Large Cutoff Research Articles

Surface tension and long range corrections of cylindrical interfaces.

The calculation of the surface tension of curved interfaces has been deeply investigated from molecular simulation during this last past decade. Recently, the thermodynamic Test-Area (TA) approach has been extended to the calculation of surface tension of curved interfaces. In the case of the cylindrical vapour-liquid interfaces of water and Lennard-Jones fluids, it was shown that the surface tension was independent of the curvature of the interface. In addition, the surface tension of the cylindrical interface is higher than that of the planar interface. Molecular simulations of cylindrical interfaces have been so far performed (i) by using a shifted potential, (ii) by means of large cutoff without periodic boundary conditions, or (iii) by ignoring the long range corrections to the surface tension due to the difficulty to estimate them. Indeed, unlike the planar interfaces there are no available operational expressions to consider the tail corrections to the surface tension of cylindrical interfaces. We propose here to develop the long range corrections of the surface tension for cylindrical interfaces by using the non-exponential TA (TA2) method. We also extend the formulation of the Mecke-Winkelmann corrections initially developed for planar surfaces to cylindrical interfaces. We complete this study by the calculation of the surface tension of cylindrical surfaces of liquid tin and copper using the embedded atom model potentials.

Reduced dissipation AUSM-family fluxes: HR-SLAU2 and HR-AUSM+-up for high resolution unsteady flow simulations

The reduced dissipation approach is applied to AUSM-family flux functions of SLAU2 (as well as its predecessor, SLAU) and AUSM+-up for high resolution simulations. In this approach, a dominant dissipation term (of the pressure flux) in each flux function is locally controlled (0 < γHR < 1, γHR: dissipation coefficient) if a cell geometry is of high quality (i.e., fully or nearly rectangular) and flow is smooth, and the original method is recovered otherwise (γHR = 1). Numerical tests demonstrate that the proposed HR (High-Resolution, or Hi-Res) -SLAU2 achieves better resolution (while maintaining robustness) for a wide-ranging Mach numbers (from Mach 6 × 10−4 to 8.1), compared with the original counterparts (γHR = 1) or an existing method (HR-Roe), whereas HR-AUSM+-up shows degraded resolution due to a large cutoff Mach number at low speeds and insufficient dissipation at super- and hypersonic speeds, although a smaller γHR is allowed. Furthermore, a new wiggle detector is proposed to improve both convergence and solution accuracy.

Characterization of polarizer made of the deep-UV birefringent crystal Ba2Mg(B3O6)2.

In optical communications and the laser industry, modulating the polarization of light requires crystals with both large birefringence and a wide transparent range. A good candidate for a deep-UV birefringent crystal is Ba2Mg(B3O6) because it has a large birefringence and short UV cutoff edge. We grew Ba2Mg(B3O6)2 crystals with sizes up to 41 mm×40 mm×7 mm using the top-seeded solution growth method. We obtained the thermal-expansion coefficients in different directions and the thermo-optic coefficients and then designed and manufactured a Glan-Taylor type polarizer to fulfill the commercial requirements.

Tunable microstrip lowpass filter with compact size and ultra‐wide stopband

A compact varactor-tuned microstrip lowpass filter (LPF) with a large cutoff frequency tuning range and an ultra-wide stopband is presented. By employing a pair of parallel coupled-lines and a low-impedance stub loaded with a varactor diode, the introduced filter can successfully realise the tunable cutoff frequency function. Besides, both radial patch resonators and stepped-impedance resonators are introduced to achieve an ultra-wide stopband in all the states in this design. A varactor-tuned microstrip LPF is designed, fabricated and measured. The measured results show that the proposed LPF provides not only a large cutoff frequency tuning range of 91.3% from 0.85 to 2.28 GHz, but also an ultra-wide stopband which extends to 20 GHz.

Renormalization group analysis of a neck-narrowing Lifshitz transition in the presence of weak short-range interactions in two dimensions

We study a system of weakly interacting electrons described by the energy dispersion $\xi(\mathbf{k}) = k_x^2 - k_y^2 - \mu$ in two dimensions within a renormalization group approach. This energy dispersion exhibits a neck-narrowing Lifshitz transition at the critical chemical potential $\mu_c=0$ where a van Hove singularity develops. Implementing a systematic renormalization group analysis of this system has long been hampered by the appearance of nonlocal terms in the Wilsonian effective action. We demonstrate that non-locality at the critical point is intrinsic, and the locality of the effective action can be maintained only away from the critical point. We also point out that it is crucial to introduce a large momentum cutoff to keep locality even away from the critical point. Based on a local renormalization group scheme employed near the critical point, we show that, as the energy scale $E$ is lowered, an attractive four-fermion interaction grows as $\log^2 E$ for $E > \mu$, whereas it retains the usual BCS growth, $-\log E$, for $E < \mu$. Starting away from the critical point, this fast growth of the pairing interaction suggests that the system becomes unstable toward a superconducting state well before the critical point is reached.

