Atomic Model Research Articles

Role of tin clustering in band structure and thermodynamic stability of GeSn by atomistic modeling

Synthesis of device-quality GeSn materials with higher Sn compositions is hindered by various factors, such as Sn segregation, clustering, and short-range ordering effects. In the present work, the impact of the clustering of Sn atoms in a GeSn semiconductor alloy was studied by density functional theory using SG15 pseudopotentials in a Synopsys QuantumATK tool, where the thermodynamic stability, effective band structure, indirect and direct bandgaps, and density of states (DOS) were computed to highlight the difference between a cluster-free random GeSn alloy and a GeSn alloy with Sn–Sn clusters. A 54-atom bulk Ge1–xSnx (x = 3.71%–27.77%) supercell was constructed with cluster-free and a first nearest neighbor Sn–Sn clustered GeSn alloy at each composition for this work. Computation using the generalized gradient approximation exchange-correlation functional showed that the thermodynamic stability of GeSn was reduced due to the clustering of Sn, which increased the formation energy of the GeSn alloys by increasing the Hartree potential energy and exchange-correlation energy. Moreover, with the effective band structure of the GeSn material at a Sn composition of ∼22%, both direct (Eg,Γ) and indirect (Eg,L) bandgaps decreased by a large margin of 40.76 and 120.17 meV, respectively, due to Sn–Sn clustering. On the other hand, Eg,Γ and Eg,L decrease is limited to 0.5 and 12.8 meV, respectively, for Sn composition of ∼5.6%. Similar impacts were observed on DOS, in an independent computation without deducing from the electronic band structure, where the width of the forbidden band reduces due to the clustering of Sn atoms in GeSn. Moreover, using the energy bandgaps of GeSn computed with the assumption of it being a random alloy having well-dispersed Sn atoms needs revision by incorporating clustering to align with the experimentally determined bandgap. This necessitates incorporating the effect of Sn atoms clustered together at varying distributions based on experimental characterization techniques such as atom probe tomography or extended x-ray absorption fine structure to substantiate the energy bandgap of the GeSn alloy at a particular composition with precision. Hence, considering the effect of Sn clusters during material characterization, beginning with the accurate energy bandgap characterization of GeSn would help in mitigating the effect of process variations on the performance characteristics of GeSn-based group IV electronic and photonic devices such as varying leakage currents in transistors and photodiodes as well as the deviation from the targeted wavelength of operation in lasers and photodetectors.

Surface Segregation in Binary Metallic Nanoparticles: Atomistic Simulation and Thermodynamic Modeling

Surface Segregation in Binary Metallic Nanoparticles: Atomistic Simulation and Thermodynamic Modeling

Automated atomic modeling in cryo-EM maps.

Automated atomic modeling in cryo-EM maps.

Structural characteristics of alpha-fetoprotein, including N-glycosylation, metal ion and fatty acid binding sites

Alpha-fetoprotein (AFP), a serum glycoprotein, is expressed during embryonic development and the pathogenesis of liver cancer. It serves as a clinical tumor marker, function as a carcinogen, immune suppressor, and transport vehicle; but the detailed AFP structural information has not yet been reported. In this study, we used single-particle cryo-electron microscopy(cryo-EM) to analyze the structure of the recombinant AFP obtained a 3.31 Å cryo-EM structure and built an atomic model of AFP. We observed and identified certain structural features of AFP, including N-glycosylation at Asn251, four natural fatty acids bound to distinct domains, and the coordination of metal ions by residues His22, His264, His268, and Asp280. Furthermore, we compared the structural similarities and differences between AFP and human serum albumin. The elucidation of AFP’s structural characteristics not only contributes to a deeper understanding of its functional mechanisms, but also provides a structural basis for developing AFP-based drug vehicles.

Tuning the Chirality Evolution in Achiral Subnanometer Systems by Judicious Control of Molecule Interactions.

Chirality evolution from molecule levels to the nanoscale in an achiral system is a fundamental issue that remains undiscovered. Here, we report the assembly of polyoxometalate (POM) clusters into chiral subnanostructures in achiral systems by programmable single-molecule interactions. Driven by the competing binding of Ca2+ and surface ligands, POM assemblies would twist into helical nanobelts, nanorings, and nanotubes with tunable helicity. Chiral molecules can be used to differentiate the formation energies of chiral isomers and immobilize the homochiral isomer, where strong circular dichroism (CD) signals are obtained in both solutions and films. Chiral helical nanobelts can be used as circularly polarized light (CPL) photodetectors due to their distinct chiroptic responsivity for right and left CPL. By the fine-tuning of interactions at single-molecule levels, the morphology and CD spectra of helical assemblies can be precisely controlled, providing an atomic precision model for investigation of the structure-chirality relationship and chirality manipulation at the nanoscale.

