2D Systems Research Articles

Intracellular proteomics and extracellular vesiculomics as a metric of disease recapitulation in 3D-bioprinted aortic valve arrays.

In calcific aortic valve disease (CAVD), mechanosensitive valvular cells respond to fibrosis- and calcification-induced tissue stiffening, further driving pathophysiology. No pharmacotherapeutics are available to treat CAVD because of the paucity of (i) appropriate experimental models that recapitulate this complex environment and (ii) benchmarking novel engineered aortic valve (AV)-model performance. We established a biomaterial-based CAVD model mimicking the biomechanics of the human AV disease-prone fibrosa layer, three-dimensional (3D)-bioprinted into 96-well arrays. Liquid chromatography-tandem mass spectrometry analyses probed the cellular proteome and vesiculome to compare the 3D-bioprinted model versus traditional 2D monoculture, against human CAVD tissue. The 3D-bioprinted model highly recapitulated the CAVD cellular proteome (94% versus 70% of 2D proteins). Integration of cellular and vesicular datasets identified known and unknown proteins ubiquitous to AV calcification. This study explores how 2D versus 3D-bioengineered systems recapitulate unique aspects of human disease, positions multiomics as a technique for the evaluation of high throughput-based bioengineered model systems, and potentiates future drug discovery.

Realization of multiple topological states and topological phase transitions in (4,0) carbon nanotube derivatives

Exploring various topological states (TS) and topological phase transitions (TPT) has attracted great attention in condensed matter physics. However, so far, there is rarely a typical material system that can be used as a platform to study the TS and TPT as the system transforms from one-dimensional (1D) nanoribbons to two-dimensional (2D) sheet then to three-dimensional (3D) bulk. Here, we first propose that some typical TS in 1D, 2D, and 3D systems can be realized in a tight-binding (TB) model. Following the TB model and further based on first-principles electronic structure calculations, we demonstrate that the structurally stable (4,0) carbon nanotube derivatives are an ideal platform to explore the semiconductor/nodal-point semimetal states in 1D nanoribbons [1D-(4,0)-C16H4 and 1D-(4,0)-C32H4], nodal-ring semimetal state in 2D sheet [2D-(4,0)-C16], and nodal-cage semimetal state in 3D bulk [3D-(4,0)-C16]. Furthermore, we calculate the characteristic band structures and the edge/surface states of 2D-(4,0)-C16 and 3D-(4,0)-C16 to confirm their nontrivial topological properties. Our work not only provides new excellent 2D and 3D members for the topological carbon material family, but also serves as an ideal template for the study of TS and TPT with the change of system dimension.

Position-dependent mass from noncommutativity and its statistical descriptions

A set of position-dependent noncommutative algebra in two dimension (2D) that describes the space near the Planck scale had been introduced [J. Phys. A: Math. Theor. 53 (2020) 115303]. This algebra predicted the existence of maximal length of graviton measurable at low energy. From this algebra, we deduce in the present paper, a new noncommutative algebra that is compatible with the deformed algebra proposed by Costa Filho et al. [Phys. Rev. A 84 (2011) 050102] to describe the Position-Dependent Mass (PDM) system in 1D. To this aim, we derive from the momentum operators, the Schrödinger-like equation which describes PDM system in null quantum well potential. The spectrum of this system is asymetrically deformed and exhibits different behaviours from the one obtained by Costa Filho et al. Thus, we observe that by increasing the PDM, the energy decreases and this decrease is more pronounced as the quantum number increases. Finally, we evaluate the thermodynamic quantities within the canonical ensemble and we show that these results are consistent with the ones recently obtained by Bensalem and Bouaziz [Phys. A Stat. Mech. Appl. 523 (2019) 583–592].

