Atomic Mechanisms Research Articles

Temperature dependence of adhesion properties at liquid-aluminum/solid interfaces

The adhesion problem of the liquid aluminum (Al) and solid surfaces in the production process has not been completely solved. In this paper, by performing the molecular dynamic simulations, we first establish models composed of liquid-Al/Al and liquid-Al/silicon (Si) systems, in which the region of solid temperature is from 100 K to 800 K. Then, the dependence between the adhesion force and the solid temperature is qualitatively investigated. The adhesion mechanism of liquid atoms is explored in terms of their diffusion behavior. The results show that there is an opposite effect of the temperature on adhesion properties between the liquid-Al/Al interface and the liquid-Al/Si interface. The thermal excitation effect induces enlargement of the probability of atomic collisions, which accounts for the increase of the adhesion force at the liquid-Al/Al interface. Conversely, the thermal excitation effect leads to the detachment of the atoms in contact with each other, which reduces the adhesion force at the liquid-Al/Si interface. Our findings reveal that the solid Al surface is aluminophilic but the solid Si surface is aluminophobic. In addition, the adhesion between liquid-Al and solid surfaces can be explained by the variation of the interfacial potential.

Dual Active Sites of Oversaturated Fe-N5 and Fe2 O3 Nanoparticles for Accelerating Redox Kinetics of Polysulfides.

The shuttling effect and sluggish reaction kinetics are the main bottlenecks for the commercial viability of lithium-sulfur (Li-S) batteries. Metal-nitrogen-carbon single atom catalysts have attracted much attention to overcoming these obstacles due to their novel electrocatalytic activity. Herein, a novel cooperative catalytic interface with dual active sites (oversaturated Fe-N5 and polar Fe2 O3 nanocrystals) are co-embedded in nitrogen-doped hollow carbon spheres (Fe2 O3 /Fe-SA@NC) is designed by fine atomic regulation mechanism. Both experimental verifications and theoretical calculations disclose that the dual active sites (Fe-N5 and Fe2 O3 ) in this catalyst (Fe2 O3 /Fe-SA@NC) tend to form "FeS" and "LiN/O" bond, synchronically enhancing chemical adsorption and interface conversion ability of polysulfides, respectively. Specially, the Fe-N5 coordination with 3D configuration and sulfiphilic superfine Fe2 O3 nanocrystals exhibit the strong adsorption ability to facilitate the subsequent conversion reaction at dual-sites. Meanwhile, the nitrogen-doped hollow carbon spheres can promote Li+ /electron transfer and physically suppress polysulfides shuttling. Consequently, Li-S battery with the Fe2 O3 /Fe-SA@NC-modified separator exhibits a high capacity retention of 78% after 800 cycles at 1C (pure S cathode, S content: 70wt.%). Furthermore, the pouch cell with this separator shows good performance at 0.1C for practical application (S loading: 4mgcm-2 ).

Initial decomposition mechanisms of 2,4,6-triamino-1,3,5-trinitrobenzene (TATB) and their kinetic isotope effect

2,4,6-triamino-1,3,5-trinitrobenzene (TATB) is an insensitive High Explosive (HE) that is widely studied to better understand the physical properties of safety and sensitivity of HE. A dominant initial decomposition mechanism of TATB is believed to be a dehydration reaction that forms mono- and di-furazans, although other mechanisms have been reported. In this work, seven initial decomposition mechanisms were modeled with ab initio simulations to calculate its free energy barriers, decomposition rates, and kinetic isotope effects. The energy barrier for mono-benzofurazan mechanisms was found to be high, >61 kcal/mol in the gas phase; however, the reaction energy can decrease significantly in a disordered condensed state. The predicted kinetic isotope effect ratio of the furazan mechanism was found to be kh/kd≈ 1.41 at 600 K, in agreement with the experiment. The NO2 scission mechanism was found to be an entropy-driven mechanism because the free energy barrier decreased significantly with temperature, making it the most energetically favorable mechanism at high temperatures in the gas phase. The results provide a better understanding of the atomistic decomposition mechanisms of TATB and may be useful for improving models of safety and sensitivity.

