Nearest-neighbor Approximation Research Articles

DTI-SNNFRA: Drug-target interaction prediction by shared nearest neighbors and fuzzy-rough approximation.

In-silico prediction of repurposable drugs is an effective drug discovery strategy that supplements de-nevo drug discovery from scratch. Reduced development time, less cost and absence of severe side effects are significant advantages of using drug repositioning. Most recent and most advanced artificial intelligence (AI) approaches have boosted drug repurposing in terms of throughput and accuracy enormously. However, with the growing number of drugs, targets and their massive interactions produce imbalanced data which may not be suitable as input to the classification model directly. Here, we have proposed DTI-SNNFRA, a framework for predicting drug-target interaction (DTI), based on shared nearest neighbour (SNN) and fuzzy-rough approximation (FRA). It uses sampling techniques to collectively reduce the vast search space covering the available drugs, targets and millions of interactions between them. DTI-SNNFRA operates in two stages: first, it uses SNN followed by a partitioning clustering for sampling the search space. Next, it computes the degree of fuzzy-rough approximations and proper degree threshold selection for the negative samples’ undersampling from all possible interaction pairs between drugs and targets obtained in the first stage. Finally, classification is performed using the positive and selected negative samples. We have evaluated the efficacy of DTI-SNNFRA using AUC (Area under ROC Curve), Geometric Mean, and F1 Score. The model performs exceptionally well with a high prediction score of 0.95 for ROC-AUC. The predicted drug-target interactions are validated through an existing drug-target database (Connectivity Map (Cmap)).

Topological quantum optical states in quasiperiodic cold atomic chains

Topological quantum optical states in one-dimensional (1D) quasiperiodic cold atomic chains are studied in this work. We propose that by introducing incommensurate modulations on the interatomic distances of 1D periodic atomic chains, the off-diagonal Aubry-Andr\'e-Harper (AAH) model can be mimicked, although the crucial difference is the existence of long-range dipole-dipole interactions. The discrete band structures with respect to the modulation phase, which plays the role of a dimension extension parameter, are calculated for finite chains beyond the nearest-neighbor approximation. It is found that the present system indeed supports nontrivial topological states localized over the boundaries. Despite the presence of long-range dipole-dipole interactions that leads to an asymmetric band structure, it is demonstrated that this system inherits the topological properties of two-dimensional integer quantum Hall systems. The spectral position, for both real and imaginary frequencies, and number of these topologically protected edge states are still governed by the gap-labeling theorem and characterized by the topological invariant, namely, the (first) Chern number, indicating the validity of bulk-boundary correspondence. Due to the fractal spectrum arising from the quasiperiodicity in a substantially wide range of system parameters, our system provides a large number of topological gaps and optical states readily for practical use. It is also revealed that a substantial proportion of the topological edge states are highly subradiant with extremely low decay rates, which therefore offer an appealing route for controlling the emission of external quantum emitters and achieving high-fidelity quantum state storage.

Extremely Fast “Solution” to the Large-Scale and Very Large-Scale Vehicle Routing Problem

A solution to the vehicle routing problem (VRP) is presented that takes only quadratic space, <i>O(n²),</i> and quadratic time, <i>O(n²)</i>, if <i>n</i> is the number of stops on a route. The input is assumed to be a list of stops of length <i>n</i> in longitude, latitude format. The output is an origin-destination (OD) matrix of size <i>O(n²)</i>, which takes <i>O(n²)</i> time to build. The element <i>(i, j)</i> in the matrix is the approximate driving distance between stop <i>i</i> and stop <i>j</i> on the route. Each approximate driving distance takes constant or <I>O(1)</I> time to compute. (The approximate driving distance appears in previous work by the author, published in URISA GIS-Pro ‘19 and CalGIS 2020.) This OD matrix is well-suited for solving large-scale and very large-scale VRP problems, since computing approximate driving distances is lightning fast. For instance, using real-world data, it took less than one (1) second to produce a route with 5,156 stops. The OD matrix can be used with any exact or approximation algorithm to find a route, including the nearest-neighbor approximation algorithm: Starting at an origin, the next closest stop is visited repeatedly, ending at the destination once all stops have been visited. Determining the next stop to visit takes linear or <i>O(n)</i> time to compute, and this is done <i>O(n)</i> times. This solution to the VRP is a polynomial-time, <i>O(n²)</i>, approximation; it is not exact, but is extremely fast.