Resonant fractional conductance through a 1D Wigner chain

In recent experiments on conductance of one-dimensional (1D) channels in ultra-clean samples, a diverse set of plateaus were found at fractions of the quantum of conductance in zero magnetic field. We consider a discrete model of strongly interacting electrons in a clean 1D system where the current between weak tunneling contacts is carried by fractionally charged solutions. While in the spinless case conductance remains unaffected by the interaction, as is typical for the strongly interacting clean 1D systems, we demonstrate that in the spinful case the peak conductance takes fractional values that depend on the filling factor of the 1D channel.

Unified Entropy-Ruled Einstein's Relation for Bulk and Low-Dimensional Molecular-Material Systems: A Hopping-to-Band Shift Paradigm.

We present a unified paradigm on entropy-ruled Einstein's diffusion-mobility relation (μ/D ratio) for 1D, 2D, and 3D free-electron solid state systems. The localization transport in the extended molecules is well approximated by the continuum time-delayed hopping factor within our unified entropy-ruled transport method of noninteracting quantum systems. Moreover, we generalize an entropy-dependent diffusion relation for 1D, 2D, and 3D systems as defined by , where heff and d are the effective entropy and dimension (d = 1, 2, 3), respectively. This generalized relation is valid for both equilibrium and nonequilibrium transport systems since the parameter heff is closely connected with the nonequilibrium fluctuation theorem-based entropy production rule. Importantly, we herein revisit the Boltzmann approach using an entropy-ruled method for mobility calculation for the universal quantum materials that is expressed as , where is the diffusion constant for band transport systems and η is the chemical potential. According to our entropy-ruled μ/D relation, the Navamani-Shockley diode equation is transformed.

Self-consistent quantum-kinetic theory for interacting drifting electrons and force-driven phonons in a 1D system

A self-consistent quantum-kinetic model is developed for studying strong-field nonlinear electron transport interacting with force-driven phonons within a nanowire system. For this model, phonons can be dragged into motion through strong electron–phonon scattering by fast-moving electrons along the opposite direction of the DC electric field. Meanwhile, the DC-field induced charge current of electrons can be either enhanced or reduced by the same electron–phonon scattering, depending on the relative direction of a DC field with respect to that of an applied temperature gradient for driving phonons. By making use of this quantum-kinetic model beyond the relaxation-time approximation, neither electron nor phonon temperature is required for describing ultrafast electron–phonon scattering and their correlated transports in this 1D electronic-lattice system.

Development and preliminary verification of a 1D–3D coupled flow and heat transfer model of OTSG

Introduction: A simulation model was developed by coupling a one-dimensional (1D) system code and 3D CFD software, to analyze the three-dimensional (3D) flow and heat transfer characteristics of the once-through steam generator (OTSG).Methods: The shell side of the OTSG was simulated by FLUENT, and the tube side was simulated by the system code LOCUST. Through spatial mapping, the 1D and 3D simulations were coupled along the outer wall of the OTSG's helically coiled tubes.Results and Discussion: This coupling method enabled the acquisition of high-resolution flow and heat transfer characteristics of the OTSG, and the error of heat flux calculation result by the coupled model is within 15%. Through coupling simulation analysis of the prototype OTSG, it was found that the inlet and outlet temperature difference reached as high as 150°C. The unevenness of the radial temperature distribution increased along the flow direction, and the wake swing effect caused by the sweeping flow of the tube bundle at the exit position was evident. The results of this study provide reference and a coupled simulation method for the engineering design and thermal-hydraulic characteristics analysis of OTSG.

Photonic Floquet Skin-Topological Effect.

Non-Hermitian skin effect and photonic topological edge states are of great interest in non-Hermitian physics and optics. However, the interplay between them is largely unexplored. Here, we propose and demonstrate experimentally the non-Hermitian skin effect constructed from the nonreciprocal flow of Floquet topological edge states, which can be dubbed "Floquet skin-topological effect." We first show the non-Hermitian skin effect can be induced by structured loss when the one-dimensional (1D) system is periodically driven. Next, based on a two-dimensional (2D) Floquet topological photonic lattice with structured loss, we investigate the interaction between the non-Hermiticity and the topological edge states. We observe that all the one-way edge states are imposed onto specific corners, featuring both the non-Hermitian skin effect and topological edge states. Furthermore, a topological switch for the skin-topological effect is presented by utilizing the phase-transition mechanism. Our experiment paves the way for realizing non-Hermitian topological effects in nonlinear and quantum regimes.

