Hundreds Of Angstroms Research Articles

The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament.

The binding of Ca2+ ions within the troponin core of the cardiac thin filament (CTF) regulates normal contraction and relaxation. Mutations within the troponin complexes are known to alter normal functions and result in the eventual development of cardiomyopathy. However, despite the importance of the problem, detailed microscopic knowledge of the mechanism of pathogenic effect of point mutations and their effects on the conformational free energy surface of CTF remains elusive. Mutations are known to transmit their effects hundreds of angstroms along this protein complex and between different component proteins. To explore the impact of point mutations on the conformational free energy barrier between the closed and blocked state of CTF, and to understand the transmission of mutation, we have carried out metadynamics simulations for the wild-type (WT) and two mutants (cardiac troponin T Arg92Trp (R92W) and Arg92Leu (R92L)). Specifically, we have investigated the conformational modification of the tropomyosin (Tm) and the troponin (Tn) complex during the closed-to-blocked state transition for both the WT and two hypertrophic cardiomyopathy causing mutations. Our calculations demonstrated that mutations within the cardiac troponin T (cTnT) protein alter conformational properties of the Tm and the other proteins of the Tn complex as well as the Ca2+ binding affinity of the cTnC protein through the indirect mediation of cardiac troponin I (cTnI). Importantly, the data revealed a significant influence of the mutations on the conformational transition free energy barriers for both the Tm and cTnC proteins. Furthermore, we found both mutations independently alter the free energy barrier of transitions of cTnT. Such alteration in the free energy upon mutation of one protein in a complex, allosterically affects the others through structural and dynamical changes, leading to a pathogenic effect on the function of the thin filament.

Quantum Size Effect in Three-Dimensional Microscopic Semiconductor Crystals

The exciton absorption spectrum of microscopic CuCl crystals grown in a transparent dielectric matrix has been studied. The size of the microscopic crystals was varied in a controlled manner from several tens of angstroms to hundreds of angstroms. There is a short-wave shift (of up to 0.1 eV) of the exciton absorption lines, caused by a quantum size effect.

Synthesis and Characterization of Carbon Microbeads.

We report a microfluidic-based droplet generation platform for synthesizing micron-sized porous carbon microspheres. The setup employs carbon materials such as graphite, carbon nanotubes, graphene, fullerenes, and carbon black as starting materials. Custom composition, structure, and function are achieved through combinations of carbon materials, cross-linkers, and additives along with variations in process parameters. Carbon materials can be assembled into spheres with a mean diameter of units to hundreds of μm with relatively tight size distribution (<25% RSD). Pore structure and size (tens to hundreds of angstrom) can be modulated by incorporating porogen/coporogen dilutants during synthesis. The microbeads have excellent mechanical stability with an elastic modulus of hundreds of MPa. They can sustain high dynamic fluid flow pressures of up to 9000 psi. This work lays the foundation for synthesizing novel tailorable and customizable carbon microbeads. It opens avenues for applying these novel materials for composite and additive manufacturing, energy, life science, and biomedical applications.

Determining the parameters of the oil film on the sea surface using remote sensing data

Oil spill accidents have gradually increased due to the continuous development of marine transportation and petroleum processing industries. Monitoring and managing marine oil spills present important economic, social, and practical implications in preventing offshore oil pollution and maintaining ecological balance.&#x0D; Remote sensing technologies play an increasingly important role in accurate detection and monitoring of oil spill slicks, assisting scientists in forecasting their trajectories, developing clean-up plans, taking timely and urgent actions, and applying effective treatments to contain and alleviate adverse effects.&#x0D; A method is proposed for remote sensing of an oil film on the sea surface based on irradiation with frequency-modulated laser radiation with a linear dependence of frequency on time. According to the spectrum of temporal changes in the intensity of the radiation reflected by the surface, the average thickness of the oil film, the distribution function of the oil film thickness, and the volume of spilled oil are determined.&#x0D; Taking into account the possibility of registering beat frequencies from fractions of a hertz to megahertz with modern instruments, we can talk about the possibility of measuring oil thicknesses from hundreds of angstroms to tens of meters using the proposed method of remote sensing. The method also makes it possible to additionally determine the thickness distribution function and the volume of spilled oil.&#x0D; The method proposed in this study has obvious advantages in terms of small sample size and processing efficiency and has great application potential in the field of maritime supervision.

