High-energy Modes Research Articles

Double Proteolysis for N- and O-glycan Analysis of Fc-fusion Protein Etanercept

Introduction. Highly glycosylated proteins are the most abundant class of modern biopharmaceuticals. A majority of such therapeuticals produced by Russian biopharmaceutical companies is biosimilars. The foundation of biosimilar manufacturing is analytical assessment of structure equivalence to an original molecule. Fc-fusions present a challenge due to their structural properties. The only biosimilar of this kind registered in Russia is etanercept – a fusion of tumor necrosis factor receptor α and Fc-fragment of IgG1. Existing approaches widely used in protein analysis do not allow accurate and reliable description of glycoylation of these proteins. Development of new approaches and principles of such analysis is necessary, as the changes in biosimilar’s molecular structure can seriously affect its efficacy and safety.Aim. Development of double proteolysis approaches for glycopeptide mapping of Fc-fusion protein etanercept using Arg-C protease.Materials and methods. Etanercept was subjected to enzymatic hydrolysis using trypsin in combination with Arg-C or Asp-N. The resulting peptides were analyzed using HPLC-MS system Xevo G2-XS QTOF (Waters Corporation, USA). The conformation of glycan structure was performed via analysis of fragment spectra of glycopeptides, acquired with high collision energy mode (MS E ). UNIFI (version 1.8) with biopharmasuetical assessment setting (Waters Corporation, USA) was used to analyze the peptide maps.Results and discussion. It was found that using the combination of trypsin with protease Arg-C leads to reliable results Using the developed approach we successfully determined the majority of O-glycosylation sites and types of O-glycans. It was shown that for an effective O-glycopeptide maping N-deglycosylation stage is required. Most abundant N-glycan structures were identified for each of three N-glycosylation sites (N149, N171, N317). It was determined, that the combination of trypsin with Arg-C allows identification of three-antenna forms despite the presence of O-glycosylation site on the analyzed peptide. General N-glycosylation profile shows comparability of results for both approaches.Conclusion. As a result of this research we developed glycopeptide mapping approaches in which a combination of proteases is used. Using these methods sites of N- and O-glycosilation and glycofoms of etanercept were accurately and reproducibly determined. Developed procedures can be applied to other types of Fc-fusion proteins, making it of broader appeal and benefit to the overall biopharmaceutical industry. These approaches provide comprehensive information useful for structure-function studies and of potential value for product comparability measurements and possibly even future manufacturing control strategies.

High-performance thin-film lithium niobate electro-optic modulator based on etching slot andultrathin silicon film.

An electro-optic modulator (EOM) is an indispensable component to connect the electric and optical fields. Here, we propose a high-performance, thin-film lithium niobate-based EOM, where the modulation waveguide is formed by an etching slot on the lithium niobate film and the deposit of an ultrathin silicon film in the slot region. Therefore, a small mode size and high mode energy can be simultaneously achieved in the LN region with a high EO coefficient, which will be beneficial to increase the EO overlap and gradually decrease in the mode size. Further, we employed a waveguide structure to construct a typical Mach-Zehnder interference-type EOM. According to the requirements of high-speed traveling wave modulation, we conduct the index matching, impedance matching, and low-loss operation. From the results, the key half-wave voltage length product and 3dB modulation bandwidth are, respectively, 1.45Vcm and 119GHz in a modulation length of 4mm. Moreover, a larger 3dB bandwidth also can be achieved by shortening the modulation length. Therefore, we believe the proposed waveguide structure and EOM will provide new ways to enhance the performance of LNOI-based EOMs.

