Impact of Atomic Defects on Ceria Surfaces on Chemical Mechanical Polishing of Silica Glass Surfaces.

This study investigates the impact of atomic defects, such as oxygen vacancies and Ce3+ ions, on cerium oxide (ceria) surfaces during chemical mechanical polishing (CMP) for silica glass finishing. Using density functional theory (DFT) and reactive molecular dynamics simulations, the interaction of orthosilicic molecules and silica glass with dry and wet ceria surfaces is explored. Defects alter the surface reactivity, leading to the dissociation of orthosilicic acid on oxygen vacancies, forming a strong Si-O-Ce bond. Hydroxylated surfaces exhibit easier oxygen vacancy formation and thermodynamically favored substitution of hydroxyl groups with orthosilicic acid. A new ReaxFF library for silica/ceria interfaces with defects is validated using DFT outcomes. Reactive MD simulations demonstrate that ceria surfaces with 30% Ce3+ ions on (111) planes exhibit higher polishing efficiency, attributed to increased Si-O-Ce bond formation. The simultaneous presence of oxygen vacancies and various acidic and basic sites on ceria surfaces enhances the polishing efficiency, involving acid-base reactions with silica. Defective surfaces show superior efficiency by removing silicate chains, contrasting with nondefective surfaces removing isolated orthosilicate units. This study provides insights into optimizing CMP processes for high-precision glass industry surface finishing.

Atomistic mechanism of structural and volume relaxation below glass transition temperature in a soda-lime silicate glass revealed by Raman spectroscopy and its DFT calculations.

To elucidate the atomistic origin of volume relaxation in soda-lime silicate glass annealed below the glass transition temperature (Tg), the experimental and calculated Raman spectra were compared. By decomposing the calculated Raman spectra into specific groups of atoms, the Raman peaks at 800, 950, 1050, 1100, and 1150 cm-1 were attributed to oxygen and silicon in Si-O-Si, non-bridging oxygen in the Q2 unit, bridging oxygen in low-angle Si-O-Si, non-bridging oxygen in the Q4 unit, and bridging oxygen in high-angle Si-O-Si, respectively. Based on these attributions, we found that by decreasing the fictive temperature by annealing below Tg - 70 K, a homogenization reaction Q2 + Q4 → 2Q3 and an increase in average Si-O-Si angle occurred simultaneously. By molecular dynamics simulation, we clarified how the experimentally demonstrated increase in average Si-O-Si angle contributes to volume shrinkage; increasing Si-O-Si angles can expand the space inside the rings, and Na can be inserted into the ring center.

New Atomistic Insights on the Chemical Mechanical Polishing of Silica Glass with Ceria Nanoparticles.

Reactive molecular dynamics simulations have been used to simulate the chemical mechanical polishing (CMP) process of silica glass surfaces with the ceria (111) and (100) surfaces, which are predominantly found in ceria nanoparticles. Since it is known that an alteration layer is formed at the glass surface as a consequence of the chemical interactions with the slurry solutions used for polishing, we have created several glass surface models with different degrees of hydroxylation and porosity for investigating their morphology and chemistry after the interaction with acidic, neutral, and basic water solutions and the ceria surfaces. Both the chemical and mechanical effects under different pressure and temperature conditions have been studied and clarified. According to the simulation results, we have found that the silica slab with a higher degree of hydroxylation (thicker alteration layer) is more reactive, suggesting that proper chemical treatment is fundamental to augment the polishing efficiency. The reactivity between the silica and ceria (111) surfaces is higher at neutral pH since more OH groups present at the two surfaces increased the Si-O-Ce bonds formed at the interface. Usually, an outermost tetrahedral silicate unit connected to the rest of the silicate network through a single bond was removed during the polishing simulations. We observed that higher pressure and temperature accelerated the removal of more SiO4 units. However, excessively high pressure was found to be detrimental since the heterogeneous detachment of SiO4 units led to rougher surfaces and breakage of the Si-O-Si bond, even in the bulk of the glass. Despite the lower concentration of Ce ions at the surface resulting in the lower amount of Si-O-Ce formed, the (100) ceria surface was intrinsically more reactive than (111). The different atomic-scale mechanisms of silica removal at the two ceria surfaces were described and discussed.