Morphological, cytotoxic and apoptotic effects of different concentrations of nisin ZP on MG63 cells in a 3-dimensional culture system

Osteosarcoma (OS) is a primary bone cancer that commonly affects young individuals. Despite treatment, it is known to be highly resistant to therapy. Nisin, a bacteriocin released by Lactococcus lactis has been shown to exhibit an apoptotic effect on cancer cells. To better represent in vivo cancer cell constructs, 3-dimensional (3D) culture systems have been used in vitro. This study aims to compare the effects of nisin on OS cell culture in both monolayered and 3D gas-permeable VECELL® G-Plate. Osteosarcoma cells (MG63) were cultured on 3D culture (G-Plate) and normal culture plates. Morphological assessments were carried out through light and scanning electron microscopic examinations. The results showed that the use of a 3D system is more reliable in the development of 3D osteosarcoma models compared to the 2-dimensional (2D) culture system. Specifically, the 3D culture demonstrated the formation of MG63 spheroids, indicating the reliability of the hanging drop methods to produce spheroidal cell morphology. Additionally, the cell viability assay showed a higher IC50 value for 2D groups compared to the 3D groups, with values of 102.56 µg/mL and 33.96 µg/mL, respectively. Finally, a dose-dependent apoptosis was noticed for the apoptotic assay, further demonstrating the effectiveness of the 3D culture system. The effectiveness of nisin ZP as an anticancer agent was observed in both 2D and 3D culture systems. However, the 3D culture system required a higher dose of nisin ZP to demonstrate its potential, indicating that this system could be a promising approach in OS intervention studies.

Numerical Evaluation of the Elastic Moduli of AlN and GaN Nanosheets.

Two-dimensional (2D) nanostructures of aluminum nitride (AlN) and gallium nitride (GaN), called nanosheets, have a graphene-like atomic arrangement and represent novel materials with important upcoming applications in the fields of flexible electronics, optoelectronics, and strain engineering, among others. Knowledge of their mechanical behavior is key to the correct design and enhanced functioning of advanced 2D devices and systems based on aluminum nitride and gallium nitride nanosheets. With this background, the surface Young's and shear moduli of AlN and GaN nanosheets over a wide range of aspect ratios were assessed using the nanoscale continuum model (NCM), also known as the molecular structural mechanics (MSM) approach. The NCM/MSM approach uses elastic beam elements to represent interatomic bonds and allows the elastic moduli of nanosheets to be evaluated in a simple way. The surface Young's and shear moduli calculated in the current study contribute to building a reference for the evaluation of the elastic moduli of AlN and GaN nanosheets using the theoretical method. The results show that an analytical methodology can be used to assess the Young's and shear moduli of aluminum nitride and gallium nitride nanosheets without the need for numerical simulation. An exploratory study was performed to adjust the input parameters of the numerical simulation, which led to good agreement with the results of elastic moduli available in the literature. The limitations of this method are also discussed.

Noncentrosymmetric two-dimensional Weyl semimetals in porous Si/Ge structures.

In this work we predict a family of noncentrosymmetric two-dimensional (2D) Weyl semimetals (WSMs) composed by porous Ge and SiGe structures. These systems are energetically stable graphenylene-like structures with a buckling, spontaneously breaking the inversion symmetry. The nontrivial topological phase for these 2D systems occurs just below the Fermi level, resulting in nonvanishing Berry curvature around the Weyl nodes. The emerged WSMs are protected byC3symmetry, presenting one-dimensional edge Fermi-arcs connecting Weyl points with opposite chiralities. Our findings complete the family of Weyl in condensed-matter physics, by predicting the first noncentrosymmetric class of 2D WSMs.