Losses of thulium atoms from optical dipole traps operating at 532 and 1064 nm

Recently thulium has been condensed to Bose-Einstein condensate. Machine learning was used to avoid a detailed study of all obstacles making cooling difficult. This paper analyses the atomic loss mechanism for the 532 nm optical trap, used in the Bose-condensation experiment, and compares it with the alternative and more traditional micron-range optical dipole trap. We also measured the scalar and tensor polarizability of thulium at 1064 nm and was found to be $167\pm 25$ a.u. ($275\pm 41\times {{10}^{-41}}\text{F }\cdot \text{ }{{\text{m}}^{\text{2}}}$) and $-4\pm 1$ a.u. ($7\pm 2\times {{10}^{-41}}\text{F }\cdot \text{ }{{\text{m}}^{\text{2}}}$).

First principles study of oxygen diffusion in plutonium dioxide, sesquioxide, and their interface under activated conditions

The oxidation corrosion of metallic plutonium, intentional or unavoidable, is a crucial issue for its actual applications. However, the atomistic mechanisms behind such oxidation remain elusive. Through a systematic first principles study of the oxygen diffusion in plutonium dioxide, sesquioxide, and their interface, we obtained some dynamic parameters of oxygen diffusion in different oxides. Moreover, we also discovered a dynamic equilibrium and an anisotropic pathway that prefers the [001] crystallographic direction for oxygen diffusion at their interface. These conclusions were in accord with the experimental results of ceria oxides, an ideal analogue of the plutonium oxides with 4f electrons. These results help us to better understand the mechanisms of oxidation corrosion of plutonium at an atomistic level, and to reveal prospects for applications of the anisotropic orientation-relevant fluorite-structured oxides.

Understanding the synergistic effect of Ni/Al2O3 on CO2 adsorption and sintering properties of CaO in sorption-enhanced steam reforming process

Sorption-enhanced steam reforming with in-situ CO2 removal by high temperature solid sorbents is an environmentally friendly and sustainable approach for hydrogen production. Ca-Ni-Al bifunctional materials with both catalytic activity and sorption activity have received extensive attention recently. However, the synergistic effect of Ni/Al2O3 on the CO2 adsorption and sintering properties of CaO sorbents have not been studied, and the atomistic mechanisms behind them still remain unclear. Here, we investigated the synergistic effect of Ni/Al2O3 on the carbonation properties and sintering resistance of CaO sorbents by experiments combined with density functional theory (DFT) calculations. Results show that the phase transformation for reduction of NiO and NiAl2O4 to Ni promotes the reaction between CaO and Al2O3, which is beneficial to the formation of the inert framework Ca12Al14O33. After adding 5 % and 15 % Ni, the BET specific surface area decreases from 11.85 to 7.59 and 4.51 m2/g, respectively. The catalytic component Ni is dispersed on the CaO surface, which blocks the pore structure and eventually leads to a decrease in CO2 capture capacity. Under high temperature calcination, Ni aggravates the sintering of CaO, which is not conducive to cyclic adsorption. The Al2O3 support can effectively improve the pore structure and maintain cycle stability of CaO sorbents. DFT calculations suggest that the catalytic component Ni, the Al2O3 support and the Ni-Al2O3 bi-component have little effect on the CO2 adsorption activity. The Ni significantly weakens the adsorption energy of Ca4O4 cluster on CaO surface from −2.58 eV to −1.57 eV, resulting in the growth of CaO grains. The strong interaction between Ca4O4 cluster and Al2O3 surface with the adsorption energy of −7.34 eV makes Ca4O4 cluster migration difficult, thereby inhibiting the agglomeration and sintering of CaO particles. Meanwhile, the addition of Ni component does not significantly reduce the anti-sintering ability of Al2O3 support on CaO sorbents. For Ni-Ca-Al bifunctional materials, the strong interaction between Ni-Ca is not conducive to the carbonation performance of CaO sorbents and the strong interaction between Ni-Al should be appropriately avoided to weaken the efficacy of Al2O3 support, which was confirmed by experiments.

