Simple Model System Research Articles

Identification of active slip modes in twinned bicrystals of GNS/Cu composite through intragranular misorientation axes analysis

Bicrystals serve as a simplified model system for studying the deformation behavior of polycrystalline materials. In this study, we fabricated graphene nanosheets (GNSs) reinforced copper (Cu) matrix laminated composites using electrophoretic deposition and subsequent vacuum hot-press sintering. Interestingly, the composite exhibited a bicrystal microstructure, with two types of adjacent crystals, i.e., denoted as crystal A (φ1 = 222.06, Φ = 40.54, φ2 = 82.5) and crystal B (φ1 = 141.36, Φ = 43.76, φ2 = 1.94), displaying a twin orientation relationship. To investigate the deformation behavior of the GNS/Cu composite, we conducted interrupted room temperature uniaxial tensile tests combined with Scanning Electron Microscope (SEM) Electron Backscatter Diffraction (EBSD) characterization. To identify the activated slip systems in the composites, we performed trace analysis, applied the Schmid Factor law, analyzed the deformation gradient tensor, and conducted intragranular misorientation axis (IGMA) analysis. The trace analysis revealed that slip systems with high Schmid Factor values were favored during tension. Moreover, the deformation gradient tensor elements of the primary slip systems in the two crystals confirmed the deformation features observed by SEM. However, crystal B exhibited a significant deviation in trace angle. Further IGMA investigation revealed that during tension, some slip systems, which were not favored by the Schmid Factor law, were also activated in crystal B. The activation of these slip systems in crystal B can be attributed to the large deviation in the trace angle. The findings in this work provide valuable insights for exploring the underlying deformation mechanisms in polycrystalline materials.

Electron Dynamics in Open Quantum Systems: The Driven Liouville-von Neumann Methodology within Time-Dependent Density Functional Theory.

A first-principles approach to describe electron dynamics in open quantum systems driven far from equilibrium via external time-dependent stimuli is introduced. Within this approach, the driven Liouville-von Neumann methodology is used to impose open boundary conditions on finite model systems whose dynamics is described using time-dependent density functional theory. As a proof of concept, the developed methodology is applied to simple spin-compensated model systems, including a hydrogen chain and a graphitic molecular junction. Good agreement between steady-state total currents obtained via direct propagation and those obtained from the self-consistent solution of the corresponding Sylvester equation indicates the validity of the implementation. The capability of the new computational approach to analyze, from first principles, non-equilibrium dynamics of open quantum systems in terms of temporally and spatially resolved current densities is demonstrated. Future extensions of the approach toward the description of dynamical magnetization and decoherence effects are briefly discussed.

In search of a precursor for crystal nucleation of hard and charged colloids.

The interplay between crystal nucleation and the structure of the metastable fluid has been a topic of significant debate over recent years. In particular, it has been suggested that even in simple model systems such as hard or charged colloids, crystal nucleation might be foreshadowed by significant fluctuations in local structure around the location where the nucleus first arises. We investigate this using computer simulations of spontaneous nucleation events in both hard and charged colloidal systems. To detect local structural variations, we use both standard and unsupervised machine learning methods capable of finding hidden structures in the metastable fluid phase. We track numerous nucleation events for the face-centered cubic and body-centered cubic crystals on a local level and demonstrate that all signs of crystallinity emerge simultaneously from the very start of the nucleation process. We thus conclude that we observe no precursor for the crystal nucleation of hard and charged colloids.

Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics

Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the “lipid raft” hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation—essentially measuring the sign (but not the amplitude) of the free-energy change upon separation—rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.

The Rheology and Textural Properties of Bakery Products Upcycling Brewers' Spent Grain.

This study aimed to evaluate the rheological properties of doughs with 50% brewers' spent grain (BSG) derived from a rye-based (RBSG) and barley-based (BBSG) beer added, and the textural profile of the related baked products. Simple model systems using BSG flour mixed with water were studied. Two bakery products, focaccia and cookies, were made as food systems using BSG in a 1:1 ratio with wheat flour (WF). Their rheological properties and texture after baking were characterized. BSG-added dough exhibited viscoelastic properties with a solid gel-like behavior. The addition of BSG increased G' > G″ and decreased the dough flexibility. BSG addition in baked RBSG focaccia increased the hardness, gumminess, and chewiness by 10%, 9%, and 12%, respectively. BBSG cookies had a 20% increase in fracturability. A positive correlation was found between the rheological metrics of the dough and the textural parameters of BBSG-added cookies. PCA analysis revealed that complex viscosity, G', G″, and cohesiveness separated BBSG focaccia from RBSG focaccia and the control. Therefore, the rheological properties of BSG dough will have industrial relevance for 3D-printed customized food products with fiber. Adding RBSG and BBSG to selected foods will increase the up-cycling potential by combining techno-functional properties.

