Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics.

The explicit real-time propagation approach for time-dependent density functional theory (RT-TDDFT) has increasingly become a popular first-principles computational method for modeling various time-dependent electronic properties of complex chemical systems. In this Perspective, we provide a nontechnical discussion of how this first-principles simulation approach has been used to gain novel physical insights into nonequilibrium electron dynamics phenomena in recent years. Following a concise overview of the RT-TDDFT methodology from a practical standpoint, we discuss our recent studies on the electronic stopping of DNA in water and the Floquet topological phase as examples. Our discussion focuses on how RT-TDDFT simulations played a unique role in deriving new scientific understandings. We then discuss existing challenges and some new advances at the frontier of RT-TDDFT method development for studying increasingly complex dynamic phenomena and systems.

Theory of moment propagation for quantum dynamics in single-particle description.

We present a novel theoretical formulation for performing quantum dynamics in terms of moments within the single-particle description. By expressing the quantum dynamics in terms of increasing orders of moments, instead of single-particle wave functions as generally done in time-dependent density functional theory, we describe an approach for reducing the high computational cost of simulating the quantum dynamics. The equation of motion is given for the moments by deriving analytical expressions for the first-order and second-order time derivatives of the moments, and a numerical scheme is developed for performing quantum dynamics by expanding the moments in the Taylor series as done in classical molecular dynamics simulations. We propose a few numerical approaches using this theoretical formalism on a simple one-dimensional model system, for which an analytically exact solution can be derived. The application of the approaches to an anharmonic system is also discussed to illustrate their generality. We also discuss the use of an artificial neural network model to circumvent the numerical evaluation of the second-order time derivatives of the moments, as analogously done in the context of classical molecular dynamics simulations.

First-Principles Approach for Coupled Quantum Dynamics of Electrons and Protons in Heterogeneous Systems.

The coupled quantum dynamics of electrons and protons is ubiquitous in many dynamical processes involving light-matter interaction, such as solar energy conversion in chemical systems and photosynthesis. A first-principles description of such nuclear-electronic quantum dynamics requires not only the time-dependent treatment of nonequilibrium electron dynamics but also that of quantum protons. Quantum mechanical correlation between electrons and protons adds further complexity to such coupled dynamics. Here we extend real-time nuclear-electronic orbital time-dependent density functional theory (RT-NEO-TDDFT) to periodic systems and perform first-principles simulations of coupled quantum dynamics of electrons and protons in complex heterogeneous systems. The process studied is an electronically excited-state intramolecular proton transfer of o-hydroxybenzaldehyde in water and at a silicon (111) semiconductor-molecule interface. These simulations illustrate how environments such as hydrogen-bonding water molecules and an extended material surface impact the dynamical process on the atomistic level. Depending on how the molecule is chemisorbed on the surface, excited-state electron transfer from the molecule to the semiconductor surface can inhibit ultrafast proton transfer within the molecule. This Letter elucidates how heterogeneous environments influence the balance between the quantum mechanical proton transfer and excited electron dynamics. The periodic RT-NEO-TDDFT approach is applicable to a wide range of other photoinduced heterogeneous processes.

Effects of κ-carrageenan gum on 3D printability and rheological properties of pork pastes.

The effects of κ-carrageenan gum (KG) on the 3D printability and rheological properties of pork pastes were investigated in this study. There were five groups with different levels of KG (0, 2, 4, 6, and 8 g/kg) named as KG-0, KG-2, KG-4, KG-6, and KG-8, respectively. The addition of KG increased the yield stress, viscosity, shear stress, recovery percentage, storage modulus, loss modulus, and initial and average flow forces (P < 0.05). The results of low-field nuclear magnetic resonance analysis revealed that addition of KG reduced T21 and T22 (P < 0.05). The best printing parameters were obtained by accuracy and stability results: printing filling percent, 90%; printing speed, 35 mm⋅s-1; layer height, 2 mm; nozzle diameter, 1.55 mm, and KG addition level, 6 g/kg. KG addition improved the hardness, springiness, chewiness, cohesiveness, adhesiveness, and density, respectively (P < 0.05). The results suggested that KG addition improved the rheological properties and 3D printability of the pork pastes.

Polypyrrole coated carbon nanotube aerogel composite phase change materials with enhanced thermal conductivity, high solar-/electro- thermal energy conversion and storage.