Piezoelectric atomization of liquids with dynamic viscosities up to 175 cP at room temperature

Piezoelectric atomization has been applied in the field of respiratory medicine delivery and chemistry. However, the wider application of this technique is limited by the viscosity of the liquid. High-viscosity liquid atomization has great potential for applications in aerospace, medicine, solid-state batteries and engines, but the actual development of atomization is behind expectations. In this study, instead of the traditional model of single-dimensional vibration as a power supply, we propose a novel atomization mechanism that uses two coupled vibrations to induce micro-amplitude elliptical motion of the particles on the surface of the liquid carrier, which produces a similar effect as localized traveling waves to push the liquid forward and induce cavitation to achieve atomization. To achieve this, a flow tube internal cavitation atomizer (FTICA) consisting of a vibration source, a connecting block and a liquid carrier is designed. The prototype can atomize liquids with dynamic viscosities up to 175 cP at room temperature with a driving frequency of 507 kHz and a voltage of 85 V. The maximum atomization rate in the experiment is 56.35 mg/min, and the average atomized particle diameter is 10 µm. Vibration models for the three parts of the proposed FTICA are established, and the vibration characteristics and atomization mechanism of the prototype were verified using the vibration displacement measurement experiment and the spectroscopic experiment. This study offers new possibilities for transpulmonary inhalation therapy, engine fuel supply, solid-state battery processing and other areas where high-viscosity microparticle atomization is needed.

Optimization of the hydrogen response characteristics of halogen-doped SnO2

The increasing demand for efficient sensing devices with facile low-cost fabrication has attracted a lot of scientific research effort in the recent years. In particular, the scientific community aims to develop new candidate materials suitable for energy-related devices, such as sensors and photovoltaics or clean energy applications such as hydrogen production. One of the most prominent methods to improve materials functionality and performance is doping key device component(s). This paper aims to examine in detail, both from a theoretical and an experimental point of view, the effect of halogen doping on the properties of tin dioxide (SnO2) and provide a deeper understanding on the atomic scale mechanisms with respect to their potential applications in sensors. Density Functional Theory (DFT) calculations are used to examine the defect processes, the electronic structure and the thermodynamical properties of halogen-doped SnO2. Calculations show that halogen doping reduces the oxide bandgap by creating gap states which agree well with our experimental data. The crystallinity and morphology of the samples is also altered. The synergy of these effects results in a significant improvement of the gas-sensing response. This work demonstrates for the first time a complete theoretical and experimental characterization of halogen-doped SnO2 and investigates the possible responsible mechanisms. Our results illustrate that halogen doping is a low-cost method that significantly enhances the room temperature response of SnO2.

Direct observation of the atomic scale mechanism of grain rotation

Direct observation of the atomic scale mechanism of grain rotation

Understanding the poisoning mechanisms of Si and Zr atoms on L12 Al3Ti (111) surface: A first-principles investigation

In order to reveal the poisoning mechanism, the adsorption and diffusion of Si and Zr atoms on the L12 Al3Ti (111) surface have been investigated using first-principles calculations. Based on the results of adsorption energy and work function, the most favorable adsorption sites for Si and Zr atoms are H4 and T1 of L12 Al3Ti (111) surface, respectively. It is revealed from electron density differences, density of states and Mulliken population that the Ti–Si covalent bonds in Si@Al3Ti(111) system the hybridization of Si 3p and Ti 3d orbitals while the Ti–Zr ionic bond in Zr@Al3Ti(111) system is come from the contribution of Ti 3d and Zr 4d orbitals. By calculating formation energy, it is found that the Si and Zr atoms prefer to incorporate the Al site of the first layer and Ti site of the second layer of L12 Al3Ti (111) surface, respectively. The energy barriers of Si and Zr atoms diffusion on or into L12 Al3Ti (111) surface are also evaluated.

