Enhancement of the mechanical and thermal transport properties of carbon nanotube yarns by boundary structure modulation.

Carbon nanotubes (CNTs) exhibit extremely high nanoscopic thermal/electrical transport and mechanical properties. However, the macroscopic properties of assembled CNTs are significantly lower than those of CNTs because of the boundary structure between the CNTs. Therefore, it is crucial to understand the relationship between the nanoscopic boundary structure in CNTs and the macroscopic properties of the assembled CNTs. Previous studies have shown that the nanoscopic phonon transport and macroscopic thermal transport in CNTs are improved by Joule annealing because of the improved boundary Van-der-Waals interactions between CNTs via the graphitization of amorphous carbon. In this study, we investigate the mechanical strength and thermal/electrical transport properties of CNT yarns with and without Joule annealing at various temperatures, analyzing the phenomena occurring at the boundaries of CNTs. The obtained experimental and theoretical results connect the nanoscopic boundary interaction of CNTs in CNT yarns and the macroscopic mechanical and transport properties of CNT yarns.

Sulfated vizantin causes detachment of biofilms composed mainly of the genus Streptococcus without affecting bacterial growth and viability.

BACKGROUND: Sulfated vizantin, a recently developed immunostimulant, has also been found to exert antibiofilm properties. It acts not as a bactericide, but as a detachment-promoting agent by reducing the biofilm structural stability. This study aimed to investigate the mechanism underlying this activity and its species specificity using two distinct ex vivo oral biofilm models derived from human saliva. RESULTS: The biofilm, composed mainly of the genus Streptococcus and containing 50 µM of sulfated vizantin, detached significantly from its basal surface with rotation at 500 rpm for only 15 s, even when 0.2% sucrose was supplied. Expression analyses for genes associated with biofilm formation and bacterial adhesion following identification of the Streptococcus species, revealed that a variety of Streptococcus species in a cariogenic biofilm showed downregulation of genes encoding glucosyltransferases involved in the biosynthesis of water-soluble glucan. The expression of some genes encoding surface proteins was also downregulated. Of the two quorum sensing systems involved in the genus Streptococcus, the expression of luxS in three species, Streptococcus oralis, Streptococcus gordonii, and Streptococcus mutans, was significantly downregulated in the presence of 50 µM sulfated vizantin. Biofilm detachment may be facilitated by the reduced structural stability due to these modulations. As a non-specific reaction, 50 µM sulfated vizantin decreased cell surface hydrophobicity by binding to the cell surface, resulting in reduced bacterial adherence. CONCLUSION: Sulfated vizantin may be a candidate for a new antibiofilm strategy targeting the biofilm matrix while preserving the resident microflora.

Effect of water aging on the anti-biofilm properties of glass ionomer cement containing fluoro-zinc-silicate fillers.

A previous study has reported that a novel fluoro-zinc-silicate glass ionomer cement (Caredyne Restore) showed superior anti-biofilm effects by interfering with bacterial adhesion. However, the active ions may degrade with time. This study aimed to assess the valid anti-biofilm effects of Caredyne Restore after being aged by water immersion for 3 weeks. Streptococcus mutans biofilm was allowed to grow on the surface before and after water aging for 24 h using a modified Robbins device flow-cell system. The results showed water aging promoted biofilm formation. Insufficient amount of fluoride and zinc ions were released from Caredyne Restore after water aging under neutral pH condition. An acidic pH is needed to exert effective anti-biofilm properties. As the release of active ions from Caredyne Restore will gradually decrease after the restoration,  the restoration may not prevent biofilm formation after 3 weeks while neutral pH is maintained by the buffering capacity of saliva.

Effects of a sub-minimum inhibitory concentration of chlorhexidine gluconate on the development of in vitro multi-species biofilms.

Following antimicrobial administrations in oral environments, bacteria become exposed to a sub-minimum inhibitory concentration (sub-MIC), which can induce in vitro single-species biofilms. This study explored the effects of chlorhexidine gluconate (CHG) at a sub-MIC on in vitro multi-species biofilms comprising Streptococcus mutans, Streptococcus oralis and Actinomyces naeslundii. CHG at a sub-MIC was found to induce in vitro biofilm growth, although the bacterial growth was not significantly different from that in the control. The gene transcription related to S. mutans multi-species biofilm formation with CHG at a sub-MIC was significantly higher than that of the control, but this was not found in S. mutans single-species biofilms. The bio-volume of extracellular polysaccharides with CHG at a sub-MIC was significantly higher than that of the control. This suggests that CHG at a sub-MIC may promote the development of multi-species biofilms by affecting the gene transcription related to S. mutans biofilm formation.

