Journal articles on the topic 'Polymorphism - Network Forming Liquids'

Abstract Characterization of phases of soft matter systems is a challenge faced in many physical chemical problems. For polymorphic fluids it is an even greater challenge. Specifically, glass forming fluids, as water, can have, besides solid polymorphism, more than one liquid and glassy phases, and even a liquid–liquid critical point. In this sense, we apply a neural network algorithm to analyze the phase behavior of a mixture of core-softened fluids that interact through the continuous-shouldered well (CSW) potential, which have liquid polymorphism and liquid–liquid critical points, similar to water. We also apply the neural network to mixtures of CSW fluids and core-softened alcohols models. We combine and expand methods based on bond-orientational order parameters to study mixtures, applied to mixtures of hardcore fluids and to supercooled water, to include longer range coordination shells. With this, the trained neural network was able to properly predict the crystalline solid phases, the fluid phases and the amorphous phase for the pure CSW and CSW-alcohols mixtures with high efficiency. More than this, information about the phase populations, obtained from the network approach, can help verify if the phase transition is continuous or discontinuous, and also to interpret how the metastable amorphous region spreads along the stable high density fluid phase. These findings help to understand the behavior of supercooled polymorphic fluids and extend the comprehension of how amphiphilic solutes affect the phases behavior.

When aged below the glass transition temperature, Tg, the density of a glass cannot exceed that of the metastable supercooled liquid (SCL) state, unless crystals are nucleated. The only exception is when another polyamorphic SCL state exists, with a density higher than that of the ordinary SCL. Experimentally, such polyamorphic states and their corresponding liquid–liquid phase transitions have only been observed in network-forming systems or those with polymorphic crystalline states. In otherwise simple liquids, such phase transitions have not been observed, either in aged or vapor-deposited stable glasses, even near the Kauzmann temperature. Here, we report that the density of thin vapor-deposited films of N,N′-bis(3-methylphenyl)-N,N′-diphenylbenzidine (TPD) can exceed their corresponding SCL density by as much as 3.5% and can even exceed the crystal density under certain deposition conditions. We identify a previously unidentified high-density supercooled liquid (HD-SCL) phase with a liquid–liquid phase transition temperature (TLL) ∼35 K below the nominal glass transition temperature of the ordinary SCL. The HD-SCL state is observed in glasses deposited in the thickness range of 25 to 55 nm, where thin films of the ordinary SCL have exceptionally enhanced surface mobility with large mobility gradients. The enhanced mobility enables vapor-deposited thin films to overcome kinetic barriers for relaxation and access the HD-SCL state. The HD-SCL state is only thermodynamically favored in thin films and transforms rapidly to the ordinary SCL when the vapor deposition is continued to form films with thicknesses more than 60 nm.

It has been studied whether machine learning interatomic potentials parameterized with only disordered configurations corresponding to liquid can describe the properties of crystalline phases and predict their structure. The study has been performed for a network-forming system SiO2, which has numerous polymorphic phases significantly different in structure and density. Using only high-temperature disordered configurations, a machine learning interatomic potential based on artificial neural networks (DeePMD model) has been parameterized. The potential reproduces well ab initio dependences of the energy on the volume and the vibrational density of states for all considered tetra- and octahedral crystalline phases of SiO2. Furthermore, the combination of the evolutionary algorithm and the developed DeePMD potential has made it possible to reproduce the really observed crystalline structures of SiO2. Such a good liquid–crystal portability of the machine learning interatomic potential opens prospects for the simulation of the structure and properties of new systems for which experimental information on crystalline phases is absent.

The random first order transition theory (RFOT) describing the transition from a supercooled liquid to an ideal glass has been actively developed over the last twenty years. This theory is formulated in a way that allows a description of the transition from the initial equilibrium state to the final metastable state without considering any kinetic processes. The RFOT and its applications for real molecular systems (multicomponent liquids with various intermolecular potentials, gel systems, etc.) are widely represented in English-language sources. However, these studies are practically not described in any Russian sources. This paper presents an overview of the studies carried out in this field. REFERENCES 1. Sanditov D. S., Ojovan M. I. Relaxation aspectsof the liquid—glass transition. Uspekhi FizicheskihNauk. 2019;189(2): 113–133. DOI: https://doi.org/10.3367/ufnr.2018.04.0383192. Tsydypov Sh. B., Parfenov A. N., Sanditov D. S.,Agrafonov Yu. V., Nesterov A. S. 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Organogelators gelate liquids by forming a network of anisotropic fibres. Hansen solubility parameters can be used to rationalize the effect of the gelator structure: the gelation and solubility domains evolve in opposite directions.