The Al-Fe Intermetallic Compounds and the Atomic Diffusion Behavior at the Interface of Aluminum-Steel Welded Joint

The formation of intermetallic compounds (IMC) at the Al/Fe interface determined the mechanical property of steel-aluminum welded joint. To understand the interfacial microstructure evolution and relate diffusion mechanism of atoms cross the Al/Fe interface, the effect of welding parameters on the interfacial IMC was studied, and the molecular dynamics method (MD) was used to simulate the diffusion process of Al and Fe atoms. Four temperatures (950 K, 1000 K, 1050 K, and 1100 K) were selected in the simulation model. The interfacial IMC are distributed in a laminar pattern, and their physical phases are mainly composed of Fe2Al5, controlling the Al/Fe atomic ratio of 5:2 in the IMC configuration, the Embedded Atom Method (EAM) potential is used to describe the interactions between Al and Fe atoms. In the Al-Fe system IMC conformation, the mean square displacement and diffusion (MSD) coefficient of Al atoms at different temperatures were small, and the main diffusion path is the Al atoms across the IMC conformation into the Fe crystal structure. The diffusion in the IMC conformation was mainly along the direction perpendicular to the interface. The diffusion mechanisms were mainly vacancy diffusion and interstitial diffusion mechanisms.

Development and Validation of a ReaxFF Reactive Force Field for Modeling Silicon–Carbon Composite Anode Materials in Lithium-Ion Batteries

Silicon–carbon (Si–C) nanocomposites have recently established themselves among the most promising next-generation anode materials for lithium (Li)-ion batteries. Indeed, combined Si and graphitic (sp2-C) phases exhibit high energy densities with reasonable electrochemical responses, while covalently bonded silicon carbide (SiC) compounds offer high mechanical stiffness to withstand structural degradation. However, to form and utilize a Si–C composite structure that effectively satisfies specific battery energy, power, and lifetime requirements, it is necessary to understand the underlying atomistic mechanisms at work within its individual phases and at their interfaces. Here, we develop and validate a reactive interatomic potential (ReaxFF) for the Li–Si–C system, trained and tested against a large, diverse collection of ab initio data. In conjunction with molecular dynamics and Monte Carlo simulations, our new force field links macroscale phenomena to the nanostructures of various hybrid Si–C systems in a wide range of lithiation, temperature, and stress conditions. As an illustration, it demonstrates that the high capacity of SiC (5882 mA h g–1) is caused by amorphous lithium carbides (e.g., a-Li4.4C), which soften the overall a-Li4.4(SiC)0.5 system while swelling it volumetrically up to 668%. Furthermore, our force field accurately depicts step-wise lithiation mechanisms and volume changes in Si–sp2-C composites throughout the lithiation domain of each host subsystem. It reveals the formation of a Li-rich interphase at their grain boundary, which favors their adhesion and increases the local Li (de)insertion voltage up to 1 V. These examples demonstrate the ability of the new Li–Si–C ReaxFF potential to provide atomistic-scale insights required for designing and optimizing a wide range of Si–C-based anode candidates for upcoming Li-ion battery technologies.

Molecular dynamics simulation of surface phenomena due to high electronic excitation ion irradiation in amorphous silica

We studied by means of an atomistic model based on molecular dynamics the thermal evolution of surface atoms in amorphous silica under high electronic excitation produced by irradiation with swift heavy ions. The model was validated with the total and differential yields measured in sputtering experiments with different ions and ion energies showing a very good quantitative prediction capability. Three mechanisms are behind the evolution of the surface region: (1) an ejection mechanism of atoms and clusters with kinetic energy exceeding their binding energy to the sample surface, which explains the experimentally observed angular distributions of emitted atoms, and the correlation of the total sputtering yield with the electronic stopping power and the incidence angle. (2) A collective mechanism of the atoms in the ion track originated by the initial atom motion outwards the track region subsequently followed by the return to the resulting low-density region in the track center. The collective mechanism describes the energy dissipation of bulk atoms and the changes in density, residual stress, defect formation and optical properties. (3) A flow mechanism resulting from the accumulation and subsequent evolution of surface atoms unable to escape. This mechanism is responsible for the crater rim formation.Graphic Evolution of the molecular dynamics simulation of amorphous silica for 12 keV/nm electronic stopping power with a hot cylinder of radius 3.0 nm and an incidence angle of 20º

