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The present work is devoted to the study of the thermostability of native DNA during binding to TiO$_{2}$ nanoparticles (NPs) at various concentrations under conditions close to physiological (0.1 M Na $^+$, pH 7) using thermal denaturation method and dynamic light scattering (DLS). The analysis of the DNA melting curves in the presence of TiO$_{2}$ NPs revealed a temperature range in which the light absorption of DNA decreases. This is explained by the formation of an ordered structure of partially unwound DNA strands on the NP surface. The DNA:TiO$_{2}$ NP nanoassemblies formed at the initial stages remained stable in the wide temperature range. The performed temperature-dependent DLS measurements of the DNA:TiO$_{2}$ NP suspension at pH 7 have not revealed the aggregation of the DNA:TiO$_{2}$ NP nanoassemblies that had been observed at pH 5., Comment: 17 pages, 5 figures. arXiv admin note: text overlap with arXiv:2308.13444

Self-interaction is a fundamental flaw of practical Kohn-Sham Density Functional Theory (KS DFT) approximations responsible for numerous qualitative and even catastrophic shortcomings. Whereas self-interaction is easy to characterize in one-electron systems, its orbital-dependent nature makes it difficult to uniquely define and decompose it and other components of the KS energy into orbital components. By starting from the orthogonal Hartree ansatz as the exchange-free self-interaction-free model, it is possible to uniquely define self-interaction and genuine exchange total energies as well as their decomposition into orbital contributions. Using Edmiston-Ruedenberg orbitals as a close numerical surrogate of the Hartree orbitals we investigate the accuracy of genuine exchange energies predicted by several levels of Jacob's ladder of functionals and their Perdew-Zunger (PZ) self-interaction corrected counterparts. Among several notable insights provided by the per-orbital breakdown of the KS energies the key is the delicate cancellation of errors between core and valence orbitals that belies the remarkable accuracy of many functionals (particularly, GGAs). Disruption of the cancellation by the PZ correction accounts for its relatively modest impact on GGAs and other semilocal functionals., Comment: 38 pages, 9 figures

To follow up on the unexpectedly-good performance of several coupled-cluster models with approximate inclusion of 3-body clusters [J. Chem. Phys. 151, 064102 (2019)] we performed a more complete assessment of the 3CC method [J. Chem. Phys. 125, 204105 (2006)] for accurate computational thermochemistry in the standard HEAT framework. New spin-integrated implementation of the 3CC method applicable to closed- and open-shell systems utilizes a new automated toolchain for derivation, optimization, and evaluation of operator algebra in many-body electronic structure. We found that with a double-zeta basis set the 3CC correlation energies and their atomization energy contributions are almost always more accurate (with respect to the CCSDTQ reference) than the CCSDT model as well as the standard CCSD(T) model. The mean absolute errors in cc-pVDZ {3CC, CCSDT, and CCSD(T)} electronic (per valence electron) and atomization energies relative to the CCSDTQ reference for the HEAT dataset [J. Chem. Phys. 121, 11599 (2004)], were {24, 70, 122} $\mu E_h/e$ and {0.46, 2.00, 2.58} kJ/mol, respectively. The mean absolute errors in the complete-basis-set limit {3CC, CCSDT, and CCSD(T)} atomization energies relative to the HEAT model reference, were {0.52, 2.00, and 1.07} kJ/mol, The significant and systematic reduction of the error by the 3CC method and its lower cost than CCSDT suggests it as a viable candidate for post-CCSD(T) thermochemistry applications, as well as the preferred alternative to CCSDT in general., Comment: 30 pages, 3 tables

The radiation mechanism underlying the prompt emission remains unresolved and can be resolved using a systematic and uniform time-resolved spectro-polarimetric study. In this paper, we investigated the spectral, temporal, and polarimetric characteristics of five bright GRBs using archival data from AstroSat CZTI, Swift BAT, and Fermi GBM. These bright GRBs were detected by CZTI in its first year of operation, and their average polarization characteristics have been published in Chattopadhyay et al. (2022). In the present work, we examined the time-resolved (in 100-600 keV) and energy-resolved polarization measurements of these GRBs with an improved polarimetric technique such as increasing the effective area and bandwidth (by using data from low-gain pixels), using an improved event selection logic to reduce noise in the double events and extend the spectral bandwidth. In addition, we also separately carried out detailed time-resolved spectral analyses of these GRBs using empirical and physical synchrotron models. By these improved time-resolved and energy-resolved spectral and polarimetric studies (not fully coupled spectro-polarimetric fitting), we could pin down the elusive prompt emission mechanism of these GRBs. Our spectro-polarimetric analysis reveals that GRB 160623A, GRB 160703A, and GRB 160821A have Poynting flux-dominated jets. On the other hand, GRB 160325A and GRB 160802A have baryonic-dominated jets with mild magnetization. Furthermore, we observe a rapid change in polarization angle by $\sim$ 90 degrees within the main pulse of very bright GRB 160821A, consistent with our previous results. Our study suggests that the jet composition of GRBs may exhibit a wide range of magnetization, which can be revealed by utilizing spectro-polarimetric investigations of the bright GRBs., Comment: 36 pages, 11 figures, Published in ApJ

