Liquid-like Structure Research Articles

Mapping and engineering RNA-controlled architecture of the multiphase nucleolus.

Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a layered multiphase liquid-like structure and the site of ribosome biogenesis. In the nucleolus, ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps that ultimately result in formation of the ribosomal small subunit (SSU) and large subunit (LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. Furthermore, by generating synthetic de novo nucleoli through an engineered rDNA plasmid system in cells, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.

Diverse Microstructures and Quasi-Ionic Liquid-like Transport Mechanisms in Concentrated "Water-in-Salt" Lithium Salt Electrolytes: A Molecular Dynamics Study.

"Water-in-salt"(WIS) electrolytes as potential green and nonflammable electrolytes are currently applied in various energy storage devices, such as lithium-ion batteries and supercapacitors. However, the microstructure at molecular scale and fast ion transport mechanism in such aqueous electrolytes are still under heavy debate due to the complex interactions among ions and water. Here, molecular dynamics simulations are used to study the microstructure and ion transport behaviors from the very dilute LiTFSI/water solution to the highly concentrated WIS electrolytes. It revealed that the diverse microstructures such as completely hydrated ions, ion complexes, and bridge-water molecules are jointly responsible for the electrochemical stability of WIS electrolytes. Diffusion model analysis showed that the Li+ ions exhibit a vehicular transport mechanism with first shell water molecules and structural diffusion mechanism with TFSI- anions. The lithium ion and its first hydration shell act as a single cationic entity. The entity forms a quasi-ionic liquid-like dynamic transport structure with associated anions. Our study challenges previous findings that the high transport dynamics of lithium ions arises from their transport in water-rich nanodomains in high-concentration WIS systems.

Ion-specific ice provides a facile approach for reducing ice friction

HypothesisIce friction plays a crucial role in both basic study and practical use. Various strategies for controlling ice friction have been developed. However, one unsolved puzzle regarding ice friction is the effect of ion–ice interplay on its tribological properties. Experiments and SimulationsHere, we conducted ice friction experiments and summarized the specific effects of hydrated ions on ice friction. By selecting cations and anions, the coefficient of ice friction can be reduced by more than 70 percent. Experimental spectra, low-field nuclear magnetic resonance (LF-NMR), density functional theory (DFT) calculations, and Molecular dynamics (MD) simulations demonstrated that the addition of ions could break the H-bonds in water. FindingsThe link between the charge density of ions and the coefficients of ice friction was revealed. A part of the ice structure was changed from an ice-like to a liquid-like interfacial water structure with the addition of ions. Lower charge density ions led to weaker ionic forces with the water molecules in the immobilized water layer, resulting in free water molecules increasing in the lubricating layer. This study provides guidance for preparing ice-making solutions with low friction coefficients and a fuller understanding of the interfacial water structure at low temperatures.

A self-healing multispectral transparent adhesive peptide glass.

Despite its disordered liquid-like structure, glass exhibits solid-like mechanical properties1. The formation of glassy material occurs by vitrification, preventing crystallization and promoting an amorphous structure2. Glass is fundamental in diverse fields of materials science, owing to its unique optical, chemical and mechanical properties as well as durability, versatility and environmental sustainability3. However, engineering a glassy material without compromising its properties is challenging4-6. Here we report the discovery of a supramolecular amorphous glass formed by the spontaneous self-organization of the short aromatic tripeptide YYY initiated by non-covalent cross-linking with structural water7,8. This system uniquely combines often contradictory sets of properties; it is highly rigid yet can undergo complete self-healing at room temperature. Moreover, the supramolecular glass is an extremely strong adhesive yet it is transparent in a wide spectral range from visible to mid-infrared. This exceptional set of characteristics is observed in a simple bioorganic peptide glass composed of natural amino acids, presenting a multi-functional material that could be highly advantageous for various applications in science and engineering.

Crossover from gas-like to liquid-like molecular diffusion in a simple supercritical fluid.

According to textbooks, no physical observable can be discerned allowing to distinguish a liquid from a gas beyond the critical point. Yet, several proposals have been put forward challenging this view and various transition boundaries between a gas-like and a liquid-like behaviour, including the so-called Widom and Frenkel lines, and percolation line, have been suggested to delineate the supercritical state space. Here we report observation of a crossover from gas-like (Gaussian) to liquid-like (Lorentzian) self-dynamic structure factor by incoherent quasi-elastic neutron scattering measurements on supercritical fluid methane as a function of pressure, along the 200 K isotherm. The molecular self-diffusion coefficient was derived from the best Gaussian (at low pressures) or Lorentzian (at high pressures) fits to the neutron spectra. The Gaussian-to-Lorentzian crossover is progressive and takes place at about the Widom line intercept (59 bar). At considerably higher pressures, a liquid-like jump diffusion mechanism properly describes the supercritical fluid on both sides of the Frenkel line. The present observation of a gas-like to liquid-like crossover in the self dynamics of a simple supercritical fluid confirms emerging views on the unexpectedly complex physics of the supercritical state, and could have planet-wide implications and possible industrial applications in green chemistry.

