Vitrification Research Articles (Page 1)

Understanding the role that structure plays in the dynamical arrest observed in glassy systems remains an open challenge. Over the past decade, machine learning (ML) strategies have emerged as an important tool for probing this structure-dynamics relationship, particularly for predicting heterogeneous glassy dynamics from local structure. A recent advancement is the introduction of the cage state, a structural quantity that captures the average positions of particles while rearrangements are forbidden. During the caging regime, linear models trained on the cage state have been shown to outperform more complex ML methods trained on initial configurations only. In this paper, we explore the properties associated with the cage state in more detail to better understand why it serves as such an effective predictor for the dynamics. In particular, we examine how the cage state in a binary hard-sphere mixture is influenced by both packing fraction and boundary conditions. Our results reveal that, as the system approaches the glassy regime, the cage state becomes increasingly influenced by long-range structural effects. This influence is evident both in its predictive power for particle dynamics and in the internal structure of the cage state, suggesting that the CS might be associated with some form of an amorphous growing structural length scale.

On the nature of the glass transition in metallic glasses after deep relaxation

Research progress on dynamic crack propagation and crack arrest models of supercritical and dense-phase CO2 pipelines

Effect of resveratrol supplementation in conventional slow freezing and kinetic vitrification media on the post-cryopreserved quality of dog epididymal spermatozoa.

Biomolecular condensates form by phase separation of biological polymers and have important functions in the cell — functions that are inherently linked to their physical properties at different scales. A notable aspect of such membraneless organelles is that their viscoelastic properties can vary by orders of magnitude, but it has remained unclear how these pronounced differences are rooted in the nanoscale dynamics at the molecular level. Here we investigate a series of condensates formed by complex coacervation of highly charged disordered proteins and polypeptides that span about two orders of magnitude in bulk viscosity. We find that their viscosity is highly correlated with protein translational diffusion and nano- to microsecond chain dynamics. Remarkably, analytical relations from polymer physics can predict condensate viscosity from diffusivity and chain dynamics, and vice versa, even for more hydrophobic disordered proteins and for synthetic polyelectrolytes, indicating a mechanistic link across several decades of length- and timescales. Atomistic simulations reveal that the observed differences in friction — a key quantity underlying these relations — reflect differences in inter-residue contact lifetimes as a function of arginine content and salt concentration, leading to the vastly different dynamics among condensates. The rapid exchange of inter-residue contacts we observe may be a general mechanism for preventing dynamic arrest in compartments densely packed with polyelectrolytes, such as the cell nucleus.

Waves and oscillations are key to information flow and processing in the brain. Recent work shows that, in addition to electrical activity, biomechanical signaling can also be excitable and support self-sustaining oscillations and waves. Here, we measured the biomechanical dynamics of actin polymerization in neural precursor cells (NPC) during their differentiation into populations of neurons and astrocytes. Using fluorescence-based live-cell imaging, we analyzed the dynamics of actin and calcium signals. The size and localization of actin dynamics adjusts to match functional needs throughout differentiation, enabling the initiation and elongation of processes and, ultimately, the formation of synaptic and perisynaptic structures. Throughout differentiation, actin remains dynamic in the soma, with many cells showing notable rhythmic character. Arrest of actin dynamics increases the slower time scale (likely astrocytic) calcium dynamics by 1) decreasing the duration and increasing the frequency of calcium spikes and 2) decreasing the time-delay cross-correlations in the networks. These results are consistent with the transition from an overdamped system to a spontaneously oscillating system and suggest that dynamic actin may dampen calcium signals. We conclude that mechanochemical interventions can impact calcium signaling and, thus, information flow in the brain.

Pressure-induced tetrahedral-octahedral transitions have been one of the central topics in high-pressure research due to the importance of SiO2and GeO2glasses in condensed matter physics and geosciences. However, the existence and role of the fivefold coordinated structural unit remains elusive. While accurate determination of the different polyhedral structures in the glasses in high-pressure experiments is a formidable challenge, we have performed a comprehensiveab initiomolecular dynamics (AIMD) simulation and the results agree well with the local structure determined by HP-XAFS experiments. With increasing pressure, the fivefold-coordinated hexahedral GeO5 unit ([5]Ge) suddenly appears with up to ∼40% polyhedrons, while the sixfold-coordinated GeO6 unit ([6]Ge) is negligible. The hexahedral[5]Ge become the dominant polyhedral species in 15-25 GPa. The results indicate that hexahedral[5]Ge plays an important role in the formation of octahedral[6]Ge and that the commonly considered tetrahedral-octahedral transition of GeO2glass at high pressure is actually a tetrahedral-hexahedral-octahedral transition. .