We revisit the problem of unphysical charge density delocalization/fractionalization induced by the self-interaction error of common approximate Kohn-Sham Density Functional Theory functionals on simulation of small to medium-size proteins in vacuum. Aside from producing unphysical electron densities and total energies, the vanishing of the HOMO-LUMO gap associated with the unphysical charge delocalization leads to an unphysical low-energy spectrum and catastrophic failure of most popular solvers for the Kohn-Sham (KS) self-consistent field (SCF) problem. We apply a robust quasi-Newton SCF solver [Phys. Chem. Chem. Phys. 26, 6557 (2024)] to obtain solutions for some of these difficult cases. The anatomy of the charge delocalization is revealed by the natural deformation orbitals obtained from the density matrix difference between the Hartree-Fock and KS solutions; the charge delocalization can occur not only between charged fragments (such as in zwitterionic polypeptides) but also may involve neutral fragments. The vanishing-gap phenomenon and troublesome SCF convergence are both attributed to the unphysical KS Fock operator eigenspectra of molecular fragments (e.g., amino acids or their side chains). Analysis of amino acid pairs suggests that the unphysical charge delocalization can be partially ameliorated by the use of {\em some} range-separated hybrid functionals, but not by semilocal or standard hybrid functionals. Last, we demonstrate that solutions without the unphysical charge delocalization can be located even for semilocal KS functionals highly prone to such defects, but such solutions have non-Aufbau character and are unstable with respect to mixing of the non-overlapping "frontier" orbitals., Comment: 27 pages, 5 figures, 4 tables

We report an implementation of the McMurchie-Davidson (MD) algorithm for 3-center and 4-center 2-particle integrals over Gaussian atomic orbitals (AOs) with low and high angular momenta $l$ and varying degrees of contraction for graphical processing units (GPUs). This work builds upon our recent implementation of a matrix form of the MD algorithm that is efficient for GPU evaluation of 4-center 2-particle integrals over Gaussian AOs of high angular momenta ($l\geq 4$) [$\mathit{J. Phys. Chem. A}\ \mathbf{127}$, 10889 (2023)]. The use of unconventional data layouts and three variants of the MD algorithm allow to evaluate integrals in double precision with sustained performance between 25% and 70% of the theoretical hardware peak. Performance assessment includes integrals over AOs with $l\leq 6$ (higher $l$ is supported). Preliminary implementation of the Hartree-Fock exchange operator is presented and assessed for computations with up to quadruple-zeta basis and more than 20,000 AOs. The corresponding C++ code is a part of the experimental open-source $\mathtt{LibintX}$ library available at $\mathbf{github.com:ValeevGroup/LibintX}$.

We have implemented noniterative triples corrections to the energy from coupled-cluster with single and double excitations (CCSD) within the 1-electron exact two-component (1eX2C) relativistic framework. The effectiveness of both the CCSD(T) and the completely renormalized (CR) CC(2,3) approaches are demonstrated by performing all-electron computations of the potential energy curves and spectroscopic constants of copper, silver, and gold dimers in their ground electronic states. Spin-orbit coupling effects captured via the 1eX2C framework are shown to be crucial for recovering the correct shape of the potential energy curves, and the correlation effects due to triples in these systems changes the dissociation energies by about 0.1--0.2 eV or about 4--7\%. We also demonstrate that relativistic effects and basis set size and contraction scheme are significantly more important in Au$_2$ than in Ag$_2$ or Cu$_2$.

