Crystal Model Research Articles

Biomimetic Synthesis of Calcium Carbonate in Bile in the presence of Amino Acids

Thermodynamic and experimental modeling of calcium carbonate crystallization in a model solution of human bile has been carried out. The process of calcium carbonate (calcite and vaterite) crystallization from solutions containing bile has been studied. It is shown that differences in the phase and group composition of the samples arise depending on the synthesis parameters. It has been established that in the presence of 1 wt. % bile, calcite is formed, and an increase in the concentration of bile in the initial solution from 5 to 100 wt. % contributes to the crystallization of vaterite. It is shown that the mass of the solid phase increases with an increase in the concentration of bile in the initial solution. The dissolution of the synthesized samples was performed in 0.9 wt. % NaCl solution and 0.05 M EDTA solution. It was found that the presence of bile components in the composition of solid samples reduces the rate of their dissolutions.

The Effect of Lidan Huashi Pills on the Glutathione Peroxidase Activity and Growth of Calcium Oxalate Crystals in the Kidneys of Rats

Objective: To explore the effects of Lidan Huashi Pills on the glutathione peroxidase (GSH-Px) activity and growth of calcium oxalate crystals in the kidneys of rats. Methods: 30 rats were randomly divided into a blank group, a model group, and an experimental group, with 10 rats in each group. The blank group was free to eat and drink water for 8 weeks; the ethylene glycol method was used for the standard calcium oxalate crystal modeling in the control group and experimental group for 4 weeks. The model group was given free feeding and physiological saline (2 ml/d) by continuous gavage for 4 weeks; the experimental group was given free feeding and Lidan Huashi Pills (450 mg/kg, 2 ml/d) by continuous gavage for 4 weeks. After 4 weeks, all rats were euthanized, and the left kidney was taken for GSH-Px level detection. The right kidney was stained with hematoxylin and eosin (H&E) to observe the formation of calcium oxalate crystals. Results: After 4 weeks of modeling, the urinary calcium levels in the model group and experimental group significantly increased compared to the blank group (868.00 ± 39.29 vs 929.40 ± 33.61, P < 0.05), indicating successful modeling. The urine calcium ion concentration in the experimental group after modeling was significantly lower than that in the model group (929.40 ± 33.61 vs 888.60 ± 25.92, P < 0.05). The grading score of calcium oxalate crystals in the model group was significantly higher than that in the blank group (P < 0.05); the grading score of calcium oxalate crystals in the experimental group was lower than that in the model group, and the difference was not statistically significant (P > 0.05). The GSH-Px activity in the left kidney of the model group was significantly lower than that of the blank group [203.49 (208.21, 144.22) vs 494.91 (431.32, 538.18), P < 0.05); the GSH-Px activity in the left kidney of the experimental group was significantly higher than that of the model group [433.60 (383.86, 504.49) vs 203.49 (208.21, 144.22), P < 0.05). Morphological observation and H&E staining suggest that the formation of right kidney crystals and inflammation in the experimental group are between the blank group and the model group. Conclusion: Lidan Huashi Pills can enhance the serum GSH-Px activity in rats and inhibit the growth of calcium oxalate crystals and inflammatory response in the kidneys, thus playing a role in preventing and treating urinary tract stones.

Linking Grain Size to Microscopic Hardening Laws in a Phenomenological Crystal Plasticity Model: A Finite Element Simulation Approach for 316L Stainless Steel

Linking Grain Size to Microscopic Hardening Laws in a Phenomenological Crystal Plasticity Model: A Finite Element Simulation Approach for 316L Stainless Steel

Simulation of time-crystal-like behavior for a few-boson chiral soliton model in a ring