The Arrhenius crossover temperature, TA, corresponds to a thermodynamic state wherein the atomistic dynamics of a liquid becomes heterogeneous and cooperative; and the activation barrier of diffusion dynamics becomes temperature-dependent at temperatures below TA. The theoretical estimation of this temperature is difficult for some types of materials, especially silicates and borates. In these materials, self-diffusion as a function of the temperature T is reproduced by the Arrhenius law, where the activation barrier practically independent on the temperature T. The purpose of the present work was to establish the relationship between the Arrhenius crossover temperature TA and the physical properties of liquids directly related to their glass-forming ability. Using a machine learning model, the crossover temperature TA was calculated for silicates, borates, organic compounds and metal melts of various compositions. The empirical values of the glass transition temperature Tg, the melting temperature Tm, the ratio of these temperatures Tg/Tm and the fragility index m were applied as input parameters. It has been established that the temperatures Tg and Tm are significant parameters, whereas their ratio Tg/Tm and the fragility index m do not correlate much with the temperature TA. An important result of the present work is the analytical equation relating the temperatures Tg, Tm and TA, and that, from the algebraic point of view, is the equation for a second-order curved surface. It was shown that this equation allows one to correctly estimate the temperature TA for a large class of materials, regardless of their compositions and glass-forming abilities.

The non-Arrhenius behavior of segmental dynamics in glass-forming liquids is one of the most profound mysteries in soft matter physics. In this article, we propose a dynamically correlated network (DCN) model to understand the growing behavior of dynamically correlated regions during cooling, which leads to the viscous slowdown of supercooled liquids. The fundamental concept of the model is that the cooperative region of collective motions has a network structure that consists of string-like parts, and networks of various sizes interpenetrate each other. Each segment undergoes dynamical coupling with its neighboring segments via a finite binding energy. Monte Carlo simulations showed that the fractal dimension of the DCNs generated at different temperatures increased and their size distribution became broader with decreasing temperature. The segmental relaxation time was evaluated based on a power law with four different exponents for the activation energy of rearrangement with respect to the DCN size. The results of the present DCN model are consistent with the experimental results for various materials of molecular and polymeric liquids.

Ionic liquids (ILs) and deep eutectic mixtures (DEMs) are potential solutions to the problems of low solubility, polymorphism, and low bioavailability of drugs. The aim of this work was to develop and investigate ketoprofen (KET)-based ILs/DEMs containing an ester local anesthetic (LA): benzocaine (BEN), procaine (PRO) and tetracaine (TET) as the second component. ILs/DEMs were prepared via a mechanosynthetic process that involved the mixing of KET with an LA in a range of molar ratios and applying a thermal treatment. After heating above the melting point and quench cooling, the formation of supercooled liquids with Tgs that were dependent on the composition was observed for all KET-LA mixtures with exception of that containing 95 mol% of BEN. The KET-LA mixtures containing either ≥ 60 mol% BEN or 95 mol% of TET showed crystallization to BEN and TET, respectively, during either cooling or second heating. KET decreased the crystallization tendency of BEN and TET and increased their glass-forming ability. The KET-PRO systems showed good glass-forming ability and did not crystallize either during the cooling or during the second heating cycle irrespective of the composition. Infrared spectroscopy and molecular modeling indicated that KET and LAs formed DEMs, but in the KET-PRO systems small quantities of carboxylate anions were present.

NMR spectroscopic literature data are used, in a wide temperature-pressure range (180–350 K and 0.1–400 MPa), to study the water polymorphism and the validity of the liquid–liquid transition (LLT) hypothesis. We have considered the self-diffusion coefficient DS and the reorientational correlation time τθ (obtained from spin-lattice T1 relaxation times), measured, respectively, in bulk and emulsion liquid water from the stable to well inside the metastable supercooled region. As an effect of the hydrogen bond (HB) networking, the isobars of both these transport functions evolve with T by changing by several orders of magnitude, whereas their pressure dependence become more and more pronounced at lower temperatures. Both these transport functions were then studied according to the Adam–Gibbs model, typical of glass forming liquids, obtaining the water configurational entropy and the corresponding specific heat contribution. The comparison of the evaluated CP,conf isobars with the experimentally measured water specific heat reveals the full consistency of this analysis. In particular, the observed CP,conf maxima and its diverging behaviors clearly reveals the presence of the LLT and with a reasonable approximation the liquid–liquid critical point (LLCP) locus in the phase diagram.

This study concerned a novel super-molecular ionic liquid synthesized by ammonium thiocyanate and caprolactam. The physical characters such as melting point and electric conductivity were investigated. Results showed that the melting point is -12.2°C at the molar ratio of 3:1 (caprolactam/ammonium thiocyanate), which is much lower than raw materials. The electric conductivities of synthesized ionic liquids were close to that of imidazole ILs. The structure of ionic liquid was characterized by IR,1HNMR and quantum chemical calculations. It was shown that the NH4+cation connected with caprolactam organic molecules by hydrogen bonds, leading to the forming of a super-molecular ion. The electrostatic attraction of super-molecular ion with anion was decreased because of the larger volume of super-molecular ion than original cation, thus the melting point decreased. The key properties that distinguish super-molecular ionic liquid from other ILs were the presence of supermolecular ion, which can be used to build up a hydrogen-bonded network. This type ion liquid was named as super-molecular ion liquid.

