Physicochemical properties of L- and DL-valine: first-principles calculations.

At present, physicochemical properties of amino acid molecular crystals are of the utmost interest. The compounds where molecules have different chirality are the focus of particular interest. This paper, presents a study on the structural and electronic properties of crystalline L- and DL-valine within the framework of density functional theory including van der Waals interactions. The results of this study showed that electronic properties of the two forms of valine are similar at zero pressure. Pressure leads to different responses in these crystals which is manifested as various deformations of molecules. The pressure effect on the infrared spectra and distribution of electron density of L- and DL-valine has been studied.

Rectified Gaussian Scale Mixtures and the Sparse Non-Negative Least Squares Problem.

In this paper, we develop a Bayesian evidence maximization framework to solve the sparse non-negative least squares problem (S-NNLS). We introduce a family of probability densities referred to as the Rectified Gaussian Scale Mixture (R-GSM), to model the sparsity enforcing prior distribution for the signal of interest. The R-GSM prior encompasses a variety of heavy-tailed distributions such as the rectified Laplacian and rectified Student-t distributions with a proper choice of the mixing density. We utilize the hierarchical representation induced by the R-GSM prior and develop an evidence maximization framework based on the Expectation-Maximization (EM) algorithm. Using the EM-based method, we estimate the hyper-parameters and obtain a point estimate for the solution of interest. We refer to this proposed method as rectified Sparse Bayesian Learning (R-SBL). We provide four EM-based R-SBL variants that offer a range of options to trade-off computational complexity to the quality of the E-step computation. These methods include the Markov Chain Monte Carlo EM, linear minimum mean square estimation, approximate message passing and a diagonal approximation. Using numerical experiments, we show that the proposed R-SBL method outperforms existing S-NNLS solvers in terms of both signal and support recovery, and is very robust against the structure of the design matrix.

A unified framework for sparse non-negative least squares using multiplicative updates and the non-negative matrix factorization problem.

We study the sparse non-negative least squares (S-NNLS) problem. S-NNLS occurs naturally in a wide variety of applications where an unknown, non-negative quantity must be recovered from linear measurements. We present a unified framework for S-NNLS based on a rectified power exponential scale mixture prior on the sparse codes. We show that the proposed framework encompasses a large class of S-NNLS algorithms and provide a computationally efficient inference procedure based on multiplicative update rules. Such update rules are convenient for solving large sets of S-NNLS problems simultaneously, which is required in contexts like sparse non-negative matrix factorization (S-NMF). We provide theoretical justification for the proposed approach by showing that the local minima of the objective function being optimized are sparse and the S-NNLS algorithms presented are guaranteed to converge to a set of stationary points of the objective function. We then extend our framework to S-NMF, showing that our framework leads to many well known S-NMF algorithms under specific choices of prior and providing a guarantee that a popular subclass of the proposed algorithms converges to a set of stationary points of the objective function. Finally, we study the performance of the proposed approaches on synthetic and real-world data.

Hydrostatic Pressure Effects on Structural and Electronic Properties of ETN and PETN from First-Principles Calculations.

We studied the structural and electronic properties of pentaerythritol tetranitrate (PETN) and erythritol tetranitrate (ETN) crystals within the framework of density functional theory with van der Waals interactions. The computed lattice parameters have good agreement with experimental data. Electronic and structural properties of the crystals under 0-20 GPa hydrostatic pressure were studied. The parameters of equations of state calculated from the theoretical data show good agreement with experiment within the studied pressure intervals. We have also calculated the detonation velocity and pressure.

Study elastic properties of the leucine and isoleuicine from first principles calculations.

I studied the elastic properties of crystalline L- and DL-forms of leucine and isoleucine within the framework of density functional theory with van der Waals interactions. The energy gaps of the considered crystals are 7.48-7.60 eV. Chiral molecules have the same chemical composition. Therefore, the study of crystalline amino acids provides a better understanding of how the structure of molecules affects mechanical properties of molecular crystals. Complete set of elastic constants for L-leucine, L-isoleucine, DL-leucine and DL-isoleucine were calculated. Linear compressibility of crystals has high anisotropy. The crystalline L- and DL-forms of leucine and isoleucine have different mechanical properties. Linear compressibility has a negative value for DL-isoleucine. My calculations predict that L-leucine and L-isoleucine are ductile compounds, while DL-leucine and DL-isoleucine are brittle compounds.