From an atomistic study of olivine under pressure to the understanding of the macroscopic energy release in earthquakes

• Assessing macroscopic seismic observables from an unusual microscopic perspective. • A common rupture mechanism for intermediate and very deep earthquakes. • Grounds to redefine commonly accepted order of magnitude for seismic efficiency. We present a multi-disciplinary study of the rupture process of deep- and intermediate-depth earthquakes in the subducting slab that develops beneath the Peruvian-Brazilian region. This contemplates the understanding of the atomistic fracture mechanism in an olivine model, its energetics budget, and the bridging of these results to the available seismic observables. A theoretical description of the stress-strain curves for the subducting material is initially provided as a key element to discern whether the rupture mechanism changes with depth or not. To this purpose, atomistic modeling was carried out through ab initio techniques for the forsterite olivine at different pressure ranges. The achieved stress-strain curves were compared to the average moment-scaled functions obtained for 43 intermediate (50 km < h < 200 km) and very deep earthquakes (500 km < h < 700 km) at the Peruvian-Brazilian subduction zone. It is found that at both depths operate a common atomistic rupture mechanism that is based on the gliding of the {001} crystal planes. Although the velocity of stress release changes with depth, this finding helps to clarify the controversial rupture process for very deep earthquakes at subduction zones. Likewise, efforts were directed to quantify the total amount of energy freed during an earthquake. Test calculations were carried out for several deep earthquakes providing rupture energy of six orders of magnitudes larger than the observable radiated seismic energy. This indicates that there might be space for redefining the commonly accepted order of magnitude for the seismic efficiency coefficient.

Selective virtual screening of hypoxia inducible factor agonists and antagonists using artificial intelligence and linear response theory.

Hypoxia inducible factor (HIF) is a heterodimeric transcription factor that mediates a signaling cascade under low oxygen concentration and prevents cell death. Under normoxia, enhanced HIF activity promotes tumorigenesis, and it is considered as a key oncogenic driver in renal cell carcinoma. Enhancing HIF activity is a therapeutic approach to treat renal anaemia, thus making both HIF activators (agonists) and inhibitors (antagonists) a potential therapeutic target under different disease conditions. While known HIF agonists and antagonists have opposing effect on the HIF activity, both binds to same cavity in the C-terminal domain of HIF (PASB domain). We identify the atomic level mechanism behind differential effect of agonists/antagonists on HIF activity using molecular dynamics simulations and linear response theory. Agonists and antagonists trigger different allosteric pathway from the PASB domain to the DNA-binding domain of HIF transcription factor. The ligand induced external forces on the protein residues explains the observed allosteric effect and used as a descriptor to predict the activation/inhibition potential of a given ligand. A large-scale structure-based virtual screening of 700 million molecules from ZINC database is performed to identify the potential new ligands of HIF. Binding energies of 10 million ligands is predicted using Autodock Vina and used to train a directed-message passing neural network (D-MPNN) to predict binding energies of the remaining molecules, hence enabling the screening of the larger portion of molecules at a reasonable computational cost. The top candidate molecules are further classified as potential inhibitors based on the forces exerted by the ligands on protein residues.

One-dimensional harmonic chain model of vibration-mode matching in solid-liquid interfacial thermal transport.

