Exploring non-adiabaticity to CO reduction reaction through ab initio molecular dynamics simulation

Non-adiabatic chemical reaction refers to the electronic excitation during reactions. This effect cannot be modeled by the ground-state Born-Oppenheimer molecular dynamics (BO-MD), where the electronic structure is at the ground state for every step of ions' movement. Although the non-adiabatic effect has been explored extensively in gas phase reactions, its role in electrochemical reactions, such as water splitting and CO2 reduction, in electrolyte has been rarely explored. On the other hand, electrochemical reactions usually involve electron transport; thus, a non-adiabatic process can naturally play a significant role. In this work, using one-step CO2 reduction as an example, we investigated the role of the non-adiabatic effect in the reaction. The reaction barriers were computed by adiabatic BO-MD and non-adiabatic real-time time dependent density functional theory (rt-TDDFT). We found that by including the non-adiabatic effect, rt-TDDFT could increase the reaction barrier up to 6% compared to the BO-MD calculated barrier when the solvent model is used to represent water. Simulations were carried out using explicit water molecules around the reaction site under different overpotentials, and similar non-adiabatic effects were found

Large polaron formation and its effect on electron transport in hybrid perovskites

Many experiments have indicated that a large polaron may be formed in hybrid perovskites, and its existence is proposed to screen the carrier-carrier and carrier-defect scattering, thus contributing to the long lifetime of the carriers. However, a detailed theoretical study of the large polaron and its effect on carrier transport at the atomic level is still lacking. In particular, how strong is the large polaron binding energy? How does its effect compare with the effect of dynamic disorder caused by the A-site molecular rotation? And how does the inorganic sublattice vibration impact the motion of the large polaron? All of these questions are largely unanswered. In this work, using CH3NH3PbI3 as an example, we implement a tight-binding model fitted from density-functional theory to describe the electron large polaron ground state and to understand the large polaron formation and transport at its strong-coupling limit. We find that the formation energy of the large polaron is around -12 meV for the case without dynamic disorder, and -55 meV by including dynamic disorder. By performing the explicit time-dependent wavefunction evolution of the polaron state, together with the rotations of CH3NH3+ and vibrations of the PbI3- sublattice, we studied the diffusion constant and mobility of the large polaron state driven by the dynamic disorder and the sublattice vibration. Two effects of the inorganic sublattice vibrations are found: on one hand, the vibration of the sublattice provides an additional driving force for carrier mobility; on the other hand, the large polaron polarization further localizes the electron, reducing its mobility. Overall, the effect of the large polaron is to slow down the electron mobility by roughly a factor of two. We believe that both dynamic disorder due to rotation of the organic molecule, and large polaron effects induced by the polarization and vibration of the inorganic sublattice, play important roles for the electronic structure and carrier dynamics of the system

Solid 3D Li-S Battery Design via Stacking 2D Conductive Microporous Coordination Polymers and Amorphous Li-S Layers

To make a lithium-sulfur (Li-S) battery practical, not only high gravimetric energy capacity is important, but also high volumetric energy capacity will be required. The currently explored Li-S cathode designs often deploy systems with liquid electrolyte infiltration, hence with relatively low volumetric capacity. In the current study, we theoretically test a compact solid three-dimensional (3D) design (more like a Li-ion battery cathode than a conventional Li-S cathode) consisted of a sandwich structure alternating between the two-dimensional (2D) Mn-hexaaminobenzene-based coordination polymer (2D Mn-HAB-CP) layer and the amorphous Li-S layer. We study the theoretical limits for both its gravimetric and volumetric energy capacity, as well as its structural stability and Li diffusion within the cathode system. To study the Li diffusion within an amorphous system, we also develop a pull-atom molecular dynamics (PA-MD) to calculate the barrier heights of such disordered systems. We reveal the mechanism that determines the Li diffusion in the amorphous layer of the system. Overall, we find such a 3D solid Li-S cathode can be practical, with sufficient large gravimetric and volumetric energy capacity, as well as the Li diffusion constant. It also solves many other common Li-S cathode problems, from Li polysulfide dissolution to electrical insulating, and structure instabilities

Effects of calcium phosphate nanocrystals on osseointegration of titainium implant in irradiated bone

Radiotherapy may compromise the integration of implant and cause implant loss. Implant surface modifications have the possibility of promoting cell attachment, cell growth, and bone formation which ultimately enhance the osseointegration process. The present study aimed to investigate the effects of calcium phosphate nanocrystals on implant osseointegration in irradiated bone. Sixteen rabbits were randomly assigned into control and nano-CaP groups, receiving implants with dual acid-etched surface or dual acid-etched surface discretely deposited of nanoscale calcium-phosphate crystals, respectively. The left leg of all the rabbits received 15 Gy radiation, followed by implants placement one week after. Four animals in each group were sacrificed after 4 and 12 weeks, respectively. Implant stability quotient (ISQ), ratio of bone volume to total volume (BV/TV), bone growth rate, and bone-to-implant contact (BIC) were evaluated. The nano-CaP group showed significantly higher ISQ (week 12, P = 0.031) and bone growth rate (week 6, P = 0.021; week 9, P = 0.001) than that in control group. No significant differences in BV/TV and BIC were found between two groups. Titanium implant surface modified with CaP nanocrystals provides a potential alternative to improve bone healing around implant in irradiated bone.published_or_final_versio