Electronic structure and chemical bond in naphthalene and anthracene.

We investigated the electronic structure of crystalline naphthalene and anthracene within the framework of density functional theory including van der Waals interactions (DFT-D). It is established that for better agreement with experimental values it is necessary to use the increased values of the van der Waals radii, which is caused by an overestimated value of the van der Waals interactions in crystalline linear oligoacenes. Utilization of the DFT-D leads to a correct account of the dispersion forces, which results in a high precision of the computed lattice parameters and cohesive energy. Based on the relaxed crystal structures, we have computed the total and deformation electron density and determined the mechanism of chemical bonds formation in crystals of naphthalene and anthracene. It has been established that the chemical bond in molecular crystals is formed under the influence of not only intramolecular but also intermolecular interactions. On the basis of the Mulliken population analysis it was revealed that two C(3) atoms in naphthalene (or C(3) and C(4) in anthracene) have a positive charge and the population of the rest of the carbon atoms increased, as compared with isolated molecule.

A Temporal Boosted YOLO-Based Model for Birds Detection around Wind Farms.

Object detection for sky surveillance is a challenging problem due to having small objects in a large volume and a constantly changing background which requires high resolution frames. For example, detecting flying birds in wind farms to prevent their collision with the wind turbines. This paper proposes a YOLOv4-based ensemble model for bird detection in grayscale videos captured around wind turbines in wind farms. In order to tackle this problem, we introduce two datasets-(1) Klim and (2) Skagen-collected at two locations in Denmark. We use Klim training set to train three increasingly capable YOLOv4 based models. Model 1 uses YOLOv4 trained on the Klim dataset, Model 2 introduces tiling to improve small bird detection, and the last model uses tiling and temporal stacking and achieves the best mAP values on both Klim and Skagen datasets. We used this model to set up an ensemble detector, which further improves mAP values on both datasets. The three models achieve testing mAP values of 82%, 88%, and 90% on the Klim dataset. mAP values for Model 1 and Model 3 on the Skagen dataset are 60% and 92%. Improving object detection accuracy could mitigate birds' mortality rate by choosing the locations for such establishment and the turbines location. It can also be used to improve the collision avoidance systems used in wind energy facilities.

Study of the Elastic Properties of the Energetic Molecular Crystals Using Density Functionals with van der Waals Corrections.

We studied the elastic properties of crystalline energetic materials within the framework of density functional theory with van der Waals interactions (DFT-D3(BJ) and rev-vdW-DF2). The full sets of elastic constants were computed. The computed parameters are in good agreement with the experimental data. Among the crystals studied in this work, FOX7 had the lowest compressibility value of 0.0034 GPa-1 and had the highest anisotropy. Crystalline pentaerythritol tetranitrate had almost isotropic mechanical properties.

SSGD: SPARSITY-PROMOTING STOCHASTIC GRADIENT DESCENT ALGORITHM FOR UNBIASED DNN PRUNING.

While deep neural networks (DNNs) have achieved state-of-the-art results in many fields, they are typically over-parameterized. Parameter redundancy, in turn, leads to inefficiency. Sparse signal recovery (SSR) techniques, on the other hand, find compact solutions to overcomplete linear problems. Therefore, a logical step is to draw the connection between SSR and DNNs. In this paper, we explore the application of iterative reweighting methods popular in SSR to learning efficient DNNs. By efficient, we mean sparse networks that require less computation and storage than the original, dense network. We propose a reweighting framework to learn sparse connections within a given architecture without biasing the optimization process, by utilizing the affine scaling transformation strategy. The resulting algorithm, referred to as Sparsity-promoting Stochastic Gradient Descent (SSGD), has simple gradient-based updates which can be easily implemented in existing deep learning libraries. We demonstrate the sparsification ability of SSGD on image classification tasks and show that it outperforms existing methods on the MNIST and CIFAR-10 datasets.