Phase change materials (PCMs) have been widely investigated as promising thermal management materials due to their high thermal storage capacity, satisfactory heat transfer rate and multi-responsive energy conversion and storage characteristics. In this work, a shape-stabilized solar-/electro- responsive thermal energy capture and storage system is proposed involving polypyrrole (PPy)-deposited carbon nanotubes (CNT) heterogeneous porous aerogel as a supporting matrix and the paraffin wax (PW) as a PCM. The composite PCMs obtained via integration of PW into aerogel supports present a relatively high thermal storage density of 160.9 J/g and outstanding phase transition stability even after 100 heating-cooling cycles. Furthermore, great enhancement of thermal conductivity (0.64 W/m-1·K-1, 2.56 times that of PW) is achieved in the composite PCMs by inducing PPy coating as a binder in the gap between CNTs. The mechanism of heat transport enhancement is explored by molecular dynamics simulation. It concludes that the in-situ polymerization of PPy through the vapor deposition method on the CNT aerogels effectively builds additional thermal transfer channels and enhances the heat transport between CNT by coordinating the carbon atom vibration. Herein, this reported stratagem may shed light on preparing composite PCMs with high thermal conductivity and multi-energy utilization functions.

A Comprehensive Analysis of Physiologic and Hormone Basis for the Difference in Room-Temperature Storability between 'Shixia' and 'Luosanmu' Longan Fruits.

Although the effects of phytohormones (mainly salicylic acid) on the storability of longan fruit have been reported, the relationship between postharvest hormone variation and signal transduction and storability remains unexplored. The basis of physiology, biochemistry, hormone content and signalling for the storability difference at room-temperature between 'Shixia' and 'Luosanmu' longan fruit were examined. 'Luosanmu' longan exhibited faster pericarp browning, aril breakdown and rotting during storage. 'Luosanmu' pericarp exhibited higher malondialdehyde but faster decreased total phenolics, flavonoid, glutathione, vitamin C, catalase activity and gene expression. Higher H2O2 and malondialdehyde but lower glutathione, glutathione-reductase and peroxidase activities, while higher activities and gene expressions of polygalacturonase, ß-galactosidase and cellulose, lower covalent-soluble pectin, cellulose and hemicellulose but higher water-soluble pectin were observed in 'Luosanmu' aril. Lower abscisic acid and methyl jasmonate but higher expressions of LOX2, JAZ and NPR1 in pericarp, while higher abscisic acid, methyl jasmonate and salicylic acid together with higher expressions of ABF, JAZ, NPR1 and PR-1 in 'Luosanmu' aril were observed. In conclusion, the imbalance between the accumulation and scavenging of active oxygen in 'Luosanmu' longan might induce faster lipid peroxidation and senescence-related hormone signalling and further the polymerization of phenolics in pericarp and polysaccharide degradation in aril.

Improving the solubility of myofibrillar proteins in water by destroying and suppressing myosin molecular assembly via glycation.

Filamentous myosin is a self-assembling polymer that prevents myofibrillar proteins (MPs) from functioning in low ionic strength media. This study was aimed at investigating if glycation has the potential to improve the solubility of MPs in water. MPs were conjugated with monosaccharides, oligosaccharides, and polysaccharides under wet reaction conditions at 37 °C. The conjugation was verified by SDS-PAGE, FT-IR and amino acid analyses. MPs conjugated with dextran (DX) exhibited a higher solubility and dispersion stability in water, which corresponded to smaller particle size and more uniform distribution (P < 0.05). According to secondary and tertiary structure analyses, the loss of α-helix structures and unfolding of the MPs appear to be the main reasons for MP solubilization. Additionally, according to the zeta-potential, confocal laser scanning microscopy, and atomic force microscopy observation results, glycation can provide electrostatic repulsion or steric hindrance to disintegrate existing filamentous myosin aggregates and inhibit further self-assembly behavior.

Nuclear-electronic orbital approach to quantization of protons in periodic electronic structure calculations.

The nuclear-electronic orbital (NEO) method is a well-established approach for treating nuclei quantum mechanically in molecular systems beyond the usual Born-Oppenheimer approximation. In this work, we present a strategy to implement the NEO method for periodic electronic structure calculations, particularly focused on multicomponent density functional theory (DFT). The NEO-DFT method is implemented in an all-electron electronic structure code, FHI-aims, using a combination of analytical and numerical integration techniques as well as a resolution of the identity scheme to enhance computational efficiency. After validating this implementation, proof-of-concept applications are presented to illustrate the effects of quantized protons on the physical properties of extended systems, such as two-dimensional materials and liquid-semiconductor interfaces. Specifically, periodic NEO-DFT calculations are performed for a trans-polyacetylene chain, a hydrogen boride sheet, and a titanium oxide-water interface. The zero-point energy effects of the protons as well as electron-proton correlation are shown to noticeably impact the density of states and band structures for these systems. These developments provide a foundation for the application of multicomponent DFT to a wide range of other extended condensed matter systems.

Purification and Characterization of the Protease from Staphylococcus xylosus A2 Isolated from Harbin Dry Sausages.