Influence of Quantum Oscillations in the Thermal Scattering Law of Zirconium Carbide on Neutron Thermalization and Criticality

Zirconium carbide (ZrC) is a candidate material for advanced high temperature reactors, including space nuclear thermal propulsion applications. Thermal scattering laws (TSLs) are generated in the incoherent approximation for carbon bound in ZrC [C(ZrC)] and zirconium bound in ZrC [Zr(ZrC)], using ab initio lattice dynamics methods. Disordered alloy theory is introduced to improve treatment of isotopic composition within the elastic scattering cross section. Localized higher-energy vibrational modes and the presence of a phonon band gap in C(ZrC) cause quantized oscillation in the TSL atypical of nonhydrogenous solids. These oscillations yield a significant likelihood of large energy downscattering and upscattering interactions such that the quanta of energy transfer affecting neutron thermalization is substantially greater than classically expected. MC21 critical mass calculations of ZrC mixtures with high-enriched uranium demonstrate an impact of TSLs when compared to a free-gas treatment for thermal neutron–driven 235U loadings. The critical mass of homogenous mixed moderator systems of ZrC and reactor-grade graphite are also sensitive to the ZrC TSL. Moreover, the effect of quantized energy exchange on the neutron spectra is found to influence the temperature feedback coefficient.

Electronic Origin of Laser-Induced Ferroelectricity in SrTiO3.

Although ultrafast control of the nonthermally driven ferroelectric transition of paraelectric SrTiO3 was achieved under laser excitation, the underlying mechanism and dynamics of the photoinduced phase transition remain ambiguous. Here, the determinant formation mechanism of ultrafast ferroelectricity in SrTiO3 is traced by nonadiabatic dynamics simulations. That is, the selective excitation of multiple phonons, induced by photoexcited electrons through the strong correlation between electronic excitation and lattice distortion, results in the breaking of the crystal central symmetry and the onset of ferroelectricity. The accompanying population transition between 3dz2 and 3dx2-y2 orbitals excites multiple phonon branches, including the two high-energy longitudinal optical modes, so as to drive the titanium ion away from the center of the oxygen octahedron and generate a metastable ferroelectric phase. Our findings reveal a cooperative electronic and ionic driving mechanism for the laser-induced ferroelectricity that provides new schemes for the optical control of ultrafast quantum states.

Exploring Platinum Speciation with X-ray Absorption Spectroscopy under High-Energy Resolution Fluorescence Detection Mode

Critical to interpreting platinum chemical speciation using X-ray absorption spectroscopy (XAS) is the availability of reference spectra of compounds with known Pt redox and coordination. Here we compare different techniques for Pt LIII-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectral regions for a large set of Pt-O-Cl-S reference compounds of known structures. The measurements were conducted in HERFD (high-energy resolution fluorescence detection, high-resolution or HR) mode, as well as in two conventional modes such as transmission (TR) and nominal-resolution total fluorescence yield (TFY or NR). Samples analyzed here included Pt0 (TR), PtIIS (HR), PtIVS2 (TR), K2PtIICl4 (HR + TR), K2PtIVCl6 (HR + TR), PtIVO2 (HR + TR), C6H12N2O4PtII (HR + TR), and aqueous solutions of K2PtIICl4 and H2PtIVCl6 (NR + TR), as well as (NH4)2PtIV(S5)3 (HR + TR). XANES spectra in HERFD mode offer a better energy resolution than in conventional modes, allowing a more accurate identification of Pt redox state and coordination geometry. EXAFS spectra in all three modes for a given compound yield identical within errors values of Pt-neighbor interatomic distances and mean square relative displacement (MSRD, σ2) parameters. In contrast, both TR and NR spectra on the one hand and HR spectra on the other hand yield distinct amplitude reduction factor (S02) values, 0.76 ± 0.04 and 0.99 ± 0.07 (1 standard error), respectively. This study contributes to the development of an open-access XAS database SSHADE.

Modal analysis of compressor cascades with sweeping jet actuator and pulsed jet for active flow control based on large Eddy simulation