Joint Effect of the Dipole–Dipole Interaction and Constant Dipole Moment on the Shape of the Field Pulse without an Envelope

An integrable model is proposed for a two-level medium with a constant dipole moment, which describes the evolution of electromagnetic field pulses without an envelope with account for the dipole–dipole interaction. In the nearest neighbor approximation, this interaction is taken into account in the form of quadratic dispersion. It is found that such a generalization of the reduced Maxwell–Bloch equations preserves the complete integrability. It is shown using the obtained exact soliton solutions as examples that the joint effect of quadratic dispersion and the constant dipole moment has a number of unique features and provides new opportunities for controlling the shape of field pulses. In particular, it is found that the shape and amplitude of a field pulse depend on the signs of the dipole–dipole interaction as well as on the sign of the constant dipole moment.

Comparative study of the electron–electron interactions on optoelectronic properties of carbon nanotube within orthogonal and nonorthogonal tight-binding model

We investigate the electron–electron (e–e) interactions effect on the optoelectronic properties of single-walled carbon nanotubes (SWCNTs). We study theoretically the effect of e–e interactions on the optoelectronic properties of zigzag carbon nanotubes and obtain some useful expressions for the band structure and optical absorption of nanotubes for the first nearest-neighbor (1NN) and second nearest-neighbor (2NN) approximation in tight-binding (TB) model. Our computational approach is based on combination of the orthogonal (o-TB) and nonorthogonal (n-TB) tight-binding method with Hubbard model for zigzag SWCNTs. In nonorthogonal tight-binding model we consider the effect of orbital overlap on optoelectronic properties of nanotubes. We also obtain the optical absorption spectrum of zigzag SWCNTs under e–e interactions effect with considering orthogonal and nonorthogonal tight-binding method for 1NN and 2NN approximation. We investigate optical absorption for the incident light polarized parallel to the tube axis and obtain all allowed optical transitions. Our results show some variations in the band structure and optical absorption spectrum of nanotubes under e–e interactions effect when we use orthogonal tight-binding model compare with nonorthogonal tight-binding model.

The effects of electric field on electronic and thermal properties of bilayer boron phosphide: Beyond nearest neighbor approximation

The behaviors electronic structure and density of states (DOS) of biased AB bilayer boron phosphide (BP) with two configuration types (BP and BB) investigated by the fifth nearest neighbor tight binding model. The bias voltage and temperature dependence of electronic contribution of the heat capacity, electrical and thermal conductivity, paramagnetic susceptibility and Lorenz number have been investigated using linear response theory. The bias voltage increases the energy band gap in BP configuration while in the BB configuration, the band gap decreases to zero at critical bias voltage and then increases again as the bias increases beyond the critical voltage. For BB configuration type, the thermal properties increases with temperature and the thermal properties is larger for stronger bias voltage in U ≤ 1.0 eV and decreases by further bias increasing in the voltage range U > 1.0 eV. The thermal properties of BP configuration increases linearly with temperature and unlike to BB configuration type, which applying the bias voltage leads to decreasing its thermal properties. The thermal properties of BB configuration type showed more sensitivity to bias and temperature than BP configuration type and their differences increases by increasing the temperature up to 1000 K.

Effect of strain on surface plasmon polaritons of a graphene cladded one-dimensional photonic crystal.

We investigate the dispersion properties of TE-polarized surface plasmon polaritons at the interface of a strained graphene cladded one-dimensional photonic crystal and a homogeneous medium. The optical conductivity of graphene under uniform planar tension is numerically calculated using the perturbation theory and the nearest-neighbor tight-binding approximation. We show that the wavelength, propagation length, and penetration depth of the surface plasmon polaritons in the homogeneous environment and the photonic crystal depend on the magnitude and orientation of the applied strain. Depending on the magnitude and direction of the tension, a Van Hove singularity may appear at the electronic band structure of the graphene in the desired frequency interval. We show that the surface mode corresponding to the Van Hove singularity has the least propagation length. We also observe that strain only affects the penetration depth of the low-frequency surface plasmon polaritons in the homogeneous medium and the high-frequency surface plasmon polaritons in the photonic crystal.

