Transient Domains Research Articles

Glassy Dynamics and Local Crystalline Order in Two-Dimensional Amorphous Silica.

We reassess the modeling of amorphous silica bilayers as a 2D classical system whose particles interact with an effective pairwise potential. We show that it is possible to reparametrize the potential developed by Roy, Heyde, and Heuer to quantitatively match the structural details of the experimental samples. We then study the glassy dynamics of the reparametrized model at low temperatures. Using appropriate cage-relative correlation functions, which suppress the effect of Mermin-Wagner fluctuations, we highlight the presence of two well-defined Arrhenius regimes separated by a narrow crossover region, which we connect to the thermodynamic anomalies and changes in the local structure. We find that the bond-orientational order grows steadily below the crossover temperature and is associated with transient crystalline domains of nanometric size. These findings raise fundamental questions about the nature of the glass structure in two dimensions and provide guidelines to interpret the experimental data.

A network of transient domains for breaking symmetry during anterior-posterior axis formation in the porcine embryo.

Breaking radial symmetry for anterior-posterior axis formation is one of the key developmental steps of vertebrate gastrulation and is established through a succession of transient domains defined by morphology or gene expression. Three such domains were interpreted recently in the rabbit to be part of a "three-anchor-point model" for axis formation. To answer the question as to whether the model is generally applicable to mammals, the dynamic expression patterns of four marker genes were analyzed in the pig, where gastrulating epiblast forms from half the inner cell mass: EOMES and PKDCC transcripts display decreasing expression intensities in the anterior hypoblast and-together with WNT3-increasing intensity in the anterior streak domain and the node; TBX6 expression changes from an initial central expression to exclusive expression in the posterior extremity of the primitive streak. The anterior streak domain has thus a molecular footprint similar to the one in the rabbit, the end node shares TBX6 between the species, while the anterior hypoblast-mirroring specific porcine epiblast derivation and fate-is marked by PKDCC instead of WNT3. The molecular similarities in transient domains point to conserved mechanisms for establishing the mammalian anterior-posterior axis and, possibly, breaking radial symmetry.

Product differentiation of Sarawak premium rice using MOS gas sensors: comparison between transient and frequency response

In Malaysia, rice, ranked as the third most crucial crop, faces challenges due to domestic consumption outpacing production, resulting in increased instances of rice adulteration. This underscores the imperative of maintaining integrity and quality standards across the entire supply chain. This study uses an electronic nose, comprising four metal oxide semiconductor (MOS) gas sensors, and employing temperature modulation, Principal Component Analysis (PCA) and supervised machine learning (classification models) to distinguish rice varieties such as Bario, Bajong, Borneo Fragrant, Biris, and Jasmine. The study evaluated 30 classifiers based on their classification and validation accuracy. Sensor data was first extracted from the transient response of sensors output voltage, yielding a 12-dimension dataset with response times of 30 s, 50 s, and 95 s. Classification models trained from this dataset achieved classification (training) accuracy of up to 100% and validation accuracy of up to 96%, where the best performing models are subspace discriminant and kernel naïve bayes classifiers. An attempt was also made to analyze the sensor data frequency response for rice classification. Comparison between the prediction results in the transient and frequency domains showed that transient response is better suited for the classification of rice.

Chiral domain dynamics and transient interferences of mirrored superlattices in nonequilibrium electronic crystals

Mirror symmetry plays a major role in determining the properties of matter and is of particular interest in condensed many-body systems undergoing symmetry breaking transitions under non-equilibrium conditions. Typically, in the aftermath of such transitions, one of the two possible broken symmetry states is emergent. However, synthetic systems and those formed under non-equilibrium conditions may exhibit metastable states comprising of both left (L) and right (R) handed symmetry. Here we explore the formation of chiral charge-density wave (CDW) domains after a laser quench in 1T-TaS2 with scanning tunneling microscopy. Typically, we observed transient domains of both chiralities, separated spatially from each other by domain walls with different structure. In addition, we observe transient density of states modulations consistent with interference of L and R-handed charge density waves within the surface monolayer. Theoretical modeling of the intertwined domain structures using a classical charged lattice gas model reproduces the experimental domain wall structures. The superposition (S) state cannot be understood classically within the correlated electron model but is found to be consistent with interferences of L and R-handed charge-density waves within domains, confined by surrounding domain walls, vividly revealing an interference of Fermi electrons with opposite chirality, which is not a result of inter-layer interference, but due to the interaction between electrons within a single layer, confined by domain wall boundaries.