This study utilized large eddy simulation (LES) to explore the mitigation effects of endwall pulsed jet (PJ) and suction-surface sweeping jet actuator (SJA) controls on corner separation. Two modal analysis methods, proper orthogonal decomposition (POD) and dynamic modal decomposition (DMD), were applied to extract the main structures in the flow field and to analyze the mechanism of the effect of an unsteady jet on flow separation. First, LES was first performed in a linear cascade to capture the pulsating information in the flow field. The spectral analysis shows the dominance of the shedding vortex dynamic feature in the measured position of the original scheme. Furthermore, the dominant flow pattern in the flow field was obtained using POD. Both unsteady jet schemes made the energy distribution in the decomposed reconstructed flow field of the POD more dispersed than that in the origin. However, POD loses the actual physical meaning of the eigenvalues and corresponding modes of that order when finding the optimal orthogonal basis. Therefore, this study used DMD to retain information reflecting the time-evolution process. The magnitude of each order of energy corresponded to the characteristic frequency of the flow field. The highest energy modal frequency was consistent with the jet frequency for both jet schemes. The results of the modal analysis showed that the PJ and its induced small-scale flow structures dominate most of the higher energy modes. These small-scale flow structures inhibit the development of transverse secondary flows at the endwall. In comparison, the dominant flow-field structure using the SJA is a large-scale streamwise vortex. The sweeping jet accelerates the corner low-energy fluid over a broader area by the induced streamwise vortex itself, thus controlling the corner separation.

Rindler bulk reconstruction and subregion duality in AdS/CFT

In this paper, we study the AdS-Rindler reconstruction. The CFT operators naively given by the holographic dictionary for the AdS-Rindler reconstruction contain tachyonic modes, which are inconsistent with the causality and unitarity of the CFT. Therefore, the subregion duality and the entanglement wedge reconstruction do not hold. We also find that the tachyonic modes in the AdS-Rindler patch lead to arbitrary high-energy or trans-Planckian modes in the global AdS. It means that the mode expansion of the Rindler patch is sensitive to the UV limit of the theory, that is, quantum gravity. In addition, the tachyonic modes are related to the existence of null geodesics connecting the past and future horizons.

Turbulent Transition of a Flow from Small to O(1) Rossby Numbers

Abstract Oceanic flows are energetically dominated by low vertical modes. However, disturbances in the form of atmospheric storms, eddy interactions with various forms of boundaries, or spontaneous emission by coherent structures can generate weak high-baroclinic modes. The feedback of the low-energy high-baroclinic modes on large-scale energetically dominant low modes may be weak or strong depending on the flow Rossby number. In this paper we study this interaction using an idealized setup by constraining the flow dynamics to a high-energy barotropic mode and a single low-energy high-baroclinic mode. Our investigation points out that at low Rossby numbers the barotropic flow organizes into large-scale coherent vortices via an inverse energy flux while the baroclinic flow accumulates predominantly in anticyclonic barotropic vortices. In contrast, with increasing Rossby number, the baroclinic flow catalyzes a forward flux of barotropic energy. The barotropic coherent vortices decrease in size and number, with a strong preference for cyclonic coherent vortices at higher Rossby numbers. On partitioning the flow domain into strain-dominant and vorticity-dominant regions based on the barotropic flow, we find that at higher Rossby numbers baroclinic flow accumulates in strain-dominant regions, away from vortex cores. Additionally, a major fraction of the forward energy flux of the flow takes place in strain-dominant regions. Overall, one of the key outcomes of this study is the finding that even a low-energy high-baroclinic flow can deplete and dissipate large-scale coherent structures at O(1) Rossby numbers.

Quantifying the surface modification induced by the argon cluster ion bombardment of KGd(WO4)2: Nd single crystal

The damage in an inorganic single crystal surface caused by gas cluster ion bombardment is still an open issue. In this work, the influence of the kinetic energy per atom in the clusters E/N on the physicochemical structure of KGd(WO4)2:Nd single crystals was evaluated using XPS, Raman spectroscopy and XRD techniques. The high-energy mode with an energy per atom in the cluster E/N of about 100 eV provides a sufficient sputtering efficiency, while the low-energy mode with an energy of a several eV provides the minimal surface damage. The results revealed no substantial damage to the subsurface crystal structure after the cluster bombardment processing. Nevertheless, the unexpected increase in the relative concentration of O atoms by 12% and depletion of K atoms by a factor of 2 in the subsurface layer of KGd(WO4)2:Nd crystals were detected. The features of surface sputtering of inorganic single crystals at different E/N-modes are discussed.

