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At least 865 records · Page 48

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Structural, Elastic, Thermodynamic, Electronic, and Magnetic Investigations of Full-Heusler Compound Ag{sub 2}CeAl: FP-LAPW Method

Structural, elastic, thermodynamic, electronic, and magnetic properties of the full-Heusler compound Ag{sub 2}CeAl were determined using generalized gradient approximation with exchange-correlation functional GGA (PBEsol) with spin-orbit coupling (SOC) correction. The elastic modulus and their pressure dependence are calculated. From the elastic parameter behavior, it is inferred that this compound is elastically stable and ductile in nature. Through the quasi-harmonic Debye model, in which the phononic effect is considered the effect of pressure P (0 to 50) and temperature T (0 to 1000) on the lattice constant, the elastic parameters, bulk modulus B, heat capacity and thermal expansion α, internal energy U, entropy S, Debye temperature 𝜃{sub D}, Helmholtz free energy A, and Gibbs free energy G are investigated. The thermodynamic properties show that the compound Ag{sub 2}CeAl is a heavy fermion material. The density of state (DOS), magnetic momentum, and band structure are computed, to investigate the magnetic and metallic characteristics. The calculated polarization of the compound is 77.34%. The obtained results are the first predictions of the physical properties for the rare-earth-based (Ce) full-Heusler Ag{sub 2}CeAl.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Magneto-electronic and Thermodynamic Properties of Quaternary NiFeMnZ (Z = In, Sn) New Spin Gapless Semiconductors

This paper deals with investigation of magneto-electronic and thermodynamic properties of new spin gapless semiconductor quaternary NiFeMnZ (Z = In, Sn) Heusler alloys. In addition, electronic properties such as band structure and density of states were studied in detail. The obtained results are based on first-principles calculations, using the full potential linearized augmented plane wave (FP-LAPW) method within well-known generalized gradient approximation (GGA) coupling with spin-orbit calculation (SOC) in framework of the density functional theory (DFT) implemented in the WIEN2k package. As results, the alloys were found to be new spin gapless semiconductors (SGSs), and both compounds in LiMgPdSn-type crystal structure are stable. The magnetic moment of NiFeMnIn and NiFeMnSn was 4.39 and 4.99 μ{sub B} per formula unit, respectively. This result is in agreement with the Slater-Pauling rule (M{sub tot} = 24 −Z{sub tot}). Furthermore, the thermodynamic properties were also predicted. All these multifunctionalities lead to crucial interest for developing future spintronics device generations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Quest for the Ultimate Anisotropic Banach Space

We present a new scale U{sub p}{sup t,s} (s<−t<0 and 1≤p<∞) of anisotropic Banach spaces, defined via Paley–Littlewood, on which the transfer operator L{sub g}φ=(g⋅φ)∘T{sup −1} associated to a hyperbolic dynamical system T has good spectral properties. When p=1 and t is an integer, the spaces are analogous to the “geometric” spaces B{sup t,|s+t|} considered by Gouëzel and Liverani (Ergod Theory Dyn Syst 26:189–217, 2006). When p>1 and −1+1/p<s<−t<0<t<1/p, the spaces are somewhat analogous to the geometric spaces considered by Demers and Liverani (Trans Am Math Soc 360:4777–4814, 2008). In addition, just like for the “microlocal” spaces defined by Baladi and Tsujii (Ann Inst Fourier 57:127–154, 2007) (or Faure–Roy–Sjöstrand in Open Math J 1:35–81, 2008), the transfer operator acting on U{sub p}{sup t,s} can be decomposed into L{sub g,b}+L{sub g,c}, where L{sub g,b} has a controlled norm while a suitable power of L{sub g,c} is nuclear. This “nuclear power decomposition” enhances the Lasota–Yorke bounds and makes the spaces U{sub p}{sup t,s} amenable to the kneading approach of Milnor–Thurson (Dynamical Systems (Maryland 1986–1987), Springer, Berlin, 1988) (as revisited by Baladi–Ruelle, Baladi in Dynamical Zeta Functions and Dynamical Determinants for Hyperbolic Maps, Monograph, 2016; Baladi and Ruelle in Ergod Theory Dyn Syst 14:621–632, 1994; Baladi and Ruelle in Invent Math 123:553–574, 1996) to study dynamical determinants and zeta functions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Density Large Deviations for Multidimensional Stochastic Hyperbolic Conservation Laws