A new universal force-field for the Li2S-P2S5 system.

Lithium thiophosphate electrolyte is a promising material for application in all-solid-state batteries. Ab initio molecular dynamics (AIMD) simulations have been used to investigate the ion conduction mechanisms in single-crystalline and glassy compounds. However, the complexity of real materials (e.g., materials with grain boundaries and multiphase glass-ceramics) causes AIMD simulations to have high computational cost. To overcome this computational limitation, we developed a new interatomic potential for classical molecular dynamics (CMD) simulations of Li solid-state electrolytes. The training datasets were generated from representative sulfide electrolytes (ß-Li3PS4, γ-Li3PS4, Li4P2S6, Li7P3S11, and Li7PS6 crystals and 70Li2S-30P2S5 glass). Using the functional forms of the Class II and Stillinger-Weber potentials, all parameters were optimized by minimizing the differences in forces on atoms, stresses, and potential energies between the CMD and AIMD results. Subsequent validation showed that the optimized parameters can reproduce the dynamics of Li+ as well as the structures of the crystalline and glassy materials. The ionic conductivity of Li7P3S11 crystal was approximately five times that of the isostoichiometric 70Li2S-30P2S5 glass, indicating that CMD simulations using the developed force-field accurately reproduced the effective conduction path in Li7P3S11 from AIMD. The developed force-field parameters make it possible to simulate complex materials including amorphous-crystalline interfaces and multiphase glass-ceramics in the CMD framework.

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study.

Molecular dynamics simulations were employed to investigate the adsorption behavior of a variety of amino-acid side-chain analogs (SCAs) and a ß-hairpin (HP7) peptide on a series of liquid-like self-assembled monolayers (SAMs) with terminal functional groups of -OH, -OCH3, -CH3, and -CF3. The relationships between the adsorption free energy of the SCAs and the interfacial properties of water on the SAMs were examined to determine the acute predictors of protein adsorption on the SAM surfaces. The structural changes of HP7 on the SAM surfaces were also investigated to understand the relationship between the surface nature and protein denaturation. It was found that the adsorption free energy of the SCAs was linearly related to the surface hydrophobicity, which was computed as the free energy of cavity formation near the SAM-water interfaces. In addition, the hydrophobic -CH3 and -CF3 SAMs produced substantial conformational changes in HP7 because of the strong hydrophobic attractions to the nonpolar side chains. The hydrophilic surface terminated by -OH also promoted structural changes in HP7 resulting from the formation of hydrogen bonds between the hydrophilic tail and HP7. Consequently, the moderate amphiphilic surface terminated by -OCH3 avoided the denaturation of HP7 most efficiently, thus improving the biocompatibility of the surface. In conclusion, these results provide a deep understanding of protein adsorption for a wide range of polymeric surfaces, and they can potentially aid the design of appropriate biocompatible coatings for medical applications.

Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters.

Metadynamics (MetaD) is a useful technique to study rare events such as crystallization. It has been only recently applied to study nucleation and crystallization in glass-forming liquids such as silicates, but the optimal set of parameters to drive crystallization and obtain converged free energy surfaces is still unexplored. In this work, we systematically investigated the effects of the simulation conditions to efficiently study the thermodynamics and mechanism of crystallization in highly viscous systems. As a prototype system, we used fused silica, which easily crystallizes to ß-cristobalite through MetaD simulations, owing to its simple microstructure. We investigated the influence of the height, width, and bias factor used to define the biasing Gaussian potential, as well as the effects of the temperature and system size on the results. Among these parameters, the bias factor and temperature seem to be most effective in sampling the free energy landscape of melt to crystal transition and reaching convergence more quickly. We also demonstrate that the temperature rescaling from T > Tm is a reliable approach to recover free energy surfaces below Tm, provided that the temperature gap is below 600 K and the configurational space has been properly sampled. Finally, albeit a complete crystallization is hard to achieve with large simulation boxes, these can be reliably and effectively exploited to study the first stages of nucleation.

Outcomes of methotrexate-associated lymphoproliferative disorders in rheumatoid arthritis patients treated with disease-modifying anti-rheumatic drugs.

