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At least 1,495 records · Page 83

Thermal energy evolution and mechanical deformation of monocrystalline yttria-stabilized zirconia nanoparticles in aerosol deposition processes

Aerosol deposition (AD) is a coating process wherein aerosol particles are impacted on a target substrate. There are fundamental differences between the AD process (cold impact), where particle translational kinetic energy is high and thermal energy is low, and thermal spray deposition (thermal impact), where translational energy is lower but thermal energy is high. To better compare cold and thermal impact effects on particles, we carried out molecular dynamics simulations using yttria-stabilized zirconia (YSZ) nanoparticles on YSZ substrates as a model system. We performed cold impact simulations at 300 K with variable impact velocity in the 500 ms –1 –1500 ms –1 range to understand how increasing translational kinetic energy affects thermal energy and mechanical evolution. We then performed thermal impact simulations at variable temperature and impact velocity, but where the total kinetic energy of the nanoparticle was equivalent to that of a 300 K, 1000 impact. In cold impact, the temperature increases in YSZ nanoparticles at a rate of 10 13 – 10 14 K s –1 , and large temperature gradients result. Conversely, in thermal impact, nanoparticle temperatures remain uniform. Furthermore, the temperature gradients during cold impact coincide with plastic deformation in nanoparticles, while with larger thermal energies, plastic deformation is reduced.

42 ENGINEERING↗

Conformational space exploration of cryo-EM structures by variability refinement

Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. Here, in order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.

59 BASIC BIOLOGICAL SCIENCES↗

Membrane hydrophobicity determines the activation free energy of passive lipid transport

The collective behavior of lipids with diverse chemical and physical features determines a membrane's thermodynamic properties. Yet, the influence of lipid physicochemical properties on lipid dynamics, in particular interbilayer transport, remains underexplored. Here, we systematically investigate how the activation free energy of passive lipid transport depends on lipid chemistry and membrane phase. Through all-atom molecular dynamics simulations of 11 chemically distinct glycerophospholipids, we determine how lipid acyl chain length, unsaturation, and headgroup influence the free energy barriers for two elementary steps of lipid transport: lipid desorption, which is rate limiting, and lipid insertion into a membrane. Consistent with previous experimental measurements, we find that lipids with longer, saturated acyl chains have increased activation free energies compared to lipids with shorter, unsaturated chains. Lipids with different headgroups exhibit a range of activation free energies; however, no clear trend based solely on chemical structure can be identified, mirroring difficulties in the interpretation of previous experimental results. Compared to liquid-crystalline phase membranes, gel phase membranes exhibit substantially increased free energy barriers. Overall, we find that the activation free energy depends on a lipid's local hydrophobic environment in a membrane and that the free energy barrier for lipid insertion depends on a membrane's interfacial hydrophobicity. Both of these properties can be altered through changes in lipid acyl chain length, lipid headgroup, and membrane phase. Thus, the rate of lipid transport can be tuned through subtle changes in local membrane composition and order, suggesting an unappreciated role for nanoscale membrane domains in regulating cellular lipid dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump

The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun’s lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Finally, sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.

59 BASIC BIOLOGICAL SCIENCES↗

Steric effects of central dogma processes on the compaction and segregation of bacterial nucleoids

The bacterial cytoplasm is characterized by a distinctive membrane-less organelle, the nucleoid, which harbors the chromosomal DNA. Here, we investigate the steric effects of dynamic processes associated with transcription and translation on the structure of this organelle using coarse-grained molecular dynamics simulations that incorporate out-of-equilibrium reactions. Our model captures the scale of the entire cell and incorporates a reaction-diffusion system for ribosomes and polyribosomes, coupling their nonequilibrium kinetics to DNA excluded volume interactions. Our findings demonstrate that out-of-equilibrium reactions increase the size of the nucleoid and the number of ribosomes in this subcellular region. In addition, we show that nucleoid size is proportional to transcriptional activity. Our model reproduces the time-dependent change in nucleoid size observed in rifampicin treatment experiments, where the pool of polyribosomes is depleted. Furthermore, we find that these active processes are essential for complete sister chromosome separation and correct nucleoid positioning within the cell. Overall, our study reveals the effects of the central dogma processes on the internal organization and localization of bacterial nucleoids.