We present numerical simulations for a chiral soliton model with N=2,3 bosons in a ring, which is a few-particle version of our previous mean-field model for a quantum time crystal. Following Syrwid, Kosior, and Sacha (SKS), the notion is that a precise position measurement of one particle can lead to spontaneous formation of a bright soliton that in a time crystal should rotate intact for at least a few revolutions around the ring. In their work SKS found spontaneous formation of a soliton due to the position measurement, but quantum fluctuations cause the soliton to subsequently decay before it has a chance to perform even one revolution of the ring. Based on this, they concluded that time-crystal dynamics are impossible for Wilczek's model of a bright soliton in a ring. In contrast, for our few-boson chiral soliton model, allowing for imprecise (weak) measurements of the particle position, we show that time-crystal-like behavior is possible, allowing for several revolutions of the spontaneously formed soliton around the ring. Published by the American Physical Society 2024

Analysis of vibrational modes and weak interactions in terahertz spectra of γ-aminobutyric acid and its isomer L-2-aminobutyric acid

Aminobutyric acid, a non-proteinogenic amino acid, is present in the human body and influences physiological functions, exhibiting promising pharmaceutical prospects. γ-Aminobutyric Acid (GABA) and its isomer, L-2-Aminobutyric Acid (L-AABA), exhibit unique characteristic absorption peaks in the 0.6 to 2.5 THz range. To elucidate the mechanisms behind these absorption peaks, this study employed Density Functional Theory (DFT) for theoretical simulations of the crystal cell models of L-AABA and GABA, achieving terahertz spectra consistent with experimental results. Additionally, the study utilized Vibrational Mode Automatic Relevance Determination (VMARD) and Interaction Region Indicator (IRI) methodologies to interpret the vibrational modes corresponding to different absorption peaks and to detail the locations and types of intermolecular interactions within the crystals. Research indicates that the combination of terahertz time-domain spectroscopy (THz-TDS) and theoretical calculations can serve as an effective method for identifying isomers of Aminobutyric Acid and detecting intermolecular weak interactions such as hydrogen bonds within these crystals.

Dual-phase polycrystalline crystal plasticity model revealing the relationship between microstructural characteristics and mechanical properties in additively manufactured maraging steel

To elucidate the relationship between microstructural characteristics and mechanical properties in additively manufactured (AM) maraging steel, this study introduces a computational approach that addresses two fundamental challenges. Firstly, it addresses the creation of representative volume elements (RVEs) that mimic the observed microstructural complexities, such as meltpool boundaries, prior austenite grains, packets and blocks of lath martensite. This is accomplished through the application of Potts Monte-Carlo methods and grain segmentation techniques in accordance with the Kurdjumov–Sachs orientation relationship. Secondly, this study develops a comprehensive crystal plasticity (CP) model encompassing both bcc and fcc plasticity. Inspired by atomistic and discrete dislocation dynamics studies, the proposed CP model incorporates characteristics intrinsic to bcc plasticity, including non-Schmid effects, dislocation and precipitate strengthening, and Hall–Petch type strengthening of elongated martensitic blocks. Utilizing the created RVEs and the proposed CP framework, finite element simulations are conducted based on an update-Lagrangian formulation. The purpose of this study is to investigate the deformation behavior, texture evolution, tension–compression asymmetry, and evolution in dislocation density in RVEs representative of as-built and heat-treated samples of maraging steel. This computational approach and its findings deepen our understanding of the intricate interplay between microstructural characteristics and mechanical properties in maraging steel and also provide valuable guidelines for refining its additive manufacturing and heat treatment processes.