Holographic Einstein ring of a charged AdS black hole

Taking into account that the real quantum materials are engineered generically at a finite chemical potential, we investigate the Einstein ring structure for the lensed response of the complex scalar field as a probe wave on the charged AdS black hole in the context of AdS/CFT. On the one hand, we find that the resulting Einstein ring radius has no variation with the chemical potential, which is similar to the behavior for the weakly interacting quantum system. On the other hand, not only can such a ring exist well within the screen, but also the temperature dependence of its radius exhibits a distinct feature in the sense that it displays an appreciable increase at low temperatures while the ring keeps unchanged right at the edge of the screen for the weakly interacting system. Note that such a Einstein ring emerges in the large frequencies and can be well captured by the photon sphere away from the black hole horizon in the geometric optics approximation, thus such a distinct feature may be regarded as a universal behavior associated with the high energy modes of the strongly coupled system which has a gravity dual.

Autotoxicity of Endogenous Organic Acid Stress in Two Ganoderma lucidum Cultivars.

Ganoderma lucidum has been used as a rare medical mushroom for centuries in China, due to its health-promoting properties. Successive cropping obstacles are common in the cultivation of G. lucidum, although the remaining nutrients in the germ substrate are sufficient for a second fruiting. Here, we aimed to study the metabolite profile of G. lucidum via nontargeted metabonomic technology. Metabonomic data revealed that organic acids played an important role in the cropping obstacles of G. lucidum, which is accordance with the pH decrease in the germ substrate. A Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis indicated that most differential acids participated in the metabolic pathways. Five acids were all significantly upregulated by two MS with high energy (MSE) modes in two cultivars, among which 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylic acid is also involved in purine metabolism regulation and microbial metabolism in diverse environments. Taken together, this work illustrated the organic acid stress generated by G. lucidum, which formed the autotoxicity feedback, and resulted in cropping obstacles. Determining the cause of the cropping obstacles in G. lucidum will promote the utilization rate of fungus substrate to realize the sustainable use of this resource.

Phase diagram and magnetic excitations of J1–J3 Heisenberg model on the square lattice

We study the phase diagram and the dynamical spin structure factor of the spin-1/2 ${J}_{1}--{J}_{3}$ Heisenberg model on the square lattice using density matrix renormalization group, exact diagonalization (ED), and cluster perturbation theory (CPT). By extrapolating the order parameters and studying the level crossings of the low-lying energy and entanglement spectra, we obtain the phase diagram of this model and identify a narrow region of quantum spin liquid (QSL) phase followed by a plaquette valence-bond solid (PVBS) state in the intermediate region, whose nature has been controversial for many years. More importantly, we use CPT and ED to study the dynamical spin structure factor in the QSL and the PVBS phase. In the QSL phase, the high-energy magnon mode completely turns into some dispersive weak excitations around the $X$ and $M$ points. For the PVBS phase, the low-energy spectrum is characterized by a gapped triplet excitation, and at the high energy, we find another branch of dispersive excitation with broad continua, which is unlike the plaquette phase in the $2\ifmmode\times\else\texttimes\fi{}2$ checkerboard model. In the latter case, the second branch of excitation is nearly flat due to the weak effective interactions between the local excitations of the plaquettes. And in the ${J}_{1}--{J}_{3}$ Heisenberg model, the uniform interactions and the spontaneously translational symmetry breaking of the PVBS phase make the difference in the excitation spectra.

The effect of electrospark deposition using zirconium electrodes on structure and properties of nickel-containing alloy obtained selective laser melting