We investigate the density large deviation function for a multidimensional conservation law in the vanishing viscosity limit, when the probability concentrates on weak solutions of a hyperbolic conservation law. When the mobility and diffusivity matrices are proportional, i.e. an Einstein-like relation is satisfied, the problem has been solved in Bellettini and Mariani (Bull Greek Math Soc 57:31–45, 2010). When this proportionality does not hold, we compute explicitly the large deviation function for a step-like density profile, and we show that the associated optimal current has a non trivial structure. We also derive a lower bound for the large deviation function, valid for a more general weak solution, and leave the general large deviation function upper bound as a conjecture.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Stochastic Resonance and First Arrival Time for Excitable Systems

We study the noise induced thermally activated barrier crossing of Brownian particles that hop in a piecewise linear potential. Using the exact analytic solutions and via numerical simulations not only we explore the dependence for the first passage time of a single particle but also we calculate the first arrival time for one particle out of N particles. The first arrival time decreases as the number of particles increases as expected. We then explore the thermally activated barrier crossing rate of the system in the presence of time varying signal. The dependence of signal to noise ratio SNR as well as the power amplification (η) on model parameters is explored. η and SNR depict a pronounced peak at particular noise strength. In the presence of N particles, η is considerably amplified as N steps up showing the weak periodic signal plays a vital role in controlling the noise induced dynamics of the system. Moreover, for the sake of generality, the viscous friction γ is considered to decrease exponentially when the temperature T of the medium increases (γ=Be{sup −AT}) as proposed originally by Reynolds (Philos Trans R Soc Lond 177:157, 1886).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Derivation of the Time Dependent Two Dimensional Focusing NLS Equation

We present a microscopic derivation of the two-dimensional focusing cubic nonlinear Schrödinger equation starting from an interacting N-particle system of Bosons. The interaction potential we consider is given by W{sub β}(x)=N{sup −1+2β}W(N{sup β}x) for some spherically symmetric and compactly supported potential W∈L{sup ∞}(ℝ{sup 2},ℝ). The class of initial wave functions is chosen such that the variance in energy is small. Furthermore, we assume that the Hamiltonian H{sub W{sub β,t}}=−∑{sub j=1}{sup N}Δ{sub j}+∑{sub 1≤j 2, or in trace norm, for more general external potentials. For trapping potentials of the form A(x)=C|x|{sup s} ,C>0, the condition H{sub W{sub β,t}}≥− CN can be fulfilled for a certain class of interactions W{sub β}, for all 0<β<((s+1)/(s+2)), see Lewin et al. (Proc Am Math Soc 145:2441–2454, 2017).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Impact of biochar application on nitrogen nutrition of rice, greenhouse-gas emissions and soil organic carbon dynamics in two paddy soils of China

Two field microcosm experiments and 15N labeling techniques were used to investigate the first-year effects of biochar addition on rice N nutrition and GHG emissions in an Inceptisol and an Ultisol. Biochar N bioavailability and effect of biochar on fertilizer nitrogen-use efficiency (NUE) were studied by 15N-enriched wheat biochar (7.8803 atom% 15N) and fertilizer urea (5 atom% 15N) (Experiment I). Corn biochar and corn stalks were applied at 12 Mg ha-1 to study their effects on GHG emissions (Experiment II). Biochar had no significant impact on rice production and less than 2% of the biochar N was available to plants in the first season. Biochar addition increased soil C and N contents and decreased urea NUE.. Seasonal cumulative CH4 emissions with biochar were similar to the controls, but significantly lower than the local practice of straw amendment. Soil emissions of N2O with biochar amendment were similar to the control in the acidic Ultisol, but significantly higher in the slightly alkaline Inceptisol. Carbon-balance calculations found no major losses of biochar-C. Low bio-availability of biochar N did not make a significant impact on rice production or N nutrition during the first year.. Replacement of straw amendments with biochar could decrease CH4 emissions and increase SOC stocks.

agriculture↗

Simulated Temperature Programmed Desorption of Acetaldehyde on CeO 2 (111): Evidence for the Role of Oxygen Vacancy and Hydrogen Transfer