Designer pair statistics of disordered many-particle systems with novel properties.

The knowledge of exact analytical functional forms for the pair correlation function g2(r) and its corresponding structure factor S(k) of disordered many-particle systems is limited. For fundamental and practical reasons, it is highly desirable to add to the existing database of analytical functional forms for such pair statistics. Here, we design a plethora of such pair functions in direct and Fourier spaces across the first three Euclidean space dimensions that are realizable by diverse many-particle systems with varying degrees of correlated disorder across length scales, spanning a wide spectrum of hyperuniform, typical nonhyperuniform, and antihyperuniform ones. This is accomplished by utilizing an efficient inverse algorithm that determines equilibrium states with up to pair interactions at positive temperatures that precisely match targeted forms for both g2(r) and S(k). Among other results, we realize an example with the strongest hyperuniform property among known positive-temperature equilibrium states, critical-point systems (implying unusual 1D systems with phase transitions) that are not in the Ising universality class, systems that attain self-similar pair statistics under Fourier transformation, and an experimentally feasible polymer model. We show that our pair functions enable one to achieve many-particle systems with a wide range of translational order and self-diffusion coefficients D, which are inversely related to one another. One can design other realizable pair statistics via linear combinations of our functions or by applying our inverse procedure to other desirable functional forms. Our approach facilitates the inverse design of materials with desirable physical and chemical properties by tuning their pair statistics.

Dynamic neighbours: a proposal of a tool to characterize phase transitions

For molecular dynamics simulations of hard particles, we define dynamic neighbours as the distinct particles that collide with a given reference one during a specific time interval. This definition allows us to determine the distribution of the number of dynamic neighbours, its average, and its standard deviation. We will show that regardless of the time window used to identify dynamic neighbours, their distribution is correlated with diffusion coefficients, structure, and configurational entropy. Thus, it is likely that the distribution of the number of dynamic neighbours may be employed as another tool to gain insights into the dynamic behaviour of hard-core systems. We tested this approach on 2D and 3D systems consisting of monodisperse and binary mixtures of hard disks and spheres. Results show that implementing dynamic neighbours to define order parameters can sharpen the signals where transitions take place.

Controlled Growth of Highly Defected Zirconium-Metal-Organic Frameworks via a Reaction-Diffusion System for Water Remediation.

The relentless growth of metal-organic framework (MOF) chemistry is paralleled by the persistent urge to control the MOFs physical and chemical properties. While this control is mostly achieved by solvothermal syntheses, room temperature procedures stand out as more convenient and sustainable pathways for the production of MOF materials. Herein, a novel approach to control the crystal size and defect numbers of a dihydroxy-functionalized zirconium-based metal-organic framework (UiO-66(OH)2) at room temperature is reported. Through a reaction-diffusion method in a 1D system, zirconium salt was diffused into an agar gel matrix containing the organic linker to form nanocrystals of UiO-66(OH)2 with tailored structural features that include crystal size distribution, surface area, and defect number. By variation of the synthesis parameters of the system, hierarchical MOF nanocrystals with an average size ranging from 30 nm up to 270 nm and surface areas between 201 and 500 m2 g-1 were obtained in a one-pot synthetic route. To stress the importance of crystal size, morphology, and structural defects on the adsorption properties of UiO-66(OH)2, the adsorption capacity of the MOF toward methylene blue dye was tested with the largest and most defected crystals achieving the best performance of 202 mg/g. The distinctive structural characteristics including the hierarchical micromesoporous frameworks, the nanosized particles, and the highly defective crystals obtained by our synthesis procedure are deemed challenging through the conventional synthesis methods. This work paves the way for engineering MOF crystals with tunable physical and chemical properties, using a green synthesis procedure, for their advantageous use in many desirable applications.