Quantum Boltzmann equation for bilayer graphene

A-B stacked bilayer graphene has massive electron and hole-like excitations with zero gap in the nearest-neighbor hopping approximation. In equilibrium, the quasiparticle occupation approximately follows the usual Fermi-Dirac distribution. In this paper we consider perturbing this equilibrium distribution so as to determine DC transport coefficients near charge neutrality. We consider the regime $\beta |\mu| \lesssim 1$ (with $\beta$ the inverse temperature and $\mu$ the chemical potential) where there is not a well formed Fermi surface. Starting from the Kadanoff-Baym equations, we obtain the quantum Boltzmann equation of the electron and hole distribution functions when the system is weakly perturbed out of equilibrium. The effect of phonons, disorder, and boundary scattering for finite sized systems are incorporated through a generalized collision integral. The transport coefficients, including the electrical and thermal conductivity, thermopower, and shear viscosity, are calculated in the linear response regime. We also extend the formalism to include an external magnetic field. We present results from numerical solutions of the quantum Boltzmann equation. Finally, we derive a simplified two-fluid hydrodynamic model appropriate for this system, which reproduces the salient results of the full numerical calculations.

Unified description of sound velocities in strongly coupled Yukawa systems of different spatial dimensionality

Sound velocities in classical single-component fluids with Yukawa (screened Coulomb) interactions are systematically evaluated and analyzed in one-, two-, and three spatial dimensions (D=1,2,3). In the strongly coupled regime, the convenient sound velocity scale is given by Q2/Δm, where Q is the particle charge, m is the particle mass, n is the particle density, and Δ=n−1/D is the unified interparticle distance. The sound velocity can be expressed as a product of this scaling factor and a dimension-dependent function of the screening parameter, κ=Δ/λ, where λ is the screening length. A unified approach is used to derive explicit expressions for these dimension-dependent functions in the weakly screened regime (κ≲3). It is also demonstrated that for stronger screening (κ≳3), the effect of spatial dimensionality virtually disappears, the longitudinal sound velocities approach a common asymptote, and a one-dimensional nearest-neighbor approximation provides a relatively good estimate for this asymptote. This result is not specific to the Yukawa potential, but equally applies to other classical systems with steep repulsive interactions. An emerging relation to a popular simple freezing indicator is briefly discussed. Overall, the results can be useful when Yukawa interactions are relevant, in particular, in the context of complex (dusty) plasmas and colloidal suspensions.

Confined electron states in two-dimensional HgTe in magnetic field: Quantum dot versus quantum ring behavior

We investigate the electron states and optical absorption in square- and hexagonal-shaped two-dimensional (2D) HgTe quantum dots and quantum rings in the presence of a perpendicular magnetic field. The electronic structure is modeled by means of the $sp^3d^5s^*$ tight-binding method within the nearest-neighbor approximation. Both bulklike and edge states appear in the energy spectrum. The bulklike states in quantum rings exhibit Aharonov-Bohm oscillations in magnetic field, whereas no such oscillations are found in quantum dots, which is ascribed to the different topology of the two systems. When magnetic field varies, all the edge states in square quantum dots appear as quasibands composed of almost fully flat levels, whereas some edge states in quantum rings are found to oscillate with magnetic field. However, the edge states in hexagonal quantum dots are localized like in rings. The absorption spectra of all the structures consist of numerous absorption lines, which substantially overlap even for small line broadening. The absorption lines in the infrared are found to originate from transitions between edge states. It is shown that the magnetic field can be used to efficiently tune the optical absorption of HgTe 2D quantum dot and quantum ring systems.

Kramers-Kronig relations for magnetoinductive waves

Kramers-Kronig relations for propagating modes are a fundamental property of many but not all structures supporting wave propagation. While Kramers-Kronig relations for a transfer function of a causal system are always satisfied, it was discovered in the past that Kramers-Kronig relations for individual modes of a system may fail, e.g., in leaky structures. Our aim in this paper is to scrutinize whether magnetoinductive waves propagating in discrete metamaterial structures by virtue of interelement coupling satisfy Kramers-Kronig relations. Starting with the dispersion relations of magnetoinductive waves in the nearest-neighbor approximation we investigated the real and imaginary parts of two complex functions: the propagation coefficient and the transfer function. In order to show that the real and imaginary parts of these functions are related to each other by the Kramers-Kronig relations we had to modify the functions by deducting from them the values of the functions at infinite frequencies. It was shown that these modified functions and their Kramers-Kronig pairs perfectly coincided. The much more complicated case of magnetoinductive wave propagation with long-range coupling assumed was also investigated. The mode structure was derived for interactions up to the third neighbor. It was shown that the Kramers-Kronig relations are not applicable to the individual modes, but are valid for the transfer functions of the waveguide after solving the excitation problem and taking all the modes into account. Our method can be applied to practically relevant cases enabling rapid evaluation of transfer functions, e.g., in metamaterials used for wireless power transfer.