Analysis of Phase Heterogeneity in Lipid Membranes Using Single-Molecule Tracking in Live Cells.

In live cells, the plasma membrane is composed of lipid domains separated by hundreds of nanometers in dynamic equilibrium. Lipid phase separation regulates the trafficking and spatiotemporal organization of membrane molecules that promote signal transduction. However, visualizing domains with adequate spatiotemporal accuracy remains challenging because of their subdiffraction limit size and highly dynamic properties. Here, we present a single lipid-molecular motion analysis pipeline (lipid-MAP) for analyzing the phase heterogeneity of lipid membranes by detecting the instantaneous velocity change of a single lipid molecule using the excellent optical properties of nanoparticles, high spatial localization accuracy of single-molecule localization microscopy, and separation capability of the diffusion state of the hidden Markov model algorithm. Using lipid-MAP, individual lipid molecules were found to be in dynamic equilibrium between two statistically distinguishable phases, leading to the formation of small (∼170 nm), viscous (2.5× more viscous than surrounding areas), and transient domains in live cells. Moreover, our findings provide an understanding of how membrane compositional changes, i.e., cholesterol and phospholipids, affect domain formation. This imaging method can contribute to an improved understanding of spatiotemporal-controlled membrane dynamics at the molecular level.

Dynamic Local Structure in Caesium Lead Iodide: Spatial Correlation and Transient Domains.

Metal halide perovskites are multifunctional semiconductors with tunable structures and properties. They are highly dynamic crystals with complex octahedral tilting patterns and strongly anharmonic atomic behavior. In the higher temperature, higher symmetry phases of these materials, several complex structural features are observed. The local structure can differ greatly from the average structure and there is evidence that dynamic 2D structures of correlated octahedral motion form. An understanding of the underlying complex atomistic dynamics is, however, still lacking. In this work, the local structure of the inorganic perovskite CsPbI3 is investigated using a new machine learning force field based on the atomic cluster expansion framework. Through analysis of the temporal and spatial correlation observed during large-scale simulations, it is revealed that the low frequency motion of octahedral tilts implies a double-well effective potential landscape, even well into the cubic phase. Moreover, dynamic local regions of lower symmetry are present within both higher symmetry phases. These regions are planar and the length and timescales of the motion are reported. Finally, the spatial arrangement of these features and their interactions are investigated and visualized, providing a comprehensive picture of local structure in the higher symmetryphases.

Fault Coverage Improvement of CMOS Analog Circuits Using Supply Current Testing Method

In this paper, a testing technique based on supply current verifying is presented, for fault detection of analog circuits containing CMOS operational amplifiers. This testing technique is employed and developed to maximize the fault coverage of the circuit under test (CUT) using transient and frequency responses of the supply current. This testing method is based on the over-sighting of the quiescent supply current (Iddq) of the CMOS operational amplifier operating in its quiescent mode and the supply current of the CMOS operational amplifier used as a Sallen-Key band pass filter in the AC and transient operating domains. The faults investigated in our study are of bridging and open circuit types that occur at the CMOS transistor level. The Pspice software was used for the CUT simulation by applying Monte-Carlo analysis in faulty and fault free conditions. Test parameters are extracted and selected to be used as input features of our classifier.