Zc(3900)as a resonance from theDD¯*interaction

In this paper it is proposed that the charged charmonium-like state ${Z}_{c}(3900)$ is a resonance above the threshold from the $D{\overline{D}}^{*}$ interaction. The $D{\overline{D}}^{*}$ interaction is described by the one-boson exchange model with light meson exchanges plus a short-range $J/\ensuremath{\psi}$ exchange. The scattering amplitude is calculated within a Bethe-Salpeter equation approach, and the poles near the $D{\overline{D}}^{*}$ threshold are searched. In the isoscalar sector, two poles found under the $D{\overline{D}}^{*}$ threshold---i.e., bound states---have the quantum numbers ${I}^{G}({J}^{\mathrm{PC}})={0}^{\ensuremath{-}}({1}^{+\ensuremath{-}})$ and ${0}^{+}({1}^{++})$. The latter can be related to the $X(3872)$. In the isovector sector, a bound state with ${I}^{G}({J}^{P})={1}^{+}({1}^{+})$ is found with a large cutoff at about 3 GeV. If a cutoff at about 2 GeV is adopted with which a pole carrying the quantum number of the $X(3872)$ is produced at an energy of about 3871 MeV, the pole for the bound state with ${1}^{+}({1}^{+})$ runs across the threshold to a second Riemann sheet and becomes a resonance above the $D{\overline{D}}^{*}$ threshold, which can be identified with the ${Z}_{c}(3900)$. With such a cutoff, the $D{\overline{D}}^{*}$ invariant mass spectrum is also investigated and the experimental results found by BESIII can be reproduced.

A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations.

A new method to account for long range electrostatic contributions is proposed and implemented for quantum mechanics/molecular mechanics long range electrostatic correction (QM/MM-LREC) calculations. This method involves the use of the minimum image convention under periodic boundary conditions and a new smoothing function for energies and forces at the cutoff boundary for the Coulomb interactions. Compared to conventional QM/MM calculations without long-range electrostatic corrections, the new method effectively includes effects on the MM environment in the primary image from its replicas in the neighborhood. QM/MM-LREC offers three useful features including the avoidance of calculations in reciprocal space (k-space), with the concomitant avoidance of having to reproduce (analytically or approximately) the QM charge density in k-space, and the straightforward availability of analytical Hessians. The new method is tested and compared with results from smooth particle mesh Ewald (PME) for three systems including a box of neat water, a double proton transfer reaction, and the geometry optimization of the critical point structures for the rate limiting step of the DNA dealkylase AlkB. As with other smoothing or shifting functions, relatively large cutoffs are necessary to achieve comparable accuracy with PME. For the double-proton transfer reaction, the use of a 22 Å cutoff shows a close reaction energy profile and geometries of stationary structures with QM/MM-LREC compared to conventional QM/MM with no truncation. Geometry optimization of stationary structures for the hydrogen abstraction step by AlkB shows some differences between QM/MM-LREC and the conventional QM/MM. These differences underscore the necessity of the inclusion of the long-range electrostatic contribution.

Running of the contact interactions in chiral N3LO potentials from subtractive renormalization

In this work a subtracted kernel renormalization procedure (SKM) is applied to the chiral NN potential up to next-to-next-to-next-to-leading-order (N3 LO) to obtain the running of the renormalized contact strengths with the subtraction scale μ and the phase shifts for all uncoupled waves with contact interaction (S,P,D). We use two potentials constructed within the framework of Weinberg's approach to ChEFT, which provide a very accurate description of NN scattering data below laboratory energies E ∼ 350 MeV, namely Epelbaum, Glöckle and Meissner (N3LO-EGM) and Entem and Machleidt (N3LO-EM). For both potentials, we consider a large cutoff (30 fm-1) and analyze the phases and the running of the contact strengths with the subtraction point μ by making a fit of the K-matrix with five subtractions to the K-matrix from the Nijmegen II potential at low energies (E ≤ 20 MeV).