Recently, the use of targeted synthetic or biological disease-modifying anti-rheumatic drugs (ts/bDMARDs) in addition to conventional synthetic (cs)DMARDs including methotrexate (MTX) for rheumatoid arthritis (RA) has increased. However, whether ts/bDMARDs are associated with the development and clinicopathological features of MTX-associated lymphoproliferative disorder (MTX-LPD) in patients with RA remains unknown. Therefore, we evaluated the clinical outcomes of 121 patients with MTX-LPD. Results showed that prior use of ts/bDMARDs was not associated with the different histopathological subtypes of MTX-LPD. Patients with polymorphic-type LPD had a better event-free survival than those with diffuse large B-cell lymphoma (DLBCL), classical Hodgkin lymphoma and peripheral T-cell lymphoma. The pathological subtype of lymphoma could predict the clinical outcome of MTX-LPD. In patients with DLBCL, the use of tumour necrosis factor-alpha (TNF-α) inhibitors prior to MTX-LPD onset was associated with a higher non-relapse mortality. Further, patients with RA previously treated with Janus kinase (JAK) inhibitors more commonly required chemotherapy than those treated with csDMARDs alone, indicating disease aggressiveness. Hence, special caution should be observed when managing patients with MTX-LPD previously treated with JAK or TNF-α inhibitors for RA.

Simulation of Catastrophic Failure in a Residual Stress Field.

Residual stress has been empirically utilized for industrial applications to control material strength and shape of fragments. The interaction between the dynamically growing cracks and the residual stress field is sufficiently complicated to prevent us from building effective models. To rigorously evaluate the release and redistribution of residual stress in the dynamic fracture process, we develop a mathematical model and a numerical analysis method for the dynamic fracture in a residual stress field. Our methodology is simple and rigorous and applicable regardless of materials and scales.

Self-assembly of the cationic surfactant n-hexadecyl-trimethylammonium chloride in methyltrimethoxysilane aqueous solution: classical and reactive molecular dynamics simulations.

A flexible aerogel polymerized from methyltrimethoxysilane (MTMS) shows great promise as a high-performance insulator owing to its substantially low thermal conductivity and mechanical flexibility, attributed to its porous microstructure and organic-inorganic hybridization, respectively, which promote its industrial applications. Conventionally, the cationic surfactant n-hexadecyltrimethylammonium chloride (CTAC) is utilized to experimentally control the nanoscale microstructure and, consequently, the flexibility of the MTMS aerogel; however, the mechanism through which CTAC prevents MTMS aggregation in the solution is not yet fully understood. This study unravels the role of CTAC in preventing MTMS aggregation in aqueous solution using both classical and reactive molecular dynamics simulations. We found that CTAC molecules can form self-aggregates even when the polymerization of MTMS progresses and then the MTMS-derived oligomer turns to be hydrophobic in aqueous solution. In summary, the self-assemblies of CTAC disperse among the MTMS associations and effectively prevent MTMS clustering, and this is considered as the key mechanism underlying the formation of a flexible microstructure of the hybrid aerogel.

Development and Application of a ReaxFF Reactive Force Field for Cerium Oxide/Water Interfaces.

Ceria (CeO2) is a well-known catalytic oxide with many environmental, energy production, and industrial applications, most of them involving water as a reactant, byproduct, solvent, or simple spectator. In this work, we parameterized a Ce/O/H ReaxFF for the study of ceria and ceria/water interfaces. The parameters were fitted to an ab initio training set obtained at the DFT/PBE0 level, including the structures, cohesive energies, and elastic properties of the crystalline phases Ce, CeO2, and Ce2O3; the O-defective structures and energies of vacancy formation on CeO2 bulk and CeO2 (111) surface, as well as the absorption and reaction energies of H2 and H2O molecules on CeO2 (111). The new potential reproduced reasonably well all the fitted properties as well as the relative stabilities of the different ceria surfaces, the oxygen vacancies formation, and the energies and structures of associative and dissociative water molecules on them. Molecular dynamics simulations of the liquid water on the CeO2 (111) and CeO2 (100) surfaces were carried out to study the coverage and the mechanism of water dissociation. After equilibration, on average, 35% of surface sites of CeO2 (111) are hydroxylated whereas 15% of them are saturated with molecular water associatively adsorbed. As for the CeO2 (100) surface, we observed that water preferentially dissociates covering 90% of the available surface sites in excellent agreement with recent experimental findings.