High electric field-induced ferroelectric loss of polymer/paraelectric barium titanate particle nanocomposites

Polymer nanodielectrics have manifested high energy densities for potential applications in film capacitors. However, ferroelectric-like large hysteresis is often observed in the bipolar polarization–electric field (P-E) loops, even though neither the polymer matrix nor the ceramic nanoparticle exhibits any intrinsic ferroelectricity. To understand this abnormal ferroelectric behavior, poly(vinyl pyrrolidone) (PVP)/60 nm BaTiO3 (BTO60) nanocomposite films were fabricated with uniform BTO60 nanoparticle dispersion. PVP was a linear dielectric polymer with an apparent dielectric constant of 6.8 and BTO60 was found to be paraelectric. When the volume fraction of BTO60 was above 30 vol%, broad ferroelectric P-E loops were yielded. Using a theoretical deconvolution of the broad P-E loops based on the Langevin-type function, three contributions were identified. First, deformational polarization generated the linear dielectric constant of nanocomposites, from which the linear dielectric constant of BTO60 nanoparticles was extracted using the Bruggeman mixing rule. Second, slim paraelectric P-E loops were obtained for the BTO60 nanoparticles. From the saturated polarization, the electric field-induced permanent dipole moment per unit cell was estimated to be 0.07–0.2 D at a poling field of 20–100 MV/m, which was significantly smaller than the dipole moment (5.3 D) of the tetragonal unit cell of BaTiO3, indicating the paraelectric nature of BTO60 nanoparticles. Third, strong particle–particle dipolar interactions induced transient ferroelectric domains among the high dielectric constant BTO60 nanoparticles, particularly when the poling electric field was high. The third contribution dominated the overall polarization process and thus accounted for the abnormal ferroelectric behavior for the linear dielectric polymer/paraelectric ceramic nanoparticle composites. The knowledge gained from this study will pave the way towards developing better strategies for polymer nanodielectrics in the applications of capacitive energy storage.

Fluorescent GD2 analog for single-molecule imaging.

Ganglioside GD2 is associated with the proliferation and migration of breast cancer cells. However, the precise role of GD2 is unclear because its tendency to form dynamic and transient domains in cell plasma membranes (PMs), called lipid rafts, makes it difficult to observe. Previously, we developed fluorescent analogs of gangliosides (e.g., GM3 and GM1), which enabled the observation of lipid raft formation for the first time using single-molecule imaging. In this report, we describe the first chemical synthesis of a fluorescent ganglioside, GD2. A biophysical analysis of the synthesized analog revealed its raft-philic character, suggesting its potential to aid single-molecule imaging-based investigations into raft-associated interactions.

Biochemical and Structural Insights into FIH-Catalysed Hydroxylation of Transient Receptor Potential Ankyrin Repeat Domains.

Transient receptor potential (TRP) channels have important roles in environmental sensing in animals. Human TRP subfamily A member 1 (TRPA1) is responsible for sensing allyl isothiocyanate (AITC) and other electrophilic sensory irritants. TRP subfamily vanilloid member 3 (TRPV3) is involved in skin maintenance. TRPV3 is a reported substrate of the 2-oxoglutarate oxygenase factor inhibiting hypoxia-inducible factor (FIH). We report biochemical and structural studies concerning asparaginyl hydroxylation of the ankyrin repeat domains (ARDs) of TRPA1 and TRPV3 catalysed by FIH. The results with ARD peptides support a previous report on FIH-catalysed TRPV3 hydroxylation and show that, of the 12 potential TRPA1 sequences investigated, one sequence (TRPA1 residues 322-348) undergoes hydroxylation at Asn336. Structural studies reveal that the TRPA1 and TRPV3 ARDs bind to FIH with a similar overall geometry to most other reported FIH substrates. However, the binding mode of TRPV3 to FIH is distinct from that of other substrates.

Alzheimer’s-Associated Upregulation of Mitochondria-Associated ER Membranes After Traumatic Brain Injury

Traumatic brain injury (TBI) can lead to neurodegenerative diseases such as Alzheimer’s disease (AD) through mechanisms that remain incompletely characterized. Similar to AD, TBI models present with cellular metabolic alterations and modulated cleavage of amyloid precursor protein (APP). Specifically, AD and TBI tissues display increases in amyloid-β as well as its precursor, the APP C-terminal fragment of 99 a.a. (C99). Our recent data in cell models of AD indicate that C99, due to its affinity for cholesterol, induces the formation of transient lipid raft domains in the ER known as mitochondria-associated endoplasmic reticulum (ER) membranes (“MAM” domains). The formation of these domains recruits and activates specific lipid metabolic enzymes that regulate cellular cholesterol trafficking and sphingolipid turnover. Increased C99 levels in AD cell models promote MAM formation and significantly modulate cellular lipid homeostasis. Here, these phenotypes were recapitulated in the controlled cortical impact (CCI) model of TBI in adult mice. Specifically, the injured cortex and hippocampus displayed significant increases in C99 and MAM activity, as measured by phospholipid synthesis, sphingomyelinase activity and cholesterol turnover. In addition, our cell type-specific lipidomics analyses revealed significant changes in microglial lipid composition that are consistent with the observed alterations in MAM-resident enzymes. Altogether, we propose that alterations in the regulation of MAM and relevant lipid metabolic pathways could contribute to the epidemiological connection between TBI and AD.Graphical