Protein interaction network analysis of mTOR signaling reveals modular organization

The mammalian target of rapamycin (mTOR) is a serine-threonine kinase that acts as a central mediator of translation and plays important roles in cell growth, synaptic plasticity, cancer, and a wide range of developmental disorders. The signaling cascade linking lipid kinases (phosphoinositide 3-kinases), protein kinases (AKT), and translation initiation complexes (EIFs) to mTOR has been extensively modeled, but does not fully describe mTOR system behavior. Here, we use quantitative multiplex coimmunoprecipitation to monitor a protein interaction network (PIN) composed of 300+ binary interactions among mTOR-related proteins. Using a simple model system of serum-deprived or fresh-media-fed mouse 3T3 fibroblasts, we observed extensive PIN remodeling involving 27+ individual protein interactions after 1h, despite phosphorylation changes observed after only 5min. Using small molecule inhibitors of phosphoinositide 3-kinase, AKT, mTOR, MEK and ERK, we define subsets of the PIN, termed "modules", that respond differently to each inhibitor. Using primary fibroblasts from individuals with overgrowth disorders caused by pathogenic PIK3CA or MTOR variants, we find that hyperactivation of mTOR pathway components is reflected in a hyperactive PIN. Our data define a "modular" organization of the mTOR PIN in which coordinated groups of interactions respond to the activation or inhibition of distinct nodes, and demonstrate that kinase inhibitors affect the modular network architecture in a complex manner, inconsistent with simple linear models of signal transduction.

Zebrafish as a high throughput model for organ preservation and transplantation research.

Despite decades of effort, the preservation of complex organs for transplantation remains a significant barrier that exacerbates the organ shortage crisis. Progress in organ preservation research is significantly hindered by suboptimal research tools that force investigators to sacrifice translatability over throughput. For instance, simple model systems, such as single cell monolayers or co-cultures, lack native tissue structure and functional assessment, while mammalian whole organs are complex systems with confounding variables not compatible with high-throughput experimentation. In response, diverse fields and industries have bridged this experimental gap through the development of rich and robust resources for the use of zebrafish as a model organism. Through this study, we aim to demonstrate the value zebrafish pose for the fields of solid organ preservation and transplantation, especially with respect to experimental transplantation efforts. A wide array of methods were customized and validated for preservation-specific experimentation utilizing zebrafish, including the development of assays at multiple developmental stages (larvae and adult), methods for loading and unloading preservation agents, and the development of viability scores to quantify functional outcomes. Using this platform, the largest and most comprehensive screen of cryoprotectant agents (CPAs) was performed to determine their toxicity and efficiency at preserving complex organ systems using a high subzero approach called partial freezing (i.e., storage in the frozen state at -10°C). As a result, adult zebrafish cardiac function was successfully preserved after 5 days of partial freezing storage. In combination, the methods and techniques developed have the potential to drive and accelerate research in the fields of solid organ preservation and transplantation.

Leveraging Charge-Transfer Interactions in Through-Space-Coupled Pentacene Dendritic Oligomer for Singlet Exciton Fission.

Singlet exciton fission in organic chromophores has received much attention during the past decade. Inspired by numerous spectroscopic studies in the solid state, there have been vigorous efforts to study singlet exciton fission dynamics in covalently bonded oligomers, which aims to investigate underlying mechanisms of this intriguing process in simplified model systems. In terms of through-space orbital interactions, however, most of covalently bonded pentacene oligomers studied so far fall into weakly interacting systems since they manifest chain-like structures based on various (non)conjugated linkers. Therefore, it remains as a compelling question to answer how through-space interactions in the solid state intervene this photophysical process since it is hypersensitive to displacements and orientations between neighboring chromophores. Herein, as one of experimental studies to answer this question, we introduced a tight-packing dendritic structure whose mesityl-pentacene constituents are coupled via moderate through-space orbital interactions. Based on the comparison with a suitably controlled dendritic structure, which is in a weak coupling regime, important mechanistic viewpoints are tackled such as configurational mixings between singlet, charge-transfer, and triplet pair states and the role of chromophore multiplication. We underscore that our through-space-coupled dendritic oligomer in a quasi-intermediate coupling regime provides a hint on the interplay of multiconfigurational excited-states, which might have drawn complexity in singlet exciton fission kinetics throughout numerous solid-state morphologies.