Phase-space ab-initio direct and reverse ballistic-electron emission spectroscopy: Schottky barriers determination for Au/Ge(100)

We develop a phase-space ab-initio formalism to compute Ballistic Electron Emission Spectroscopy current–voltage I(V)’s in a metal–semiconductor interface. We consider injection of electrons into the conduction band for direct bias (V>0) and injection of holes into the valence band or injection of secondary Auger electrons into the conduction band for reverse bias (V<0). Here, an ab-initio description of the semiconductor inversion layer (spanning hundreds of Angstroms) is needed. Such formalism is helpful to get parameter-free best-fit values for the Schottky barrier, a key technological characteristic for metal–semiconductor rectifying interfaces. We have applied the theory to characterize the Au/Ge(001) interface; a double barrier is found for electrons injected into the conduction band – either directly or created by the Auger process – while only a single barrier has been identified for holes injected into the valence band.

Zitterbewegung effect in graphene with spacially modulated potential

The Zitterbewegung (ZB) effect is investigated in graphene with spacially modulated potential near the original Dirac point (ODP) and extra Dirac points (EDPs). Our calculations show that to get the large ZB oscillations, the wave packet center must be at the angle $\theta_0=0$ for EDPs located at zero-energy, or $\theta_0=\pi/2$ for both ODP and EDPs at finite energy $\varepsilon=m\pi$ ($m$ integer). By varying the parameters ($q_2, \mathbb{V}$) of the periodic potential and the initial momentum ($\kappa_0, \theta_0$) of Gaussian wave packet, it is found that the frequency of the ZB oscillations is in the range $[10^{7}~\text{Hz}, 10^{13}~\text{Hz}$] depending on what type of EDP is generated and the amplitude reaches hundreds of angstroms but their attenuation becomes very slow. More analysis of the frequency shows the possibilities in experimentally realizing the ZB effect in our system.

Scattering of ultracold neutrons from rough surfaces of metal foils

The transparency of metal foils for ultracold neutrons (UCNs) plays an important role in the design of future high-density UCN sources, which will feed a number of fundamental physics experiments. In this work, we describe and discuss the measured transmission of a collimated beam of very slow neutrons (UCNs and very cold neutrons) through foils of Al, Cu, and Zr of various thicknesses at room temperature. Our goal was to separate scattering and absorption in the sample bulk from surface scattering, and to quantify the contribution of the surface. We were able to demonstrate that the surface roughness of these foils caused a significant fraction of UCN scattering. The surface roughness parameter $b$ extracted from UCN measurements was shown to be of the same order of magnitude as the surface parameter determined by atomic-force microscopy. They lie in the order of several hundreds of angstroms. Using the formalism developed here, transmission data from previous neutron-optical experiments were re-analyzed and their surface roughness parameter $b$ was extracted.

Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts.

Membrane-embedded sensor histidine kinases (HKs) and chemoreceptors are used ubiquitously by bacteria and archaea to percept the environment, and are often crucial for their survival and pathogenicity. The proteins can transmit the signal from the sensor domain to the catalytic kinase domain reliably over the span of several hundreds of angstroms, and regulate the activity of the cognate response regulator proteins, with which they form two-component signaling systems (TCSs). Several mechanisms of transmembrane signal transduction in TCS receptors have been proposed, dubbed (swinging) piston, helical rotation, and diagonal scissoring. Yet, despite decades of studies, there is no consensus on whether these mechanisms are common for all TCS receptors. Here, we extend our previous work on Escherichia coli nitrate/nitrite sensor kinase NarQ. We determined a crystallographic structure of the sensor-TM-HAMP fragment of the R50S mutant, which, unexpectedly, was found in a ligand-bound-like conformation, despite an inability to bind nitrate. Subsequently, we reanalyzed the structures of the ligand-free and ligand-bound NarQ and NarX sensor domains, and conducted extensive molecular dynamics simulations of ligand-free and ligand-bound wild type and mutated NarQ. Based on the data, we show that binding of nitrate to NarQ causes, first and foremost, helical rotation and diagonal scissoring of the α-helices at the core of the sensor domain. These conformational changes are accompanied by a subtle piston-like motion, which is amplified by a switch in the secondary structure of the linker between the sensor and TM domains. We conclude that helical rotation, diagonal scissoring, and piston are simply different degrees of freedom in coiled-coil proteins and are not mutually exclusive in NarQ, and likely in other nitrate sensors and TCS proteins as well.