New Insights for Parasitic Effects of Label-Free Biosensors Based on Capacitive Micromachined Ultrasonic Transducers

Capacitive micromachined ultrasonic transducers (CMUTs) are regarded as an attractive candidate in bio-applications such as imaging and molecule monitoring. However, the previous researches on biochemical sensing are mostly air-coupled application based on a CMUTs array because cell-to-cell mutual radiation and large motional loss in liquid environment are able to produce nonignorable noise. For a CMUTs cell, its characteristics (e.g., electrical, mechanical, and acoustic) are susceptible to parasitic effects owning to the physically capacitive dielectric dispersion, motional damping, and connection loss. Neglecting the parasitic effects on multidomain characteristics of CMUTs leads to significant robustness errors. Furthermore, finite element method (FEM) is not sufficient enough to model such parasitic effects when considering an integrated circuit interface and the evaluation of system responses. This article highlights a lumped element model (LEM) to analyze the behaviors of a label-free biosensor based on a single CMUTs cell directly operating in liquid. We successfully explore the performance of the biosensor with different types of parasitic effects in transient and frequency domains through LEM and FEM. The parasitic effects on mass loading of sensing layer and biomolecule such as deoxyribonucleic acid (DNA) and Immunoglobulin G (IgG) probes are predicted by LEM based on their surface mass densities. The proposed approach is capable of analyzing the variation’s margin of CMUTs-based biosensors to improve robustness for parasitic extraction in liquid.

A Numerical Study of a Pico Hydro Turbine

Pico hydro turbines are suitable for low head applications in power plants since their efficiency is more stable than other turbine types. In some situations, computational fluid dynamics (CFD) has also been utilized as well as experimental studies for the performance prediction of water turbines at a pico scale. Also, CFD methods are getting much closer to real conditions in terms of steady-state with moving references and transient domains with rotor movements. For this purpose, electricity production related to the flow in a PHT was investigated numerically. This study presents six degrees of freedom (6-DOF) and moving reference frame (MRF) methods to predict the maximum conditions of a pico scale two-dimensional turbine by comparing the torque and angular velocities on the runner based on the turbine output power of 1 W determined by an experimental study. Besides, the effect of the torque, angular velocity, tip speed ratio, and turbine body profile was investigated comprehensively. In this regard, MRF and 6-DOF methods were performed to validate and compare the numerical model with the experimental results. Also, the results obtained from 6-DOF and MRF methods were compared to experimental study. It is concluded that PHT is generating 0.3 W power under 6.47 rad/s angular velocity with 6-DOF method, however; this value corresponds to 31.4 rad/s angular velocity against 1 W with the MRF method. Also, the maximum velocity of the turbine was 6.1 m/s according to the simulation result. It is accepted that the turbine maximum velocity inlet was 0.53 m/s based on the experimental study. As a conclusion, numerical results for the pico hydro turbine were reasonable taking the experimental study into account. It is also concluded that there is a tip speed ratio of 2.36 with the MRF method and 0.48 with the 6-DOF method between water tangential velocity and runner velocity for the turbine model.