Odd-even trends in the series of new bis(α,ω-alkanediamine)dibromocadmium(II) coordination polymers: Crystal structure and thermal decomposition

In this paper, organic-inorganic coordination polymers of the CdBr2(H2N-(CH2)n-NH2) general formula, where n = 4 – 10 and 12, were studied. All the materials were synthesized as very fine powders from metal salt and diamine solutions following an analogous simple procedure. Scanning electron microscopy (SEM) images and recorded powder X-ray diffraction patterns (PXRD) allowed for the assessment of the purity and crystallinity of the products. Based on the collected diffraction data, lattice parameters and symmetry were determined. For five of the synthesized compounds (n = 4, 6, 7, 8, and 12) that were of relatively high purity and sufficient crystallinity, crystal structure models were determined and refined. It was found that the structure symmetry depends on the parity of the number of carbon atoms in the diamine molecules. Structures of the investigated compounds belonging to the even series are centrosymmetric while the ones from the odd series are not (P21 space group). Structures’ symmetry of compounds based on even diamines decreases from P2/m to P1¯ with increasing length of the organic molecules. Diamine molecules are aligned parallel to the diagonals of the (010) faces of the unit cell and there is an almost perfectly linear correlation between the value of a lattice parameter and the number of C atoms. There are, however, separate trends for even or odd series. Differential scanning calorimetry (DSC) and non-ambient PXRD measurements provided information about the thermal decomposition of the materials. The temperature of decomposition decreases with the growing length of diamine molecules and achieves the lowest value (176 °C, 449 K) for the compound with 1,12-diaminododecane (the longest diamine among the studied ones) while the sample with 1,4-diaminobutane is the most stable one (up to around 284 °C, 557 K). The studied compounds also show odd-even separate trends concerning the decomposition temperature. The compounds with even diamines start to decompose at relatively higher temperatures than the ones belonging to the odd series.

A two-scale approach for assessing the role of defects in fatigue crack nucleation in metallic structures

Metal structures often exhibit macroscopic defects from which cracks can nucleate during cyclic loading. The current work presents a two-scale approach to enable the prediction of crack nucleation from such defects by taking into account local microstructure features. The geometrical description of the defect and associated non-homogeneous strain fields are modeled using a macroscale model which employs a continuum elastoplastic material model for cyclic deformation. The cyclic deformation of the microstructure near the defect is modeled using a mesoscale model which employs a crystal plasticity material model and uses multiple realizations to address the statistical microstructure variability. The boundary conditions of the mesoscale model are extracted from the macroscale model. By simulating the deformation of the microstructure using the strain fields near the defect and by introducing a fatigue indicator parameter for crack nucleation, along with the weakest-link based upscaling methodology, the developed approach enables the prediction of the distribution of crack nucleation life. The approach is used for analyzing different defects for crack nucleation by considering local grain orientations. The predictions are shown to not only capture phenomena such as scatter, size effects, etc. qualitatively, but also agree with a classical engineering approach and experimentally reported data sets quantitatively.

Biofouling and biomineralization of tubular concretions attached to Longquan celadon from Shengbeiyu shipwreck, China (14th Century CE): a multi-analytical case study

A comprehensive multi-analytical investigation was conducted on a piece of Longquan celadon excavated from the Shengbeiyu shipwreck site in the East China Sea. This study focused on a representative type of tubular bio-concretions attached to the submerged celadon, believed to have been formed through the construction activities of a marine tubeworm belonging to the benthic phylum of Polychaeta Annelids. The research examined the microstructure, composition and adhesion form of these tubular bio-concretions, aiming to elucidate their developmental and attachment patterns from a biomineralization and biofouling perspective. The tubular bio-concretions were found to have a bimineralic composition, with notably higher content of aragonite than calcite, and display diverse yet highly ordered microstructures. The presence of organic matter within the bio-concretions indicates an organic matrix-controlled crystallization model, commonly observed in the construction of benthic calcareous tubes. Microscopic analyses revealed the primary degradation microstructures and corresponding phases of the glaze to which calcareous tubes attached. These findings closely resembled the corrosion characteristics observed in submerged ceramic glaze without bio-concretion attachments, as documented in earlier studies. OM and SEM observations also indicated that the calcareous tubes intricately intermeshed with the cracked glaze layer of the celadon. Additionally, Raman spectroscopic analysis detected the presence of proteins at the interface, likely residual adhesives secreted by fouling organisms to cement themselves to the settlement substrata, suggesting the occurrence of organic-mediated bio-adhesion mechanisms. These results shed new light on the formation process of bio-concretions and their interaction with attached underwater ceramics. A simplified formation mechanism of this biologically-induced degradation has been discussed.