A Simple Model for the High Temperature Oxidation Kinetics of Silicon Nanoparticle Aggregates

Silicon nanoparticles are an emerging and promising material in many fields including electronics, catalysis, and biomaterial engineering. Synthesis in the gas phase via aerosol routes allows tuning and engineering material features such as primary particle size distribution, agglomerate size distribution, crystallite size, and morphology. Proper control of these features as well as post-synthesis processing such as surface oxidation is very relevant for making the nanoparticles chemically stable. Therefore, a kinetic expression for determining the extent of oxidation in silicon nanoparticles is necessary. Significant work has been devoted to understanding the kinetics of monocrystalline silicon, and generally accepted models such as the one by Deal and Grove provide a very accurate description of bulk silicon oxidation. However, these models are not as accurate for the first hundreds of angstroms of the oxidation. While this might be acceptable for bulk wafers, it has critical results for silicon nanoparticles with diameters around such range. Furthermore, many applications involve silicon nanoparticle aggregates with a shape far away from perfect spheres. For this reason, in this work, we propose an expression for the parabolic oxidation kinetics of polycrystalline silicon nanoparticle aggregates at 1000 °C with surface area in the range of 3 to 19 m2/g. and crystallite sizes from 50 to 70 nm. The activation energy of the process is also reported to be linked to the crystallite size.

Superconducting in Equal Molar NbTaTiZr-Based High-Entropy Alloys

Superconducting (SC) in equal molar NbTaTiZr-based high-entropy alloys (HEAs) that were added with Fe, Ge, Hf, Si, and/or V was observed. According to investigation on crystal structure, composition, and the relationship between critical temperature and e/a ratio, as indicated in Matthias’ empirical rule, the main superconducting phase was that enriched with Nb and Ta. The coherence length (ξ) that was calculated from the carrier density reveals that ξvalue has the same order of magnitude of several hundreds of Angstroms as those binary Nb-Ti and Nb-Zr alloys showed.

The Ribosome as an Allosterically Regulated Molecular Machine.

The ribosome as a complex molecular machine undergoes significant conformational rearrangements during the synthesis of polypeptide chains of proteins. In this review, information obtained using various experimental methods on the internal consistency of such rearrangements is discussed. It is demonstrated that allosteric regulation involves all the main stages of the operation of the ribosome and connects functional elements remote by tens and even hundreds of angstroms. Data obtained using Förster resonance energy transfer (FRET) show that translocation is controlled in general by internal mechanisms of the ribosome, and not by the position of the ligands. Chemical probing data revealed the relationship of such remote sites as the decoding, peptidyl transferase, and GTPase centers of the ribosome. Nevertheless, despite the large amount of experimental data accumulated to date, many details and mechanisms of these phenomena are still not understood. Analysis of these data demonstrates that the development of new approaches is necessary for deciphering the mechanisms of allosteric regulation of the operation of the ribosome.

Energy Dissipation and Nonthermal Diffusion on Interstellar Ice Grains

Abstract Interstellar dust grains are known to facilitate chemical reactions by acting as a meeting place and adsorbing energy. This process strongly depends on the ability of the reactive species to effectively diffuse over the surface. The cold temperatures around 10 K strongly hamper this for species other than H and H2. However, complex organic molecules have been observed in the gas phase at these cold conditions, indicating that their formation, as well as their return to the gas phase, should be effective. Here, we show how the energy released following surface reactions can be employed to solve both problems by inducing desorption or diffusion. To this purpose, we have performed thousands of Molecular Dynamics simulations to quantify the outcome of an energy dissipation process. Admolecules on top of a crystalline water surface have been given translational energy between 0.5 and 5 eV. Three different surface species are considered (CO2, H2O, and CH4), spanning a range in binding energies, number of internal degrees of freedom, and molecular weights. The admolecules are found to be able to travel up to several hundreds of angstroms before coming to a stand still, allowing for follow-up reactions en route. The probability of travel beyond any particular radius, as determined by our simulations, shows the same r dependence for all three admolecule species. Furthermore, we have been able to quantify the desorption probability, which depends on the binding energy of the species and the translational excitation. We provide expressions that can be incorporated in astrochemical models to predict grain surface formation and return into the gas phase of these products.