Structural origin of thermal shrinkage in soda-lime silicate glass below the glass transition temperature: A theoretical investigation by microsecond timescale molecular dynamics simulations.

Microscopic dynamical features in the relaxation of glass structures are one of the most important unsolved problems in condensed matter physics. Although the structural relaxation processes in the vicinity of glass transition temperature are phenomenologically expressed by the Kohlrausch-Williams-Watts function and the relaxation time can be successfully interpreted by Adam-Gibbs theory and/or Narayanaswamy's model, the atomic rearrangement, which is the origin of the volume change, and its driving force have not been elucidated. Using the microsecond time-scale molecular dynamics simulations, this study provides insights to quantitatively determine the origin of the thermal shrinkage below Tg in a soda-lime silicate glass. We found that during annealing below Tg, Na ions penetrate into the six-membered silicate rings, which remedies the acute O-O-O angles of the energetically unstable rings. The ring structure change makes the space to possess the cation inside the rings, but the ring volume is eventually reduced, which results in thermal shrinkage of the soda-lime silica glass. In conclusion, the dynamical structural relaxation due to the cation displacement evokes the overall volume relaxation at low temperature in the glassy material.

Safety and Seropositivity after Live Attenuated Vaccine in Adult Patients Receiving Hematopoietic Stem Cell Transplantation.

Vaccination against vaccine-preventable diseases (VPDs) is highly recommended for hematopoietic stem cell transplantation (HSCT) recipients by several guidelines; however, the safety and seropositivity after live attenuated vaccines remain unclear in adult HSCT recipients. We analyzed titers of antibodies against measles, rubella, mumps, and varicella zoster virus (VZV) from Japanese adult patients who underwent allogeneic HSCT (allo-HSCT) (n = 74), autologous HSCT (auto-HSCT) (n = 39), or chemotherapy (n = 93). The seropositive rates for measles, rubella, mumps, and VZV in allo-HSCT recipients were 20.2%, 36.4%, 5.4%, and 55.4%, respectively. These rates were equivalent to those in auto-HSCT recipients but were significantly lower than those in patients receiving chemotherapy. Antibody titers tended to gradually decrease with time. Twenty-nine allo-HSCT recipients and 8 auto-HSCT recipients received live attenuated vaccines against VPDs for which they tested seronegative. The titers of antibodies against measles, rubella, and mumps significantly increased after 2 shots of vaccine, and the seropositive rate increased up to 19%, 30%, and 27%, respectively. Three patients (8.1%) experienced mild adverse events, which resolved promptly, indicating safe administration of the live attenuated vaccines. In multivariate analysis, history of chronic graft-versus-host disease was significantly associated with high seropositivity for measles as well as high seroconversion rate for measles after vaccination. Live attenuated vaccines against VPDs were safely administered in seronegative adult HSCT recipients. A further observational study is crucial to evaluate the efficacy of vaccination in seronegative HSCT patients.

Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study.

A good understanding of the surface hydrophobicity of fluorinated materials is useful for their application as coating materials. The present study investigates the surface hydrophobicity of perfluoroalkyl acrylate (PFA) thin films using molecular dynamics simulations. Surface hydrophobicity is characterized by examining the contact angle of a water droplet on PFA surfaces and the cavity formation free energy in the vicinity of the surface. It is found that the calculated microscopic contact angles are in good agreement with the experimental results and partially capture the difference in the hydrophobicity of the surface arising from the variation of packing density and side chain length of PFA. The variations of cavity formation free energy in the vicinity of the surface elucidate that the surface hydrophobicity is mainly governed by the packing density rather than the chain length of PFA. The hydrophobicity generally increases with decreasing the packing density to some extent and then turns to decrease as further reducing the packing density. At higher packing density, the surface hydrophobicity slightly decreases with increasing the chain length, while at the lower packing density, the surface hydrophobicity is increased when chain length of PFA is longer than six carbons. Furthermore, we found that the influence of packing density on the surface hydrophobicity is directly related to the variation of the surface roughness and chain flexibility, that is, the surface hydrophobicity increases with increase in the surface roughness, while the chain flexibility plays a secondary role in the enhancement by affecting the stability of water staying near the interface. The study provides a significant insight into the local hydrophobicity and microscopic structure of the PFA surfaces, which would be useful for the application of surface modification.