Sampling Real-Time Atomic Dynamics in Metal Nanoparticles by Combining Experiments, Simulations, and Machine Learning.

Even at low temperatures, metal nanoparticles (NPs) possess atomic dynamics that are key for their properties but challenging to elucidate. Recent experimental advances allow obtaining atomic-resolution snapshots of the NPs in realistic regimes, but data acquisition limitations hinder the experimental reconstruction of the atomic dynamics present within them. Molecular simulations have the advantage that these allow directly tracking the motion of atoms over time. However, these typically start from ideal/perfect NP structures and, suffering from sampling limits, provide results that are often dependent on the initial/putative structure and remain purely indicative. Here, by combining state-of-the-art experimental and computational approaches, how it is possible to tackle the limitations of both approaches and resolve the atomistic dynamics present in metal NPs in realistic conditions is demonstrated. Annular dark-field scanning transmission electron microscopy enables the acquisition of ten high-resolution images of an Au NP at intervals of 0.6 s. These are used to reconstruct atomistic 3D models of the real NP used to run ten independent molecular dynamics simulations. Machine learning analyses of the simulation trajectories allow resolving the real-time atomic dynamics present within the NP. This provides a robust combined experimental/computational approach to characterize the structural dynamics of metal NPs in realistic conditions.

Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission

Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlyingmembrane as it progresses through the GTPase cycle to sever vesicles from the plasmamembrane.Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of theassembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembledas a 2-start helix with an inner lumen of 3.4nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using theGTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.

Mechanism of single-stranded DNA annealing by RAD52–RPA complex

RAD52 is important for the repair of DNA double-stranded breaks1,2, mitotic DNA synthesis3–5 and alternative telomere length maintenance6,7. Central to these functions, RAD52 promotes the annealing of complementary single-stranded DNA (ssDNA)8,9 and provides an alternative to BRCA2/RAD51-dependent homologous recombination repair10. Inactivation of RAD52 in homologous-recombination-deficient BRCA1- or BRCA2-defective cells is synthetically lethal11,12, and aberrant expression of RAD52 is associated with poor cancer prognosis13,14. As a consequence, RAD52 is an attractive therapeutic target against homologous-recombination-deficient breast, ovarian and prostate cancers15–17. Here we describe the structure of RAD52 and define the mechanism of annealing. As reported previously18–20, RAD52 forms undecameric (11-subunit) ring structures, but these rings do not represent the active form of the enzyme. Instead, cryo-electron microscopy and biochemical analyses revealed that ssDNA annealing is driven by RAD52 open rings in association with replication protein-A (RPA). Atomic models of the RAD52–ssDNA complex show that ssDNA sits in a positively charged channel around the ring. Annealing is driven by the RAD52 N-terminal domains, whereas the C-terminal regions modulate the open-ring conformation and RPA interaction. RPA associates with RAD52 at the site of ring opening with critical interactions occurring between the RPA-interacting domain of RAD52 and the winged helix domain of RPA2. Our studies provide structural snapshots throughout the annealing process and define the molecular mechanism of ssDNA annealing by the RAD52–RPA complex.

Discrete-to-continuum modeling of spider silk fiber composites

This work presents a discrete-to-continuum approach to the constitutive response of composite materials formed by embedding a network of spider silk fibers in a matrix material. A multiscale model that makes use of the virial stress concept of statistical mechanics is formulated, which accounts for hyperelastic constitutive equations of the component materials. The finite element implementation of the given constitutive equations is also carried out. Numerical simulations show the response of a silk composite formed by embedding a spider orb web in a matrix material, and illustrate the main features of the proposed model. In the presence of a weak matrix, the force–displacement response of a silk composite is compared with that deriving from an atomistic modeling of the spider orb web. A simulation of the response of a composite equipped with an elastomeric matrix is also discussed.