Strong and tough semi-crystalline poly(aryl ether nitrile) with low coefficient of thermal expansion

The crystallization of poly (aryl ether nitrile) (PEN) has an essential impact on improving heat resistance, mechanical properties, chemical resistance, and dielectric properties. However, during the synthesis process, high crystallinity PEN is prone to precipitate out, which makes it difficult to carry out the synthesis reaction, which poses a significant challenge to synthesizing high crystallinity and high molecular weight PEN. In this work, hydroquinone (HQ) as the main phenolic monomer and 4,4′-biphenol (BP) as the second phenolic monomer were used to solve the technical difficulties in synthesis by copolymerization. The crystalline PEN with high molecular weight and significant crystallinity was obtained by regulating the molar ratio of BP to HQ. The effects of isothermal heat treatment on its crystalline, mechanical, and thermal properties were investigated. The influence laws of molecular chain structure and heat treatment process on the properties of PEN films were revealed. Among them, when the isothermal treatment temperature was 270 °C and the HQ: BP was 85:15, the mechanical strength reached 130 MPa, and the elongation at break could be up to an astonishing 50 %. Besides, the CTE value from 50 °C–150 °C is 40.84 ppm/°C, which is lower than most thermoplastics. Therefore, PEN with the HQ to BP molar ratio of 85:15 is suitable for large-scale production, providing new crystalline plastic specifications for high-performance special engineering plastics. A crystal bridge-tie chain model is summarized by the properties of HQ/BP-PEN films under different crystallization conditions, which provides an idea for preparing stiff and tough films.

Physically based modelling of orientation deviation effect on mechanical behavior for dual‐phase single‐crystal superalloy

AbstractThis work systematically investigates the orientation deviation effect on the elastoplastic deformation of a dual‐phase, nickel‐based single‐crystal superalloy through a combined experimental study and crystal plasticity finite element modelling method (CPFEM). Physically based, dual‐phase microstructural model was developed based on scanning electron microscopy (SEM), which was implemented by finite element (FE) modelling using a representative volume element (RVE) with periodic boundary conditions. An extended equivalent yield criterion coupled with CPFEM was adopted to describe the non‐uniform yield behavior induced by octahedral and cubic slip systems. The predicted results have shown that both the bulk behavior and localized stress–strain nature are orientation deviation dependent and that the first Euler angle plays a more important role in elastoplastic behavior than the second Euler angle. This study has thus advanced the basic understanding of the relationship between orientation deviation and the bulk deformation behavior of the dual‐phase nickel‐based single crystal.

Fabrication of tips for scanning probe magnetometry by diamond growth

The use of quantum sensors is promising detailed insights into physical phenomena such as magnetism or superconductivity. One example of such quantum sensors is a microscopic diamond tip containing nitrogen vacancy (NV) centers, which is capable of producing correlated measurements of vectorial magnetic fields and the sample topography on the nanoscale. In this study, we present a chemical vapor deposition (CVD) process to produce diamond tips with NV centers by overgrowing microstructured diamond substrates. The resulting diamond tips exhibit a radius of curvature of approximately 10 nm, suitable for use as a probe in an atomic force microscope. The magnetic sensitivity of the CVD-grown diamond tips is characterized with pulsed measurements of the optically detected magnetic resonance, which yield a minimum magnetic sensitivity of 60 µT Hz−1 . The growth of the diamond microstructures is observed to differ from the commonly used geometric model predicting CVD growth of bulk diamond crystals. We identify an empirical model for the growth behavior of the microstructures by taking into account processes described in the step flow growth model for crystals. Additionally, we demonstrate the applicability of the developed CVD growth process to membrane substrates required for the preparation of magnetometry-capable diamond tips.