Multiphoton ionization and dissociation of diazirine: a theoretical and experimental study.

Multiphoton ionization and dissociation processes in diazirine have been studied experimentally via 304-325 nm two-photon absorption and theoretically by using the EOM-CCSD and B3LYP methods. The electronic structure calculations identified two excited valence states and four Rydberg states in the region 4.0-8.5 eV. In one-photon excitation, the strongest absorption is to the 2(1)A(1)(3p(x) <-- n) Rydberg state, whereas in two-photon absorption at comparable energies the first photon excites the low-lying 1(1)B(2) (pi* <-- n) valence state, from which the strongest absorption is to the dissociative valence 1(1)A(2) (pi* <-- sigma(NN)) state. The diazirine ion is calculated to be rather unstable, with a binding energy of only 0.73 eV and a geometry that resembles a weakly bound CH(2)(+)...N(2) complex. In the experimental studies, resonance-enhanced multiphoton ionization (REMPI) experiments show no ions at the parent diazirine mass but only CH(2)(+) ions from dissociative photoionization. It is proposed that weak one-photon absorption to the 1(1)B(2) state is immediately followed by more efficient absorption of another photon to reach the 1(1)A(2) state from which competition between ionization and fast dissociation takes place. Strong signals of CH(+) ions are also detected and assigned to 2 + 1 REMPI via the D(2)Pi (v' = 2) <-- <-- X(2)Pi (v'' = 0) two-photon transition of CH fragments. Velocity map CH(+) images show that CH(X, v'' = 0, N'') fragments are born with substantial translational energy, indicating that they arise from absorption of two photons in diazirine. It is argued that two-photon processes via the 1(1)B(2) intermediate state are very efficient in this wavelength range, leading predominantly to dissociation of diazirine from the 1(1)A(2) state. The most likely route to CH(X) formation is isomerization to isodiazirine followed by dissociation to CH + HN(2). In agreement with other theoretical papers, we recommend revisions of the heats of formation of diazirine and diazomethane.

Vibronic structure and ion core interactions in Rydberg states of diazomethane: an experimental and theoretical investigation.

Vibronic transitions to the 21A2(3py <-- pi) Rydberg state of CH2N2, CD2N2, and CHDN2 were recorded by 2 + 1 REMPI spectroscopy, and kinetic energy distributions (eKE) of photoelectrons from ionization of selected vibronic levels were determined by velocity map imaging. Normal-mode frequencies were obtained for the 21A2(3py) Rydberg state and for the cation. Mixed levels of the 21A2(3py) and 21B1(3pz) of the three isotopologs were identified by photoelectron imaging and analyzed. The equilibrium geometries and harmonic vibrational frequencies of the electronic states of neutral diazomethane were calculated by CCSD(T)/cc-pVTZ, and B3LYP/6-311G(2df,p). The latter method was also used to calculate isotope shifts for the ground-state neutral and cation. Geometry and frequencies of the ground state of the cation were calculated by CCSD(T)/cc-pVTZ, using the unrestricted (UHF) reference. The equilibrium structures, frequencies, and isotope shifts of the 21A2(3py) and 21B1(3pz) Rydberg states were calculated by EOM-EE-CCSD/6-311(3+,+)G(2df). In all cases where comparisons with experimental results were available, the agreement between theory and experiment was very good allowing a full analysis of trends in structure and vibrational frequencies in going from the neutral species to the excited Rydberg states, 21A2(3py) and 21B1(3pz), and the cation. Although the 21A2(3py) and 21B1(3pz) states have planar C2v symmetry like the ion, they exhibit differences in geometry due to the specific interactions of the electron in the 3py and 3pz orbitals with the nuclei charge distributions of the ion core. Moreover, trends in normal-mode frequencies in the ground states of the neutral and ion and the 21A2(3py) and 21B1(3pz) Rydberg states are consistent with removing an electron from the bonding piCN-orbital, which also has an antibonding character with respect to NN. To explain the observed trends, the vibrational modes are divided into two groups that involve displacements mainly (i) along the CNN framework and (ii) in the CH2 moiety. Trends in the first group are due mostly to the effect of the lower CN and NN bond orders, whereas those in the second group are due to the interaction between the positively charged hydrogens and the Rydberg electron density, and the hybridization of the carbon. Within each group, marked differences in behavior between the in-plane and out-of-plane modes are observed.