The nature of excitations in liquids has been a subject of debate for a long time. In liquids, phonons are extremely short-lived and marginalized. Instead, recent research results indicate that local topological or configurational excitations (anankeons) are the elementary excitations in high temperature metallic liquids. Local topological excitations are those which locally alter the atomic connectivity network by cutting or forming atomic bonds, and are directly tied to the atomistic origin of viscosity in the liquid. The local potential energy landscape (PEL) of anankeons represents the probability weighted projection of the global PEL to a single atom. The original PEL is an insightful concept, but is highly multi-dimensional and difficult to characterize or even to visualize. A description in terms of the local PEL for anankeons appears to offer a simpler and more effective approach toward this complex problem. At the base of these advances, is the recognition that atomic discreteness and the topology of atomic connectivity are the most crucial features of the structure in liquids, which current nonlinear continuum theories cannot fully capture. These discoveries could open the way to the explanation of various complex phenomena in liquids, such as atomic transport, fragility, and the glass transition, in terms of these excitations.

Understanding in a unified manner the generic and chemically specific aspects of activated dynamics in diverse glass-forming liquids over 14 or more decades in time is a grand challenge in condensed matter physics, physical chemistry, and materials science and engineering. Large families of conceptually distinct models have postulated a causal connection with qualitatively different “order parameters” including various measures of structure, free volume, thermodynamic properties, short or intermediate time dynamics, and mechanical properties. Construction of a predictive theory that covers both the noncooperative and cooperative activated relaxation regimes remains elusive. Here, we test using solely experimental data a recent microscopic dynamical theory prediction that although activated relaxation is a spatially coupled local–nonlocal event with barriers quantified by local pair structure, it can also be understood based on the dimensionless compressibility via an equilibrium statistical mechanics connection between thermodynamics and structure. This prediction is found to be consistent with observations on diverse fragile molecular liquids under isobaric and isochoric conditions and provides a different conceptual view of the global relaxation map. As a corollary, a theoretical basis is established for the structural relaxation time scale growing exponentially with inverse temperature to a high power, consistent with experiments in the deeply supercooled regime. A criterion for the irrelevance of collective elasticity effects is deduced and shown to be consistent with viscous flow in low-fragility inorganic network-forming melts. Finally, implications for relaxation in the equilibrated deep glass state are briefly considered.

Recent developments in machine learning have enabled accurate predictions of the dynamics of slow structural relaxation in glass-forming systems. However, existing machine learning models for these tasks are mostly designed such that they learn a single dynamic quantity and relate it to the structural features of glassy liquids. In this study, we propose a graph neural network model, “BOnd TArgeting Network,” that learns relative motion between neighboring pairs of particles, in addition to the self-motion of particles. By relating the structural features to these two different dynamical variables, the model autonomously acquires the ability to discern how the self motion of particles undergoing slow relaxation is affected by different dynamical processes, strain fluctuations and particle rearrangements, and thus can predict with high precision how slow structural relaxation develops in space and time.

Two polymorphs of tripotassium erbium disilicate, K3ErSi2O7, were synthesized by high-temperature flux crystal growth during the exploration of the flux technique for growing new alkali rare-earth elements (REE) containing silicates. Their crystal structures were determined by single-crystal X-ray diffraction analysis. One of them (denoted 1) crystallizes in the space group P63/mmc and is isostructural with disilicates K3LuSi2O7, K3ScSi2O7 and K3YSi2O7, while the other (denoted 2) crystallizes in the space group P63/mcm and is isostructural with disilicates K3NdSi2O7, K3REESi2O7 (REE = Gd–Yb), K3YSi2O7, K3(Y0.9Dy0.1)Si2O7 and K3SmSi2O7. In the crystal structure of polymorph 1, the Er cations are in an almost perfect octahedral coordination, while in the crystal structure of polymorph 2, part of the Er cations are in a slightly distorted octahedral coordination and the other part are in an ideal trigonal prismatic coordination environment. Sharing six corners, disilicate Si2O7 groups in the crystal structure of polymorph 1 link six ErO6 octahedra, forming a three-dimensional network and nine-coordinated potassium cations are located in its holes. In the crystal structure of polymorph 2, the disilicate Si2O7 groups connect four ErO6 octahedra, as well as one ErO6 trigonal prism. Three differently coordinated potassium cations are situated between them. Different site symmetries of the erbium cations in the crystal structures of polymorphs 1 and 2 affect their photoluminescence properties. Only polymorph 2 exhibits luminescence. Intense narrow lines in the emission spectrum are a result of the 4f–4f transition. The green emission line at 560 nm is the result of the Er3+ transition 4S3/2→4I15/2, and the luminescence line at 690 nm is the result of a 4F9/2→4I15/2 transition. The crystal morphologies of the two polymorphs are similar. Crystals of polymorph 1 are in the form of a hexagonal prism in combination with a hexagonal base, while crystals of polymorph 2 contain a dihexagonal prism in combination with a hexagonal base, although poorly developed faces of the dihexagonal pyramid can also be noticed.