The existence of the spinodal decomposition phenomenon in the Fe-P metallic glasses (MGs) has long been debated, and the fundamental physical mechanism underlying the ductile-to-brittle transition, which is closely related to the chemical composition of Fe-P MGs, has remained unresolved. In this study, we employ molecular dynamics (MD) simulations based on empirical potentials, ab initio molecular dynamics (AIMD) based on density functional theory (DFT), and the CALYPSO structure search software, which utilizes a particle swarm optimization algorithm, to systematically investigate the rapid solidification, tensile fracture behavior, and geometric configurations of ground-state atomic clusters in Fe-P MGs with six different chemical compositions (Fe84P16, Fe73P27, Fe64P36, Fe50P50, Fe36P64, Fe14P86). Our results demonstrate that spinodal decomposition is an intrinsic atomic structural feature of the Fe-P MGs, rather than an artifact of empirical potential functions. This unique atomic structure arises from the strong electronic interactions between Fe atoms, which are governed by a mix of metallic and ionic bonding. Additionally, microcracks are found to preferentially propagate along P-enriched regions, owing to the high energy, reduced structural stability, and extremely weak electronic interactions between P atoms within these clusters. These factors collectively promote crack initiation and growth, fundamentally contributing to the ductile-to-brittle transition in Fe-P MGs. This work establishes a robust theoretical framework for understanding the intrinsic mechanical behavior of Fe-P MGs and provides valuable guidance for future research.

Biomolecular condensates form by phase separation of biological polymers and have important functions in the cell-functions that are inherently linked to their physical properties at different scales. A notable aspect of such membraneless organelles is that their viscoelastic properties can vary by orders of magnitude, but it has remained unclear how these pronounced differences are rooted in the nanoscale dynamics at the molecular level. Here, we investigate a series of condensates formed by complex coacervation of highly charged disordered proteins and polypeptides that span about two orders of magnitude in bulk viscosity. We find that their viscosity is highly correlated with protein translational diffusion and nano- to microsecond chain dynamics. Remarkably, analytical relations from polymer physics can predict condensate viscosity from diffusivity and chain dynamics, and vice versa, even for more hydrophobic disordered proteins and for synthetic polyelectrolytes, indicating a mechanistic link across several decades of length- and timescales. Atomistic simulations reveal that the observed differences in friction-a key quantity underlying these relations-reflect differences in interresidue contact lifetimes as a function of arginine content and salt concentration, leading to the vastly different dynamics among condensates. The rapid exchange of interresidue contacts we observe may be a general mechanism for preventing dynamic arrest in compartments densely packed with polyelectrolytes, such as the cell nucleus.

Abstract Study question Whether the extracellular vesicle characteristics differ before and after vitrification in human blastocysts and evaluate the impact of embryos biopsy (EB). Summary answer Extracellular vesicles’ (EVs) characteristics produced by blastocyst maintain similar profiles before and after vitrification (VT) and are not affected by embryo biopsy (EB). What is known already The current knowledge of EVs composition and their role in embryo development and competence for implantation is established in IVF produced embryos. Nonetheless, there is limited information on how the vitrification (VT) process affects the EV production machinery or whether embryo biopsy (EB), required for preimplantation genetic testing (PGT), influences the characteristics of EVs both prior to and following VT. Study design, size, duration The study was conducted in a private fertility center in 2024 in collaboration with a public research organization. A total of 144 embryos’ spent media samples were analyzed using the Leprechaun device technology. The samples were distributed in four main groups of study: Embryos not subjected to EB before (Group 1a) and after VT (Group 1b), and embryos biopsied also before (Group 2a) and after VT (Group 2b). Participants/materials, setting, methods Patients were recruited and theirs embryos’ spent media were collected for molecular study of the secreted EVs. Analysis of CD9, CD63 and CD81 tetraspanin expression was performed using the Leprechaun device technology and the EVs were further analyzed to study the expression of representative markers of pluripotency (Nanog), cell death (Annexin-V) and immune response (HLA-G). EVs characteristics were compared before and after vitrification, considering biopsied and non-biopsied embryos, and performing the corresponding statistical analysis. Main results and the role of chance Our results indicate that most of the EVs produced by the embryos under all conditions express the CD63 membrane tetraspanin, whereas other tetrapanins are considerably less abundant. We can observe that the number, size and composition in representative markers of the CD63 containing vesicles do not differ significatively before and after VT process, and this stability is not altered by the EB performed for preimplantation genetic testing (PGT). Differences in EVs cargo and composition were observed only between biopsied and non-biopsied embryos before VT, particularly concerning Nanong and Annexin-V content, suggesting that the biopsy procedure may influence EVs composition. Nevertheless, these minor differences were no longer evident in the spent medium of devitrified embryos following embryo transfer, indicating a probable restoration of EVs production after VT. Limitations, reasons for caution The major limitations are related to the sample size and the technological approach employed, which does not enable a comprehensive analysis of all EV characteristics. Additionally, caution should be also taken as variations in IVF procedures, especially in EB ant VT, may influence the outcomes. Wider implications of the findings This study shows that EVs characteristics are quite similar before and after vitrification and also reveals only subtle differences between biopsied and not biopsied embryos. This suggest that EVs production is not altered by VT or EB process, implying that these laboratory procedures do not impair EVs production and composition. Trial registration number No