A coarse-grained simulation study of the structures, energetics, and dynamics of linear and circular DNA with its ions.

We have studied the structural, energetics, and dynamical properties of a variety of linear and circular DNA fragments using a solvent-mediated coarse-grained (CG) model of DNA with explicit ions recently developed by us [Naômé et al., J. Chem. Theory Comput., 2014, 10, 3541-3549]. We particularly examined the treatment of electrostatics and determined that a large cutoff is necessary to properly reproduce the DNA flexibility. Moreover, it is crucial to include long-ranged electrostatic interactions: a Particle Mesh Ewald scheme at low resolution is sufficient to avoid structural artifacts. We calculated the ring closure probabilities, as j-factors, for DNA fragments of different lengths from equilibrium, as well as restrained molecular dynamics (MD) simulations. The latter force integration method provided accurate results without model fitting. We generated topology and energy maps for DNA minicircles of various lengths and helical densities, at low and high ion concentrations. A general trend for structure compaction is observed, driven by an increase in writhing as the ionic concentration increases. Finally, we applied a reconstruction procedure to generate detailed molecular structures from the various superhelical conformations generated by the CG MD of the DNA minicircles. These pre-equilibrated reconstructed atomistic structures can serve as starting material for atomistic simulations.

Multi-million atom Monte Carlo simulation of oxide materials and solid solutions

We propose a method for the simulation of large ionic systems with long-range forces using the Monte Carlo method. This method employs a domain decomposition strategy for subdividing the simulation cell and parallelisation of these subdomains using a thread based strategy. This is thus ideally suited to modern day multi-core architectures.Evaluation of the long range interactions that is incompatible with a domain decomposition strategy has been replaced by the direct calculation of the Coulomb sum (Fennell and Gezelter, 2006). We compare this approach with that of “standard” Monte Carlo simulations that employ the Ewald technique. A relatively large two-body cutoff is required to reproduce the Ewald results accurately. Finally, as a pilot application, we demonstrate that our novel approach can be applied to very large simulation cells (>1 million atoms); results for enthalpies, are presented for a typical non-ideal oxide solid solution (MnO–MgO) as a function of composition and highlight the formation of nano-sized domains in the very large simulation cells. Well defined structures such as exsolution lamellae are not observed.

Generalization of Darcy's law for Bingham fluids in porous media: from flow-field statistics to the flow-rate regimes.

In this paper, we numerically investigate the statistical properties of the nonflowing areas of Bingham fluid in two-dimensional porous media. First, we demonstrate that the size probability distribution of the unyielded clusters follows a power-law decay with a large size cutoff. This cutoff is shown to diverge following a power law as the imposed pressure drop tends to a critical value. In addition, we observe that the exponents are almost identical for two different types of porous media. Finally, those scaling properties allow us to account for the quadratic relationship between the pressure gradient and velocity.

Role of gravity in the collapse of a wave function: A probe into the Diósi-Penrose model

We investigate the Di\'osi-Penrose (DP) proposal for connecting the collapse of the wave function to gravity. The DP model needs a free parameter, acting as a cutoff to regularize the dynamics, and the predictions of the model highly depend on the value of this cutoff. The Compton wavelength of a nucleon seems to be the most reasonable cutoff value since it justifies the nonrelativistic approach. However, with this value, the DP model predicts an unrealistically high rate of energy increase. Thus, either one is forced to choose a much larger cutoff, which is not physically justified and totally arbitrary, or one needs to include dissipative effects in order to tame the energy increase. Taking the analogy with dissipative collisional decoherence seriously, we develop a dissipative generalization of the DP model. We show that even with dissipative effects, the DP model contradicts known physical facts, unless either the cutoff is kept artificially large or one limits the applicability of the model to massive systems. We also provide an estimation for the mass range of this applicability.

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations.