Ab Initio Investigation of Charge Trapping Across the Crystalline- Si -Amorphous- Si O2 Interface

Accurate microscopic description of the charge-trapping process from semiconductor to defects in the dielectric-oxide layer is of paramount importance for understanding many microelectronic devices such as complementary metal-oxide-semiconductor (CMOS) transistors, as well as electrochemical reactions. Unfortunately, most current microscopic descriptions of such processes are based on empirical models with parameters fitted to experimental device performance results or simplified approximations like the Wentzel-Kramers-Brillouin (WKB) method. Some critical questions are still unanswered, including: What controls the charge-hopping rate, the coupling strength between the defect level to semiconductor level, or the energy difference? How does the hopping rate decay with defect-semiconductor distance? What is the fluctuation of the defect level, especially in amorphous dielectrics? Many of these questions can be answered by ab initio calculations. However, to date, there are few ab initio studies for this problem mainly due to technical challenges from atomic-structure construction to large-system calculations. Here, using the latest advances in calculation methods and codes, we study the carrier-trapping problem using density-functional theory (DFT) based on the Heyd-Scuseria-Ernzerhof (HSE) exchange correlation functional. The valence bond random-switching method is used to construct the crystalline-Si-amorphous-SiO2 (c-Si/a-SiO2) interfacial atomic structure, and the HSE yields a band offset that agrees well with experiments. The hopping rate is calculated with the Marcus theory, and the hopping-rate dependences on the gate potential and defect distances are revealed, as well as the range of fluctuation results from amorphous structural variation. We also analyze the result with the simple WKB model and find a major difference in the description of the coupling constant decay with the defect-semiconductor distance. Our results provide the ab initio simulation insights for this important carrier-trapping process for device operation

Effect of different rhBMP-2 and TG-VEGF ratios on the formation of heterotopic bone and neovessels

Bioengineered bone substitutes might represent alternatives to autologous bone grafts in medically compromised patients due to reduced operation time and comorbidity. Due to the lack of an inherent vascular system their dimension is limited to the size of critical bone size defect. To overcome this shortcoming, the experiment tried to create heterotopic bone around vessels. In vivo, a two-component fibrin and thrombin gel containing recombinant bone morphogenic protein (rhBMP-2) and transglutamate vascular endothelial growth factor (TG-VEGF) in different ratios, respectively, was injected into a dimensionally stable membrane tube, wrapped around the femoral vessel bundle in twelve New Zealand white rabbits. Sacrifice occurred eight weeks postoperatively. Microcomputed tomography of the specimens showed significantly increased bone volume in the rhBMP-2 to TG-VEGF ratio of 10 to 1 group. Histology showed new bone formation in close proximity to the vessel bundle. Immunohistochemistry detected increased angiogenesis within the newly formed bone in the rhBMP-2 to TG-VEGF ratios of 3 to 1 and 5 to 1. Heterotopic bone was engineered in vivo around vessels using different rhBMP-2 and TG-VEGF ratios in a fibrin matrix injected into a dimensionally stable membrane tube which prevented direct contact with skeletal muscles.published_or_final_versio

On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

N-Acetyl-L-Glutamate Kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network model representation, which shows that the conformational mechanisms for substrate binding by NAGK strongly correlate with the intrinsic dynamics of the enzyme in the unbound form. We further analyzed the potential mechanisms of allosteric signalling within NAGK using a Markov model for network communication. Comparative analysis of the dynamics of family members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establish signal transduction are highly conserved among family members, in support of the paradigm sequence→structure→dynamics→function © 2010 Marcos et al

Polymorphic Structures of Alzheimer's β-Amyloid Globulomers

Misfolding and self-assembly of Amyloid-β (Aβ) peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphic Aβ structures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation.Here, we model a series of molecular structures of Aβ globulomers assembled by monomer and dimer building blocks using our peptide-packing program and explicit-solvent molecular dynamics (MD) simulations. Structural and energetic analysis shows that although Aβ globulomers could adopt different energetically favorable but structurally heterogeneous conformations in a rugged energy landscape, they are still preferentially organized by dynamic dimeric subunits with a hydrophobic core formed by the C-terminal residues independence of initial peptide packing and organization. Such structural organizations offer high structural stability by maximizing peptide-peptide association and optimizing peptide-water solvation. Moreover, curved surface, compact size, and less populated β-structure in Aβ globulomers make them difficult to convert into other high-order Aβ aggregates and fibrils with dominant β-structure, suggesting that they are likely to be off-pathway species to amyloid fibrils. These Aβ globulomers are compatible with experimental data in overall size, subunit organization, and molecular weight from AFM images and H/D amide exchange NMR.Our computationally modeled Aβ globulomers provide useful insights into structure, dynamics, and polymorphic nature of Aβ globulomers which are completely different from Aβ fibrils, suggesting that these globulomers are likely off-pathway species and explaining the independence of the aggregation kinetics between Aβ globulomers and fibrils