Knowledge of pressure-induced structural changes in glasses is important in various scientific fields as well as in engineering and industry. However, polyamorphism in glasses under high pressure remains poorly understood because of experimental challenges. Here we report new experimental findings of ultrahigh-pressure polyamorphism in GeO2 glass, investigated using a newly developed double-stage large-volume cell. The Ge–O coordination number (CN) is found to remain constant at ∼6 between 22.6 and 37.9 GPa. At higher pressures, CN begins to increase rapidly and reaches 7.4 at 91.7 GPa. This transformation begins when the oxygen-packing fraction in GeO2 glass is close to the maximal dense-packing state (the Kepler conjecture = ∼0.74), which provides new insights into structural changes in network-forming glasses and liquids with CN higher than 6 at ultrahigh-pressure conditions.

Two topics are described for structure analyses of glass and liquid using a combination of conical nozzle levitation (CNL) technique and diffraction experiments. The structure of high-purity bulk forsterite (Mg2SiO4) glass synthesized by a CNL technique has been determined by a combination of high-energy x-ray, neutron diffraction, and reverse Monte Carlo (RMC) modeling technique. The 3-dimensional atomic configuration derived from RMC modeling revealed that unusual network structure. In order to study structures of high-temperature and undercooled liquids, a CNL system has been developed and integrated with the two-axis diffractometer for glass, liquid, and amorphous materials at SPring-8, which is one of the third-generation synchrotron source. High-energy x-ray diffraction experiments were performed to obtain reliable diffraction data for the liquid phase of metallic glass-forming Zr-Cu binary alloys.

Li-ion batteries are currently considered promising energy storage devices for the future. However, the use of liquid electrolytes poses certain challenges, including lithium dendrite penetration and flammable liquid leakage. Encouragingly, solid electrolytes endowed with high stability and safety appear to be a potential solution to these problems. Among them, ionic liquids (ILs) packed in metal organic frameworks (MOFs), known as ILs@MOFs, have emerged as a hybrid solid-state material that possesses high conductivity, low flammability, and strong mechanical stability. ILs@MOFs plays a crucial role in forming a continuous interfacial conduction network, as well as providing internal ion conduction pathways through the ionic liquid. Hence, ILs@MOFs can not only act as a suitable ionic conduct main body, but also be used as an active filler in composite polymer electrolytes (CPEs) to meet the demand for higher conductivity and lower cost. This review focuses on the characteristic properties and the ion transport mechanism behind ILs@MOFs, highlighting the main problems of its applications. Moreover, this review presents an introduction of the advantages and applications of Ils@MOFs as fillers and the improvement directions are also discussed. In the conclusion, the challenges and suggestions for the future improvement of ILs@MOFs hybrid electrolytes are also prospected. Overall, this review demonstrates the application potential of ILs@MOFs as a hybrid electrolyte material in energy storage systems.

Single crystals of tetra(isopropylammonium) decachlorotricadmate(II) as a rare example of a two-dimensional cadmium(II) halide network of [Cd3Cl10]_n^{4 - } have been synthesized and characterized by means of calorimetry and X-ray diffraction. The crystals exhibit polymorphism in a relatively narrow temperature range (three phase transitions at 353, 294 and 259 K). Our main focus was to establish the mechanism of these successive transformations. The crystal structure was solved and refined in the space group Cmce at 375 K (Phase I), Pbca at 320 K (Phase II) and P212121 (Phase III) at 275 K in the same unit-cell metric. The structure is composed of face-sharing polyanionic [Cd3Cl10]4− units which are interconnected at the bridging Cl atom into four-membered rings forming a unique two-dimensional network of [Cd3Cl10]_n^{4 - }. The interstitial voids within the network are large enough to accommodate isopropylammonium cations and permit thermally activated rotations. While in Phase I isopropylammonium tetrahedra rotate almost freely about the C—N bond, the low-temperature phases are the playground of competition between the thermally activated disorder of isopropylammonium cations and stabilizing N—H...Cl hydrogen-bond interactions. The transition from Phase I to II is dominated by a displacive mechanism that leads to significant rearrangement of the polyanionic units. Cation order–disorder phenomena become prominent at lower temperatures.