An efficient computational procedure to obtain a more stable glass structure.

A huge gap in time between the experiment and the atomistic simulation restricts us from accessing a realistic glass structure, because the glass state is highly dependent on the cooling rate. In this study, to improve computational efficiency, we propose a simple but effective procedure, which enables us to explore a deeper basin in the energy landscape of glassy materials without a substantial increase in the computational cost. This method combines canonical ensemble molecular dynamics (MD) and energy minimization while controlling the stress of the MD system, and it is called the quasi-slow-quenching (QSQ) method. Herein, we measured the performance of the QSQ method using a binary silicate, (SiO2)80(Na2O)20, and we observed that a more stable configuration can be obtained in comparison with the conventional isobaric-isothermal MD method. The stable glass model appears to possess a lower glass transition temperature (Tg), confirming that the QSQ method finds a deeper local minimum closer to the super-cooled glass state. We also conducted further validation tests for various oxide glasses, including silicate, borate, phosphate, and their mixtures, and we verified that the QSQ method consistently enables the glassy materials to attain energetically more stable configurations and denser structures.

[Recurring Sweet syndrome in a patient with Philadelphia chromosome-positive acute lymphoblastic leukemia].

Sweet syndrome is a rare inflammatory disease with rapid onset of painful, edematous skin eruptions, and neutrophilia. Concerning hematological disorders, Sweet syndrome often presents in patients with myeloid diseases, but it is rarely observed in patients with lymphoid diseases. Here we describe a 72-year-old male with Philadelphia chromosome-positive acute lymphoblastic leukemia who suffered recurring Sweet syndrome. Following induction chemotherapy, granulocyte colony-stimulating factors (G-CSFs) were administered due to febrile neutropenia. A few weeks thereafter, skin eruption emerged on the palmar and dorsal surfaces of his hands, and skin biopsy confirmed Sweet syndrome. His symptoms improved with the short-term use of prednisolone. After recovering from the neutropenia, the patient received percutaneous coronary intervention (PCI) due to unstable angina that developed after the induction chemotherapy. During PCI, coronary artery dissection caused cardiopulmonary arrest. The patient recovered with intensive care. However, blood tests on the following day revealed marked neutrophilia. The skin eruption re-emerged on both hands, which was consistent with Sweet syndrome. Sweet syndrome repeatedly occurred after the recovery of neutropenia due to chemotherapy. We suggest that the intrinsic increase in G-CSF in response to inflammation might have caused recurring Sweet syndrome in this patient.

A study on the plasticity of soda-lime silica glass via molecular dynamics simulations.

Molecular dynamics (MD) simulations were applied to construct a plasticity model, which enables one to simulate deformations of soda-lime silica glass (SLSG) by using continuum methods. To model the plasticity, stress induced by uniaxial and a variety of biaxial deformations was measured by MD simulations. We found that the surfaces of yield and maximum stresses, which are evaluated from the equivalent stress-strain curves, are reasonably represented by the Mohr-Coulomb ellipsoid. Comparing a finite element model using the constructed plasticity model to a large scale atomistic model on a nanoindentation simulation of SLSG reveals that the empirical method is accurate enough to evaluate the SLSG mechanical responses. Furthermore, the effect of ion-exchange on the SLSG plasticity was examined by using MD simulations. As a result, it was demonstrated that the effects of the initial compressive stress on the yield and maximum stresses are anisotropic contrary to our expectations.

Polymorphic Sirpa is the genetic determinant for NOD-based mouse lines to achieve efficient human cell engraftment.

Current mouse lines efficient for human cell xenotransplantation are backcrossed into NOD mice to introduce its multiple immunodeficient phenotypes. Our positional genetic study has located the NOD-specific polymorphic Sirpa as a molecule responsible for its high xenograft efficiency: it recognizes human CD47 and the resultant signaling may cause NOD macrophages not to engulf human grafts. In the present study, we established C57BL/6.Rag2(nullIl2rgnull) mice harboring NOD-Sirpa (BRGS). BRGS mice engrafted human hematopoiesis with an efficiency that was equal to or even better than that of the NOD.Rag1(nullIl2rgnull) strain, one of the best xenograft models. Consequently, BRGS mice are free from other NOD-related abnormalities; for example, they have normalized C5 function that enables the evaluation of complement-dependent cytotoxicity of antibodies against human grafts in the humanized mouse model. Our data show that efficient human cell engraftment found in NOD-based models is mounted solely by their polymorphic Sirpa. The simplified BRGS line should be very useful in future studies of human stem cell biology.