Equivalence between particles and fields: A general statistical mechanics theory for short and long range many‐body forces

While in vacuum fundamental and dispersion inter‐molecular forces can be in principle of infinite range, in the bulk, however, they are of rather short‐range, typically between a few angstroms to a few hundreds of angstroms. Yet colloidal particles, nano‐particles, and supramolecules, like enzymes, thousand or hundreds of thousands of angstroms apart, seem to recognize each other and self‐assembly, according with their shapes and sizes, in a wide variety of complex structures. In this paper we discuss this long‐range molecular recognition mechanism through a general liquid theory, based on the recognition of the equivalence between particles and fields, and molecular simulations. In particular we show results of a counter‐intuitive attraction between like‐charged colloidal particles and compare them with experimental results.

Long Periodic Helimagnetic Ordering in CrM3S6 (M = Nb and Ta)

We report long periodic chiral helimagnetic orderings in ferromagnetic inorganic compounds CrM3S6 (M = Nb and Ta) with a chiral space group of P6322. Magnetization in polycrystalline samples and high resolution powder neutron diffraction were measured. Our powder neutron diffraction measurements in CrM3S6 successfully separated nuclear and magnetic satellite peaks, having the period of hundreds of angstroms along the c— axis. Therefore, we propose that the magnetic ordering in ferromagnetic CrM3S6 is not ferromagnetic, but long periodic chiral helimagnetic ordering.

Insight into the multiscale structure of pre-stretched recast Nafion® membranes: Focus on the crystallinity features

The structure of solution cast Nafion® membranes that were uniaxially stretched, and then thermally annealed was studied over an extended observation window, from a few angstroms to several hundreds of angstroms, using both Small-Angle X-Ray Scattering (SAXS) and Wide-Angle X-Ray Diffraction (WAXD). This Nafion® membrane preparation allowed highlighting new structural features, never reported previously. Indeed, while SAXS data evidenced moderate effect of stretching with different behaviors of the matrix and ionomer peaks, WAXD spectra showed a strong stretching induced anisotropy of the crystalline phase. These results defy the Nafion® structural models and call for further theoretical and experimental developments taking into account these new data.

Influence of synthetic lubricant fluids on the frictional coefficient

The use of lubricant and coolant fluids permits improved machining quality and longer life of metal� cutting machines. The primary functions of such flu� ids are to reduce the temperature in the cutting zone and to minimize the frictional coefficient. These roles are interdependent: with increase in temperature, the adhesive component increases; with increase in fric� tional coefficient, the cutting temperature rises. Metalworking enterprises use different lubricant and coolant fluids for different operation. Watersolu� ble (emulsions and synthetic fluids) and oilbased mixtures are used, with concentrations of 2-10% (1). Synthetic lubricant and coolant fluids are of most interest, since they present fewer biohazards than do emulsions. The lubricating action of the fluids is mainly seen at chip-cutter contact and also blank-cutter contact. It is associated with the fluids' ability to participate in physical, chemical, and physicochemical interactions with the activated surfaces in the contact zone and to form hydrodynamic, physical (adsorptive), and chem� ical lubricant films. Depending on the cutting condi� tions, such films may be formed individually or simul� taneously. Physical and chemical lubricant films are said to be boundary films. Their thickness varies from to tens to hundreds of Angstrom. Their shear resistance is higher than for hydrodynamic films. When hydrodynamic lubricant films are formed in metal cutting (for exam� ple, in the lowspeed cutting of copper), the frictional surfaces are separated by a few microns of fluid. The viscosity of the lubricant and coolant fluid is of most importance here and must be optimal. Sometimes, the viscosity may be compensated by additions of sulfur, chlorine, or phosphorus compounds. The lubricant and coolant fluid may be selected by determining the actual frictional coefficient of fluids in machining some material and also their cooling properties, so as to improve the quality of machining (the dimensional and shape precision, the surface roughness and microstructure, etc.). The actual frictional coefficients of synthetic lubri� cant and coolant fluids in conditions resembling their working conditions may be determined on an II 5018 frictional machine, using a frictional shoe (T15K6 hard alloy) and a roller (steel 45). In the present work, we consider Biosil S, Isogrind�130EP, AkremonD�1, KonkrepolVTs, and Ekol�3 fluids, at a concentration of 10%. The force on the shoe P = 800 N; the roller speed n = 250 rpm. The table presents the results for the machining of steel 45 using synthetic lubricant and coolant fluids.