Chang, Mu-Hung [Univ. of Tennessee, Knoxville, TN ↗

Converting PBO fibers into carbon fibers by ultrafast carbonization

Here, we report an ultrafast transformation of poly(p-phenylene-2,6-benzobisoxazole) (PBO) fibers into car- bon fibers (CFs) by direct carbonization that eliminates high-cost oxidation in traditional CF conversion. Ultrafast heating and cooling render PBO-derived CFs superlative mechanical properties. ReaxFF atomistic-scale reactive molecular dynamics simulations unveil the PBO to CF conversion mechanism in which ultrafast heating suppresses the O-contained gas release, facilitating all-carbon rings alignment during the carbonization of PBO. These results offer new guidelines for identifying and evaluating alternative CF precursors and fresh perspectives on smart manufacturing of CFs.

42 ENGINEERING↗

Dislocation-graphene interactions in Cu/graphene composites and the effect of boundary conditions: a molecular dynamics study

Here, in this paper, systematic molecular dynamics simulations were employed to study dislocation-graphene interactions in Cu/graphene systems using two carefully selected configurations: (i) edge dislocations in the pileup interacting with graphene during nanoindentation and (ii) complex dislocations interacting with graphene in compression of layered nanopillars. The intrinsic and extrinsic size effects were investigated with respect to varying the Cu lamella thickness and pillar sizes, revealing an anomalous extrinsic size effect: the smaller, the weaker. To understand which boundary conditions are physically consistent, both free and periodic graphene were considered. It was seen that edge dislocations in the pileup continuously transmitted across the free graphene through Cu/graphene interfacial sliding and graphene reorientation, whereas transmission was very difficult for periodic graphene as its in-plane deformation was required. In compression of Cu/graphene nanopillars, the strengthening effect of free graphene was found to be less obvious than that of the periodic case, which could be attributed to free graphene edges acting as dislocation sources after the compressed Cu overflowed the graphene sheet from all directions. We therefore conclude that the strengthening effect of periodic graphene inclusions appears to be overestimated, such that free graphene should be more appropriate.

36 MATERIALS SCIENCE↗

Atomistic modeling of tensile deformation and fracture of carbon fibers: Nanoscale stress redistribution, effect of local structural characteristics and nanovoids

The mechanisms of tensile deformation and fracture of carbon fibers are investigated in large-scale molecular dynamics simulations. The simulations performed for computational samples with different structural characteristics enable analysis of the structural sensitivity of the mechanical properties. It is found that the carbon fiber nanostructure can be represented by a fine (nanoscale) mixture of stiff and soft regions. Despite the nanoscale structural heterogeneity of the computational fibers, their fracture strain and tensile strength exceed the experimental values by almost an order of magnitude. Here, this observation is explained by the ability of the carbon fiber nanostructure, largely consisting of curved and folded layers of turbostratic carbon, to exhibit continuous nanoscale load redistribution during the deformation. The transient, fluid nature of a percolating cluster of stress-holding structural elements prevents stress localization at the early stage of the deformation and enables the fiber nanostructure to adapt to the increasing load. Overall, the results of the simulations suggest that the design of advanced carbon fiber manufacturing and post-processing methods focused on the elimination of critical mesoscopic structural defects (internal voids, foreign inclusions, and surface flaws) can yield a substantial increase in the strength and fracture strain of carbon fibers.

36 MATERIALS SCIENCE↗

Diethylenetriamine-functionalized graphene oxide: Insights into ion adsorption and applications in rare earth element separation

The growing demand for critical minerals and materials requires atom- and energy-efficient, selective separations to overcome the challenges posed by the similar chemical and physical properties of the rare earth elements (REEs) and their low concentrations in unconventional domestic feedstocks. Here, in this study, we developed diethylenetriamine-functionalized graphene oxide (DETA-GO) as a membrane material for REE adsorption and separation. Synthesis conditions were optimized to maximize nitrogen incorporation while also preserving GO dispersibility for facile membrane fabrication. We investigated the mechanism of amine functionalization, the nitrogen-bonding configurations, the organization of the interlayer transport channels, and the resulting effects on ion and water transport for REE separations. Neat-GO and DETA-GO multilayer laminate membranes were fabricated by vacuum filtration onto polymer supports. To investigate the effects of amine functionalization, the membranes were characterized using scanning electron microscopy, Raman, Fourier transform infrared, and X-ray photoelectron spectroscopy, as well as grazing-incidence X-ray diffraction measurements. Ion permeation experiments with representative lanthanum (La 3+ ) and ytterbium (Yb 3+ ) solutions revealed enhanced ion adsorption and water transport through DETA-GO membranes compared to neat-GO. The strong affinity of the membranes for multivalent REEs was also validated with conductivity and inductively coupled plasma mass spectrometry measurements. Atomistic insight into the role of amine functionalization in modulating nanochannel architecture and long-term stability, optimizing adsorption sites, and regulating REE and water transport was obtained using classical molecular dynamics simulations. Collectively, our joint experimental and theoretical study demonstrates the potential of DETA-GO membranes for selective REE separations, offering insights into ion-binding mechanisms, water-transport properties, and nanochannel optimization for the recovery of critical materials from aqueous feedstocks.