Probing Electronic Effects in Tridentate Copper(I) Complexes by CIVP Spectroscopy.

Ligand electronic effects play an important role in catalysis, where small changes to ligand structure can bring about large changes in catalytic activity. Therefore, accurate experimental quantification of ligand electronic properties plays a crucial role in understanding and tuning chemical reactivity. In this work, we used cryogenic ion vibrational predissociation (CIVP) spectroscopy to experimentally quantify electronic effects in terpyridine ligands, as simple model systems, by measuring CIVP spectra of their copper complexes tagged by N2 molecules. We used the N2 stretching vibration as a reporter chromophore to probe electronic effects of the investigated ligands and employed quantum chemical calculations to better understand how different substituents influence the vibrational frequencies of the stretching vibration of the chromophore. Our data show that the electronic character, as well as position and number of substituents, can affect the N≡N vibrational frequency, and that the N≡N bond serves as a sensitive probe for electronic and steric effects.

Field-tuned quantum renormalization of spin dynamics in the honeycomb lattice Heisenberg antiferromagnet YbCl3

The basis for our understanding of quantum magnetism has been the study of elegantly simple model systems. However, even for the antiferromagnetic honeycomb lattice with isotropic spin interactions–one of the simplest model systems–a detailed understanding of quantum effects is still lacking. Here, using inelastic neutron scattering measurements of the honeycomb lattice material YbCl3, we elucidate how quantum effects renormalize the single-magnon and multimagnon excitations and how this renormalization can be tuned and ultimately driven to the classical limit by applying a magnetic field. Additionally, our work reveals that the quantum effects tuned by the magnetic field not only renormalize the magnetic excitations but also induce a distinctive sharp feature inside the multimagnon continuum. From a more general perspective, this result demonstrates that structures within magnetic continua can occur over a wide experimental parameter space and can be used as a reliable means of identifying quantum phenomena.

Dynamic coarse-graining of linear and non-linear systems: Mori-Zwanzig formalism and beyond.

To investigate the impact of non-linear interactions on dynamic coarse graining, we study a simplified model system featuring a tracer particle in a complex environment. Using a projection operator formalism and computer simulations, we systematically derive generalized Langevin equations (GLEs) describing the dynamics of this particle. We compare different kinds of linear and non-linear coarse-graining procedures to understand how non-linearities enter reconstructed GLEs and how they influence the coarse-grained dynamics. For non-linear external potentials, we show analytically and numerically that the non-Gaussian parameter and the incoherent intermediate scattering function will not be correctly reproduced by the GLE if a linear projection is applied. This, however, can be overcome by using non-linear projection operators. We also study anharmonic coupling between the tracer and the environment and demonstrate that the reconstructed memory kernel develops an additional trap-dependent contribution. Our study highlights some open challenges and possible solutions in dynamic coarse graining.

Simple models for neuroscience research discoveries: how often are these models used in Africa?

Background: Simple animal model systems such as Drosophila, Caenorhabditis Elegans and Zebrafish have enabled numerous breakthroughs in understanding human health and disease. Owing to their cheap maintenance cost, adopting these model systems will improve research in Africa. However, the extent to which these models are used across Africa is unknown. This study aimed to identify how often these models are used in Africa. Methods: We downloaded all the PUBMED-indexed publications from the year 2000 to 2021 that have an African affiliation and have mentioned Drosophila, C. elegans or Zebrafish. We manually curated the information on the experimental use of these model systems, author affiliations and details of funding from research publications. Descriptive statistics was used to describe the major hotspots for the use of the model systems and funders, and the pattern of local and international collaborations. Results: Of the 1851 publications in which at least one of the models was mentioned, only 168 used at least one for the actual investigation. With an average of 21 articles per country, South Africa, Nigeria, Kenya, Egypt, Morocco, and Tunisia contributed 75% of these studies. The remaining 25% were contributed by seven other countries. Analysis of funding information revealed that 24.4% of the studies were exclusively locally funded, 28.57% exclusively internationally funded, 15.5% received both local and international funding, and the rest (31.5%) were unfunded, revealing that there is satisfactory access to funds for simple animal model studies, especially from external funders. By analysing the pattern of collaborations, we show that collaborations with researchers from other continents predominate over intra-Africa collbaorations. Conclusions: Our work provides data on the current state of research using simple model systems in African laboratories and argues that incorporating these models will advance biomedical science research in Africa.