Nonreciprocal Propagation of Solitons in a Chiral Medium

The evolution of polarization of a light pulse in a system consisting of two-level atoms located on symmetric helices twisted into a bundle has been considered. The interaction of induced dipoles is taken into account by additional third order differential terms in Maxwell’s equations in the nearest neighbor approximation. An integrable generalization of the reduced Maxwell-Bloch equations has been derived under the conditions of almost unidirectional propagation. The analysis of the solutions obtained has shown that the evolution of field pulses critically depends on the direction of their propagation or on the chirality of the medium.

Functional parameter measurements in children with ataxia telangiectasia.

To collect preliminary functional data on ataxia telangiectasia and create a disease specific scale: the Ataxia Telangiectasia Functional Scale (ATFS). Retrospective information on patients with ataxia telangiectasia referred to the Assistive Technology Unit was included. Functional mobility scales (the Gross Motor Function Classification System [GMFCS] and the Functional Mobility Scale [FMS]-5, FMS-50, FMS-500) and activities of daily living [ADL] parameters were recorded. We created a 51-point ATFS, that consisted of three ambulation items adapted for ataxia telangiectasia in the frame of FMS (home, school, outdoors), five ADL items, and one schooling item. Twenty-seven participants (17 males, 10 females; mean age 10y 8mo [SD 5y 1mo], range 1y 9mo-25y 6mo), were enrolled; 168 measurements were recorded. Patients walked at a mean age of 1year 4months (SD 5y 4mo) and lost ambulatory capacity at 8years 8months (SD 2y 1mo). GMFCS level and FMS-5, FMS-50, FMS-500 assessments correlated with age (Spearman's correlations r=0.555, -0.617, -0.639, -0.662 respectively, p<0.01 for all), but plateaued after 12years of age. ATFS mean score was 37.46 (SD 7.88) and increased with age (Spearman's correlation r=0.585, p<0.01). The scale showed threestages of disease progression. In this pilot study we show longitudinal functional data of ambulation and ADL skills in ataxia telangiectasia, and created a framework for a functional scale. This functional scale closely approximated disease course, but further validation is required. The Gross Motor Function Classification System and the Functional Mobility Scale are ill-suited for ataxia telangiectasia assessments. Three functional mobility scales (home, school, outdoors) suited to ataxia telangiectasiawere created. The Ataxia Telangiectasia Functional Scale (ATFS) combines mobility and items of activities of daily living. The ATFS closely approximates the three-stage progression of the disorder.

Electrical conductivity of undoped bilayer Graphene: Beyond nearest neighbor approximation

We have addressed density of states and electrical conductivity of undoped biased bilayer graphene for both AA and AB stacking in the context of tight binding model hamiltonian. The effects of next nearest neighbor hopping amplitude for electrons and gap parameter on electronic density of states and electrical conductivity have been investigated. Green’s function approach has been implemented to find the behavior of electrical conductivity of bilayer graphene within linear response theory. We have found the temperature dependence of electrical conductivity for different values of gap parameter and bias voltage in the presence of neat nearest neighbor hopping integral. Our results for density of states of bilayer graphene in the presence of gap parameter show the increase of bias voltage reduces the band gap width. Also a peak in the dependence of thermal conductivity on temperature has been observed for all physical parameters. An anisotropic behavior for electrical conductivity of unbiased simple bilayer graphene in the presence of gap parameter has been resulted.