Cascade reaction networks within audible sound induced transient domains in a solution

Spatiotemporal control of chemical cascade reactions within compartmentalized domains is one of the difficult challenges to achieve. To implement such control, scientists have been working on the development of various artificial compartmentalized systems such as liposomes, vesicles, polymersomes, etc. Although a considerable amount of progress has been made in this direction, one still needs to develop alternative strategies for controlling cascade reaction networks within spatiotemporally controlled domains in a solution, which remains a non-trivial issue. Herein, we present the utilization of audible sound induced liquid vibrations for the generation of transient domains in an aqueous medium, which can be used for the control of cascade chemical reactions in a spatiotemporal fashion. This approach gives us access to highly reproducible spatiotemporal chemical gradients and patterns, in situ growth and aggregation of gold nanoparticles at predetermined locations or domains formed in a solution. Our strategy also gives us access to nanoparticle patterned hydrogels and their applications for region specific cell growth.

Imaging Cu2+ binding to charged phospholipid membranes by high-throughput second harmonic wide-field microscopy.

The interaction of divalent copper ions (Cu2+) with cell membranes is crucial for a variety of physiological processes of cells, such as hormone synthesis and cellular energy production. These interactions would not be possible without membrane hydration. However, the role of water has not received a lot of attention in membrane studies. Here, we use high-throughput wide-field second harmonic (SH) microscopy to study the interaction between Cu2+ and hydrated freestanding Montal-Müller lipid membranes. The symmetric lipid membranes are composed of 1,2-diphytanoyl-sn-glycero-3-phosphocholine and either 1,2-diphytanoyl-sn-glycero-3-phosphate or 1,2-diphytanoyl-sn-glycero-3-phospho L-serine and are brought into contact with divalent Cu2+, which are added to one leaflet while maintaining the ionic strength balance. We observe transient domains of high SH intensity. In these areas, Cu2+ ions bind to the charged head groups, leading to charge neutralization on one side of the membrane. This exposes the ordered water at the non-interacting side of the membrane interface, which can be used to compute the interfacial membrane potential difference. We find that the domains of lipids with phosphatidic acid head groups display a higher interfacial membrane potential than those with phosphatidylserine head groups, which converts into higher dynamic electrostatic free energies and binding constants.

Observing the spontaneous formation of a sub-critical nucleus in a phase-change amorphous material from ab initio molecular dynamics

Phase-change materials (PCMs) are finding wide applications in emerging technologies such as nonvolatile phase-change random-access memory and in-memory computing devices by utilising the ultrafast and reversible amorphous-to-crystal transition. The crystallisation of the amorphous state is much slower compared to the crystal melting, hence representing a bottleneck in the further development of new technologies. Here, we disclose the detailed crystallisation pathway of amorphous Ge2Sb2Te5 (GST) via ab initio molecular dynamics simulations. By probing the local order with a highly sensitive metric, we detect the formation of a sub-critical nucleus formed by the spontaneous aggregation of highly ordered octahedral-like atoms. Specifically, we observe that Sb atoms recover octahedral-like geometry quicker than Ge atoms, implying that the different mobility of different species plays a central role in the overall process. With respect to other less locally-ordered (hence transient) domains, this stable precursor is characterised by lower energy, is resilient to melting, and acts as a skeleton over which the critical nucleus further develops. The detailed understanding of the kinetics of homogeneous nucleation in GST opens the doorway for the development of more efficient PCM-based storage devices by a rational composition design and, ultimately, for the boosting of the speed and efficiency of computing architectures.

Expression patterns of signalling molecules and transcription factors in the early rabbit embryo and their significance for modelling amniote axis formation

The anterior-posterior axis is a central element of the body plan and, during amniote gastrulation, forms through several transient domains with specific morphogenetic activities. In the chick, experimentally proven activity of signalling molecules and transcription factors lead to the concept of a ‘global positioning system’ for initial axis formation whereas in the (mammotypical) rabbit embryo, a series of morphological or molecular domains are part of a putative ‘three-anchor-point model’. Because circular expression patterns of genes involved in axis formation exist in both amniote groups prior to, and during, gastrulation and may thus be suited to reconcile these models, the expression patterns of selected genes known in the chick, namely the ones coding for the transcription factors eomes and tbx6, the signalling molecule wnt3 and the wnt inhibitor pkdcc, were analysed in the rabbit embryonic disc using in situ hybridisation and placing emphasis on their germ layer location. Peripheral wnt3 and eomes expression in all layers is found initially to be complementary to central pkdcc expression in the hypoblast during early axis formation. Pkdcc then appears — together with a posterior-anterior gradient in wnt3 and eomes domains — in the epiblast posteriorly before the emerging primitive streak is marked by pkdcc and tbx6 at its anterior and posterior extremities, respectively. Conserved circular expression patterns deduced from some of this data may point to shared mechanisms in amniote axis formation while the reshaping of localised gene expression patterns is discussed as part of the ‘three-anchor-point model’ for establishing the mammalian body plan.