We present a catalog of 150 variable stars, including 13 stars with exoplanet candidates. 37 stars were identified as variables for the first time. As a result of a 2.5-year photometric survey of exoplanets, we have obtained and analyzed light curves for almost 50 thousand stars in fields around white dwarfs WD 0009+501 and GRW +708247. Here we describe observations and data processing, the search for variable stars, their cross-identification with other catalogs and classification. The catalog is published in open access and contains the primary classification of variability, light curves and their parameters., Comment: 10 pages, 3 figures, 2 tables

We develop the Perron-Frobenius theory using a variational approach and extend it to a set of arbitrary matrices, including those that are neither irreducible nor essentially positive, and non-preserved cones. We introduce a new concept called a quasi-eigenvalue of a matrix, which is invariant under orthogonal transformations of variables, and has various useful properties, such as determining the largest value of the real parts of the eigenvalues of a matrix. We extend Weyl's inequality for the eigenvalues to the set of arbitrary matrices and prove the new stability result to the Perron root of irreducible nonnegative matrices under arbitrary perturbations. As well as this, we obtain new types of estimates for the ranges of the sets of eigenvalues and their real parts., Comment: 15 pages

Two main results are presented: 1) a new class of applied problems that lead to equations with $(p,q)$-Laplace is presented; 2) a method for solving nonlinear boundary value problems involving $(p,q)$-Laplace with measurable unbounded coefficients is introduced. In the main result, the existence, uniqueness, and stability of the nonnegative weak solution to the equations of the form $$ -{\rm div}(\rho|\nabla u|^{q-2} \nabla u)-{\rm div}(|\nabla u|^{p-2}\nabla u)=\lambda b |u|^{q-2}u,~~p>q $$ are proven. Additionally, an explicit formula that expresses the solution of the equation through the inverse optimal solution of the spectral problem $$-{\rm div}(\rho|\nabla \phi|^{q-2}\nabla \phi)=\lambda b|\phi|^{q-2}\phi$$ is presented. The advantage of the method is that the inverse optimal problem has a visible geometry and a simple variational structure, which makes it easy to solve it and, as a consequence, find a solution to the associated nonlinear boundary value problem., Comment: 13 pages

Sparse tensor networks are commonly used to represent contractions over sparse tensors. Tensor contractions are higher-order analogs of matrix multiplication. Tensor networks arise commonly in many domains of scientific computing and data science. After a transformation into a tree of binary contractions, the network is implemented as a sequence of individual contractions. Several critical aspects must be considered in the generation of efficient code for a contraction tree, including sparse tensor layout mode order, loop fusion to reduce intermediate tensors, and the interdependence of loop order, mode order, and contraction order. We propose CoNST, a novel approach that considers these factors in an integrated manner using a single formulation. Our approach creates a constraint system that encodes these decisions and their interdependence, while aiming to produce reduced-order intermediate tensors via fusion. The constraint system is solved by the Z3 SMT solver and the result is used to create the desired fused loop structure and tensor mode layouts for the entire contraction tree. This structure is lowered to the IR of the TACO compiler, which is then used to generate executable code. Our experimental evaluation demonstrates very significant (sometimes orders of magnitude) performance improvements over current state-of-the-art sparse tensor compiler/library alternatives.

(Abridged) In this paper, we present a project of multi-channel wide-field optical sky monitoring system with high temporal resolution -- Small Aperture Imaging Network Telescope (SAINT) -- mostly built from off-the-shelf components and aimed towards searching and studying optical transient phenomena on the shortest time scales. The instrument consists of 12 channels each containing 30cm (F/1.5) objectives mounted on separate mounts with pointing speeds up to 50deg/s. Each channel is equipped with a 4128x4104 pixel, and a set of photometric $griz$ filters and linear polarizers. At the heart of every channel is a custom built reducer-collimator module allowing rapid switching of an effective focal length of the telescope -- due to it the system is capable to operate in either wide-field survey or narrow-field follow-up modes. In the first case, the field of view of the instrument is 470 square degrees and the detection limits (5$\sigma$ level at 5500$\AA$) are 12.5-21 mag for exposure times of 20 ms - 20 min correspondingly. In the second, follow-up regime, all telescopes are oriented towards the single target, and SAINT becomes an equivalent to a 1m telescope, with the field of view reduced to 11$'$ x 11$'$, and the exposure times decreased down to 0.6 ms. Different channels may then have different filters installed, thus allowing a detailed study -- acquiring both color and polarization information -- of a target object with highest possible temporal resolution. The operation of SAINT will allow acquiring an unprecedented amount of data on various classes of astrophysical phenomena, from near-Earth to extragalactic ones, while its multi-channel design and the use of commercially available components allows easy expansion of its scale, and thus performance and detection capabilities., Comment: 27 pages, 8 figures, 7 tables. Accepted to Photonics