Proteomic-miRNA Biomics Profile Reveals 2D Cultures of Human iPSC-Derived Neural Progenitor Cells More Sensitive than 3D Spheroid System Against the Experimental Exposure to Arsenic.

The iPSC-derived 3D models are considered to be a connective link between 2D culture and in vivo studies. However, the sensitivity of such 3D models is yet to be established. We assessed the sensitivity of the hiPSC-derived 3D spheroids against 2D cultures of neural progenitor cells. The sub-toxic dose of Sodium Arsenite (SA) was used to investigate the alterations in miRNA-proteins in both systems. Though SA exposure induced significant alterations in the proteins in both 2D and 3D systems, these proteins were uncommon except for 20 proteins. The number and magnitude of altered proteins were higher in the 2D system compared to 3D. The association of dysregulated miRNAs with the target proteins showed their involvement primarily in mitochondrial bioenergetics, oxidative and ER stress, transcription and translation mechanism, cytostructure, etc., in both culture systems. Further, the impact of dysregulated miRNAs and associated proteins on these functions and ultrastructural changes was compared in both culture systems. The ultrastructural studies revealed a similar pattern of mitochondrial damage, while the cellular bioenergetics studies confirm a significantly higher energy failure in the 2D system than to 3D. Such a higher magnitude of changes could be correlated with a higher amount of internalization of SA in 2D cultures than in 3D spheroids. Our findings demonstrate that a 2D culture system seems better responsive than a 3D spheroid system against SA exposure.

The extracellular matrix supports breast cancer cell growth under amino acid starvation by promoting tyrosine catabolism.

Breast tumours are embedded in a collagen I-rich extracellular matrix (ECM) network, where nutrients are scarce due to limited blood flow and elevated tumour growth. Metabolic adaptation is required for cancer cells to endure these conditions. Here, we demonstrated that the presence of ECM supported the growth of invasive breast cancer cells, but not non-transformed mammary epithelial cells, under amino acid starvation, through a mechanism that required macropinocytosis-dependent ECM uptake. Importantly, we showed that this behaviour was acquired during carcinoma progression. ECM internalisation, followed by lysosomal degradation, contributed to the up-regulation of the intracellular levels of several amino acids, most notably tyrosine and phenylalanine. This resulted in elevated tyrosine catabolism on ECM under starvation, leading to increased fumarate levels, potentially feeding into the tricarboxylic acid (TCA) cycle. Interestingly, this pathway was required for ECM-dependent cell growth and invasive cell migration under amino acid starvation, as the knockdown of p-hydroxyphenylpyruvate hydroxylase-like protein (HPDL), the third enzyme of the pathway, opposed cell growth and motility on ECM in both 2D and 3D systems, without affecting cell proliferation on plastic. Finally, high HPDL expression correlated with poor prognosis in breast cancer patients. Collectively, our results highlight that the ECM in the tumour microenvironment (TME) represents an alternative source of nutrients to support cancer cell growth by regulating phenylalanine and tyrosine metabolism.

Commensurate and incommensurate 1D interacting quantum systems

Single-atom imaging resolution of many-body quantum systems in optical lattices is routinely achieved with quantum-gas microscopes. Key to their great versatility as quantum simulators is the ability to use engineered light potentials at the microscopic level. Here, we employ dynamically varying microscopic light potentials in a quantum-gas microscope to study commensurate and incommensurate 1D systems of interacting bosonic Rb atoms. Such incommensurate systems are analogous to doped insulating states that exhibit atom transport and compressibility. Initially, a commensurate system with unit filling and fixed atom number is prepared between two potential barriers. We deterministically create an incommensurate system by dynamically changing the position of the barriers such that the number of available lattice sites is reduced while retaining the atom number. Our systems are characterised by measuring the distribution of particles and holes as a function of the lattice filling, and interaction strength, and we probe the particle mobility by applying a bias potential. Our work provides the foundation for preparation of low-entropy states with controlled filling in optical-lattice experiments.