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

Taming Two-Dimensional Polymerization by a Machine-Learning Discovered Crystallization Model.

Rapidly synthesizing high-quality two-dimensional covalent organic frameworks (2D COFs) is crucial for their practical applications. While strategies such as slow monomer addition have been developed based on an empirical understanding of their formation process, quantitative guidance remains absent, which prohibits precise optimizations of the experimental conditions. Here, we use a machine-learning approach that overcomes the challenges associated with bottom-up model derivation for the non-classical 2D COF crystallization processes. The resulting model, referred to as NEgen1, establishes correlations among the induction time, nucleation rate, growth rate, bond-forming rate constants, and common solution synthesis conditions for 2D COFs that grow by a nucleation-elongation mechanism. The results elucidate the detailed competition between the nucleation and growth dynamics in solution, which has been inappropriately described previously by classical, empirical models with assumptions invalid for 2D COF polymerization. By understanding the dynamic processes at play, the NEgen1 model reveals a simple strategy of gradually increasing monomer addition speed for growing large 2D COF crystals. This insight enables us to rapidly synthesize large COF-5 colloids, which could only be achieved previously by prolonged reaction times or by introducing chemical modulators. These results highlight the potential for systematically improving the crystal quality of 2D COFs, which has wide-reaching relevance for many of the applications where 2D COFs are speculated to be valuable.

Taming Two‐Dimensional Polymerization by a Machine‐Learning Discovered Crystallization Model

Rapidly synthesizing high‐quality two‐dimensional covalent organic frameworks (2D COFs) is crucial to their practical applications. Here, we use a machine‐learning approach that overcomes the challenges associated with bottom‐up model derivation for the non‐classical 2D COF crystallization processes. The resulting model, referred to as NEgen1, establishes correlations among the induction time, nucleation rate, growth rate, bond‐forming rate constants, and common solution synthesis conditions for 2D COFs that grow by a nucleation‐elongation mechanism. The results elucidate the detailed competition between the nucleation and growth dynamics in solution, which has been inappropriately described previously by classical, empirical models with assumptions invalid for 2D COF polymerization. By understanding the dynamic processes at play, the NEgen1 model reveals a simple strategy of gradually increasing monomer addition speed for growing large 2D COF crystals. This insight enables us to rapidly synthesize large COF‐5 colloids, which could only be achieved previously by prolonged reaction times or by introducing chemical modulators. These results highlight the potential for systematically improving the crystal quality of 2D COFs, which has wide‐reaching relevance for many of the applications for which 2D COFs are speculated to be valuable.

Efficient identification of a flow-induced crystallization model for injection molding simulation

Efficient identification of a flow-induced crystallization model for injection molding simulation

Auxiliary Rather Than Dominant. The Role of Direct Dy-S Coordination in Single-Molecule Magnet Unveiled via ab initio Study.

The role of Dy-S coordination in a single-molecule magnet (SMM) is investigated via an ab initio study in a group of mononuclear structures. The SMM performance of this group is well interpreted via a concise criterion consisting of long quantum tunneling of magnetization (QTM) time τQTM and high effective barrier for magnetic reversal Ueff. The best SMMs in the selected group, i.e., 1Dy (CCDC refcode: PUKFAF) and 2Dy (CCDC refcode: NIKSEJ), are just those holding the longest τQTM and the highest Ueff simultaneously. Further analysis based on the crystal field model and ab initio magneto-structural exploration indicates that the influence of Dy-S coordination on the SMM performance of 1Dy is weaker than that of axial Dy-O coordination. Thus, Dy-S coordination is more likely to play an auxiliary role rather than a dominant one. However, if placed at the suitable equatorial position, Dy-S coordination could provide important support for good SMM performance. Consequently, starting from 1Dy, we built two new structures where Dy-S coordination only exists at the equatorial position and two axial positions are occupied by strong Dy-O/Dy-F coordination. Compared to 1Dy and 2Dy, these new ones are predicted to have significantly longer τQTM and higher Ueff, as well as a nearly doubled blocking temperature TB. Thus, they are probable candidates of SMM having clearly improved performance.