Lipoxygenases have been implicated in cardiovascular disease. A rare single-nucleotide polymorphism causing T560M exchange has recently been described, and this mutation leads to a near null variant of the enzyme encoded for by the ALOX15 gene. When we inspected the three-dimensional structure of the rabbit ortholog, we localized Thr-560 outside the active site and identified a hydrogen bridge between its side chain and Gln-294. This interaction is part of a complex hydrogen bond network that appears to be conserved in other mammalian lipoxygenases. Gln-294 and Asn-287 are key amino acids in this network, and we hypothesized that disturbance of this hydrogen bond system causes the low activity of the T560M mutant. To test this hypothesis, we first mutated Thr-560 to amino acids not capable of forming side chain hydrogen bridges (T560M and T560A) and obtained enzyme variants with strongly reduced catalytic activity. In contrast, enzymatic activity was retained after T560S exchange. Enzyme variants with strongly reduced activity were also obtained when we mutated Gln-294 (binding partner of Thr-560) and Asn-287 (binding partner of Gln-294 and Met-418) to Leu. Basic kinetic characterization of the T560M mutant indicated that the enzyme lacks a kinetic lag phase but is rapidly inactivated. These data suggest that the low catalytic efficiency of the naturally occurring T560M mutant is caused by alterations of a hydrogen bond network interconnecting this residue with active site constituents. Disturbance of this bonding network increases the susceptibility of the enzyme for suicidal inactivation.

We have prepared a series of pyridinium-based gemini amphiphiles. They exhibit thermotropic liquid–crystalline behavior depending on their alkyl chain lengths and anion species. By adjusting the alkyl chain lengths and selecting suitable anions, we have obtained an ionic amphiphile that exhibits a normal-type bicontinuous cubic phase from 38 °C to 12 °C on cooling from an isotropic phase. In the bicontinuous cubic liquid–crystalline assembly, the pyridinium-based ionic parts align along a gyroid minimal surface forming a 3D continuous ionic domain while their ionophobic alkyl chains form 3D branched nanochannel networks. This ionic compound can form homogeneous mixtures with a lithium salt and the resultant mixtures keep the ability to form normal-type bicontinuous cubic phases. Ion conduction measurements have been performed for the mixtures on cooling. It has been revealed that the formation of the 3D branched ionophobic nanochannels does not disturb the ion conduction behavior in the ionic domain while it results in the conversion of the state of the mixtures from fluidic liquids to quasi-solids, namely highly viscous liquid crystals. Although the ionic conductivity of the mixtures is in the order of 10–7 S cm–1 at 40 °C, which is far lower than the values for practical use, the present material design has a potential to pave the way for developing advanced solid electrolytes consisting of two task-specific nanosegregated domains: One is an ionic liquid nano-domain with a 3D continuity for high ionic conductivity and the other is ionophobic nanochannel network domains for high mechanical strength.

Hyaluronic acid is a mucopolysaccharide encountered in most body fluids and extracellular matrix. The aim of our review is to summarize current evidence about chemico-physical properties of hyaluronic acid, highlighting biomedical applications of hyaluronan derivatives. It is a glycosaminoglycan made of repeating disaccharide units containing a carboxylate group, four hydroxyl groups and one carboxylate group, with hydrophilic properties. Its particular structure with multiple coils forming an entangled network results in unique pseudoplastic and viscoelastic characteristics. Its viscous and elastic behavior, depending on the applied strain, makes hyaluronan widely applicable in biomedical field. The large amount of functions and applications is determined by the physico-chemical properties, which allows a polymorphism of the hyaluronic acid structures depending on the molecular weight variations, concentration and ionic status. It is currently used in ophthalmology, orthopedics and rheumatology, in plastic surgery, surgery and otolaryngology as well. Already widely used in clinical practice, hyaluronic acid proves to be often the best solution for difficult medical problems. Future developments in nanomedicine and drug delivery linked to hyaluronic acid are emerging.

Posttranslational modifications (PTMs) of α-synuclein (α-syn), e.g., phosphorylation, play an important role in modulating α-syn pathology in Parkinson’s disease (PD) and α-synucleinopathies. Accumulation of phosphorylated α-syn fibrils in Lewy bodies and Lewy neurites is the histological hallmark of these diseases. However, it is unclear how phosphorylation relates to α-syn pathology. Here, by combining chemical synthesis and bacterial expression, we obtained homogeneous α-syn fibrils with site-specific phosphorylation at Y39, which exhibits enhanced neuronal pathology in rat primary cortical neurons. We determined the cryo-electron microscopy (cryo-EM) structure of the pY39 α-syn fibril, which reveals a fold of α-syn with pY39 in the center of the fibril core forming an electrostatic interaction network with eight charged residues in the N-terminal region of α-syn. This structure composed of residues 1 to 100 represents the largest α-syn fibril core determined so far. This work provides structural understanding on the pathology of the pY39 α-syn fibril and highlights the importance of PTMs in defining the polymorphism and pathology of amyloid fibrils in neurodegenerative diseases.

