and is about five, 21 and 25 times faster compared with CRYSOL, FoXS and SAStbx, respectively, when tested on data from SASBDB. On average, Pepsi-SAXS demonstrates comparable accuracy in terms of χ² to CRYSOL and FoXS when tested on BioIsis and SASBDB profiles. Together with a small allowed variation of adjustable parameters, this demonstrates the effectiveness of the method. Pepsi-SAXS is available at http://team.inria.fr/nano-d/software/pepsi-saxs.

Multipolar interference effects in nanophotonics

Scattering of electromagnetic waves by an arbitrary nanoscale object can be characterized by a multipole decomposition of the electromagnetic field that allows one to describe the scattering intensity and radiation pattern through interferences of dominating multipole modes excited. In modern nanophotonics, both generation and interference of multipole modes start to play an indispensable role, and they enable nanoscale manipulation of light with many related applications. Here, we review the multipolar interference effects in metallic, metal-dielectric and dielectric nanostructures, and suggest a comprehensive view on many phenomena involving the interferences of electric, magnetic and toroidal multipoles, which drive a number of recently discussed effects in nanophotonics such as unidirectional scattering, effective optical antiferromagnetism, generalized Kerker scattering with controlled angular patterns, generalized Brewster angle, and non-radiating optical anapoles. We further discuss other types of possible multipolar interference effects not yet exploited in the literature and envisage the prospect of achieving more flexible and advanced nanoscale control of light relying on the concepts of multipolar interference through full phase and amplitude engineering.This article is part of the themed issue 'New horizons for nanophotonics'.

Tilting and moving-object lens for a 3D electron microscope

I investigated the tilting and movement of the objective lens of a 3D electron microscope electrically as an extension of the moving-objective lens concept. The electric or magnetic potential along the tilted optical axis is analytically expressed by a multipole potential expansion about the fixed central axis. The field distributions for axially symmetric dipole and quadrupole components are numerically shown, where the optical axis of a bell-shaped magnetic lens is tilted around the lens center by up to 60°. The hexapole and octapole components are also shown at a tilt angle of 45°.

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations

We review recent developments of fast analytical methods for macroscopic electrostatic calculations in biological applications, including the Poisson-Boltzmann (PB) and the generalized Born models for electrostatic solvation energy. The focus is on analytical approaches for hybrid solvation models, especially the image charge method for a spherical cavity, and also the generalized Born theory as an approximation to the PB model. This review places much emphasis on the mathematical details behind these methods.

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains

The two-site coarse-grained model for the interactions of charged side chains, to be used with our coarse-grained UNRES force field for protein simulations proposed in the accompanying paper, has been extended to pairs of oppositely charged side chains. The potentials of mean force of four pairs of molecules modeling charged amino-acid side chains, i.e., propionate-n-pentylamine cation (for aspartic acid-lysine), butyrate-n-pentylamine cation (for glutamic acid-lysine), propionate-1-butylguanidine (for aspartic acid-arginine), and butyrate-1-butylguanidine (for glutamic acid-arginine) pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expression was fitted to the potentials of mean force. Compared to pairs of like-charged side chains discussed in the accompanying paper, an average quadrupole-quadrupole interaction term had to be introduced to reproduce the Coulombic interactions, and a multistate model of charge distribution had to be introduced to fit the potentials of mean force of all oppositely charged pairs well. The model reproduces all salt-bridge minima and, consequently, is likely to improve the performance of the UNRES force field.

Plasmonics of 3-D nanoshell dimers using multipole expansion and finite element method

The spatial and spectral responses of the plasmonic fields induced in the gap of 3-D nanoshell dimers of gold and silver are comprehensively investigated and compared via theory and simulation using the multipole expansion (ME) and the finite element method (FEM) in COMSOL, respectively. The E-field in the dimer gap was evaluated and compared as a function of shell thickness, interparticle distance, and size. The E-field increased with decreasing shell thickness, decreasing interparticle distance, and increasing size, with the error between the two methods ranging from 1 to 10%, depending on the specific combination of these three variables. This error increases several fold with increasing dimer size, as the quasi-static approximation breaks down. A consistent overestimation of the plasmon's fwhm and red shifting of the plasmon peak occurs with FEM, relative to ME, and it increases with decreasing shell thickness and interparticle distance. The size effect that arises from surface scattering of electrons is addressed and shown to be especially prominent for thin shells, for which significant damping, broadening, and shifting of the plasmon band is observed; the size effect also affects large nanoshell dimers, depending on their relative shell thickness, but to a lesser extent. This study demonstrates that COMSOL is a promising simulation environment to quantitatively investigate nanoscale electromagnetics for the modeling and designing of surface-enhanced Raman scattering (SERS) substrates.

The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks

Hubs are highly connected proteins in a protein-protein interaction network. Previous work has implicated disordered domains and high surface charge as the properties significant in the ability of hubs to bind multiple proteins. While conformational flexibility of disordered domains plays an important role in the binding ability of large hubs, high surface charge is the dominant property in small hubs. In this study, we further investigate the role of the high surface charge in the binding ability of small hubs in the absence of disordered domains. Using multipole expansion, we find that the charges are highly distributed over the hub surfaces. Residue enrichment studies show that the charged residues in hubs are more prevalent on the exposed surface, with the exception of Arg, which is predominantly found at the interface, as compared to non-hubs. This suggests that the charged residues act primarily from the exposed surface rather than the interface to affect the binding ability of small hubs. They do this through (i) enhanced intra-molecular electrostatic interactions to lower the desolvation penalty, (ii) indirect long - range intermolecular interactions with charged residues on the partner proteins for better complementarity and electrostatic steering, and (iii) increased solubility for enhanced diffusion-controlled rate of binding. Along with Arg, we also find a high prevalence of polar residues Tyr, Gln and His and the hydrophobic residue Met at the interfaces of hubs, all of which have the ability to form multiple types of interactions, indicating that the interfaces of hubs are optimized to participate in multiple interactions.