A simultaneous Eigen valued expression to model the three coupled electronic states with triply and doubly degenerate seams together I

AbstractThe accurate modeling of triply and doubly degenerate seam together while computing the coupled multiple potential energy surfaces globally remains a challenging task due to the unavailability of a suitable model function taking care of this aspect. In this paper, we present such a function capable of predicting many‐fold electronic degeneracies simultaneously as well as the features found away from the vicinity of such degeneracies if present in the coupled surfaces disregarding the symmetry requirements. The basis of the proposed model comes from the analytical diagonalization of a real valued diagonally symmetric diabatic matrix and thus, the resulting three symbolic Eigen valued functions form the basis of model to be used in this work. From the analytical model, an attempt was made to provide an analytical expression for the adiabatic‐diabatic transformation angle. Few applications were considered starting from the simple physical model systems to actual realistic molecule illustrating how the present model function are being applied to them to show the presence of degeneracies among the three electronic states.

Fast bit flipping based on stability transition of coupled spins.

A bipartite spin system is proposed for which a fast transfer from one defined state into another exists. For sufficient coupling between the spins, this implements a bit-flipping mechanism, which is much faster than that induced by tunneling. The states correspond in the semiclassical limit to equilibrium points with a stability transition from elliptic-elliptic stability to complex instability for increased coupling. The fast transfer is due to the spiraling characteristics of the complex unstable dynamics. Based on the classical system we find an approximate scaling relation for the transfer time, which even applies in the deep quantum regime. By investigating a simple model system, we show that the classical stability transition is reflected in a fundamental change in the structure of the eigenfunctions.

Perspectives on a Few Puzzles in Phase Transformations: When Should the Farthest Reach the Earliest?

We briefly review the facts concerning two important aspects of phase transitions, namely, critical and coarsening phenomena. A discussion of the universal features, highlighting the current challenges, is provided. Following this, we elaborate on a topic of much recent interest, viz., the Mpemba effect, a puzzle that found mention even in the works of Aristotle. After a description of the debated case of faster freezing of a hotter sample of liquid water, into ice, than a colder one, when quenched to the same subzero temperature, we discuss more modern interest. There one asks, should a hotter body of a material equilibrate faster than a colder one when quenched to a common lower temperature? Within this broad scenario, we focus on magnetic systems. A surprising observation of the effect during the para- to ferromagnetic transition, in a simple model system, viz., the nearest-neighbor Ising model, without any built-in frustration, is described. Some associated future directions are pointed out. A discussion is provided by considering the effect as a kinetic outcome in the background of critical phenomena. A picture is drawn by putting emphasis on the role of spatial correlations in the initial configurations alongside discussing the importance of frustration and metastability in evolution from one state to another. In connection with dynamical freezing, concerning metastability, we have introduced the complex Ginzburg-Landau equation that has relevance in phase transitions, chemical oscillations, and elsewhere. For this model and a few other cases also, we have described how a lack of order or correlation in certain parameters can lead to quicker evolution.

Self-Similarity and Spatial Periodicity in Cerebral Cortical Patterning: Structural Design Notes for Neural Tissue Architects

Tissue engineering is a powerful tool with which to systematically identify the determinants of biological functions. Applied to the design and fabrication of biomimetic brains, tissue engineering serves to disentangle the complex anatomy of neural circuits and pathways by recapitulating structure-function relationships in simplified model systems. The complex neuroanatomy of the cerebral cortex, with its enigmatic columnar and stratified cytoarchitectonic organization, represents a major challenge toward isolating the minimal set of elements that are required to assemble neural tissues with cognitive functions. Whereas considerable efforts have highlighted important genetic and physical correlates of early cortical tissue patterning, no substantive attempt to identify the determinants of how the cortices acquire their relatively conserved, narrow range of numbered layers is evident in the literature. Similarly, it is not yet clear whether cortical columns and laminae are functionally relevant or epiphenomena of embryonic neurodevelopment. Here, we demonstrate that spatial frequencies (m−1) derived from the width-to-height ratios of cerebral cortical columns predict sinusoids with a narrow range of spatial cycles over the average cortical thickness. The resulting periodicities, denoted by theoretical wavenumbers, reflect the number of observed cortical layers among humans and across several other species as revealed by a comparative anatomy approach. We present a hypothesis that cortical columns and their periodic layers are emergent of the intrinsic spatial dimensions of neurons and their nested, self-similar aggregate structures including minicolumns. Finally, we discuss the implications of periodic tissue patterns in the context of neural tissue engineering.

Chirality-controlled spin scattering through quantum interference.