Dark GRBs constitute a significant fraction of the GRB population. In this paper, we present the multiwavelength analysis of an intense two-episodic GRB 150309A observed early on to ~114 days post-burst. Despite the strong gamma-ray emission, no optical afterglow was detected for this burst. However, we discovered near-infrared afterglow ($K_{\rm S}$-band), ~5.2 hours post burst, with the CIRCE instrument mounted at the 10.4m GTC. We used Fermi observations of GRB 150309A to understand the prompt emission mechanisms and jet composition. We performed the early optical observations using the BOOTES robotic telescope and late-time afterglow observations using the GTC. A potential faint host galaxy is also detected at optical wavelength using the GTC. We modelled the potential host galaxy of GRB 150309A in order to explore the environment of the burst. The time-resolved spectral analysis of Fermi data indicates a hybrid jet composition consisting of a matter-dominated fireball and magnetic-dominated Poynting flux. GTC observations of the afterglow revealed that the counterpart of GRB 150309A was very red, with H-$K_{\rm S}$ > 2.1 mag (95 $\%$ confidence). The red counterpart was not discovered in any bluer filters of Swift UVOT, indicative of high redshift origin. This possibility was discarded based on multiple arguments, such as spectral analysis of X-ray afterglow constrain z < 4.15 and a moderate redshift value obtained using spectral energy distribution modelling of the potential galaxy. The broadband afterglow SED implies a very dusty host galaxy with deeply embedded GRB (suggesting $A_{\rm V}$ $\gtrsim$ 35 mag). The environment of GRB 150309A demands a high extinction towards the line of sight, demanding dust obscuration is the most probable origin of optical darkness and the very red afterglow of GRB 150309A. This result makes GRB 150309A the highest extinguished GRB known to date., Comment: 14 pages, 10 figures, 3 tables, accepted for publication in Astronomy & Astrophysics (A&A)

We report an independent Doppler confirmation of the TESS planet candidate orbiting an F-type main sequence star TOI-1408 located 140 pc away. We present a set of radial velocities obtained with a high-resolution fiber-optic spectrograph FFOREST mounted at the SAO RAS 6-m telescope (BTA-6). Our self-consistent analysis of these Doppler data and TESS photometry suggests a grazing transit such that the planet obscures its host star by only a portion of the visible disc. Because of this degeneracy, the radius of TOI-1408.01 appears ill-determined with lower limit about $\sim$1 R$_{\rm Jup}$, significantly larger than in the current TESS solution. We also derive the planet mass of $1.69\pm0.20$~$M_{\rm Jup}$ and the orbital period $\sim4.425$ days, thus making this object a typical hot Jupiter, but with a significant orbital eccentricity of $0.259\pm0.026$. Our solution may suggest the planet is likely to experience a high tidal eccentricity migration at the stage of intense orbital rounding, or may indicate possible presence of other unseen companions in the system, yet to be detected., Comment: 5 pages, 3 figures

TiO$_{2}$ nanoparticles (NPs) have unique photocatalytic properties, which are used in food industries, medicine, biosensorics, and solar energy conversion. Since the toxic properties of TiO$_{2}$ NPs have been insufficiently studied, additional information on the molecular mechanisms of their biological action on the structure and stability of biological macromolecules is needed, especially concerning DNA. In this work exploiting the differential UV-visible spectroscopy, the effect of the heating (from 20 till 90 $^0$C) and concentration of TiO$_{2}$ NPs ((1-3)$\times$10$^-$$^4$ M) on a conformation of native DNA adsorbed on TiO$_{2}$ NPs in a buffer solution (pH 5) is studied. Analysis of dynamic light scattering (DLS) data for the DNA:TiO$_{2}$ NPs suspension revealed that when the temperature increases the separated DNA:TiO$_{2}$ NP nanoassemblies form nanoaggregates. Correlation between the thermal dependency of the DLS data and thermal DNA denaturation measurements indicated that the appearance of the single-stranded unwound regions in double-stranded DNA in the suspension with temperature rise promotes the effective formation of the DNA:TiO$_{2}$ NPs nanoaggregates., Comment: 14 pages, 5 figures