Theoretical and experimental investigations of the electronic Rydberg states of diazomethane: assignments and state interactions.

The electronic states of diazomethane in the region 3.00-8.00 eV have been characterized by ab initio calculations, and electronic transitions in the region 6.32-7.30 eV have been examined experimentally using a combination of 2 + 1 REMPI spectroscopy and photoelectron imaging in a molecular beam. In the examined region, three Rydberg states of 3p character contribute to the transitions, 2(1)A2(3p(y) <-- pi), 2(1)B1(3p(z) <-- pi), and 3(1)A1(3p(x) <-- pi). The former two states are of mostly pure Rydberg character and exhibit a resolved K structure, whereas the 3(1)A1(3p(x) <-- pi) state is mixed with the valence 2(1)A1(pi* <-- pi) state, which is unbound and is strongly predissociative. Analyses of photoelectron kinetic energy distributions indicate that the ground vibrational level of the 2(1)B1(3p(z)) state is mixed with the 2(1)A2(3p(y)) nu(9) level, which is of B1 vibronic symmetry. The other 2(1)A2(3p(y)) vibronic states exhibit pure Rydberg character, generating ions in single vibrational levels. The photoelectron spectra of the 3(1)A1(3p(x) <-- pi) state, on the other hand, give rise to many states of the ion as a result of strong mixing with the valence state, as evidenced also in the ab initio calculations. The equilibrium geometries of the electronic states of neutral diazomethane were calculated by CCSD(T), using the cc-pVTZ basis, and by B3LYP, using the 6-311G(2df,p) basis. Geometry and frequencies of the ground state of the cation were calculated by CCSD(T)/cc-pVTZ, using the unrestricted (UHF) reference. Vertical excitation energies were calculated using EOM-CCSD/6-311(3+,+)G* at the B3LYP optimized geometry. The theoretical results show that the 2(1)A2(3p(y) <-- pi) and 2(1)B1(3p(z) <-- pi) states have geometries similar to the ion, which has C(2v) symmetry, with slight differences due to the interactions of the electron in the 3p orbital with the nuclei charge distributions. The geometry of the 3(1)A1(3p(x) <-- pi) state is quite different and has Cs symmetry. The experimental and theoretical results agree very well, both in regard to excitation energies and to vibrational modes of the ion.

Imaging the state-specific vibrational predissociation of the C2H2-NH3 hydrogen-bonded dimer.

The state-to-state vibrational predissociation (VP) dynamics of the hydrogen-bonded ammonia-acetylene dimer were studied following excitation in the asymmetric CH stretch. Velocity map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) were used to determine pair-correlated product energy distributions. Following vibrational excitation of the asymmetric CH stretch fundamental, ammonia fragments were detected by 2 + 1 REMPI via the B1E'' <-- X1A1' and C'1A1' <-- X1A1' transitions. The fragments' center-of-mass (c.m.) translational energy distributions were determined from images of selected rotational levels of ammonia with one or two quanta in the symmetric bend (nu2 umbrella mode) and were converted to rotational-state distributions of the acetylene co-fragment. The latter is always generated with one or two quanta of bending excitation. All the distributions could be fit well when using a dimer dissociation energy of D0 = 900 +/- 10 cm(-1). Only channels with maximum translational energy <150 cm(-1) are observed. The rotational excitation in the ammonia fragments is modest and can be fit by temperatures of 150 +/- 50 and 50 +/- 20 K for 1nu2 and 2nu2, respectively. The rotational distributions in the acetylene co-fragment pair-correlated with specific rovibrational states of ammonia appear statistical as well. The vibrational-state distributions, however, show distinct state specificity among channels with low translational energy release. The predominant channel is NH3(1nu2) + C2H2(2nu4 or 1nu4 + 1nu5), where nu4 and nu5 are the trans- and cis-bend vibrations of acetylene, respectively. A second observed channel, with much lower population, is NH3(2nu2) + C2H2(1nu4). No products are generated in which the ammonia is in the vibrational ground state or the asymmetric bend (1nu4) state, nor is acetylene ever generated in the ground vibrational state or with CC stretch excitation. The angular momentum (AM) model of McCaffery and Marsh is used to estimate impact parameters in the internal collisions that give rise to the observed rotational distributions. These calculations show that dissociation takes place from bent geometries, which can also explain the propensity to excite fragment bending levels. The low recoil velocities associated with the observed channels facilitate energy exchange in the exit channel, which results in statistical-like fragment rotational distributions.