Understanding the atomistic mechanism of interfacial thermal transport at solid-liquid interfaces is a key challenge in thermal management at the nanoscale. A recent molecular-dynamics study demonstrated that interfacial thermal resistance (ITR) at the interface between a solid and a surfactant solution can be minimized by adjusting the molecular mass of the surfactant. In the present study, we explain the mechanism of this ITR minimization in view of vibration-mode matching using a one-dimensional (1D) harmonic chain model of a solid-liquid interface having an interfacial adsorption layer of surfactant molecules. The equation of motion for the 1D chain is described by a classical Langevin equation and is analytically solved by the nonequilibrium Green's function (NEGF) method. The resultant ITR is expressed in a form of vibrational matching, and its relationship to the overlap of the vibrational density of states is also discussed. The analysis leads to a conclusion that the damping coefficient η in the Langevin equation should be a finite and sufficiently large value to represent the rapid damping of vibration modes at solid-liquid interfaces. This conclusion provides a clue to seamlessly extend the conventional NEGF-phonon transmission picture of solid-solid interfacial thermal transport, which assumes η to be infinitesimal, to solid-liquid interfaces.

Mechanisms of ribosome stalling and unstalling studied by MD simulations.

The reasons for ribosomes being stalled in certain conformational states are manifold. Many bound antibiotics impede the conformational changes necessary for progression thereby trapping the ribosome in a specific state. Stalled conformations can lead to homogeneous ensembles and are therefore especially accessible to structure determination by cryo-EM and X-ray crystallography. To address mechanisms of stalling, we use all-atom Molecular Dynamics simulations of the stalled structures (e.g., including the antibiotic) and of structures after in-silico removal of the cause for stalling (e.g. removing the antibiotic or introducing a mutation). The comparison of the acquired ensembles allows us to formulate hypotheses of the atomistic mechanism, which can then be tested in experiments. In collaborations with experimental groups, we identified the stalling mechanism of Erm leader peptides in presence of macrolide antibiotics that induces the expression of a downstream macrolide resistance determinant. mRNAs which lack a stop codon result in ribosomes stalled at the 3’ end of the mRNA. Alternative ribosome-rescue factor B (ArfB) rescues stalled ribosomes by tRNA-peptide hydrolysis, thus releasing the peptide. ArfB consists of an N-terminal domain with the GGQ motif required for the hydrolysis, a C-terminal domain which acts as a sensor for the empty mRNA entry channel, and a linker connecting the domains. In simulations of wild-type ArfB, we found an alpha helix (residues 80-99) stabilizing the tRNA CCA-tail in a hydrolysis-competent conformation. Cutting the linker, or introducing mutations of conserved linker residues results in a shifted helix and consequently different CCA-tail conformations. We suggest that the placement of the C-terminal domain in the empty mRNA entry channel determines the position of the linker which, in turn, restricts the conformation of the alpha helix and stabilizes the tRNA in a hydrolysis-competent conformation.

Atomistic mechanisms for catalytic transformations of NO to NH3, N2O, and N2 by Pd

The industrial pollutant NO is a potential threat to the environment and to human health. Thus, selective catalytic reduction of NO into harmless N2, NH3, and/or N2O gas is of great interest. Among many catalysts, metal Pd has been demonstrated to be most efficient for selectivity of reducing NO to N2. However, the reduction mechanism of NO on Pd, especially the route of N−N bond formation, remains unclear, impeding the development of new, improved catalysts. We report here the elementary reaction steps in the reaction pathway of reducing NO to NH3, N2O, and N2, based on density functional theory (DFT)-based quantum mechanics calculations. We show that the formation of N2O proceeds through an Eley-Rideal (E−R) reaction pathway that couples one adsorbed NO* with one non−adsorbed NO from the solvent or gas phase. This reaction requires high NO* surface coverage, leading first to the formation of the trans-(NO)2* intermediate with a low N−N coupling barrier (0.58 eV). Notably, trans-(NO)2* will continue to react with NO in the solvent to form N2O, that has not been reported. With the consumption of NO and the formation of N2O* in the solvent, the Langmuir-Hinshelwood (L-H) mechanism will dominate at this time, and N2O* will be reduced by hydrogenation at a low chemical barrier (0.42 eV) to form N2. In contrast, NH3 is completely formed by the L-H reaction, which has a higher chemical barrier (0.87 eV). Our predicted E-R reaction has not previously been reported, but it explains some existing experimental observations. In addition, we examine how catalyst activity might be improved by doping a single metal atom (M) at the NO* adsorption site to form M/Pd and show its influence on the barrier for forming the N−N bond to provide control over the product distribution.