The temperature programmed desorption of acetaldehyde adsorbed on partially reduced CeO 2 (111) has been studied in detail using microkinetic modeling based on self-consistent, periodic density functional theory calculations at the GGA-PW91+U level. Previous experimental studies (Chen et al. J. Phys. Chem. C 115: 3385, 2011; Calaza et al. J. Am. Chem. Soc. 134: 18034, 2012) have shown that, whereas on fully oxidized CeO 2 (111) acetaldehyde desorbs molecularly with a peak temperature of 210 K, the polymerization and enolization of acetaldehyde dominate the surface reactivity on partially reduced CeO 2 (111), resulting in acetaldehyde desorption at higher temperatures. Here we propose a comprehensive reaction mechanism that is consistent with the spectroscopic evidence of the identities of the surface intermediates and with the observed desorption activities, including the formation of ethylene and acetylene. Besides acetaldehyde (CH 3 CHO) and its enolate (CH 2 CHO), several other C 2 H x O species are proposed as key intermediates which are not seen spectroscopically, including ethoxy (CH 3 CH 2 O), ethyleneoxy (CH2CH2O), and formylmethylene (CHCHO). Our study suggests that oxygen vacancies play the critical role of activating the carbonyl bond and thereby facilitating b C–H bond scissions in acetaldehyde, leading to enolization, intermolecular hydrogen transfer, deoxygenation, and potentially C–C coupling reactions.

Zhao, Chuanlin↗

A W-Geometry Ortho-TOF MS with High Resolution and Up to 100% Duty Cycle for MS/MS

Orthogonal injection time-of-flight (orthoTOF) mass spectrometry (MS) is the most prevalent form of TOFMS, owing to its greater control over incoming ion energy, the ability to correct for aberrations in incoming ion velocity and position, and its ability to provide an entire mass spectrum within a single scan. However, the duty cycle of orthoTOFMS is low compared with scanning analyzers, which can have 100% duty cycle when measuring a single type of ion. Typical duty cycles for orthoTOFMS range from 1% to 30%, depending on instrument geometry. Generally, as instrument resolution increases, duty cycle decreases. Additionally, the greatest duty cycle is achieved for the highest m/z ion recorded in the spectrum, and decreases for all other ions as a function of m/z. In a prior publication [Loboda, A.V.; Chernushevich, I.V. J. Am. Soc. Mass Spectrom. 20, 1342–1348 (20)], a novel trapping/release method for restoring the duty cycle of a V-geometry orthoTOFMS to near 100% (referred to as “Zeno pulsing”) was presented. Here, we apply that method to a W-TOF geometry analyzer with analog detection. Across a m/z range of 100–2000, sensitivity gains of ~5–20 are observed, for total ion currents approaching ~10{sup 7} ions·s{sup −1}. Zeno pulsing, or similar strategies for restoring duty cycle, will continue to be important as instrument resolution in orthoTOFMS is increased through the use of ion mirrors. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Easy, Fast, and Reproducible Quantification of Cholesterol and Other Lipids in Human Plasma by Combined High Resolution MSX and FTMS Analysis

Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and for the monitoring of metabolic health. Here, we compared the performance of three mass spectrometric approaches available for direct detection and quantification of cholesterol in extracts of human plasma. These approaches are high resolution full scan Fourier transform mass spectrometry (FTMS) analysis, parallel reaction monitoring (PRM), and novel multiplexed MS/MS (MSX) technology, where fragments from selected precursor ions are detected simultaneously. Evaluating the performance of these approaches in terms of dynamic quantification range, linearity, and analytical precision showed that the MSX-based approach is superior to that of the FTMS and PRM-based approaches. To further show the efficacy of this approach, we devised a simple routine for extensive plasma lipidome characterization using only 8 μL of plasma, using a new commercially available ready-to-spike-in mixture with 14 synthetic lipid standards, and executing a single 6 min sample injection with combined MSX analysis for cholesterol quantification and FTMS analysis for quantification of sterol esters, glycerolipids, glycerophospholipids, and sphingolipids. Using this simple routine afforded reproducible and absolute quantification of 200 lipid species encompassing 13 lipid classes in human plasma samples. Notably, the analysis time of this procedure can be shortened for high throughput-oriented clinical lipidomics studies or extended with more advanced MS{sup ALL} technology (Almeida R. et al., J. Am. Soc. Mass Spectrom. 26, 133–148 [1]) to support in-depth structural elucidation of lipid molecules. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Influence of Background H{sub 2}O on the Collision-Induced Dissociation Products Generated from [UO{sub 2}NO{sub 3}]{sup +}