Imaging study of vibrational predissociation of the HCl-acetylene dimer: pair-correlated distributions.

The state-to-state predissociation dynamics of the HCl-acetylene dimer were studied following excitation in the asymmetric C-H (asym-CH) stretch and the HCl stretch. Velocity map imaging (VMI) and resonance enhanced multiphoton ionization (REMPI) were used to determine pair-correlated product energy distributions. Different vibrational predissociation mechanisms were observed for the two excited vibrational levels. Following excitation in the of the asym-CH stretch fundamental, HCl fragments in upsilon = 0 and j = 4-7 were observed and no HCl in upsilon = 1 was detected. The fragments' center-of-mass (c.m.) translational energy distributions were derived from images of HCl (j = 4-7), and were converted to rotational state distributions of the acetylene co-fragment by assuming that acetylene is generated with one quantum of C-C stretch (nu(2)) excitation. The acetylene pair-correlated rotational state distributions agree with the predictions of the statistical phase space theory, restricted to acetylene fragments in 1nu(2). It is concluded that the predissociation mechanism is dominated by the initial coupling of the asym-CH vibration to a combination of C-C stretch and bending modes in the acetylene moiety. Vibrational energy redistribution (IVR) between acetylene bending and the intermolecular dimer modes leads to predissociation that preserves the C-C stretch excitation in the acetylene product while distributing the rest of the available energy statistically. The predissociation mechanism following excitation in the Q band of the dimer's HCl stretch fundamental was quite different. HCl (upsilon = 0) rotational states up to j = 8 were observed. The rovibrational state distributions in the acetylene co-fragment derived from HCl (j = 6-8) images were non-statistical with one or two quanta in acetylene bending vibrational excitation. From the observation that all the HCl(j) translational energy distributions were similar, it is proposed that there exists a constraint on conversion of linear to angular momentum during predissociation. A dimer dissociation energy of D(0) = 700 +/- 10 cm(-1) was derived.

Atomic force microscopy detection of molecular complexes in multiprotein P450cam containing monooxygenase system.

The application of atomic force microscopy (AFM) technique in proteomic research, identification and visualization of individual molecules and molecular complexes within the P450cam containing monooxygenase system was demonstrated. The method distinguishes between the binary protein complexes and appropriate monomeric proteins and, also, between the binary and ternary complexes. The AFM images of the components of a cytochrome P450cam containing monooxygenase system - cytochrome P450cam (P450cam), putidaredoxin (Pd) and putidaredoxin reductase (PdR) - were obtained on a mica support. The molecules of P450cam, Pd and PdR were found to have typical heights of 2.6 +/- 0.3 nm, 2.0 +/- 0.3 and 2.8 +/- 0.3 nm, respectively. The measured heights of the binary Pd/PdR and P450cam/PdR complexes were 4.9 +/- 0.3 nm and 5.1 +/- 0.3 nm, respectively. The binary P450cam/Pd complexes were found to have a typical height of about (3.9 / 5.7 nm) and the ternary PdR/Pd/P450cam complexes, a typical height of about 9.1 +/- 0.3 nm.