Abstract Background: Current hybridization protocols on microarrays are slow and need skilled personnel. Microfluidics is an emerging science that enables the processing of minute volumes of liquids to perform chemical, biochemical, or enzymatic analyzes. The merging of microfluidics and microarray technologies constitutes an elegant solution that will automate and speed up microarray hybridization. Methods: We developed a microfluidic flow cell consisting of a network of chambers and channels molded into a polydimethylsiloxane substrate. The substrate was aligned and reversibly bound to the microarray printed on a standard glass slide to form a functional microfluidic unit. The microfluidic units were placed on an engraved, disc-shaped support fixed on a rotational device. Centrifugal forces drove the sample and buffers directly onto the microarray surface. Results: This microfluidic system increased the hybridization signal by ∼10fold compared with a passive system that made use of 10 times more sample. By means of a 15–min automated hybridization process, performed at room temperature, we demonstrated the discrimination of 4 clinically relevant Staphylococcus species that differ by as little as a single-nucleotide polymorphism. This process included hybridization, washing, rinsing, and drying steps and did not require any purification of target nucleic acids. This platform was sensitive enough to detect 10 PCR-amplified bacterial genomes. Conclusion: This removable microfluidic system for performing microarray hybridization on glass slides is promising for molecular diagnostics and gene profiling.

Yielding behavior in amorphous solids has been investigated in computer simulations using uniform and cyclic shear deformation. Recent results characterize yielding as a discontinuous transition, with the degree of annealing of glasses being a significant parameter. Under uniform shear, discontinuous changes in stresses at yielding occur in the high annealing regime, separated from the poor annealing regime in which yielding is gradual. In cyclic shear simulations, relatively poorly annealed glasses become progressively better annealed as the yielding point is approached, with a relatively modest but clear discontinuous change at yielding. To understand better the role of annealing on yielding characteristics, we perform athermal quasistatic cyclic shear simulations of glasses prepared with a wide range of annealing in two qualitatively different systems—a model of silica (a network glass) and an atomic binary mixture glass. Two strikingly different regimes of behavior emerge. Energies of poorly annealed samples evolve toward a unique threshold energy as the strain amplitude increases, before yielding takes place. Well-annealed samples, in contrast, show no significant energy change with strain amplitude until they yield, accompanied by discontinuous energy changes that increase with the degree of annealing. Significantly, the threshold energy for both systems corresponds to dynamical cross-over temperatures associated with changes in the character of the energy landscape sampled by glass-forming liquids.

We investigate the jamming transition observed in vibrated granular systems composed of millimeter size glass beads. When a granular system is submitted to vibrations with decreasing intensity, it evolves in a way similar to glass-forming liquids: from a low viscosity, liquid-like state, it evolves into an amorphous jammed state. This evolution is observed by the means of an immersed oscillator acting as a torsion pendulum in forced mode. The complex susceptibility of the oscillator is measured as a function of the probe forcing frequency and of the vibration intensity. Focusing on the strongly vibrated states, we observe that there are two different dynamic regions. The first is a high fluidization regime, where the internal friction is found to be proportional to the ratio between the pulsation and the vibration intensity: . In this region, the system shows an apparent viscous friction . In the second, low fluidization, regime, we observe a more complex behavior, and the measured internal friction appears to be well described by a relation of the form: . In this second case, the key role is played by a critical breakaway stress, σcr, needed to break the network of chains of forces that form between the grains. Finally, if vibration intensities are still reduced, we also observe that onset of jamming is clearly distinguishable: we observe a sharp increase in the apparent dynamic modulus together with a peak in internal friction. This transition presents important similarities to those observed in glasses, and it leads to the second (low vibrations) regime, where the key role is played by the square root of the vibration intensity.

In pumpkin (Cucurbita moschata), the naked or hull-less seed phenotype has great benefits for breeding this crop for oil or snack use. We previously identified a naked seed mutant in this crop. In this study, we report genetic mapping, identification, and characterization of a candidate gene for this mutation. We showed that the naked seed phenotype is controlled by a single recessive gene (N). The bulked segregant analysis identified a 2.4 Mb region on Chromosome 17 with 15 predicted genes. Multiple lines of evidence suggested that CmoCh17G004790 is the most probable candidate gene for the N locus which encodes a NAC transcription factor WALL THICKENING PROMOTING FACTOR 1 (CmNST1). No nucleotide polymorphism or structural variation was found in the genomic DNA sequences of CmNST1 between the mutant and the wildtype inbred line (hulled seed). However, the cDNA sequence cloned from developing seed coat samples of the naked seed mutant was 112 bp shorter than that from the wildtype which is due to seed coat-specific alternative splicing in the second exon of the mutant CmNST1 transcript. The expression level of CmNST1 in the developing seed coat was higher in the mutant than in the wildtype during early seed coat development which was reversed later. Transcriptomic profiling with RNA-Seq at different stages of seed development in the mutant and wildtype revealed a critical role of CmNST1 as a master regulator for the lignin biosynthesis pathway during seed coat development while other NAC and MYB transcription factors were also involved in forming a regulatory network for the building of secondary cell walls. This work provides a novel mechanism for the well-characterized NST1 transcription factor gene in regulating secondary cell wall development. The cloned gene also provides a useful tool for marker-assisted breeding of hull-less C. moschata varieties.