Glass transition in metallic glasses facilitated by static loading

We study a model of diffusive oscillators whose internal states are subject to a periodic drive. These models are inspired by the dynamics of deformable particles with pulsating sizes, where repulsion leads to arrest the internal pulsation at high density. We reveal that, despite the absence of any repulsion between the diffusive oscillators, our model still captures the emergence of dynamical arrest. We demonstrate that arrest here stems from the discrete nature of internal states, which enforces an effective energy landscape analogous to that of deformable particles. Moreover, we show that the competition between arrest and synchronization promotes spiral waves reminiscent of the pulsating states of deformable particles. Using analytical coarse graining, we derive and compare the collective dynamics of diffusive oscillators with that of deformable particles. This comparison leads to rationalizing the emergence of spirals in terms of a rotational invariance at the coarse-grained level, and to elucidating the role of hydrodynamic fluctuations.

Glass transition in metallic glasses facilitated by static loading

We investigate theoretically the critical role of thermal fluctuations in maintaining a narrow gap between a very narrow capillary tube and a highly confined enclosed membrane vesicle. We quantitatively find that the size of the slender gap between a tightly fitting incompressible vesicle and an enclosing cylindrical tube depends on a subtle interplay between membrane area dilation and vesicle fluctuations. This work is therefore likely to be of crucial importance for investigating the paradigmatic properties of highly confined membrane vesicles inside a very narrow capillary tube. Additionally, fluid flow can also occur in this gap, giving rise to a finite vesicle mobility along a narrow capillary tube. Typically, for most (small to moderate) fluid velocities, we find that (in the vesicle fluctuation dominated regime) the gap size remains essentially insensitive to fluid flow. However, for relatively large fluid velocities, it is approximately found (in the fluid flow dominated regime) that the gap size grows with increasing fluid velocity as a power law, and we are able to evaluate the extra hydrodynamic pressure drop due to the presence of the vesicle, as well as the vesicle's relative mobility. This work is thus also likely to be highly relevant for considerations of the stalling and dynamic arrest of tightly confined vesicles in narrow constrictions. Possible applications of this work might thus also include biological transport, microfluidics, and drug delivery.

The development and extension of microcracks in rocks affect the integrity and stability of rock mass construction. External dynamic loads with different loading rates lead to different dynamic fracture characteristics of rock fractures. In this study, a large-sized PMMA specimen with an arc boundary was proposed. The time at which the crack started and spread was determined using drop hammer impact testing and crack growth meter testing. Subsequently, the microscopic characteristics of the crack fracture surfaces were analyzed using a scanning electron microscope. Finally, the dynamic fracture toughness of the crack tip of the PMMA specimen was calculated using the finite-element method. Both experimental and numerical studies indicated that the arc boundary of the specimen demonstrated effective capabilities for arresting propagating cracks, and as the loading rate increased, the crack velocity also increased, while the crack initiation time decreased. The crack no longer propagated along the original crack surface after the crack arrest. The peak compressive stress along the crack trajectories increased with the loading rate. During the early stages of crack propagation, the highest compressive stress was observed for the 65° specimen. Conversely, during the later stages of the crack propagation, the 125° specimen exhibits the highest compressive stress. The dynamic arrest toughness of the crack is greater than the dynamic initiation and propagation toughness of the crack. As the loading rates increased, the dynamic initiation and propagating toughness of the crack also increased, while the dynamic arrest toughness of the crack changed little with the loading rate.