TransientZitterbewegungof graphene superlattices

We investigate Zitterbewegung (ZB) behavior in a graphene superlattice with generations of massless Dirac fermions having highly anisotropic group velocities, which results from a graphene subject to one-dimensional periodic potentials. It is shown that with tuning parameters of the periodic potential, the frequency of ZB oscillations can be of order ${10}^{12}$ Hz, the amplitude can increase to hundreds of angstroms, and their attenuation can become much slower. The required parameters of the graphene superlattice can be realized under current experimental conditions, thus providing a good system for probing the ZB effect experimentally.

Ballistic and molecular dynamics simulations of aluminum deposition in micro-trenches

Two different feature scale modeling frameworks are utilized for the study of aluminum (Al) deposition profiles inside micro-trenches. The first framework, which is applied in metal-organic chemical vapor deposition (MOCVD) of Al, couples a ballistic model for the local flux calculation, a surface chemistry model, and a profile evolution algorithm. The calculated conformity of the deposited film is compared with experimental results corresponding to Al MOCVD from dimethylethylamine alane (DMEAA). The outcome of the comparison is that the effective sticking coefficient of DMEAA is in the range of 0.1–1. There is also a strong indication that surface reaction kinetics follows Langmuir–Hinshelwood or Eley–Rideal mechanism. The second framework, which is applied in physical vapor deposition of Al, implements 2D molecular dynamics (MD) simulations. The simulations are performed in a “miniaturized” domain of some hundreds of Angstroms and are used to explore micro-trench filling during magnetron sputtering deposition of Al on a rotated substrate. Most of the experimental results are qualitatively reproduced by the MD simulations; the rotation, aspect ratio, and kinetic energy effects are correctly described despite the completely different length scales of simulation and experiment. The sticking probability of Al is calculated 0.6 for the conditions of the experiments.

PRECISION SPECTROPHOTOMETRY AT THE LEVEL OF 0.1%

Accurate relative spectrophotometry is critical for many science applications. Small wavelength scale residuals in the flux calibration can significantly impact the measurements of weak emission and absorption features in the spectra. Using Sloan Digital Sky Survey data, we demonstrate that the average spectra of carefully selected red-sequence galaxies can be used as a spectroscopic standard to improve the relative spectrophotometry precision to 0.1% on small wavelength scales (from a few to hundreds of Angstroms). We achieve this precision by comparing stacked spectra across tiny redshift intervals. The redshift intervals must be small enough that any systematic stellar population evolution is minimized and less than the spectrophotometric uncertainty. This purely empirical technique does not require any theoretical knowledge of true galaxy spectra. It can be applied to all large spectroscopic galaxy redshift surveys that sample a large number of galaxies in a uniform population.

Modeling Electrostatically Induced Collapse Transitions in Carbon Nanotubes

Molecular dynamics simulations demonstrate how a mechanically bistable single-walled carbon nanotube can act as a variable-shaped capacitor. If the voltage is tuned so that collapsed and inflated states are degenerate, the tube's susceptibility to diverse external stimuli--temperature, voltage, trapped atoms--diverges following a universal curve, yielding an exceptionally sensitive sensor or actuator. The boundary between collapsed and inflated states can shift hundreds of angstroms in response to a single gas atom inside the tube. Several potential nanoelectromechanical devices could be based on this electrically tuned crossover between near-degenerate collapsed and inflated configurations.