Effect of a novel glass ionomer cement containing fluoro-zinc-silicate fillers on biofilm formation and dentin ion incorporation.

OBJECTIVES: This study is aimed at evaluating the effect of a new glass ionomer cement (GIC) containing fluoro-zinc-silicate fillers on biofilm formation and ion incorporation. MATERIALS AND METHODS: Streptococcus mutans biofilms were developed on two GIC materials: Caredyne Restore (CD) and Fuji VII (FJ); and hydroxyapatite (HA) for 24 h at 37 °C using a flow cell system. The morphological structure and bacterial viability were analyzed using a confocal laser scanning microscopy. Bacterial adhesion during the initial 2 h was also assessed by viable cell counting. To study the ion incorporation, restored cavities prepared on the root surfaces of human incisors were subjected to the elemental mapping of the zinc and fluoride ions in the GIC-dentin interface using a wavelength-dispersive X-ray spectroscopy electron probe microanalyzer. RESULTS: Morphological observations revealed that biofilm formation in the CD group was remarkably inhibited compared with the HA and FJ groups, exhibiting sparse, thinner biofilm clusters. The microorganisms adhering to the CD group were significantly inhibited, revealing 2.9 ± 0.4 for CD, 4.9 ± 0.2 for FJ, and 5.4 ± 0.4 log colony-forming units (CFU) for HA. The CD zinc ion incorporation depth was 72.2 ± 8.0 µm. The fluoride penetration of CD was three times deeper than that of FJ; this difference was statistically significant (p < 0.05). CONCLUSIONS: Enhanced by the incorporation of zinc and fluoride ions, the new GIC inhibited biofilm formation by interfering with bacterial adhesion. CLINICAL RELEVANCE: A novel GIC comprised of fluoro-zinc-silicate fillers may improve clinical outcomes, such as root caries and minimally invasive dentistry.

Adjunct use of mouth rinses with a sonic toothbrush accelerates the detachment of a Streptococcus mutans biofilm: an in vitro study.

BACKGROUND: The aim of this in vitro study was to examine the possible enhancement of the biofilm peeling effect of a sonic toothbrush following the use of an antimicrobial mouth rinse. METHODS: The biofilm at a noncontact site in the interdental area was treated by sound wave convection with the test solution or by immersion in the solution. The biofilm peeling effect was evaluated by determining the bacterial counts and performing morphological observations. A Streptococcus mutans biofilm was allowed to develop on composite resin discs by cultivation with stirring at 50 rpm for 72 h. The specimens were then placed in recesses located between plastic teeth and divided into an immersion group and a combination group. The immersion group was treated with phosphate buffer, chlorhexidine digluconate Peridex™ (CHX) mouth rinse or Listerine® Fresh Mint (EO) mouth rinse. The combination group was treated with CHX or EO and a sonic toothbrush. RESULTS: The biofilm thickness was reduced by approximately one-half compared with the control group. The combination treatment produced a 1 log reduction in the number of bacteria compared to the EO immersion treatment. No significant difference was observed in the biofilm peeling effect of the immersion group compared to the control group. CONCLUSIONS: The combined use of a sonic toothbrush and a mouth rinse enhanced the peeling of the biofilm that proliferates in places that are difficult to reach using mechanical stress.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION.

Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance.

Excess Hydrogen Bond at the Ice-Vapor Interface around 200 K.

Phase-resolved sum-frequency generation measurements combined with molecular dynamics simulations are employed to study the effect of temperature on the molecular arrangement of water on the basal face of ice. The topmost monolayer, interrogated through its nonhydrogen-bonded, free O-H stretch peak, exhibits a maximum in surface H-bond density around 200 K. This maximum results from two competing effects: above 200 K, thermal fluctuations cause the breaking of H bonds; below 200 K, the formation of bulklike crystalline interfacial structures leads to H-bond breaking. Knowledge of the surface structure of ice is critical for understanding reactions occurring on ice surfaces and ice nucleation.

π+-π+ stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces.

The interfacial structure of room temperature ionic liquids (RTILs) controls many of the unique properties of RTILs, such as the high capacitance of RTILs and the efficiency of charge transport between RTILs and electrodes. RTILs have been experimentally shown to exhibit interfacial molecular layering structures over a 10 Å length scale. However, the driving force behind the formation of these layered structures has not been resolved. Here, we report ab initio molecular dynamics simulations of imidazolium RTIL/air and RTIL/graphene interfaces along with force field molecular dynamics simulations. We find that the π+-π+ interaction of imidazolium cations enhances the layering structure of RTILs, despite the electrostatic repulsion. The length scales of the molecular layering at the RTIL/air and RTIL/graphene interfaces are very similar, manifesting the limited effect of the substrate on the interfacial organization of RTILs.