A computational methodology to account for the liquid film thickness evolution in Direct Numerical Simulation of prefilming airblast atomization

Prefilming airblast atomization is becoming widely used in current aero engines. Fundamental studies on the actual annular configuration of airblast atomizers are difficult to realize. For this reason, researchers have also focused on planar configurations. In this regard, the Karlsruhe Institute of Technology (KIT) developed a test rig to conduct experimental activities, conforming a large database with results for different working fluids and operating conditions. Such data allow two-phase flow modelers to validate their calculations concerning primary atomization on these devices. The present investigation proposes a Direct Numerical Simulation (DNS) study on the KIT planar configuration through the Volume of Fluid (VOF) method within the PARIS Simulator code. The novelty compared to DNS works reported in the literature resides in the use of a boundary condition that allows accounting not only for the gas inflow turbulence but also for the spatio-temporal evolution of the liquid film thickness at the DNS inlet and its related effect on turbulence. The proposed methodology requires computing precursor single-phase and two-phase flow Large-Eddy Simulations on the prefilmer flow, with the assumption that the flow between computational domains is one-way coupled. Results are compared to DNS that only account for a constant (both timewise and spanwise) liquid film thickness at the domain inlet, validating the full methodology workflow. The proposed methodology is shown to improve the qualitative description of the atomization mechanism, as the different stages of breakup (liquid accumulation behind the prefilmer edge, bag formation, bag breakup, ligament formation and ligament breakup) coexist spanwise for a given temporal snapshot. This implies a more continuous atomization than the one predicted by the constant film thickness case, which showed the same breakup stage to be present along the prefilmer span for a given instant and led to a more discretized set of atomization events. The proposed workflow allows quantifying the influence of the liquid film flow evolution above the prefilmer surface on primary breakup frequency and relevant atomization features.

Different pKa Shifts of Internal GLU8 in Human β-Endorphin Amyloid Revealing a Coupling of Internal Ionization and Stepwise Fibril Disassembly.

As a functional amyloid, human β-endorphin amyloid fibril features a β-solenoid conformation and store peptide hormones within acidic secretory granules, which would be released into the blood through fibril disassembly when the cellular milieu pH increases from acidic to neutral level on exocytosis. To gain detailed atomic mechanism of β-endorphin amyloid fibrils' pH-responsive disassembly, we conduct constant pH molecular dynamics simulations to investigate the structural and dynamical properties of β-endorphin amyloid fibrils in experiencing the environmental pH changes. Our results demonstrate a clear pKa shift of the internal ionizable residue of GLU8, and this shift becomes even more pronounced when it is buried more deeply in the amyloid fibrils. The unusual pKa of GLU8 reveals that its protonation state changes from the protonated state in the acidic secretory granule to the deprotonated state in the neutral pH conditions in the blood, where the deprotonation of GLU8 leads to unfavorable interactions within the hydrophobic core of the amyloid and subsequent fibril disassembly. The different pKa shifts of GLU8 relative to its positions in the amyloid fibril indicate that the β-endorphin amyloid fibril disassembly is a stepwise process, accounting for the experimental observation that the disassembly always initiates from the outermost layer. This study reveals the critical role of the protonation state of GLU8 in amyloid fibrils' pH-responsive disassembly, and provides clear insights for understanding the structural transitions of amyloids in hormone secretion. This study also provides theoretical basis for designing pH-sensitive biological tools for specific use with precise positioning of ionizable residues into the hydrophobic interior of proteins.