Protective coatings were applied by electrospark deposition (ESD) using zirconium electrodes to improve the performance of the Ni-containing alloy obtained using the selective laser melting (SLM) technology. The kinetics of mass transfer was studied in 5 different frequency-energy processing modes. An analog-to-digital converter was used to determine the average number of pulse discharges, single-pulse energy, and the total energy of pulse discharges for 1 min of processing (ΣЕ) for all the modes used. In low-energy processing modes (ΣЕ = 1459÷2915 J), a weak mass transfer was observed, and the cathode weight gain was recorded only in the first minutes. As the processing time increased, a decrease in the substrate weight was observed. The roughness of coatings (Ra) varied in the range of 3.9–7.2 μm. In high-energy modes (ΣЕ = 5197÷17212 J), due to intense electrode heating, a steady cathode weight gain was observed, but the formed coatings featured by increased roughness: Ra = 7.4÷8.6 μm. The Ra parameter for the original SLM samples was 10.7 μm. The formed coatings featured by a thickness of 15–30 μm, high continuity (up to 100 %), hardness of 9.0–12.5 GPa, elastic modulus of 122–145 GPa, and friction coefficient of 0.36–0.49. The ESD processing promoted an increase in wear resistance of the SLM alloy by 7.5–20 times, and oxidation resistance by 10–20 % (t = 1150 °C, τ = 30 h). It was found that the coating obtained in the low-energy ESD mode with energy ΣЕ = 2915 J featured the best performance (hardness, modulus of elasticity, roughness, wear resistance and oxidation resistance).

Changes in the hydrogen nuclear kinetic energy across the several phases of methylammonium lead tribromide.

We present an experimental investigation of methylammonium lead tribromide single crystals in the orthorhombic, tetragonal, and cubic phases based on inelastic and deep inelastic neutron scattering experiments. We show how the average hydrogen nuclear kinetic energy, mainly affected by zero-point vibrational energies, shows differences larger compared to the changes simply related to temperature effects when moving from one phase to another. In particular, the Gaussian contribution to the average nuclear kinetic energy is larger in the tetragonal phase compared to the cubic and orthorhombic ones. Moreover, we find that the vibrational densities of states of MAPbBr3 single crystals in the orthorhombic phase are compatible with previously reported results on powder samples, and that the only vibrational modes that show slightly different frequencies compared to MAPbI3 are those in the energy range between 100 and 300cm-1, related to librational/rotational modes. As these shifts are of about 10cm-1 and do not affect any higher-energy vibrational mode, we conclude that the zero-point energies and average nuclear kinetic energies in the two-hybrid organic/inorganic perovskites are expected to be approximately the same within a harmonic framework.

Monte Carlo Simulation and Experimental Determination of Tissue Phantom Ratio for Photon Beams delivered from Medical Linear Accelerator

For an external radiotherapy procedure, the tissue phantom ratio (TPR20,10) is used as a quality index. This work presents an estimate of TPR20,10 using two cylindrical ionization chambers (NE2571 Farmer and PTW30013) in three high-energy photon modes (6, 10 and 15 MV) using both the Monte Carlo (MCNP) process and the experimental setup. The MCNP (version MCNP5) was used for the simulation of photon beams delivered by Varian-2300CD for the determination of TPR20,10 according to technical report series (TRS) 398. Again applying the same protocol TPR20,10 values were measured experimentally with NE2571 Farmer and PTW30013 chambers for the same medical linear accelerator (LINAC). The differences of TPR20, 10 between MCNP and experimental values were found for NE2571 Farmer chamber within 4.17 percent, 2.9 percent and 2.5 percent and similarly, these were within 3.89 percent, 2.71 percent and 1.98 percent at 6, 10 and 15 MV respectively for PTW30013. The TPR20,10 values simulated by our calculated MCNP demonstrated strong agreement with our experimental results.

Origin of Protein Quake: Energy Waves Conducted by a Precise Mechanical Machine.

A long-standing challenge in protein biophysics is to understand protein quake in myoglobin─the structural dynamics responsible for redistributing the excess heme energy after photolysis. Despite extensive efforts, the molecular mechanism of this process remains elusive. Using the energy flow theory, we uncovered a fundamental new phenomenon: the heme energy is redistributed by sinusoidal waves with a ubiquitous fundamental frequency and two overtones. The energy waves emanate from the heme into the myoglobin backbone via a conduit of five consecutive dihedrals of the proximal histidine and then travel quickly along the backbone to reach sidechains across the protein. This mechanism is far more effective than the diffusion-based mechanism from previous studies because waves are systematic while diffusion is random. To propagate energy waves, coordinates must cooperate, resulting in collective modes that are singular vectors of the generalized work functional. These modes show task partitioning: a handful of high-energy modes generate large-scale breathing motion, which loosens up the protein matrix to enable hundreds of low-energy vibrational modes for energy transduction.