Molecular mechanics and dynamics simulations use distance based cutoff approximations for faster computation of pairwise van der Waals and electrostatic energy terms. These approximations traditionally use a precalculated and periodically updated list of interacting atom pairs, known as the “nonbonded neighborhood lists” or nblists, in order to reduce the overhead of finding atom pairs that are within distance cutoff. The size of nblists grows linearly with the number of atoms in the system and superlinearly with the distance cutoff, and as a result, they require significant amount of memory for large molecular systems. The high space usage leads to poor cache performance, which slows computation for large distance cutoffs. Also, the high cost of updates means that one cannot afford to keep the data structure always synchronized with the configuration of the molecules when efficiency is at stake. We propose a dynamic octree data structure for implicit maintenance of nblists using space linear in the number of atoms but independent of the distance cutoff. The list can be updated very efficiently as the coordinates of atoms change during the simulation. Unlike explicit nblists, a single octree works for all distance cutoffs. In addition, octree is a cache-friendly data structure, and hence, it is less prone to cache miss slowdowns on modern memory hierarchies than nblists. Octrees use almost 2 orders of magnitude less memory, which is crucial for simulation of large systems, and while they are comparable in performance to nblists when the distance cutoff is small, they outperform nblists for larger systems and large cutoffs. Our tests show that octree implementation is approximately 1.5 times faster in practical use case scenarios as compared to nblists.

A Compensatory Approach of the Fixed Localization in EnKF

Abstract While fixed covariance localization can greatly increase the reliability of the background error covariance in filtering by suppressing the long-distance spurious correlations evaluated by a finite ensemble, it may degrade the assimilation quality in an ensemble Kalman filter (EnKF) as a result of restricted longwave information. Tuning an optimal cutoff distance is usually very expensive and time consuming, especially for a general circulation model (GCM). Here the authors present an approach to compensate the demerit in fixed localization. At each analysis step, after the standard EnKF is done, a multiple-scale analysis technique is used to extract longwave information from the observational residual (referred to the EnKF ensemble mean). Within a biased twin-experiment framework consisting of a global barotropical spectral model and an idealized observing system, the performance of the new method is examined. Compared to a standard EnKF, the hybrid method is superior when an overly small/large cutoff distance is used, and it has less dependence on cutoff distance. The new scheme is also able to improve short-term weather forecasts, especially when an overly large cutoff distance is used. Sensitivity studies show that caution should be taken when the new scheme is applied to a dense observing system with an overly small cutoff distance in filtering. In addition, the new scheme has a nearly equivalent computational cost to the standard EnKF; thus, it is particularly suitable for GCM applications.

High-performance AlGaInP tunneling heterostructure-emitter bipolar transistor

In this paper, a high-performance heterostructure-emitter bipolar transistor employing an AlGaInP quaternary compound tunneling layer is fabricated and demonstrated. In the studied device, a 50Å n-AlGaInP tunneling emitter layer together with a 200Å n-GaAs layer forms the heterostructure emitter to decrease the collector–emitter offset voltage. On the other hand, due to the relatively large valence band discontinuity (∼0.4eV) at AlGaInP/GaAs heterojunction and the small hole transmission coefficient across the AlGaInP tunneling layer, most of holes injecting from base to emitter will be blocked at AlGaInP/GaAs heterojunction and then high collector current and current gain are achieved. The experimental results exhibit a large collector current of 92mA, a large current gain of 446, and a relatively low offset voltage of only 45mV, respectively. Furthermore, a large current-gain cutoff frequency ft up to 63.7GHz is obtained for the device with a thin tunneling layer.

Large field inflation and double α-attractors

We consider a broad class of inflationary models that arise naturally in supergravity. They are defined in terms of a parameter $\alpha$ that determines the curvature and cutoff of these models. As a function of this parameter, we exhibit that the inflationary predictions generically interpolate between two attractor points. At small cutoff $\alpha$, the resulting inflationary model is of plateau-type with $n_s = 1 - 2 / N$ and $r = 12 \alpha / N^2$. For $\alpha = 1$, these predictions coincide with predictions of the Starobinsky model and Higgs inflation. In contrast, for large cutoff $\alpha$, the theory asymptotes to quadratic inflation, with $n_s = 1 - 2 / N$, $r = 8 / N$. Both universal predictions can be attributed to a stretching of the moduli space. For intermediate values of $\alpha$, the predictions interpolate between these two critical points, thus covering the sweet spots of both Planck and BICEP2.