Abstract Background: The Mdm2 protein is an E3 ubiquitin ligase that directly interacts with p53 protein leading to its degradation. The expression of MDM2 is controlled by p53 activity through an autoregulatory feedback loop. In addition, a single nucleotide polymorphism (SNP) in the MDM2 promoter modulates its expression and is associated with the risk of cancer. Emerging evidence emphasizes the metabolic activities of MDM2 to be essential for the maintenance of cellular homeostasis. We hypothesized that MDM2 maintains the metabolic homeostasis of hematopoietic stem cells (HSCs) and its downregulation in TP53-mutant leukemias leads to metabolic vulnerabilities independent of p53. Investigation of the metabolic role of MDM2 in hematopoietic stem cells can provide valuable insight into the pathology of TP53 mutant leukemias. Methods: To understand the function of Mdm2 in HSCs, we generated a conditional mouse model driven by Vav-Cre to genetically label and trace the fate of HSCs after heterozygous deletion of Mdm2 in early development and adult bone marrow. We utilized fluorescence microscopy, flow cytometry, apoptosis assays and RNA-seq to functionally characterize the fate of HSCs after heterozygous deletion of Mdm2. Using Trp53 floxed allele and a new Trp53 mutant allele that switches from wildtype to Trp53R172H mutant, we deleted and/or mutated Trp53 gene concomitantly in Mdm2 haplo-insufficient HSCs. Additionally, MDM2 copy number as well as MDM2 SNP309 status were determined in 95 samples from p53 mutant AML patients and 24 controls. Results: Heterozygous deletion of Mdm2 in hematopoietic stem cells (Vav-Cre;mTmG;Mdm2 fl/+) resulted in massive apoptosis of emerging hematopoietic progenitor cells in the aorta-gonad-mesonephros (AGM) region at E11.5. Strikingly, hematopoietic cells residing in fetal liver displayed minimal apoptosis evident by a few TUNEL positive cells. Colony forming assays revealed a myeloid biased hematopoiesis in Mdm2 haplo-insufficient HSCs. Vav-Cre;Mdm2 fl/+ mice displayed a marked reduction in Lin -/CD150 +/c-Kit +/Sca-1 + HSCs cells and significant decrease in peripheral blood counts. Deletion of Trp53 in these mice (Vav-Cre;Trp53 fl/fl;Mdm2 fl/+) resulted in marked decrease in CD19+ B lymphocytes cells whereas the population of CD11b+ myeloid cells did not change. The population of Lin neg-c-Kit + hematopoietic stem/progenitor cells isolated from the bone marrow of Vav-Cre;Mdm2 fl/+ mice displayed marked downregulation of cholesterol biosynthesis and mevalonate pathway (-log2 pvalue=20). Strikingly, 85% of genes involved in cholesterol biosynthesis (29 genes) were downregulated in Vav-Cre;Mdm2 fl/+ mice. Homozygous deletion of Trp53 in Vav-Cre;Mdm2 fl/+ mice did not rescue the metabolic alterations driven by Mdm2 haplo-insufficiency. In addition, the gene signature of oxidative phosphorylation(oxphos), was remarkably upregulated in Vav-Cre;Mdm2 fl/+ mice independent of p53. We further demonstrate that Cre-mediated induction of a Trp53R172 mutation in Mdm2 haplo-insufficient mice resulted in malignant transformation of HSCs leading to acute myeloid leukemia (AML). Of note, mice with homozygote Trp53 mutation and/or deletion without Mdm2- haplo-insufficiency developed lymphoma and not leukemia. In human, MDM2 loss of heterozygosity (MDM2 LOH) in AML was always concomitant with TP53 missense mutations (log2 odds ratio>3, p<.001), and not TP53 deletions or truncations whereas in lymphomas, MDM2 LOH and TP53 mutations were mutually exclusive. Conclusion: Using a genetic model, we have shown that Mdm2 haplo-insufficiency in HSCs leads to apoptosis and clonal selection towards myeloid biased hematopoiesis. Mechanistically, Mdm2 haplo-insufficiency resulted in a metabolic switch from cholesterol biosynthesis to oxphos in HSCs. Notably, this metabolic reprograming is not rescued by deletion of Trp53. However, mutation of Trp53 in Mdm2 haplo-insufficient hematopoietic stem cells resulted in leukemic transformation of HSCs leading to acute myeloid leukemia. Lastly, we demonstrate that MDM2 SNP309 is associated with TP53 mutation in AML and provide clinical evidence that MDM2 loss of heterozygosity is concomitant with TP53 mutations in AML with lower survival compared to TP53 mutant patients with diploid MDM2. Our findings demonstrate a p53-independent role for Mdm2 in metabolic maintenance of hematopoietic stem/progenitor cells. Figure 1 Figure 1. Disclosures Khoury: Kiromic: Research Funding; Angle: Research Funding; Stemline Therapeutics: Research Funding. Andreeff: Glycomimetics: Consultancy; Medicxi: Consultancy; Karyopharm: Research Funding; ONO Pharmaceuticals: Research Funding; Senti-Bio: Consultancy; Reata, Aptose, Eutropics, SentiBio; Chimerix, Oncolyze: Current holder of individual stocks in a privately-held company; Syndax: Consultancy; Amgen: Research Funding; Daiichi-Sankyo: Consultancy, Research Funding; Breast Cancer Research Foundation: Research Funding; Novartis, Cancer UK; Leukemia & Lymphoma Society (LLS), German Research Council; NCI-RDCRN (Rare Disease Clin Network), CLL Foundation; Novartis: Membership on an entity's Board of Directors or advisory committees; Oxford Biomedica UK: Research Funding; AstraZeneca: Research Funding; Aptose: Consultancy.