Communication: Constant uncertainty molecular dynamics: A simple and efficient algorithm to incorporate quantum nature into a real-time molecular dynamics simulation.

We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.

The surface roughness, but not the water molecular orientation varies with temperature at the water-air interface.

We examine the temperature dependence of the interfacial molecular structure at the water-air interface by combining experimental and simulated sum-frequency generation (SFG) spectroscopy. The experimental SFG spectra of the OH-stretching mode show a decrease in the amplitude at ∼3300 cm(-1) with increasing temperature, while the 3700 cm(-1) 'free OH' SFG feature is insensitive to temperature changes. The simulated spectra are in excellent agreement with experiment. A comparison between interfacial SFG spectra and bulk infrared/Raman spectra reveals that the variation of the SFG signal due to the temperature change is not caused by a temperature-dependent OH bond orientation of the interfacial water molecules, but can be fully accounted for by the temperature dependence of the optical response of water. These results indicate that while the thickness of the interfacial region varies with temperature, the molecular organization of interfacial water at the water-air interface is surprisingly insensitive to temperature changes.

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Calculating two-dimensional THz-Raman-THz and Raman-THz-THz signals for various molecular liquids: the samplers.

Recently, two-dimensional (2D) THz-Raman spectroscopy has been used to investigate the intermolecular modes of liquid water. We examine such 2D spectroscopy signals by means of full molecular dynamics (MD) simulations. In this way, we carry out a detailed analysis of intermolecular interactions that play an essential role in many important chemical processes. We calculate 2D Raman-THz-THz (RTT), THz-Raman-THz (TRT), and 2D Raman signals for liquid water, methanol, formamide, acetonitrile, formaldehyde, and dimethyl sulfoxide using an equilibrium-non-equilibrium hybrid MD simulation algorithm originally developed for 2D Raman spectroscopy. These signals are briefly analyzed in terms of anharmonicity and nonlinear polarizability of vibrational modes on the basis of the 2D Raman signals calculated from a Brownian oscillator model with a nonlinear system-bath interaction. We find that the anharmonic contribution is dominant in the RTT case, while the nonlinear polarizability contribution is dominant in the TRT case. For water and methanol, we observed vibrational echo peaks of librational motion in the 2D TRT signals. The predicted signal profiles and intensities that we obtained provide valuable information that can be applied to 2D spectroscopy experiments, allowing them to be carried out more efficiently.

Nuclear Quantum Dynamics of Three-Dimensional Condensed-Phase Systems by Constant Uncertainty Molecular Dynamics.

Constant uncertainty molecular dynamics (CUMD), which was developed to include nuclear quantum effects (NQEs) in molecular dynamics (MD) simulations, is extended to three-dimensional condensed-phase systems. Its applicability was verified via CUMD simulations of bulk water and ice Ih with the q-TIP4P/F potential model. The simulated radial distribution functions, proton momentum distributions, and infrared spectra were compared with those of previous studies in which the simulations were carried out on the basis of the imaginary-time path-integral formalism. We found that CUMD can function as an alternative trajectory-based simulation method for including static and dynamic NQEs in MD simulations of three-dimensional condensed-phase systems.

A Combined Reaction Path Search and Hybrid Solvation Method for the Systematic Exploration of Elementary Reactions at the Solid-Liquid Interface.

We present a combined simulation method of single-component artificial force induced reaction (SC-AFIR) and effective screening medium combined with the reference interaction site model (ESM-RISM), termed SC-AFIR+ESM-RISM. SC-AFIR automatically and systematically explores the chemical reaction pathway, and ESM-RISM directly simulates the precise electronic structure at the solid-liquid interface. Hence, SC-AFIR+ESM-RISM enables us to explore reliable reaction pathways at the solid-liquid interface. We applied it to explore the dissociation pathway of an H2O molecule at the Cu(111)/water interface. The reaction path networks of the whole reaction and the minimum energy paths from H2O to H2 + O depend on the interfacial environment. The qualitative difference in the energy diagrams and the resulting change in the kinematically favored dissociation pathway upon changing the solvation environments are discussed. We believe that SC-AFIR+ESM-RISM will be a powerful tool to reveal the details of chemical reactions in surface catalysis and electrochemistry.

A Horizontal Sequential Cutting Method to Estimate the Effectiveness of Dentin Disinfection by Using Confocal Laser Scanning Microscopy.