Quantifying particle size and turbulent scale dependence of dust flux in the Sahara using aircraft measurements

The first size-resolved airborne measurements of dust fluxes and the first dust flux measurements from the central Sahara are presented and compared with a parameterization by Kok (2011a). High-frequency measurements of dust size distribution were obtained from 0.16 to 300 µm diameter, and eddy covariance fluxes were derived. This is more than an order of magnitude larger size range than previous flux estimates. Links to surface emission are provided by analysis of particle drift velocities. Number flux is described by a −2 power law between 1 and 144 µm diameter, significantly larger than the 12 µm upper limit suggested by Kok (2011a). For small particles, the deviation from a power law varies with terrain type and the large size cutoff is correlated with atmospheric vertical turbulent kinetic energy, suggesting control by vertical transport rather than emission processes. The measured mass flux mode is in the range 30–100 µm. The turbulent scales important for dust flux are from 0.1 km to 1–10 km. The upper scale increases during the morning as boundary layer depth and eddy size increase. All locations where large dust fluxes were measured had large topographical variations. These features are often linked with highly erodible surface features, such as wadis or dunes. We also hypothesize that upslope flow and flow separation over such features enhance the dust flux by transporting large particles out of the saltation layer. The tendency to locate surface flux measurements in open, flat terrain means these favored dust sources have been neglected in previous studies.

High cell density cultivations by alternating tangential flow (ATF) perfusion for influenza A virus production using suspension cells

High cell densities in animal cell culture can be obtained by continuous perfusion of fresh culture medium across hollow fiber membranes that retain the cells. Careful selection of the membrane type and cut-off allows to control accumulation of target molecules and removal of low molecular weight compounds. In this report, perfusion with the scalable ATF (alternating tangential filtration, Refine Technology) system was evaluated for two suspension cell lines, the avian cell line AGE1.CR and the human cell line CAP. Both were cultivated in chemically defined media optimized for batch cell growth in a 1L stirred tank bioreactor connected to the smallest ATF unit (ATF2) and infected with cell line-adapted human influenza A virus (A/PR/8/34 (H1N1), typical diameter: 80–100nm).At concentrations of about 25 million cells/mL three different membrane cut-offs (50kDa, 0.2μm and 0.5μm) were tested and compared to batch cultivations performed at 5 million cells/mL. For medium and large cut-offs no cell-density effect could be observed with cell-specific virus yields of 1428–1708 virions/AGE1.CR cell (infected with moi 0.001) and 1883–4086 virions/CAP cell (moi of 0.025) compared to 1292 virions/AGE1.CR cell and 3883 virions/CAP cell in batch cultures. Even at a concentration of 48 million AGE1.CR cells/mL (cut-off: 0.2μm) a cell-specific yield of 1266 virions/cell was reached. Only for the small cut-off (50kDa) used with AGE1.CR cells a decrease in cell-specific yield was measured with 518 virions/cell. Surprisingly, the ratio of infectious to total virions seemed to be increased in ATF compared to batch cultures. AGE1.CR cell-derived virus particles were present in the permeate (0.2 and 0.5μm cut-off), whereas CAP cell-derived virions were not, suggesting possible differences in morphology, aggregation or membrane properties of the virions released by the two cell lines.To our knowledge, this is the first study that illustrates the potential of ATF-based perfusion of chemically defined media across cell-retaining membranes for production of an influenza A vaccine.

Fluctuation analysis in complex networks modeled by hidden-variable models: necessity of a large cutoff in hidden-variable models.

It is becoming more and more clear that complex networks present remarkable large fluctuations. These fluctuations may manifest differently according to the given model. In this paper we reconsider hidden-variable models which turn out to be more analytically treatable and for which we have recently shown clear evidence of non-self-averaging, the density of a motif being subject to possible uncontrollable fluctuations in the infinite-size limit. Here we provide full detailed calculations and we show that large fluctuations are only due to the node-hidden variables variability while, in ensembles where these are frozen, fluctuations are negligible in the thermodynamic limit and equal the fluctuations of classical random graphs. A special attention is paid to the choice of the cutoff: We show that in hidden-variable models, only a cutoff growing as N(λ) with λ ≥ 1 can reproduce the scaling of a power-law degree distribution. In turn, it is this large cutoff that generates non-self-averaging.

The Born Series for S-wave Quartet nd Scattering at Small Cutoff Values

Perturbative expansions, the Born series, of the scattering length and the amplitude of $S$-wave neutron-deuteron scattering for spin quartet channel below deuteron breakup threshold are studied in pionless effective field theory at small cutoff values. A three-body contact interaction is introduced when the integral equation is solved using the small cutoffs. After renormalizing the three-body interaction by using the scattering length, we expand the integral equation as the ordinary and inverted Born series. We find that the scattering length and the phase shift are considerably well reproduced with a few terms of the inverted Born series at relatively large cutoff values, $\Lambda\simeq 100$ MeV.