Developing a comprehensive understanding of the reactivity of uranium-containing species remains an important goal in areas ranging from the development of nuclear fuel processing methods to studies of the migration and fate of the element in the environment. Electrospray ionization (ESI) is an effective way to generate gas-phase complexes containing uranium for subsequent studies of intrinsic structure and reactivity. Recent experiments by our group have demonstrated that the relatively low levels of residual H{sub 2}O in a 2-D, linear ion trap (LIT) make it possible to examine fragmentation pathways and reactions not observed in earlier studies conducted with 3-D ion traps (Van Stipdonk et al. J. Am. Soc. Mass Spectrom. 14, 1205–1214, 2003). In the present study, we revisited the dissociation of complexes composed of uranyl nitrate cation [U{sup VI}O{sub 2}(NO{sub 3})]{sup +} coordinated by alcohol ligands (methanol and ethanol) using the 2-D LIT. With relatively low levels of background H{sub 2}O, collision-induced dissociation (CID) of [U{sup VI}O{sub 2}(NO{sub 3})]{sup +} primarily creates [UO{sub 2}(O{sub 2})]{sup +} by the ejection of NO. However, CID (using He as collision gas) of [U{sup VI}O{sub 2}(NO{sub 3})]{sup +} creates [UO{sub 2}(H{sub 2}O)]{sup +} and UO{sub 2}{sup +} when the 2-D LIT is used with higher levels of background H{sub 2}O. Based on the results presented here, we propose that product ion spectrum in the previous experiments was the result of a two-step process: initial formation of [U{sup VI}O{sub 2}(O{sub 2})]{sup +} followed by rapid exchange of O{sub 2} for H{sub 2}O by ion-molecule reaction. Our experiments illustrate the impact of residual H{sub 2}O in ion trap instruments on the product ions generated by CID and provide a more accurate description of the intrinsic dissociation pathway for [U{sup VI}O{sub 2}(NO{sub 3})]{sup +}. .

74 ATOMIC AND MOLECULAR PHYSICS↗

Nonreciprocal spin-wave propagation in YIG/GGG: a limit on the DMI parameter

Materials with low damping, such as Yttrium Iron Garnet (YIG), are of interest in connection with spintronic devices. A promising structure for information storage is the Skyrmion, a domain wall quasi-particle. It has been shown that the stabilization of a Skyrmion can be energetically favorable with the addition of spin-orbit coupling (SOC) through the Dzyaloshinsky-Moriya Interaction (DMI). This interaction should be largest in metals, but still present in insulators. In order to produce spintronic devices using YIG, we must evaluate the DMI interaction inherent in the substrate used to grow the YIG, which is generally Gadolinium Gallium Garnet (GGG). In this study, we measure nonreciprocal spin wave propagation in a thick YIG film in order to place a limit on the DMI parameter in a YIG/GGG bilayer.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

An Analysis of FPGA LUT Bias and Entropy for Physical Unclonable Functions

Process variations within Field Programmable Gate Arrays (FPGAs) provide a rich source of entropy and are therefore well-suited for the implementation of Physical Unclonable Functions (PUFs). However, careful considerations must be given to the design of the PUF architecture as a means of avoiding undesirable localized bias effects that adversely impact randomness, an important statistical quality characteristic of a PUF. Here in this paper, we investigate a ring-oscillator (RO) PUF that leverages localized entropy from individual look-up table (LUT) primitives. A novel RO construction is presented that enables the individual paths through the LUT primitive to be measured and isolated at high precision, and an analysis is presented that demonstrates significant levels of localized design bias. The analysis demonstrates that delay-based PUFs that utilize LUTs as a source of entropy should avoid using FPGA primitives that are localized to specific regions of the FPGA, and instead, a more robust PUF architecture can be constructed by distributing path delay components over a wider region of the FPGA fabric. Compact RO PUF architectures that utilize multiple configurations within a small group of LUTs are particularly susceptible to these types of design-level bias effects. The analysis is carried out on data collected from a set of identically designed, hard macro instantiations of the RO implemented on 30 copies of a Zynq 7010 SoC.

97 MATHEMATICS AND COMPUTING↗

Effect of spin rotation coupling on spin transport

We have studied the spin rotation coupling (SRC) as an ingredient to explain different spin-related issues. This special kind of coupling can play the role of a Dresselhaus like coupling in certain conditions. Consequently, one can control the spin splitting, induced by the Dresselhaus like term, which is unusual in a semiconductor heterostructure. Within this framework, we also study the renormalization of the spin-dependent electric field and spin current due to the k{sup →}⋅p{sup →} perturbation, by taking into account the interband mixing in the rotating system. In this paper we predict the enhancement of the spin-dependent electric field resulting from the renormalized spin rotation coupling. The renormalization factor of the spin electric field is different from that of the SRC or Zeeman coupling. The effect of renormalized SRC on spin current and Berry curvature is also studied. Interestingly, in the presence of this SRC-induced SOC it is possible to describe spin splitting as well as spin galvanic effect in semiconductors. -- Highlights: •Studied effect of spin rotation coupling on the spin electric field, spin current and Berry curvature. •In the k{sup →}⋅p{sup →} framework we study the renormalization of spin electric field and spin current. •For an inertial system we have discussed the spin splitting. •Expression for the Berry phase in the inertial system is discussed. •The inertial spin galvanic effect is studied.