Health and ecological risk assessment of heavy metals in water and sediments within a data scarce urban catchment in Tanzania – A case of Ngerengere River, Morogoro Municipality

Low-, middle- and high-income countries, exhibit indications of risks associated with water quality. The study investigated heavy metal concentrations in surface water and sediments within the Ngerengere River and its tributaries (Kikundi, Bigwa, and Morogoro) drain within in the Morogoro Municipality of Tanzania, an Urban Catchment Area (UCA) with limited available data mainly because of inadequate monitoring and reporting capabilities. Analysis of health and ecological risks associated with heavy metal pollution was also carried out using health risk assessments models, pollution indices, and multivariate analysis techniques. Between the dry and wet seasons of 2023, water and sediment samples from (13) sampling stations strategically established along the Ngerengere river and its tributaries were analyzed for six heavy metals (Pb, Cr, Ni, Cd, Cu and Zn) using the Atomic Absorption Spectrophotometer Model Perking Elmer 850 Graphite Furnace and Perking Elmer AS 800 Auto-sampler coupled with a computer interface for operational, displaying and reading the results. The calculated degree of water contamination (Cd) values in river water in both dry and wet seasons ranged from 0 to 6.803 indicating low and high degrees of contamination respectively. Heavy metal concentration in sediment decreases in the order of Zn>Ni>Cr>Cu>Cd>Pb. The non-cancer risk index (HI) via ingestion and dermal pathways in dry and wet seasons for both children and adult groups was <1 hence no non-cancer risk, However, cumulative dermal and ingestion exposure in both children and adults indicated potential cancer risk in dry and wet season. The analysis of ecological risks associated with heavy metal enrichment in the sediment indicated high enrichment of sediments with Cd, Ni and Zn. Conclusively, in wet months, risk indices tend to be low, while in dry months, they typically remain high.

Molecular-Level Insight into the Chlorofluorocarbons Adsorption by Defective Covalent Organic Polymers.

Halocarbons have important industrial applications, but because of their contribution to global warming and the fact that they can cause ozone depletion, they are considered highly toxic. Hence, the techniques that can capture and recover the used halocarbons with energy-efficient methods have been recently received greater attention. In this contribution, we report the capture of dichlorodifluoromethane (R12), which has high global warming and ozone depletion potential, using covalent organic polymers (COPs). The defect-engineered COPs were synthesized and demonstrated outstanding sorption capacities, ~226 wt % of R12 combined with linear-shaped adsorption isotherms. We further identified the plausible microscopic adsorption mechanism of the investigated COPs via grand canonical Monte Carlo simulations applied to non-defective and a collection of atomistic models of the defective COPs. The modeling work suggests that significant R12 adsorption performance is attributed to a gradual increment of porosities due to isolated/interconnected micro-/meso-pore channels and the change of the long-range ordering of both COPs. The successive hierarchical-pore-filling mechanism promotes R12 molecular adsorption via moderate van der Waals adsorbate-adsorbent interactions in the micropores of both COPs at low pressure followed by adsorbate-adsorbate interactions in the extra-voids created at moderate to high pressure ranges. This continuous pore-filling mechanism makes defective COPs as promising sorbents for halocarbon adsorption.

Atomic Models of Dense Plasmas, Applications, and Current Challenges

Modeling plasmas in terms of atoms or ions is theoretically appealing for several reasons. When it is relevant, the notion of atom or ion in a plasma provides us with an interpretation scheme of the plasma’s internal functioning. From the standpoint of quantitative estimation of plasma properties, atomic models of plasma allow one to extend many theoretical tools of atomic physics to plasmas. This notably includes the statistical approaches to the detailed accounting for excited states, or the collisional-radiative modeling of non-equilibrium plasmas, which is based on the notion of atomic processes. This paper is focused on the theoretical challenges raised by the atomic modeling of dense, non-ideal plasmas. It is intended to give a synthetic and pedagogical view on the evolution of ideas in the field, with an accent on the theoretical consistency issues, rather than an exhaustive review of models and experimental benchmarks. First we make a brief, non-exhaustive review of atomic models of plasmas, from ideal plasmas to strongly-coupled and pressure-ionized plasmas. We discuss the limitations of these models and pinpoint some open problems in the field of atomic modeling of plasmas. We then address the peculiarities of atomic processes in dense plasmas and point out some specific issues relative to the calculation of their cross-sections. In particular, we discuss the modeling of fluctuations, the accounting for channel mixing and collective phenomena in the photoabsorption, or the impact of pressure ionization on collisional processes.