We present a high-performance evaluation method for 4-center 2-particle integrals over Gaussian atomic orbitals with high angular momenta ($l\geq4$) and arbitrary contraction degrees on graphical processing units (GPUs) and other accelerators. The implementation uses the matrix form of McMurchie-Davidson recurrences. Evaluation of the 4-center integrals over four $l=6$ ($i$) Gaussian AOs in the double precision (FP64) on an NVIDIA V100 GPU outperforms the reference implementation of the Obara-Saika recurrences (${\tt Libint}$) running on a single Intel Xeon core by more than a factor of 1000, easily exceeding the 73:1 ratio of the respective hardware peak FLOP rates while reaching almost 50\% of the V100 peak. The approach can be extended to support AOs with even higher angular momenta; for lower angular momenta ($l\leq3$) additional improvements will be reported elsewhere. The implementation is part of an open-source ${\tt LibintX}$ library feely available at https://github.com/ValeevGroup/LibintX., Comment: 23 pages

We present an efficient quasi-Newton orbital solver optimized to reduce the number of gradient (Fock matrix) evaluations. The solver optimizes orthogonal orbitals by sequences of unitary rotations generated by the (preconditioned) limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm incorporating trust-region step restriction. Low-rank structure of the inverse (approximate) Hessian is exploited not only in L-BFGS but also when solving the trust-region problem. The efficiency of the proposed ``Quasi-Newton Unitary Optimization with Trust-Region'' (QUOTR) method is compared to that of the standard Roothaan-Hall approach accelerated by the Direct Inversion of Iterative Subspace (DIIS), and other exact and approximate Newton solvers for mean-field (Hartree-Fock and Kohn-Sham) problems.

Here we present eight new candidates for exoplanets detected by the transit method at the Special Astrophysical Observatory of the Russian Academy of Sciences. Photometric observations were performed with a 50-cm robotic telescope during the second half of 2020. We detected transits with depths of $\Delta m = 0.056-0.173^m$ and periods $P = 18.8^h-8.3^d$ in the light curves of stars with magnitudes of $m = 14.3-18.8^m$. All considered stars are classified as dwarfs with radii of $R_* = 0.4-0.6 R_{sun}$ (with the uncertainty for one star up to $1.1 R_{sun}$). We estimated the candidate radii (all are greater than 1.4 times the Jovian radius), semi-major axes of their orbits ($0.012-0.035 AU$), and other orbital parameters by modelling. We report the light curves with transits for two stars obtained in 2022 based on individual observations., Comment: 16 pages, 14 figures, 3 tables

With the growing reliance of modern supercomputers on accelerator-based architectures such a GPUs, the development and optimization of electronic structure methods to exploit these massively parallel resources has become a recent priority. While significant strides have been made in the development of GPU accelerated, distributed memory algorithms for many-body (e.g. coupled-cluster) and spectral single-body (e.g. planewave, real-space and finite-element density functional theory [DFT]), the vast majority of GPU-accelerated Gaussian atomic orbital methods have focused on shared memory systems with only a handful of examples pursuing massive parallelism on distributed memory GPU architectures. In the present work, we present a set of distributed memory algorithms for the evaluation of the Coulomb and exact-exchange matrices for hybrid Kohn-Sham DFT with Gaussian basis sets via direct density-fitted (DF-J-Engine) and seminumerical (sn-K) methods, respectively. The absolute performance and strong scalability of the developed methods are demonstrated on systems ranging from a few hundred to over one thousand atoms using up to 128 NVIDIA A100 GPUs on the Perlmutter supercomputer., Comment: 45 pages, 9 figures

This Comment identifies errors in the formalism/implementation reported in Ref. 1 and discusses some aspects of that work that were not fully specified in the original publication. This Comment also provides reference numerical results for a simple system to ease future implementation of the approach by other researchers., Comment: 3 pages

To improve the efficiency of Gaussian integral evaluation on modern accelerated architectures FLOP-efficient Obara-Saika-based recursive evaluation schemes are optimized for the memory footprint. For the 3-center 2-particle integrals that are key for the evaluation of Coulomb and other 2-particle interactions in the density-fitting approximation the use of multi-quantal recurrences (in which multiple quanta are created or transferred at once) is shown to produce significant memory savings. Other innovation include leveraging register memory for reduced memory footprint and direct compile-time generation of optimized kernels (instead of custom code generation) with compile-time features of modern C++/CUDA. Performance of conventional and CUDA-based implementations of the proposed schemes is illustrated for both the individual batches of integrals involving up to Gaussians with low and high angular momenta (up to $L=6$) and contraction degrees, as well as for the density-fitting-based evaluation of the Coulomb potential. The computer implementation is available in the open-source LibintX library., Comment: 37 pages, 2 figures, 6 tables