74 ATOMIC AND MOLECULAR PHYSICS↗

A highly efficient and durable air electrode for intermediate-temperature reversible solid oxide cells

Solid oxide cells (SOCs) are considered the most efficient system for reversible conversion between chemical and electrical energy, thus having potential to be an attractive technology for a sustainable energy future. To achieve high round-trip efficiency, highly efficient and durable air electrode materials are needed to minimize energy loss associated with oxygen reduction reaction (ORR) and oxygen evolution reaction (OER). Here we report a bi-functional air electrode material, PrBa 0.9 Co 1.96 Nb 0.04 O 5+δ , demonstrating outstanding electrochemical performance (e.g., achieving peak power densities of over 1.5 and 1 W cm –2 , respectively, for Gd 0.1 Ce 0.9 O 1.95 and BaZr 0.1 Ce 0.7 Y 0.1 Yb 0.1 O 3-δ based fuel cells at 600 °C) while maintaining excellent stability (e.g., having a degradation rate of 40 mV per 1,000 h for H 2 O electrolysis cells). Finally, the excellent property of the new electrode is attributed to the improved stability from Nb doping and the enhanced electrocatalytic activity from tuning Ba deficiency, as confirmed by experimental results and computational analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modelling wind power spatial-temporal correlation in multi-interval optimal power flow: A sparse correlation matrix approach

The significantly increasing deployment of wind power necessitates that system operation considers the spatial-temporal correlation of power forecast from different wind power plants. How to model this spatial-temporal correlation in the actual system dispatch is challenging. In this paper, a sparse correlation matrix is utilized to efficiently model the spatial-temporal correlation of wind power forecast in the generation dispatch model. A novel, adjustable, and distributionally-robust chance-constrained multi-interval optimal power flow (ADRCC-MIOPF) model is proposed to obtain reliable economic dispatch (ED) solutions. The spatial-temporal correlation of wind power plants power forecasts is represented by the sparse correlation covariance matrix obtained from historical, time series wind power forecast error data. The chance constraints in the ADRCC-MIOPF model are transformed into a set of second-order-cone (SOC) constraints in which an adjustable coefficient in the chance constraints controls the robustness of the ADRCC-MIOPF model to the wind power forecast errors distribution. Case studies performed on the PJM 5-bus system and IEEE 118-bus system verify the proposed method to improve the system security and reduce the cost especially under the high wind penetration levels. All the cases can be solved within several minutes for both the small and large cases which validates the efficiency of the proposed sparse matrix model. In addition, considering the spatial-temporal correlation of wind power forecast and the distributional robustness of wind power forecast error leads to a more reliable economic dispatch with lower system violations.

17 WIND ENERGY↗

Battery state of health monitoring by estimation of the number of cyclable Li-ions

Herein this paper introduces a method to monitor battery state of health (SOH) by estimating the number of cyclable Li-ions, a health-relevant electrochemical variable. SOH monitoring is critical to battery management in balancing the trade-off between maximizing system performance and minimizing battery degradation. The decrease of cyclable Li-ions indicates the effect on the SOH of degradation mechanisms that consume cyclable Li-ions. The unavailability of the number of cyclable Li-ions through non-invasive measurements makes its estimation necessary for in-situ SOH monitoring. In this paper, the extended Kalman filter (EKF) is used to estimate the number of cyclable Li-ions as an unknown battery parameter. The single particle model (SPM), a simplified battery electrochemical model, is used as the model in the EKF to achieve a computational complexity suitable for on-line estimation. Simulations are performed under typical electric vehicle current trajectories using an example parameter set for a hybrid-electric-vehicle battery. In the simulations, the battery is represented by the Doyle–Fuller–Newman (DFN) model, an electrochemical model with higher fidelity than the SPM. To comply with the practice, instead of using the same parameters as the DFN model in the SPM, parameterization of the SPM is performed before estimation of the number of cyclable Li-ions. The simulations show high estimation accuracy of the number of cyclable Li-ions using the EKF, even with the structural and parametric differences between the DFN model and the SPM, under both the ideal conditions and various non-ideal conditions (i.e., SOC estimation error, additional modeling error, and measurement noise).

25 ENERGY STORAGE↗