The level scheme of the neutron-rich \(^{87}\)Se isotope has been extended up to 2397 keV excitation energy. The isotope of interest was produced in a neutron-induced fission reaction of a \(^{235}\)U target at the Institut Laue-Langevin in Grenoble. During the analysis, six new gamma transitions were identified by employing multifold gamma-ray coincidence relationships, measured with the FIPPS array. Based on the gamma angular correlations technique, tentative spin-parity assignments have been proposed for the low-lying levels. Abstract Published by the Jagiellonian University 2025 authors

Data on the structure of sulphur isotopes close to the neutron drip-line are rather scarce. The excited states of the very neutron-rich \(^{46}\)S and \(^{47}\)S nuclei have been investigated by in-beam gamma-ray spectroscopy at the Radioactive Isotope Beam Factory at the RIKEN Nishina Center. After multi-nucleon knockout reactions on the liquid-hydrogen MINOS target, the \(2^{+}_{1}\rightarrow 0^{+}_{1}\) gamma transition of \(^{46}\)S, already reported in literature, has been confirmed. Additionally, two new gamma rays have been assigned to this isotope and one gamma line has been observed in \(^{47}\)S. Abstract Published by the Jagiellonian University 2025 authors

ABSTRACT This research focuses on examining the glass transition and crystallization kinetics in quaternary Se80In5Te15-xSbx chalcogenide glasses (with x = 0, 3, 6, and 9) prepared via melt-quenching techniques and analyzed using Differential Scanning Calorimetry. The glass transition temperature (Tg) and crystallization temperature (Tc) were investigated at different heating rates. Energy-dispersive X-ray spectroscopy (EDS) and elemental mapping confirmed the presence of desired elements in the synthesized glasses, while HRXRD and FESEM verified their amorphous and crystalline nature. Results showed that both Tg and Tc increase with higher heating rates. The activation energies for crystallization (ΔEc) and structural relaxation (ΔEt) were determined based on the dependence of Tg and Tc on heating rates. Thermal stability across compositions was also studied and found to vary with Sb content. The calculated various thermal parameters ensure that the prepared samples show an electrical threshold switching behaviour for phase change memory applications.

Low-energy excitations play a key role in all condensed-matter systems, yet there is limited understanding of their nature in glasses, where they correspond to local rearrangements of groups of particles. Here, we introduce an algorithm to systematically uncover these excitations up to the activation energy scale relevant to structural relaxation. We use it in a model system to measure the density of states on a scale never achieved before, confirming that this quantity shifts to higher energy under cooling, precisely as the activation energy does. Second, we show that the excitations' energetic and spatial features allow one to predict with great accuracy the dynamic propensity, i.e., the location of future relaxation dynamics. Finally, we find that excitations have a primary field whose properties, including the displacement of the most mobile particle, scale as a power-law of their activation energy and are independent of temperature. Additionally, they exhibit an outer deformation field that depends on the material's stability and, therefore, on temperature. We build a scaling description of these findings. Overall, our analysis supports that excitations play a crucial role in regulating relaxation dynamics near the glass transition, effectively suppressing the transition to dynamical arrest predicted by mean-field theories while also being strongly influenced by it.

To compare the effectiveness of slow freezing (SF) and vitrification (VT) for ovarian tissue cryopreservation using a xenograft model. From September 2020 to August 2023, ovarian tissues from patients aged 18 to 37 undergoing benign ovarian surgery were divided into three groups. Group 1: fresh tissues (FC) were immediately fixed for analysis. Group 2 (SF/VT): tissues were cryopreserved by SF or VT without transplantation. Group 3 (SF-T/VT-T): tissues were cryopreserved using SF or VT, followed by transplantation into NOD-SCID mice for one week, after which the tissues were collected and analyzed. A total of 49 ovarian tissue fragments were analyzed. Regardless of the cryopreservation technique, follicle survival, development, function, and vascularization were significantly reduced compared to the FC group, particularly after transplantation (p < 0.001). The survival rate of follicles in the SF-T group was notably higher (90.9%) than in the VT-T group (82.6%) (p < 0.001). For cell proliferation, indicated by Ki-67 positivity, the SF-T group showed a higher median number of positive follicles (2.5; range: 0-18) compared to the VT-T group (2; range: 0-11) (p = 0.04). Neo-vascularization, assessed via CD31 positivity, was significantly greater in the SF-T group (61%) than in the VT-T group (47%) (p = 0.016). Additionally, the median number of AMH-positive follicles was significantly higher in the SF-T group (3; range: 0-23) compared to the VT-T group (2; range: 0-25) (p = 0.03). Both SF and VT are feasible methods for ovarian tissue cryopreservation. SF may be the preferred cryopreservation technique for fertility preservation in cases tissue transplantation is anticipated.