The protease generated from Staphylococcus (S.) xylosus A2, which was isolated from Harbin dry sausages, was purified and characterized. The molecular weight of the purified protease was approximately 21.5 kDa, and its relative activity reached the highest at pH 6.0 and 50 °C. At pH 4.0−8.0 and temperatures of 20−50 °C, the protease was stable. Its activity was significantly improved by Ca2+ and Zn2+ ions (p < 0.05). The Michaelis constant and maximum velocity of the protease were 2.94 mg/mL and 19.45 U/mL·min, respectively. The thermodynamic parameters analysis suggested that the protease showed better catalytic properties at 40 °C. Moreover, the protease could hydrolyze meat proteins, and obtained hydrolysate is non-cytotoxic to the HEK-293 cells. These findings provide a theoretical basis for understanding the enzymatic characterization of S. xylosus A2 protease and its future application in fermented meat products.

Effect of the protease from Staphylococcus carnosus on the proteolysis, quality characteristics, and flavor development of Harbin dry sausage.

The effect of the addition of different levels of S. carnosus protease (0, 0.15, 0.30, 0.45 and 0.60 g/kg raw meat) on the proteolysis, quality characteristics, and flavor development of Harbin dry sausage was investigated. The results showed that the S. carnosus protease addition to Harbin dry sausage effectively promoted the degradation of meat proteins into peptides and free amino acids, thus resulting in tenderization and inhibiting fat oxidation. Moreover, the S. carnosus protease addition could promote the development of key flavor compounds such as some ketones, acids and esters. Sausage with S. carnosus protease levels of 0.45 g/kg exhibited the most attractive sensory attributes. Molecular docking showed that the S. carnosus protease can interact with myosin heavy chains. In summary, the S. carnosus protease addition can improve quality characteristics and flavor profile of Harbin dry sausage.

Interaction between protease from Staphylococcus epidermidis and pork myofibrillar protein: Flavor and molecular simulation.

This study investigated the influence of a protease from Staphylococcus (S.) epidermidis on the hydrolysis and flavor development in pork myofibrillar protein (MP). The surface hydrophobicity, fluorescence, Fourier transform infrared spectra, and atomic force microscopy analysis indicated that hydrolysis significantly changed surface hydrophobicity and secondary structure of MP (p < 0.05), and improved the stability of MP in water. The contents of free amino acid from MP, especially glutamic and alanine, significantly increased (p < 0.05), and the production of volatile compound such as aldehydes, alcohols and acid were promoted under the action of protease. MP treated with S. epidermidis protease is non-cytotoxic to the HEK-293 cells. Molecular docking analysis suggested that the interaction between the protease and actin was spontaneous and mainly involved hydrogen bonding forces. In summary, this study provides a theoretical basis for the future application of S. epidermidis protease in fermented meat products.

Effects of Modified Atmosphere Packaging with Various CO2 Concentrations on the Bacterial Community and Shelf-Life of Smoked Chicken Legs.

The effects of modified atmosphere packaging (MAP) with various CO2 concentrations on the bacterial community and shelf-life of smoked chicken legs during 25 d of storage at 4 °C were evaluated herein. Four treatments were stored in pallets (PAL) and MAP under 20% (M20), 60% (M60), and 100% (M100) CO2, respectively. The results indicated that the MAP treatments provided the legs with higher redness and hardness and lower yellowness, luminance, and lipid oxidation, compared with the PAL treatment. In addition, the MAP treatments effectively inhibited the growth of viable bacteria, delayed bacterial spoilage, and extended the shelf-life of the samples. The M60 and M100 treatments had a better inhibition effect on bacteria. In terms of bacterial community, Carnobacterium, Pseudomonas, Brochothrix, and Lactococcus were the most predominant genera in the 25 d-stored MAP samples, with Carnobacterium maltaromaticum, Pseudomonas fragi, Shewanella baltica, and Lactococcus piscium being the dominant species. However, while the inhibition effects of the M60 and M100 treatments on the bacterial community at Day 25 were similar, the outer package of the M100 treatment collapsed. Overall, the M60 treatment may be a promising approach to improving the quality and extending the shelf-life of smoked chicken legs.

Modeling Liquid Water by Climbing up Jacob's Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials.

Within the framework of Kohn-Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob's ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric-isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.

Physiological, Morphological and Antioxidant Responses of Pediococcus pentosaceus R1 and Lactobacillus fermentum R6 Isolated from Harbin Dry Sausages to Oxidative Stress.