Shear localization in gradient high-entropy alloy at high strain rates: Crystal plasticity modeling

Gradient-structured metals have attracted a lot of attention due to their good synergy between strength and ductility. However, whether they can be used as a candidate for effective prevention of shear localization failure during high strain rate deformations is still an open question. Corresponding to the particular mechanisms of dynamic recrystallization and twinning at high strain rates, a physically based constitutive model of crystal plasticity is developed, including a new evolution equation for dislocation density and a twinning model, to investigate the detailed process of shear localization of gradient-structured CoCrFeMnNi high-entropy alloys (HEAs). A physically based strain gradient theory is considered to capture the strengthening effect of gradient structures. The competition between microstructural softening and strengthening effects is quantified to reveal the effects of gradient-structure on shear localization and shear localization can be significantly delayed in gradient-structured HEAs. This study contributes to the understanding of the influence of gradient-structure on shear localization and provides insights for further optimization of the mechanical behavior of gradient-structures at high strain rates to develop strong and ductile metals and alloys for dynamic applications.

Predicting tensile behavior and fatigue life of laser shock peened titanium alloy by crystal plasticity model

Laser shock peening (LSP) could improve fatigue resistance of metals, but the complex surface microstructures created by LSP make it extremely challenging to predict the mechanical behavior. Here, we present a crystal-plasticity (CP) modeling framework to predict the tensile behavior and fatigue life of LSPed titanium alloy, in which LSP induced three strengthening mechanisms (i.e., residual stress, grain-size gradient, and dislocation) are fully involved. The fatigue life is evaluated by incorporating CP finite-element results and a modified Tanaka–Mura model. The three strengthening mechanisms of LSP and their individual contribution to the tensile and fatigue properties are quantitatively clarified. The predicted tensile behavior and fatigue life of LSPed titanium alloys are demonstrated to agree well with experimental results. In terms of tensile property, the major strengthening contribution is ascribed to the LSP induced grain-size gradient, followed by dislocation and residual stress. As for fatigue life, all predictions are within the ±2 times error band. It is found that balancing residual stress with grain size and dislocation is crucial for improving fatigue life. This work provides a predictive approach for evaluating tensile and fatigue performance of LSPed alloys, and is insightful for fatigue life enhancement by LSPed microstructure engineering.

Linear relaxation method with regularized energy reformulation for phase field models

In this paper, we establish a novel linear relaxation method with regularized energy reformulation for phase field models, which we name the RRER method. We employ the molecular beam epitaxy (MBE) model and the phase-field crystal (PFC) model as test beds, along with several coupled phase field models, to illustrate the concept. Our proposed RRER strategy is applicable to a broad class of phase field models that can be derived through energy variation. The RRER method consists of two major steps. First, we introduce regularized auxiliary variables to reformulate the original phase field models into equivalent forms where the free energy is transformed under the auxiliary variables. Then, we discretize the reformulated PDE model under these variables on a staggered time mesh for the phase field models. We incorporate the energy reformulation idea in the first step and the linear relaxation concept in the second step to derive a general numerical algorithm for phase field models that is linear and second-order accurate. Our approach differs from the classical invariant energy quadratization (IEQ) and scalar auxiliary variable (SAV) approaches, as we don't need to take time derivatives for the auxiliary variables. The resulting schemes are linear, i.e., only linear algebraic systems need to be solved at each time step. Rigorous theoretical analysis demonstrates that these resulting schemes satisfy the modified discrete energy dissipation laws and preserve the discrete mass conservation for the PFC and MBE models. Furthermore, we present numerical results to demonstrate the effectiveness of our method in solving phase field models.