Halalopathy: Stimulation of the Immune System Through Enrichment of Potential Energy

The human mind is highly exposed to different sources of information. According to halalopathy, supportive information enriches potential, while distracting information increases entropy. Potential energy and entropy are inversely proportional. The enrichment of potential energy creates favourable circumstances for prevention and recovery, while the accumulation of entropy accelerates aging and the development of diseases. The availability of potential energy plays a crucial role in how the immune system can exist and behave. Fight mode i.e., high potential energy mode where errors and defects are detected and corrected simultaneously. Fright mode in which potential energy is dispersed and entropy is accelerated, causing the immune system to respond randomly and attack indiscriminately. The flight mode, in which potential energy is suppressed, leads to a slowing down of the immune response, thereby bypassing many defects and mutations. The main objective of halalopathy is to develop methods and strategies to enrich the potential, keep the fight mode active and thus stimulate the immune system for better prevention and recovery.

The effect of laser surface treatment of titanium samples on the adhesive strength of adhesive joints

The article considers the strength of adhesive joints of specimens made of OT-4 titanium alloys, the surface of which has been treated with laser radiation. The paper presents the results of the dependence of the macro- and microgeometry of the obtained surface, chemical composition, wetting angle and adhesion strength of adhesive joints under shear on laser processing modes. The purpose of this work is to determine the optimal parameters of laser processing for obtaining high strength adhesive joints. The results obtained can be used for gluing spacecraft structural elements. The studies were carried out on the adhesive pair «Titan – Titan». Depending on the processing mode, characteristic surface textures were identified, which were combined into groups «B», «K» and «C». High-energy modes of laser surface treatment of samples before gluing lead to a significant increase in the strength characteristics of the adhesive joint (up to 70 %) due to an increase in the area of the gluing surface and mechanical locking of the adhesive in the microrelief of the texture of the samples. In addition, the use of this method, in comparison with mechanical and chemical methods, significantly increases the productivity of surface treatment.

Dissipation-Engineered Family of Nearly Dark States in Many-Body Cavity-Atom Systems.

Three-level atomic systems coupled to light have the capacity to host dark states. We study a system of V-shaped three-level atoms coherently coupled to the two quadratures of a dissipative cavity. The interplay between the atomic level structure and dissipation makes the phase diagram of the open system drastically different from the closed one. In particular, it leads to the stabilization of a continuous family of dark and nearly dark excited many-body states with inverted atomic populations as the steady states. The multistability of these states can be probed via their distinct fluctuations and excitation spectra, as well as the system's Liouvillian dynamics which are highly sensitive to ramp protocols. Our model can be implemented experimentally by encoding the two higher-energy modes in orthogonal density-modulated states in a bosonic quantum gas. This implementation offers prospects for potential applications like the realization of quantum optical random walks and microscopy with subwavelength spatial resolution.

Flat phonon modes driven ultralow thermal conductivities in Sr3AlSb3 and Ba3AlSb3 Zintl compounds

Searching for compounds with intrinsic low lattice thermal conductivity has been proven a successful strategy for achieving high thermoelectric performance. Herein, employing density functional theory calculations combined with electron and phonon Boltzmann transport theories, we report that Sr3AlSb3 and Ba3AlSb3 within the Zintl 3–1–3 compositional family exhibit record low thermal conductivities of 0.78 and 0.55 W/mK at room temperature, respectively. These low thermal conductivities are rooted in low-energy optical phonon modes with strong anharmonicity and the emergence of high-energy flat optical phonon modes with zero contribution to the lattice thermal conductivity. Heavier cationic atoms are found to soften low-lying optical phonon modes, which enhance phonon scattering and, therefore, favor a lower thermal conductivity. These combined characteristics lead to high and balanced figure of merit values around 2.3 for Zintl Ba3AlSb3 at both optimal p-type and n-type doping and high temperature. Our work highlights the important role of flat optical phonon modes on designing promising thermoelectric materials with intrinsic low thermal conductivity.