Interband transitions in narrow-gap carbon nanotubes and graphene nanoribbons

We use the robust nearest-neighbor tight-binding approximation to study the same footing interband dipole transitions in narrow-bandgap carbon nanotubes (CNTs) and graphene nanoribbons (GNRs). It is demonstrated that curvature effects in metallic single-walled CNTs and edge effects in gapless GNRs not only open up bandgaps, which typically correspond to THz frequencies, but also result in a giant enhancement of the probability of optical transitions across these gaps. Moreover, the matrix element of the velocity operator for these transitions has a universal value (equal to the Fermi velocity in graphene) when the photon energy coincides with the bandgap energy. Upon increasing the excitation energy, the transition matrix element first rapidly decreases (for photon energies remaining in the THz range but exceeding two bandgap energies, it is reduced by three orders of magnitude), and thereafter it starts to increase proportionally to the photon frequency. A similar effect occurs in an armchair CNT with a bandgap opened and controlled by a magnetic field applied along the nanotube axis. There is a direct correspondence between armchair GNRs and single-walled zigzag CNTs. The described sharp photon-energy dependence of the transition matrix element, together with the van Hove singularity at the bandgap edge of the considered quasi-one-dimensional systems, makes them promising candidates for active elements of coherent THz radiation emitters. The effect of Pauli blocking of low-energy interband transitions caused by residual doping can be suppressed by creating a population inversion using high-frequency (optical) excitation.

Interaction of solitons with a qubit in an anisotropic Heisenberg spin chain

The interaction between solitons, propagating in a magnetic chain, with a qubit is studied. The spin chain is described by the Heisenberg model in a nearest-neighbour approximation with anisotropy. The quantum bit (qubit) is modeled by a two level quantum system. The equation for the evolution of the qubit is obtained. The role of the parameters of the soliton for the quantum bit dynamics is investigated. The results are analyzed using a geometrical representation for the qubit as a Bloch sphere.

Soliton-impurity interaction in two coupled ferromagnetic chains

The propagation of soliton excitations in a system of two magnetic chains with impurities is studied. The inhomogeneous chains coupled through ferromagnetic interaction between the opposite spins are described by a Heisenberg model in the nearest-neighbor approximation. The presence of the impurities leads to linear perturbing terms in the evolutionary equations. We investigated numerically the influence of the soliton parameters, the interchain coupling and the defect strength on the soliton dynamics. The conditions of perfect soliton switching are obtained.

Nearest neighbor approximation and the distribution function of "free" electrons over distances and velocities in atomic plasma

Nearest neighbor approximation and the distribution function of "free" electrons over distances and velocities in atomic plasma

On electronic conductance of partially unzipped armchair nanotubes: further analysis

An investigation of the electronic conductance, based on the nearest-neighbor tight-binding approximation for non-interacting π-electrons, is presented for a junction generated by partial unzipping along the zigzag direction of armchair nanotube. An exact solution of the transmission problem has been found through the scalar discrete Wiener–Hopf method, by exploiting a symmetry of the structure for the reduction of 2 × 2 matrix kernel. The electronic probability distribution, far away from the junction on either side of it, is obtained in closed form via mode-matching. As the main result of the paper, an analytical expression for the reflection and transmission coefficients, as well as the scattering matrix, previously obtained via computational methods in earlier studies, is provided using the Chebyshev polynomials. It is found that the highly simplified nearest neighbor tight binding model of the ribbon/tube junction does not allow a mixing of the parity based on even and odd modes. The paper includes several graphical illustrations and analytical derivations.

Optimal Minimum Euclidean Distance-Based Precoder for NOMA With Finite-Alphabet Inputs

Non-orthogonal multiple access (NOMA) scheme with Gaussian input signals, which have no constellation constraint on the input alphabets, has been investigated intensively, whereas the research on finite input constellations is relatively few. This paper focuses on the power allocation in practical NOMA application with finite-alphabet inputs. We propose a practical power allocation scheme for downlink NOMA scenario based on the merit of maximizing the minimum Euclidean distance (MMED) by adopting the constellation-constrained (CC) capacity. Applying the nearest neighbor approximation and Jensen's inequality, we prove that optimal CC capacity can be achieved under the MMED criterion at high signal-to-noise ratio (SNR). Instead of updating power allocation coefficient instantaneously, a preset fixed power factor α MMED derived from the MMED criterion is preferred and thus reduces the complexity of overall system implementation. We take two cases into consideration, namely, Gaussian broadcast channel (GBC) and fading broadcast channel (FBC). We model close channel conditions, which are challenging for conventional NOMA as the GBC scenario, and model near-far effect as well Rayleigh fading as the FBC scenario. In these two cases, we show that the optimal performance can be guaranteed at high SNR without the knowledge of channel state information (CSI). We study the power coefficient pairs for the most commonly used Mary quadrature amplitude modulation (M-QAM) constellations based on the MMED criterion. We explore the relationship between the power allocation coefficients and the sizes of constellations. The numerical simulations on CC sum capacity and capacity regions are provided to validate our analysis.