As functional starter cultures and potential probiotics, the ability of lactic acid bacteria to resist oxidative stress is essential to maintain viability and functional properties. This study investigates the effects of H2O2 at different concentrations (0, 1, 2, and 3 mM) on the physiological, morphological, and antioxidant properties of Pediococcus pentosaceus R1 and Lactobacillus fermentum R6 isolated from Harbin dry sausages. The increase in H2O2 concentration induced a significant increase in reactive oxygen species and a decrease in intracellular ATP levels (p < 0.05). Based on scanning electron microscopy, transmission electron microscopy, and electric conductivity analysis, H2O2 stress caused cell deformation, the destruction of cell membrane integrity, partial loss of the cytoplasm, and an increase in the cell conductivity of both strains. H2O2 stress with 1 mM or 2 mM concentrations could effectively improve the scavenging rates of free radicals, the activities of superoxide dismutase and glutathione peroxide, and the total antioxidant capacity of both strains (p < 0.05). In conclusion, an appropriate oxidative stress contributed to the activation of the antioxidant defense system of both strains, conferred strains a better effect in inhibiting the oxidation of fermented foods, and improved the health of the host.

Stabilization of Hydroxide Ions at the Interface of a Hydrophobic Monolayer on Water via Reduced Proton Transfer.

We report a joint study using surface-specific sum-frequency vibrational spectroscopy and ab initio molecular dynamics simulations, respectively, on a pristine hydrophobic (sub)monolayer hexane-water interface, namely, the hexane/water interface with varied vapor pressures of hexane and different pHs in water. We show clear evidence that hexane on water revises the interfacial water structure in a way that stabilizes the hypercoordinated solvation structure and slows down the migration of hydroxide ion (OH^{-}) relative to that in bulk water. This mechanism effectively attracts the OH^{-} to the water-hydrophobic interface with respect to its counterion. The result illustrates the striking difference of proton transfer of hydrated OH^{-} at the interface and in the bulk, which is responsible for the intrinsic charging effect at the hydrophobic interface.

Aqueous solvation of the chloride ion revisited with density functional theory: impact of correlation and exchange approximations.

The specificity of aqueous halide solvation is fundamental to a wide range of bulk and interfacial phenomena spanning from biology to materials science. Halide polarizability is thought to drive the ion specificity, and if so, it is essential to have an accurate description of the electronic properties of halide ions in water. To this end, the solvation of the chloride anion, Cl- has been reinvestigated with state-of-the-art density functional theory. Specifically, the PBE-D3, PBE0-D3, and SCAN functionals have been employed to probe the impact of correlation and exchange approximations. Anticipating the findings, adding exact exchange improves the electronic structure, but simultaneously significantly reduces the Cl- polarizability, resulting in an over-structured Cl-O radial distribution function (RDF) and longer water H-bond lifetimes to Cl-. SCAN does not yield as much improvement in the energetics of Cl- relative to bulk water, but does result in a smaller reduction of the polarizability and thus a less structured Cl-O RDF, which agrees better with experiment. Special consideration is therefore warranted in assessing the impact of exchange on the energy, charge density, and the charge density response when designing and testing hybrid functionals for aqueous halide solvation.

Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water-Air Interface.

Density functional theory-based molecular dynamics simulations are increasingly being used for simulating aqueous interfaces. Nonetheless, the choice of the appropriate density functional, critically affecting the outcome of the simulation, has remained arbitrary. Here, we assess the performance of various exchange-correlation (XC) functionals, based on the metrics relevant to sum-frequency generation spectroscopy. The structure and dynamics of water at the water-air interface are governed by heterogeneous intermolecular interactions, thereby providing a critical benchmark for XC functionals. We find that the XC functionals constrained by exact functional conditions (revPBE and revPBE0) with the dispersion correction show excellent performance. The poor performance of the empirically optimized density functional (M06-L) indicates the importance of satisfying the exact functional condition. Understanding the performance of different XC functionals can aid in resolving the controversial interpretation of the interfacial water structure and direct the design of novel, improved XC functionals better suited to describing the heterogeneous interactions in condensed phases.

Importance of van der Waals effects on the hydration of metal ions from the Hofmeister series.

The van der Waals (vdW) interaction plays a crucial role in the description of liquid water. Based on ab initio molecular dynamics simulations, including the non-local and fully self-consistent density-dependent implementation of the Tkatchenko-Scheffler dispersion correction, we systematically studied the aqueous solutions of metal ions (K+, Na+, and Ca2+) from the Hofmeister series. Similar to liquid water, the vdW interactions strengthen the attractions among water molecules in the long-range, leading to the hydrogen bond networks softened in all the ion solutions. However, the degree that the hydration structure is revised by the vdW interactions is distinct for different ions, depending on the strength of short-range interactions between the hydrated ion and surrounding water molecules. Such revisions by the vdW interactions are important for the understanding of biological functionalities of ion channels.

Peracetylated sugar derivatives show high solubility in liquid and supercritical carbon dioxide.

[structure: see text] Acetylated sugars derivatives exhibit high solubility in liquid and supercritical carbon dioxide (scCO(2)). Peracetylated sorbitol and beta-D-galactose are soluble under mild conditions in scCO(2), high pressures are required to dissolve peracetylated beta-cyclodextrin, and peracetoxyalkyl chains impart CO(2)-solubility to amides.