Mechanism of transient stagnant formation in convection of binary mixtures

Two-dimensional convection rolls are usually stable near the critical Rayleigh number in single component fluids. However, in binary mixtures, it has been reported that the roll patterns become unstable over time and that stagnant domains are transiently formed. The formation of transient stagnant domains (TSD) occurs in systems where one component is more viscous than the other. Meanwhile, the mechanism of the TSD formation has been unclear yet. Here, we use experiments using well-mixed silicone oils and colloidal suspensions to show that the formation of transient stagnant regions is chiefly related to the concentration dependence of the kinematic viscosity rather than spatially averaged properties. Furthermore, we find that the concentration dependence of density is also related to the formation of stagnant regions. The coupling between density, viscosity and concentration fluctuations may play an important role for thermal convection in multi-component mixtures.

The Origin of Lipid Rafts.

The time-averaged lateral organization of the lipids and proteins that make up mammalian cell membranes continues to be the subject of intense interest and debate. Since the introduction of the fluid mosaic model almost 50 years ago, the "lipid raft hypothesis" has emerged as a popular concept that has captured the imagination of a large segment of the biomembrane community. In particular, the notion that lipid rafts play a pivotal role in cellular processes such as signal transduction and membrane protein trafficking is now favored by many investigators. Despite the attractiveness of lipid rafts, their composition, size, lifetime, biological function, and even the very existence remain controversial. The central tenet that underlies this hypothesis is that cholesterol and high-melting lipids have favorable interactions (i.e., they pull together), which lead to transient domains. Recent nearest-neighbor recognition (NNR) studies have expanded the lipid raft hypothesis to include the influence that low-melting lipids have on the organization of lipid membranes. Specifically, it has been found that mimics of cholesterol and high-melting lipids are repelled (i.e., pushed away) by low-melting lipids in fluid bilayers. The picture that has emerged from our NNR studies is that lipid mixing is governed by a balance of these "push and pull" forces, which maximizes the number of hydrocarbon contacts and attractive van der Waals interactions within the membrane. The power of the NNR methodology is that it allows one to probe these push/pull interaction energies that are measured in tens of calories per mole.

Real-Time Dynamics Modeling of Cryogenic Ball Bearings With Thermal Coupling

Abstract Real-time dynamic modeling of cryogenic ball bearings, where the rotating inner race accelerates to the operating speed, is based on integration of classical differential equations of motion of bearing elements, when experimentally measured ball/race traction behavior is used to compute the imposed acceleration on the rolling elements. The dynamic performance simulation provides a realistic coupling between traction behavior in the ball-to-race contacts and dynamics of bearing element motion as the bearing goes through the transient speed variation. However, due to vastly different mechanical and thermal time scales, heat generation in the bearing is time-averaged over a relatively large thermal time-step to model temperature fields as a step change, while the bearing motion is simulated in real-time. The emphasis is on dynamic modeling with thermal coupling in a static sense. Under stable conditions, the step change in temperature field converges to operating value as the bearing approaches a dynamic steady-state condition, which demonstrates acceptable significance of the dynamic simulation with coupled thermal interactions. Both all steel and hybrid ball bearings for liquid oxygen (LOX) turbo pump applications are modeled. Bearing performance simulations are closely modeled over experimental time cycles in both transient and steady-state domains. Steady-state solutions are shown to be independent of initial conditions to demonstrate acceptable convergence of time domain integrations. Model predictions of heat transferred to circulating LOX is within the range of variation in experimental data. Parametric evaluation of bearing performance as a function of operating conditions demonstrate that while the ball/race contact stress is higher in a hybrid bearing, contact heat generation is significantly lower in comparison with that in the all steel bearings.