INTRODUCTION: This study aimed to develop a technique to create sequential slices, allowing the fluorescent visualization of bacterial viability in all parts of an infected dentin. METHODS: Cylindrical dentin blocks were prepared from freshly extracted human teeth with a single-rooted canal. Each block was immersed in 5% sodium hypochlorite (NaOCl) and 17% EDTA for 5 minutes before being infected with Enterococcus faecalis. The bacteria were allowed to develop inside dentin specimens for 28 days under anaerobic conditions. The specimens were exposed in 2% NaOCl for either 2 minutes or 20 minutes at 20°C, 37°C, and 45°C, respectively. After staining with calcein AM (Thermo Fisher Scientific, Waltham, MA) and propidium iodide, the samples were cryoembedded, mounted on an adhesive film, and sectioned at a thickness of 10 µm along the running of the dentinal tubules. Stacks of fluorescent images were collected in the z dimension using confocal laser scanning microscopy, and the maximum affected distance from a root canal was measured from the 3-dimensional reconstructed image. The reliability of this technique was verified by comparison with a dye bleaching test. RESULTS: Horizontal sequential sections preserving 3-dimensional bacterial distribution and their viabilities could be made without decalcification. The treatment time contributed to the penetration of NaOCl into dentinal tubules, whereas temperature did not significantly affect the penetration. The judgment by confocal laser scanning microscopic analysis was consistent with that of a dye bleaching test. CONCLUSIONS: The horizontal sectioning method has the advantage of creating sequential sections, allowing information to be imaged at every portion.

Two-dimensional fifth-order Raman spectroscopy of liquid formamide: Experiment and Theory.

The fifth-order two-dimensional (2D) Raman spectrum of liquid formamide has been obtained. The absolute signal levels, qualitative features, as well as quantitative aspects of the 2D spectrum are found to be in good agreement with recent molecular dynamics calculations. The most important singular feature is the relatively strong rephasing signal observed along the diagonal. This finding illustrates the more structured nature of the hydrogen bond network of liquid formamide in comparison with simple liquids as exemplified by CS(2). The theoretical calculations have been extended to include comparisons of different potentials that illustrate the sensitivity of the experiment to the anharmonic motions in the liquid state. The theoretical results point out the key features in the 2D spectrum that probe the essential details in the intermolecular potential. The experiment has been demonstrated to provide new insight into collective effects operating in hydrogen bonded liquids and opens up the exploration of other liquids with this approach.

Definition of Free O-H Groups of Water at the Air-Water Interface.

Free O-H groups of water are often found at the water-hydrophobic medium interface, e.g. for water contact with hydrophobic protein residues, or at the water-air interface. In surface-specific vibrational spectroscopic studies using sum-frequency generation (SFG) spectroscopy, free O-H groups are experimentally well characterized in the O-H stretch region by a sharp 3700 cm-1 peak. Although these free O-H groups are often defined as the O-H groups which are not hydrogen-bonded to other water molecules, a direct correlation between such non-hydrogen-bonded O-H groups and the 3700 cm-1 SFG response has been lacking. Our data show that commonly used hydrogen bond definitions do not adequately capture the free O-H groups contributing to the 3700 cm-1 peak. We thus formulate a new definition for capturing the subensemble of the surface free O-H groups using the intermolecular distance and the angle formed by the water dimer, through the comparison of the ∼3700 cm-1 SFG response and the responses from the selected free O-H groups at the HOD-air interface. Using these optimized free O-H group definitions, we infer the fraction of interfacial water molecules with free O-H groups of 28%, a vibrational lifetime of the free O-H groups of 1.3 ps, and the angle formed by the free O-H groups and the surface normal of 67° at the water-air interface. We expect that this improved free O-H group definition can be helpful in exploring the structure and dynamics of the interfacial water.

Coupling between intra- and intermolecular motions in liquid water revealed by two-dimensional terahertz-infrared-visible spectroscopy.

The interaction between intramolecular and intermolecular degrees of freedom in liquid water underlies fundamental chemical and physical phenomena such as energy dissipation and proton transfer. Yet, it has been challenging to elucidate the coupling between these different types of modes. Here, we report on the direct observation and quantification of the coupling between intermolecular and intramolecular coordinates using two-dimensional, ultra-broadband, terahertz-infrared-visible (2D TIRV) spectroscopy and molecular dynamics calculations. Our study reveals strong coupling of the O-H stretch vibration, independent of the degree of delocalization of this high-frequency mode, to low-frequency intermolecular motions over a wide frequency range from 50 to 250 cm-1, corresponding to both the intermolecular hydrogen bond bending (≈ 60 cm-1) and stretching (≈ 180 cm-1) modes. Our results provide mechanistic insights into the coupling of the O-H stretch vibration to collective, delocalized intermolecular modes.