A method of sub-Doppler spectroscopy is proposed, based on the peculiarities of narrowing over time of the velocity distribution of optically excited atoms (molecules) of a rarefied gas medium in a ...thin cell after exposure to a sufficiently short pulse of broadband radiation. Recording of narrow sub-Doppler resonances at the central frequencies of quantum transitions from the atomic state excited by such a pump pulse is carried out by subsequent probe monochromatic light pulses. The optimal conditions for the implementation of this spectroscopy method occur when the radiation decay time of an optically excited atomic level exceeds the characteristic time of flight of atoms between the walls of the thin cell under consideration, the inner thickness of which is many times smaller than its transverse dimensions.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, SIK, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The MD simulation package Amber offers an attractive platform to refine crystallographic structures of proteins: (i) state-of-the-art force fields help to regularize protein coordinates and ...reconstruct the poorly diffracting elements of the structure, such as flexible loops; (ii) MD simulations restrained by the experimental diffraction data provide an effective strategy to optimize structural models of protein crystals, including explicitly modeled interstitial solvent as well as crystal contacts. Here, we present the new crystallography module xray, released as a part of the Amber 2023 package. This module contains functions to calculate and scale structure factors (including the contributions from bulk solvent), evaluate the maximum-likelihood-type crystallographic potential, and compute its derivative forces. The X-ray functionality of Amber no longer relies on external dependencies so that the full advantage of GPU acceleration can be taken. This makes it possible to refine in a short time hundreds of crystal models, including supercell models comprised of multiple unit cells. The new automated Amber-based refinement procedure leads to an appreciable improvement in R free (in some cases, by as much as 0.067) as well as MolProbity scores.
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IJS, KILJ, NUK, PNG, UL, UM
We introduce a perturbed augmented Lagrangian method framework, which is a convenient tool for local analyses of convergence and rates of convergence of some modifications of the classical augmented ...Lagrangian algorithm. One example to which our development applies is the proximal augmented Lagrangian method. Previous results for this version required twice differentiability of the problem data, the linear independence constraint qualification, strict complementarity, and second-order sufficiency; or the linear independence constraint qualification and strong second-order sufficiency. We obtain a set of convergence properties under significantly weaker assumptions: once (not twice) differentiability of the problem data, uniqueness of the Lagrange multiplier, and second-order sufficiency (no linear independence constraint qualification and no strict complementarity); or even second-order sufficiency only. Another version to which the general framework applies is the smoothed augmented Lagrangian method, where the plus-function associated with penalization of inequality constraints is approximated by a family of smooth functions (so that the subproblems are twice differentiable if the problem data are). Furthermore, for all the modifications, inexact solution of subproblems is handled naturally. The presented framework also subsumes the basic augmented Lagrangian method, both exact and inexact.
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CEKLJ, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Excitation of atoms from the ground quantum level to a metastable state by traveling monochromatic radiation in a thin gas cell, the internal thickness of which is much smaller than its radius, is ...studied theoretically. Sub-Doppler resonances are detected and analyzed that arise in the population of a metastable atomic level due to light-induced Rabi oscillations on a given optical transition and specific features of transit-time relaxation of atoms in a considered cell with a rarified gas upon scanning the radiation frequency. Such nontrivial resonances can be recorded in fluorescence of atoms with the help of an additional probe light beam. A method is proposed for a direct measurement of the Rabi frequency from spectral intervals between detected sub-Doppler resonances. The results obtained can be applied in atomic spectroscopy for the precision determination of components of dipole moment matrix elements, as well as for the Einstein coefficients and oscillator strengths related to these components, for quantum transitions between the ground and metastable levels of atoms.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, SIK, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
As is well known, when initialized close to a nonsingular solution of a smooth nonlinear equation, the Newton method converges to this solution superlinearly. Moreover, the common Armijo linesearch ...procedure used to globalize the process for convergence from arbitrary starting points, accepts the unit stepsize asymptotically and ensures fast local convergence. In the case of a singular and possibly even nonisolated solution, the situation is much more complicated. Local linear convergence (with asymptotic ratio of 1/2) of the Newton method can still be guaranteed under reasonable assumptions, from a starlike, asymptotically dense set around the solution. Moreover, convergence can be accelerated by extrapolation and overrelaxation techniques. However, nothing was previously known on how the Newton method can be coupled in these circumstances with a linesearch technique for globalization that locally accepts unit stepsize and guarantees linear convergence. It turns out that this is a rather nontrivial issue, requiring a delicate combination of the analyses on acceptance of the unit stepsize and on the iterates staying within the relevant starlike domain of convergence. In addition to these analyses, numerical illustrations and comparisons are presented for the Newton method and the use of extrapolation to accelerate convergence speed.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, ODKLJ, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
A well known solution of heterotic string theory is the spinning Kerr–Sen black hole (KSBH) characterized by a string parameter ξ. Kerr black hole is recovered at ξ=0. The purpose of this paper is to ...investigate the effect of ξ on a new diagnostic of relative time delay (RTD) to see how the latter deviates from that in general relativity. Assuming KSBH as the spinning lens partner in PSR–BH binary systems, which provide the best laboratory for testing the time delay predictions, we study here the RTD up to third PPN order in 1∕r in the thin-lens approximation. We work out a useful generalization of the RTD formulas applicable to the experimentally viable finite distance lens scales, while terms higher than the zeroth order are shown to contain the effect of ξ. We shall also relate RTD to the observable image magnification factor determined by β∕θE, where β is the angular separation between the source and the observer and θE is the ”Einstein angle” determined by an ”effective” non-aligned static lens equivalent to the original aligned spinning lens. Numerical estimates for two typical binary lens systems show μsec level delay at the zeroth order consistent with predictions in the literature. However, the string effect at higher orders is too tiny to be measurable even in the far future leading to the conclusion that the stringy and general relativity BHs are yet observationally indistinguishable.