Chirality-induced spin selectivity has been reported in many experiments, but a generally accepted theoretical explanation has not yet been proposed. Here, we introduce a simple model system of a straight cylindrical free-electron wire containing a helical string of atomic scattering centers with spin-orbit interaction. The advantage of this simple model is that it allows deriving analytical expressions for the spin scattering rates, such that the origin of the effect can be easily followed. We find that spin-selective scattering can be viewed as resulting from the constructive interference of partial waves scattered by the spin-orbit terms. We demonstrate that forward scattering rates are independent of spin, while back scattering is spin dependent over wide windows of energy. Although the model does not represent the full details of electron transmission through chiral molecules, it clearly reveals a mechanism that could operate in chiral systems.

ALS plasma reduces the viability of NSC34 cells via altering mRNA expression of VEGF: A short report

IntroductionAmyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disorder that progressively leads to motor neuron degeneration at the neuromuscular junctions, resulting in paralysis in the patients. The clinical diagnosis of ALS is time taking and further delays the therapeutics that can be helpful if the disease is diagnosed at an early stage. Changes in plasma composition can be reflected upon CSF composition and hence, can be used to study the diagnosis and prognosis markers for the disease. AimTo develop a simple model system using motor neuron like cell line after plasma induction. MethodNeuroblastoma × Spinal Cord hybridoma cell line (NSC34) was cultured under appropriate conditions. 10% ALS patients’ plasma was added to the media, and cells were conditioned for 12 h. Cell survival analysis and differential gene expression of a panel of molecules (published previously, VEGF, VEGFR2, ANG, OPTN, TDP43, and MCP-1) were done. ResultsALS patients’ plasma impacted the life of the cells and reduced survival to nearly 50% after induction. VEGF was found to be significantly down-regulated in the cells, which can be explained as a reason for reduced cell survival. ConclusionALS plasma altered the expression of an essential neuroprotective and growth factor VEGF in NSC34 cells leading to reduced viability.

Transcriptional changes in specific subsets of Drosophila neurons following inhibition of the serotonin transporter

The transcriptional effects of SSRIs and other serotonergic drugs remain unclear, in part due to the heterogeneity of postsynaptic cells, which may respond differently to changes in serotonergic signaling. Relatively simple model systems such as Drosophila afford more tractable microcircuits in which to investigate these changes in specific cell types. Here, we focus on the mushroom body, an insect brain structure heavily innervated by serotonin and comprised of multiple different but related subtypes of Kenyon cells. We use fluorescence-activated cell sorting of Kenyon cells, followed by either bulk or single-cell RNA sequencing to explore the transcriptomic response of these cells to SERT inhibition. We compared the effects of two different Drosophila Serotonin Transporter (dSERT) mutant alleles as well as feeding the SSRI citalopram to adult flies. We find that the genetic architecture associated with one of the mutants contributed to significant artefactual changes in expression. Comparison of differential expression caused by loss of SERT during development versus aged, adult flies, suggests that changes in serotonergic signaling may have relatively stronger effects during development, consistent with behavioral studies in mice. Overall, our experiments revealed limited transcriptomic changes in Kenyon cells, but suggest that different subtypes may respond differently to SERT loss-of-function. Further work exploring the effects of SERT loss-of-function in other circuits may be used help to elucidate how SSRIs differentially affect a variety of different neuronal subtypes both during development and in adults.

Enhanced resistive switching of silver copper iodide thin films prepared by interfacial phase formation

Resistive random-access memory (ReRAM), an alternative to conventional charge storage memory, employs the switching of a resistive material between high-resistance and low-resistance states, which can be generated by the formation/dissolution of metal filaments bridging the two electrodes in the cell. Silver iodide (AgI) is a promising solid electrolyte for ReRAM cells, but its application is hindered by poor photostability and low electrical conductivity. Herein, a Cu-substituted β-AgI system, β′-Ag0.7Cu0.3I, was successfully prepared via sequential deposition of a Cu metal layer onto a AgI thin film by a galvanic reaction, which induced the spontaneous incorporation of Cu+ cations into the AgI lattice. Cu substitution at the Cu–AgI heterojunction interface is a novel way to modulate the chemical composition and improve the resistive switching properties of intrinsic polycrystalline AgI thin films. We compared the resistive switching properties of a ReRAM thin film devices based on β′-Ag0.7Cu0.3I with those based on pristine β-AgI. This device exhibited enhanced performance with high ON/OFF ratio (∼104) and low working voltage compared with the β-AgI-based device. These results strongly suggest that binary metal halide materials can serve as simple model systems for the efficient formation of metal filaments and have potential low-cost, low-power memory applications.