Adsorbent↗

Rational Enzyme Design for Controlled Functionalization of Acetylated Xylan for Cell-Free Polymer Biosynthesis

Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.

93 SC - Biological and Environmental Research (BER↗

When SLIPS meets TIPS: An endogenous lubricant-infused surface by taking the diluent as the lubricant

Slippery lubricant-infused porous surfaces (SLIPSs) hold great promise in fields requiring adhesion resistance such as self-cleaning, anti-fouling, anti-icing, and anti-scaling. However, their road to practical application is still blocked by the complicated fabrication process and the restricted coating area. To address these challenges, we propose a new concept of endogenous SLIPS in which the porous structure grows from the solution coating of polypropylene/caprylyl methicone undergoing a thermally induced phase separation (TIPS) process. Caprylyl methicone serves as the diluent during TIPS as well as the lubricant in the SLIPS so that the coating can be fabricated in one step and unrestrictedly. Furthermore, the dissolution and phase separation mechanisms have been revealed by molecular dynamic simulation and in situ microscopic observation. Such SLIPSs exhibits impressive sliding property even for sticky and viscous liquids and exhibit extremely low ice adhesion in anti-icing tests.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Highly efficient interface stabilization for ambient-temperature quasi-solid-state sodium metal batteries

Solid-state sodium (Na) batteries (SSSBs) using sulfide-based solid electrolytes (SSEs) hold tremendous promise due to their high theoretical specific capacity, enhanced safety and abundant resources. However, detrimental interfacial issues between SSEs and Na metal present a major challenge to the advancement of sulfide-based SSSBs. To address interfacial issues, we demonstrate an efficient approach by incorporating an ionic liquid electrolyte ((PYR/Na)TFSI) as interlayer to stabilize the Na metal/SSE interface. The presence of the (PYR/Na)TFSI interlayer enables the formation of a stable solid electrolyte interphase (SEI) to prevent the harmful reactions and inhibit Na dendrites. Combination of ab initio molecular dynamics simulations and X-ray photoelectron spectroscopy revealed that this stable SEI is largely composed of reduced products of TFSI -, such as NaF and CF 3 . As a result, the symmetric cells exhibited stable Na plating/striping cycling for 300 h at 0.1 mA cm -2 . In addition, FeS2||Na quasi-solid-state batteries delivered an impressive specific capacity of over 300 mAh g -1 under the current density of 20 mA g -1 at room temperature. Under a higher current density (100 mA g -1 ), such batteries performed with long-term cycling stability and maintained a specific capacity of around 103 mAh g -1 after 330 cycles. This work demonstrates the novel perspective of using an ionic liquid interlayer to address interfacial issues, contributing to the advancement of high-performance SSSBs for the next-generation energy storage systems.

25 ENERGY STORAGE↗

Effective direct steam regeneration of bis-iminoguanidine solid sorbent used for carbon dioxide capture

A cost-effective, energy-efficient sorbent regeneration process for phase-changing guanidines used for CO 2 capture was developed based on direct-steam stripping. This approach enhances the regeneration rate, simplifies the overall CO 2 capture process, and reduces the energy cost compared to conventional conductive thermal regeneration. A direct-steam sorbent regeneration reactor was developed, demonstrating that aqueous bis(iminoguanidines) (BIG) sorbents, e.g., methylglyoxal-bis(iminoguanidine) (MGBIG) and glyoxal-bis(iminoguanidine) (GBIG), could be efficiently regenerated with up to ~ 99 % CO 2 recovery through direct-steam stripping. Using low-temperature steam at 100 °C, a 4.5 times faster regeneration rate for GBIG carbonate sorbent (e.g., 30 min for 10 g) was demonstrated compared to conductive-heating (e.g., 135 min for 10 g) at 130 °C. Additionally, fully regenerated MGBIG converts into an aqueous MGBIG solution when the steam condenses onto the sorbent surface. Condensed steam with the guanidine can be easily recycled as an aqueous solution into the gas–liquid contactor to achieve a continuous-flow CO 2 -capture process. Molecular dynamics simulation was employed to provide a better understanding of the process. Higher heat transfer rates from steam to guanidine carbonate, compared to air heating, were attributed to the vibration resonance of water molecules within MGBIG with that of vapor molecules and the effective transfer of kinetic energy from vapor to solid. Technoeconomic analysis demonstrated that direct-steam stripping significantly decreases the CO 2 capture cost by 50 % compared to traditional conductive heating methods. Further, enhanced mass transfer facilitated by low-temperature steam and subsequent condensation effectively heats up the H 2 O-containing BIG-carbonate crystals, facilitating the desorption of CO 2 from the solid crystals, thereby leading to fast, effective, and energy-efficient sorbent regeneration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Vapor-phase self-assembly for generating thermally stable single-atom catalysts