The effect of the network-to-molecular structural transformation with increasing phosphorus content in P xSe 100-x (30 {less than or equal to} x {less than or equal to} 67) supercooled liquids on their shear-mechanical response is investigated using oscillatory shear rheometry. While network liquids with 30 {less than or equal to} x {less than or equal to} 40 are characterized by shear relaxation via a network bond scission/renewal process, a Maxwell scaling of the storage (G') and loss (G') shear moduli and a frequency-independent viscosity at low frequencies, a new relaxation process emerges in liquids with intermediate compositions (45 {less than or equal to} x {less than or equal to} 50). This process is attributed to an interconversion between network and molecular structural moieties. Predominantly molecular liquids with x {greater than or equal to} 63, on the other hand, are characterized by a departure from the Maxwell behavior as the storage modulus shows a linear frequency scaling G'(ω) ~ ω over nearly the entire frequency range below the G'-G' crossover and a nearly constant ratio of G˝/G´ in the terminal region. Moreover, the dynamic viscosity of these rather fragile molecular liquids shows significant enhancement over that of network liquids at frequencies below the dynamical onset and does not reach a frequency-independent regime even at frequencies that are four orders of magnitude lower than that of the onset. Such power-law relaxation behavior of the molecular liquids is ascribed to an extremely broad distribution of relaxation timescales with the coexistence of rapid rotational motion of individual molecules and cooperative dynamics of transient molecular clusters, with the latter being significantly slower than the shear relaxation timescale.

AbstractSilicate liquid immiscibility leading to formation of mixtures of distinct iron-rich and silica-rich liquids is common in basaltic and andesitic magmas at advanced stages of magma evolution. Experimental modeling of the immiscibility has been hampered by kinetic problems and attainment of chemical equilibrium between immiscible liquids in some experimental studies has been questioned. On the basis of symmetric regular solutions model and regression analysis of experimental data on compositions of immiscible liquid pairs, we show that liquid–liquid distribution of network-modifying elements K and Fe is linked to the distribution of network-forming oxides SiO2, Al2O3 and P2O5 by equation: $$\log K_{{\text{d}}}^{{\text{K/Fe}}} = \, 3.796\Delta X_{{{\text{SiO}}_{2} }}^{{{\text{sf}}}} + \, 4.85\Delta X_{{{\text{Al}}_{2} {\text{O}}_{3} }}^{{{\text{sf}}}} + \, 7.235\Delta X_{{{\text{P}}_{2} {\text{O}}_{5} }}^{{{\text{sf}}}} - \, 0.108,$$ log K d K/Fe = 3.796 Δ X SiO 2 sf + 4.85 Δ X Al 2 O 3 sf + 7.235 Δ X P 2 O 5 sf - 0.108 , where $$K_{{\text{d}}}^{{\text{K/Fe}}}$$ K d K/Fe is a ratio of K and Fe mole fractions in the silica-rich (s) and Fe-rich (f) immiscible liquids: $$K_{d}^{{\text{K/Fe}}} = \, \left( {X_{{\text{K}}}^{s} /X_{{\text{K}}}^{f} } \right)/ \, \left( {X_{{{\text{Fe}}}}^{s} /X_{{{\text{Fe}}}}^{f} } \right)$$ K d K/Fe = X K s / X K f / X Fe s / X Fe f and $$\Delta X_{{\text{i}}}^{sf}$$ Δ X i sf is a difference in mole fractions of a network-forming oxide i between the liquids (s) and (f): $$\Delta X_{i}^{sf} = X_{i}^{s} - X_{i}^{f}$$ Δ X i sf = X i s - X i f . We use the equation for testing chemical equilibrium in experiments not included in the regression analysis and compositions of natural immiscible melts found as glasses in volcanic rocks. Departures from equilibrium that the test revealed in crystal-rich multiphase experimental products and in natural volcanic rocks imply kinetic competition between liquid–liquid and crystal–liquid element partitioning. Immiscible liquid droplets in volcanic rocks appear to evolve along a metastable trend due to rapid crystallization. Immiscible liquids may be closer to chemical equilibrium in large intrusions where cooling rates are lower and crystals may be spatially separated from liquids.