Tribological properties and evolutionary mechanisms of a nanocrystalline Al-Mg-Si alloy at room and cryogenic temperatures

A nanocrystalline Al-Mg-Si alloy model was established to reveal the temperature effect in nanotribology using atomistic simulations. Compared to room temperature, the samples at cryogenic temperature (CT) exhibited an increase in both the coefficient of friction (COF) and wear resistance. At CT, the thermal activation of interface atoms reduced, thereby inhibiting surface grain rotation and sliding within the atomistic model. There was grain coarsening (suppressed at CT) instead of grain refinement typically observed for surface grains. The results also indicated that changes in load influenced the COF response, with higher loads resulting in higher COF values. The friction laws in simulation and experiment are similar.

Unraveling thermodynamic anomalies of water: A molecular simulation approach to probe the two-state theory with atomistic and coarse-grained water models.

Thermodynamic and dynamic anomalies of water play a crucial role in supporting life on our planet. The two-state theory attributes these anomalies to a dynamic equilibrium between locally favored tetrahedral structures (LFTSs) and disordered normal liquid structures. This theory provides a straightforward, phenomenological explanation for water's unique thermodynamic and dynamic characteristics. To validate this two-state feature, it is critical to unequivocally identify these structural motifs in a dynamically fluctuating disordered liquid. In this study, we employ a recently introduced structural parameter (θavg) that characterizes the local angular order within the first coordination shell to identify these LFTSs through molecular dynamics simulations. We employ both realistic water models with a liquid-liquid critical point (LLCP) and a coarse-grained water model without an LLCP to study water's anomalies in low-pressure regions below 2 kbar. The two-state theory consistently describes water's thermodynamic anomalies in these models, both with and without an LLCP. This suggests that the anomalies predominantly result from the two-state features rather than criticality, particularly within experimentally accessible temperature-pressure regions.

Tight-packing of large pilin subunits provides distinct structural and mechanical properties for the Myxococcus xanthus type IVa pilus

Type IVa pili (T4aP) are ubiquitous cell surface filaments important for surface motility, adhesion to surfaces, DNA uptake, biofilm formation, and virulence. T4aP are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While major pilins of structurally characterized T4aP have lengths of <165 residues, the major pilin PilA of Myxococcus xanthus is unusually large with 208 residues. All major pilins have a conserved N-terminal domain and a variable C-terminal domain, and the additional residues of PilA are due to a larger C-terminal domain. We solved the structure of the M. xanthus T4aP (T4aPMx) at a resolution of 3.0 Å using cryo-EM. The T4aPMx follows the structural blueprint of other T4aP with the pilus core comprised of the interacting N-terminal α1-helices, while the globular domains decorate the T4aP surface. The atomic model of PilA built into this map shows that the large C-terminal domain has more extensive intersubunit contacts than major pilins in other T4aP. As expected from these greater contacts, the bending and axial stiffness of the T4aPMx is significantly higher than that of other T4aP and supports T4aP-dependent motility on surfaces of different stiffnesses. Notably, T4aPMx variants with interrupted intersubunit interfaces had decreased bending stiffness, pilus length, and strongly reduced motility. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4aP that expands the environmental conditions in which the T4aP system functions.

Structure growth, stability and adsorption properties of (AgZn3)n clusters

ABSTRACT Recently, an effective syngas catalyst composed of AgZn3 clusters is reported, in which the CO and H2 generation may occur at the Zn sites and the hollow sites between Ag and Zn. Hence, the atomic model of the AgZn3 is worth established to further investigate the catalytic mechanism. Here, we take advantage of the genetic algorithm with the density functional theory to unbiasedly search configurations of (AgZn3)n (n = 1–6) clusters. It is found that (AgZn3)n clusters evolve from hollow cages to close-packed structures, with Zn atoms gradually occupying the core positions. The Eb and Δ2E analyses show that the (AgZn3)3 has a higher stability than that of its neighbors. The AIMD simulations demonstrate that the (AgZn3)3 shows a favorable stability at 700 K. The molecular orbitals reveal that 21 valence electrons of the (AgZn3)3 fill superatomic orbits resulting in an electronic configuration of 1S21P61D102S21F1. The adsorptions of CO on the bridge sites of (AgZn3)3 are much higher in energy than the top adsorptions, but the red shift of the stretching frequency of C-O is more obvious in the former. Our results are verified that the Zn sites and bridge sites between Ag and Zn are active sites for CO.