Preparation of thermally stable metal single-atom catalysts (SACs) is a challenge in heterogeneous catalysis, especially on conventional supports that provide a weak metal-support interaction. In this work, we report that a modified support MgAl 2 O 4 can stabilize Pt single atoms by a mechanism of vapor-phase self-assembly in a high-temperature treatment (800°C, air). The experimental results on the formation mechanism and the structure are validated by DFT and ab initio molecular dynamics simulations. We infer that stable triangular K 3 O 3 structures help stabilize Pt single atoms at high temperatures in oxidizing conditions, exhibiting excellent reactivity for methane oxidation. The obtained Pt/K/MgAl 2 O 4 SAC presents excellent stability in methane oxidation after steam treatment at elevated temperatures, whereas the Pt/MgAl 2 O 4 nanocatalyst suffers from rapid deactivation due to Pt nanoparticle growth. Now this work paves the way for preparing thermally stable and highly active SACs using conventional high-surface-area supports, despite the weak metal-support interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering a photoenzyme to use red light

Photoenzymatic reactions involving flavin-dependent “ene”-reductases (EREDs) rely on protein-templated charge transfer (CT) complexes between the cofactor and substrate for radical initiation. These complexes typically absorb in the blue region of the electromagnetic spectrum. Here, we engineered an ERED to form CT complexes that absorb red light. Mechanistic studies indicate that red-light activity is due to the growth of a red-absorbing shoulder off the previously identified cyan absorption feature. Molecular dynamics simulations, docking, and excited-state calculations suggest that the cyan feature involves a π→π* transition on flavin, whereas the red-light absorption is a π→π* transition between flavin and the substrate. Furthermore, differences in the electronic transition are due to changes in the substrate-binding conformation and allosteric tuning of the electronic structure of the cofactor-substrate complex. Microenvironment tuning of the CT complex for red-light activity is observed with other engineered photoenzymatic reactions, highlighting this effect’s generality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Limiting velocities and transonic dislocations in Mg

To accurately predict the mechanical response of materials, especially at high strain rates, it is important to account for dislocation velocities in these regimes. Under these extreme conditions, it has been hypothesized that dislocations can move faster than the speed of sound. However, the presence of such dislocations remains elusive due to challenges associated with measuring these experimentally. In this work, molecular dynamics simulations were used to investigate the dislocation velocities for the basal edge, basal screw, prismatic edge, and prismatic screw dislocations in Mg in the sub-, trans-, and supersonic regimes. Also, our results show that only prismatic edge dislocations achieve supersonic velocities. Furthermore, this work demonstrates that the discrepancy between the theoretical limiting velocity and the MD results for Mg is due to its sensitivity to large hydrostatic stress around the dislocation core, which was not the case for fcc metals such as Cu.

36 MATERIALS SCIENCE↗

Extended defects-enhanced oxygen diffusion in ThO 2

Oxygen self-diffusion is key to understanding stoichiometry and defect structures in oxide nuclear fuels. Experimentally, low activation-barrier oxygen migration was found in ThO 2 , a candidate nuclear fuel, possibly due to short-circuit diffusion mechanisms. Here, we perform extensive molecular dynamics simulations to show that various types of extended defects can enhance oxygen self-diffusion with a much-reduced activation barrier in ThO 2 . In this work, we consider extended defects including 1D (dislocation), 2D (grain boundary), and 3D (void) defects. Due to the distinct characteristics of each type of extended defect, the modulation of oxygen diffusion varies. Further, these results provide a quantitative description of oxygen transport, which is significantly enhanced within a close distance (nanometer scale) from the extended defects. Among all these considered defects, grain boundary, particularly the low-energy $Σ$3 twin boundary, exhibits the strongest effect on increasing oxygen transport.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