Evidence of Multiple Crystallization Pathways in Lithium Disilicate: A Metadynamics Investigation.

Metadynamics simulations driven by using two X-ray diffraction peaks identified three alternative crystallization pathways of the lithium disilicate crystal from the melt. The most favorable one passes through the formation of disordered layered structures undergoing internal ordering in a second step. The second pathway involves the formation of phase-separated structures composed of nuclei of ß-cristobalite crystals surrounded by lithium-rich phases in which metasilicate chains are formed. The conversion of these structures to the stable lithium disilicate crystal involves an intermediate structure whose silicate layers are connected by silicate rings with the energy barrier of 2.5 kJ/mol per formula unit (f.u.). The third pathway is highly unlikely because of the huge energy barrier involved (20 kJ/mol per f.u.). This path also involves the passage through a phase-separated structure of an indefinite silica region surrounded mainly by amorphous lithium oxide.

Three-dimensional ordering of water molecules reflecting hydroxyl groups on sapphire (001) and α-quartz (100) surfaces.

Water molecules on oxide surfaces influence the chemical reactivity and molecular adsorption behavior of oxides. Herein, three-dimensional atomic force microscopy (3D-AFM) and molecular dynamics simulations are used to visualize the surface hydroxyl (OH) groups and their hydration structures on sapphire (001) and α-quartz (100) surfaces at the atomic-scale. The obtained results revealed that the spatial density distributions and hydrogen-bonding strengths of surface OH groups affect their local hydration structures. In particular, the force curves obtained by 3D-AFM suggest that the hydration forces of water molecules intensify at sites where water molecules strongly interact with the surface OH groups. The insights obtained in this study deepen our understanding of the affinities of Al2O3 and SiO2 for water molecules and contribute to the use of 3D-AFM in the investigation of atomic-scale hydration structures on various surfaces, thereby benefiting a wide range of research fields dealing with solid-liquid interfaces.

Composition Effect on Interfacial Reactions of Sodium Aluminosilicate Glasses in Aqueous Solution.

Understanding the underlying reaction mechanisms responsible for aluminosilicate glass dissolution in aqueous environments is crucial for designing glasses for technological applications ranging from architecture windows and touch screens to nuclear waste disposal. This study investigated the glass composition effect on the interfacial reactions of sodium aluminosilicate (NAS) glasses using molecular dynamics (MD) simulations with recently developed reactive potentials. Glass-water interfacial models of six NAS glasses with varying Al2O3/Na2O ratios were investigated for up to 4 nanoseconds (ns) to elucidate the interfacial reaction mechanisms at ambient temperature. The results showed that the coordination defects, such as undercoordinated Si and Al, as well as non-bridging oxygens (NBOs) accumulated at the glass surfaces, play a crucial role in the initial hydration reaction process of the glasses. They promote the formation of silanol (Si-OH) and aluminol (Al-OH) species together with the Na+⇔ H+ ion-exchange reactions. The z-density profiles of H2O and H+ ions affirmed the water/H+ propagation into the glass up to 2 nanometers after 4 ns reactions. The penetration depth depends on the composition and shows a nonlinear dependence, suggesting that the subsequent water penetration, particularly into the bulk glass, is supported by the availability of random channels. Aluminol formations, including Al-OH or Al-OH2 near the surface, were found to form mainly through the hydrolysis of Al-O-Al bonds and hydration of Al+-NBO- units. While water molecules are involved in initial interfacial reactions, water penetration into the bulk glass region is primarily achieved by proton transfer. Compared to highly mobile proton transfer involving silanol groups, proton transfer associated with [AlO4]- species is much more limited, particularly in the bulk glass region. These new insights into the role of aluminum in interfacial reactions of the NAS glasses can help to understand the initial dissolution mechanisms and in designing more durable glasses.