Vibrational properties of disordered stealthy hyperuniform 1D atomic chains

Disorder hyperuniformity is a recently discovered exotic state of many-body systems that possess a hidden order in between that of a perfect crystal and a completely disordered system. Recently, this novel disordered state has been observed in a number of quantum materials including amorphous 2D graphene and silica, which are endowed with unexpected electronic transport properties. Here, we numerically investigate 1D atomic chain models, including perfect crystalline, disordered stealthy hyperuniform (SHU) as well as randomly perturbed atom packing configurations to obtain a quantitative understanding of how the unique SHU disorder affects the vibrational properties of these low-dimensional materials. We find that the disordered SHU chains possess lower cohesive energies compared to the randomly perturbed chains, implying their potential reliability in experiments. Our inverse partition ratio (IPR) calculations indicate that the SHU chains can support fully delocalized states just like perfect crystalline chains over a wide range of frequencies, i.e. ω∈(0,100) cm−1, suggesting superior phonon transport behaviors within these frequencies, which was traditionally considered impossible in disordered systems. Interestingly, we observe the emergence of a group of highly localized states associated with ω∼200 cm−1, which is characterized by a significant peak in the IPR and a peak in phonon density of states at the corresponding frequency, and is potentially useful for decoupling electron and phonon degrees of freedom. These unique properties of disordered SHU chains have implications in the design and engineering of novel quantum materials for thermal and phononic applications.

Activation of Cryptochrome 4 from Atlantic Herring.

Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor.

Adsorption of Ciprofloxacin on Clay Minerals in Argentinian Santa Rosa-Corrientes Soils.

The presence of antibiotics in soils is increasing drastically in last decades due to the intensive farming industry and excessive human consumption. Clay minerals are one of the soil components with great adsorption capacity for organic pollutants. The study of interactions between antibiotics and mineral surfaces will give us scientific knowledge of these pollutants through soils. In this work, we study the adsorption of the antibiotic ciprofloxacin in the clay mineral fraction of soils from the Argentinian zone of Santa Rosa (Corrientes), in a collaborative research of experiments and atomistic modelling calculations of the intercalation of ciprofloxacin in the interlayer space of montmorillonite. Adsorption and desorption isotherms were performed and compared with different isotherm models. Additionally, enthalpy, entropy, and free energy were determined from equilibrium constants at a function of temperature. All these experiments and calculations lead to the conclusions that two adsorption types of ciprofloxacin are found on clay minerals: one weakly sorbed that is released during the desorption experiments, and other one strongly joined that remains in the soil.

Myosin's powerstroke transitions define atomic scale movement of cardiac thin filament tropomyosin.

Dynamic interactions between the myosin motor head on thick filaments and the actin molecular track on thin filaments drive the myosin-crossbridge cycle that powers muscle contraction. The process is initiated by Ca2+ and the opening of troponin-tropomyosin-blocked myosin-binding sites on actin. The ensuing recruitment of myosin heads and their transformation from pre-powerstroke to post-powerstroke conformation on actin produce the force required for contraction. Cryo-EM-based atomic models confirm that during this process, tropomyosin occupies three different average positions on actin. Tropomyosin pivoting on actin away from a TnI-imposed myosin-blocking position accounts for part of the Ca2+ activation observed. However, the structure of tropomyosin on thin filaments that follows pre-powerstroke myosin binding and its translocation during myosin's pre-powerstroke to post-powerstroke transition remains unresolved. Here, we approach this transition computationally in silico. We used the myosin helix-loop-helix motif as an anchor to dock models of pre-powerstroke cardiac myosin to the cleft between neighboring actin subunits along cardiac thin filaments. We then performed targeted molecular dynamics simulations of the transition between pre- and post-powerstroke conformations on actin in the presence of cardiac troponin-tropomyosin. These simulations show Arg 369 and Glu 370 on the tip of myosin Loop-4 encountering identically charged residues on tropomyosin. The charge repulsion between residues causes tropomyosin translocation across actin, thus accounting for the final regulatory step in the activation of the thin filament, and, in turn, facilitating myosin movement along the filament. We suggest that during muscle activity, myosin-induced tropomyosin movement is likely to result in unencumbered myosin head interactions on actin at low-energy cost.