•String induced deviation in relative time delay differs from Kerr black holes.•Relative time delay as a diagnostic of deviation from general relativity.•Application of relative time delay to binary systems.•Thin-lens approximation provides description of realistic lensing situations.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
•Concentration of deep electron traps is in the range of 1019 cm−3 posing challenges for electrostatic control of HfO2- and HZO-based ferroelectric devices.•Trap energy distribution universally ...exhibit three characteristic optical energy levels: around 2 eV, 3 eV, and 4 eV below the oxide CB.•The observed traps are likely intrinsic to HfO2 lattice rather than related to dopants or ZrO2 sub-network.
Electron traps in HfO2-based ferroelectric layers are known to be a major performance-degrading factor. We use room temperature charge injection and photodepopulation techniques to reveal the trap density and energy distribution in ferroelectric HfO2 and HfZrO4. The concentration of occupied electron traps is in the order of 1019 cm−3 for all analyzed samples which provides the lower limit of the defect concentration in the film. Energy distributions universally exhibit three characteristic optical energy levels: around 2 eV, 3 eV, and 4 eV below the HfO2 conduction band edge. The latter energy level was not observed previously and, according to previous DFT calculations, is too deep to be either of polaronic or O-vacancy-related nature. Nevertheless, the trap energy spectrum remains very similar in all studied samples suggesting the same sorts of the dominant electron traps both in HfO2 and HfZrO4 probably related to intrinsic defects of the HfO2 sub-network.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The effect of transtraumatic epidural electrostimulation (TEES) above (T5) and below (L2) spinal cord injury in the lower thoracic region (T8-T9) in combination with treadmill exercise in pigs was ...evaluated using electrophysiological examination methods and behavioral tests. Two weeks after spinal cord injury, motor evoked potentials of
m. soleus
were recorded during electrostimulation at the level of T5 and L2 segments, which indicated activation of spinal cord structures above and below the focus of injury. After 6 weeks of TEES in combination with physical training, restoration of the characteristics of M-response and H-reflex of the soleus muscle in response to stimulation of the sciatic nerve, improvement of joint mobility, and appearance of voluntary motor activity in the hindlimbs were observed. Neuromodulation with TEES had been proven to be an effective way to stimulate posttraumatic spinal cord regeneration and can be used in the development of a neurorehabilitation protocol for patients with spinal cord injury.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
We have investigated the behavior of second RNA-recognition motif (RRM2) of neuropathological protein TDP43 under the effect of oxidative stress as modeled in vitro. Toward this end we have used the ...specially adapted version of H/D exchange experiment, NMR relaxation and diffusion measurements, dynamic light scattering, controlled proteolysis, gel electrophoresis, site-directed mutagenesis and microsecond MD simulations. Under oxidizing conditions RRM2 forms disulfide-bonded dimers that experience unfolding and then assemble into aggregate particles (APs). These particles are strongly disordered, highly inhomogeneous and susceptible to proteolysis; some of them withstand the dithiothreitol treatment. They can recruit/release monomeric RRM2 through thiol-disulfide exchange reactions. By using a combination of dynamic light scattering and NMR diffusion data we were able to approximate the size distribution function for the APs. The key to the observed aggregation behavior is the diminished ability of disulfide-bonded RRM2 dimers to refold and their increased propensity to misfold, which makes them vulnerable to large thermal fluctuations. The emerging picture provides detailed insight on how oxidative stress can contribute to neurodegenerative disease, with unfolding, aggregation, and proteolytic cleavage as different facets of the process.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
MD simulations can provide uniquely detailed models of intrinsically disordered proteins (IDPs). However, these models need careful experimental validation. The coefficient of translational diffusion ...Dtr, measurable by pulsed field gradient NMR, offers a potentially useful piece of experimental information related to the compactness of the IDP’s conformational ensemble. Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4). We found that the predicted values of Dtr, as obtained from mean-square displacement of the peptide in the MD simulations, are largely determined by the viscosity of the MD water (which has been reinvestigated as a part of our study). Beyond that, our analysis of the diffusion data indicates that MD simulations of N-H4 in the TIP4P-Ew water give rise to an overly compact conformational ensemble for this peptide. In contrast, TIP4P-D and OPC simulations produce the ensembles that are consistent with the experimental Dtr result. These observations are supported by the analyses of the 15N spin relaxation rates. We also tested a number of empirical methods to predict Dtr based on IDP’s coordinates extracted from the MD snapshots. In particular, we show that the popular approach involving the program HYDROPRO can produce misleading results. This happens because HYDROPRO is not intended to predict the diffusion properties of highly flexible biopolymers such as IDPs. Likewise, recent empirical schemes that exploit the relationship between the small-angle x-ray scattering-informed conformational ensembles of IDPs and the respective experimental Dtr values also prove to be problematic. In this sense, the first-principle calculations of Dtr from the MD simulations, such as demonstrated in this work, should provide a useful benchmark for future efforts in this area.
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