Single-cell mapping of lipid metabolites using an infrared probe in human-derived model systems

Understanding metabolic heterogeneity is the key to uncovering the underlying mechanisms of metabolic-related diseases. Current metabolic imaging studies suffer from limitations including low resolution and specificity, and the model systems utilized often lack human relevance. Here, we present a single-cell metabolic imaging platform to enable direct imaging of lipid metabolism with high specificity in various human-derived 2D and 3D culture systems. Through the incorporation of an azide-tagged infrared probe, selective detection of newly synthesized lipids in cells and tissue became possible, while simultaneous fluorescence imaging enabled cell-type identification in complex tissues. In proof-of-concept experiments, newly synthesized lipids were directly visualized in human-relevant model systems among different cell types, mutation status, differentiation stages, and over time. We identified upregulated lipid metabolism in progranulin-knockdown human induced pluripotent stem cells and in their differentiated microglia cells. Furthermore, we observed that neurons in brain organoids exhibited a significantly lower lipid metabolism compared to astrocytes.

Strain-induced ferroelectric polarization reversal without undergoing geometric inversion in blue SiSe monolayer.

Ferroelectricity in two-dimensional (2D) systems generally arises from phonons and has been widely investigated. On the contrary, electronic ferroelectricity in 2D systems has been rarely studied. Using first-principles calculations, the ferroelectric behavior of the buckled blue SiSe monolayer under strain are explored. It is found that the direction of the out-of-plane ferroelectric polarization can be reversed by applying an in-plane strain. And such polarization switching is realized without undergoing geometric inversion. Besides, the strain-triggered polarization reversal emerges in both biaxial and uniaxial strain cases, indicating it is an intrinsic feature of such a system. Further analysis shows that the polarization switching is the result of the reversal of the magnitudes of the positive and negative charge center vectors. And the variation of buckling is found to play an important role, which results in the switch. Moreover, a non-monotonic variation of band gap with strain is revealed. Our findings throws light on the investigation of novel electronic ferroelectric systems.

Controlling the electronic and magnetic properties of the GeAs monolayer by generating Ge vacancies and doping with transition-metal atoms.

Controlling the electronic and magnetic properties of two-dimensional (2D) materials is a key step to make new multifunctional candidates for practical applications. In this work, defects and doping with transition metals (TMs = V, Cr, Mn, and Fe) at Ge sublattices are proposed in order to develop novel features in the hexagonal germanium arsenide (GeAs) monolayer. The pristine GeAs monolayer is a non-magnetic indirect gap semiconductor with an energy gap of 1.20(1.82) eV as provided by PBE(HSE06)-based calculations. A single Ge vacancy metallizes the monolayer, preserving its non-magnetic nature. In contrast, significant magnetization with a total magnetic moment of 1.96 μ B is achieved by a pair of Ge vacancies. Herein, the computed band structures assert the half-metallic behavior of the defective system. Similarly, half-metallicity is also obtained by V, Mn, and Fe doping. Meanwhile, the Cr-doped GeAs monolayer is classified as a diluted magnetic semiconductor 2D system. In these cases, magnetic properties are produced mainly by TM-3d electrons with total magnetic moments between 2.00 and 4.00 μ B. Further, the effects of substituting a pair of Ge atoms with a pair of TM atoms (pTMGe systems) are also investigated. Results indicate the ferromagnetic half-metallicity of the pVGe system, meanwhile antiferromagnetic ordering is stable in the remaining cases. In all cases, TM impurities transfer charge to the host GeAs monolayer since they are surrounded by As atoms, which are more electronegative than dopant atoms. Results presented herein may introduce new 2D systems - made from the non-magnetic GeAs monolayer - for spintronic applications with suitable electronic and magnetic features controlled mainly by transition metals.