Advance effect of magnetic field on the rheological properties of manganese zinc ferrite ferrofluid

The rheological characteristics of manganese zinc (Mn-Zn) ferrite magnetic nanofluid synthesized using co-precipitation technique were examined in the absence and presence of magnetic fields. The research formulates required conditions needed for the formation of a gelly-like structure. The impact of magnetic field and temperature on the rheological properties of Mn-Zn ferrite ferrofluid is investigated. When a magnetic field was applied, higher magnetoviscoelasticity and magnetoviscosity were formed. Analysis was also done on other rheological parameters, such as the damping factor, which is crucial for regulating and restricting vibrations in a system. A stiff, gel-like structure is produced when a magnetic field is applied, and the gel-like quality grows as the magnetic field increases; when the magnetic field is removed, the gel-like and rigidity of the structure is lost. At low temperatures, the liquid phase is dominated by solid-like particles, whereas at high temperatures, the liquid-like structure is dominant. This study reveals the conditions required for the creation of high viscous effect and the viscoelastic behavior induced by the field offers important insights for optimizing the Mn-Zn ferrite ferrofluid for a range of applications. Other criterial for gel-like structure formation such as low torque and deflection angle of the ferrofluid were also established.

Stability, thermodynamic, electronic, and thermoelectric properties of triclinic Cu[formula omitted]Se structure

The conversion of heat into electricity using the thermoelectric effect is a crucial issue to tackle the ever-increasing global energy consumption. Cu2Se is one of the high-performance thermoelectric materials due to its liquid-like atomic structure, which minimizes the phonon-derived thermal conductivity. Nevertheless, the unambiguous atomic structure of the low-temperature phase, α-Cu2Se, remains controversial. By employing a combination of theoretical approaches including an evolutionary algorithm for structural searching, density functional theory, and lattice dynamics, the α-Cu2Se phase is proposed to crystalize in the dynamically stable triclinic Cu2Se structure (s.g. P1) which can be regarded as a monoclinic polymorph (s.g. P21/c†) through slight distortion. The corresponding heat capacity (CV) and Debye temperature (ΘD) are 0.37 J/g K and 276 K, respectively, indicating low thermal conductivity in the material. The semiconducting P1 phase possesses an indirect gap of 1.0 eV. Additionally, based on the Boltzmann transportation theory, fundamental thermoelectric parameters around the transition temperature (300–500 K) are investigated. Beyond the semiconducting phase, a novel metallic phase identified as the triclinic P1̄ phase is also discovered, exhibiting a two-dimensional (2D) crystal geometry.

Structure and short-time diffusion of concentrated suspensions consisting of silicone-stabilised PMMA particles: a quantitative analysis taking polydispersity effects into account.

We characterise structure and dynamics of concentrated suspensions of silicone-stabilised PMMA particles immersed in index-matching decalin-tetralin mixtures by means of static and quasielastic light scattering experiments. These particles can reproducibly be prepared via a comparatively easy route and are thus promising model systems with hard-sphere interaction. We demonstrate the hard-sphere behaviour of dense suspensions of these systems rigorously taking polydispersity effects into account. Structure factors S(Q) can in the entire range of volume fractions with liquid-like structure quantitatively be modelled using a multi-component Percus-Yevick ansatz regarding the particle size distribution and the form factor assuming a core-shell model with a scattering length density gradient in the PMMA core. Herewith, hydrodynamic functions H(Q) are in the whole accessible Q-range beyond the second maximum of H(Q) quantitatively modelled using a rescaled δγ-approach for all investigated volume fractions. With these data, previously provided characterisation of dilute systems is extended: the excellent agreement of structural and dynamic properties with theoretical predictions for hard spheres demonstrates the suitability of these particles as a model system for hard spheres.

Characteristics of temperature-dependent shear flow in an ultrasonicated ferrofluid

The rheological effect of manganese zinc (Mn-Zn) ferrite ferrofluid was studied and the impact of temperature on the magnetoviscosity and viscoelastic system of manganese-zinc ferrite ferrofluid generated by co-precipitation process is investigated. At 25 ◦C, a ferrofluid structure that is both hard and elastic is produced. As the temperature rises, the fluid structure loses its elasticity and becomes semi-rigid. When a low relaxation modulus is applied, the fluid behavior, which is temperature-dependent, exhibits the development of linear stress relaxation and steady state flow. When a greater relaxation modulus is used, non-steady state flow results. At a high temperature of 50 ◦C, steady state flow is quickly obtained, whereas at a low temperature, equilibrium or steady state is attained more slowly. At low temperatures, the fluid exhibits a solid-like structure, whereas at high temperatures, a liquid-like structure forms as the fluid’s viscosity decreases. With the creation of yield stress in the region with high shear rates, shear stress increases with temperature, and yield stress increases with temperature. The viscoelastic system is underdamped, and the amount of fluid deflected at 25 ◦C is small, which prevents the disruption of the fluid’s rheology. This develops as a result of the presence of a small deflection angle, which facilitates the development of high magnetoviscosity at low temperature. High viscous effect forms at low temperatures due to the creation of low shear stress and low deflection angle at temperature 25 ◦C. The sample has a single phase and FCC structure, which X-ray diffraction research has verified.

Storage and Diffusion of Carbon Dioxide in the Metal Organic Framework MOF-5─A Semi-empirical Molecular Dynamics Study.

Metal-organic frameworks (MOFs) have attracted increasing attention due to their high porosity for exceptional gas storage applications. MOF-5 belongs to the family of isoreticular MOFs (IRMOFs) and consists of Zn4O6+ clusters linked by 1,4-benzenedicarboxylate. Due to the large number of atoms in the unit cell, molecular dynamics simulation based on density functional theory has proved to be too demanding, while force field models are often inadequate to model complex host-guest interactions. To overcome this limitation, an alternative semi-empirical approach using a set of approximations and extensive parametrization of interactions called density functional tight binding (DFTB) was applied in this work to study CO2 in the MOF-5 host. Calculations of pristine MOF-5 yield very good agreement with experimental data in terms of X-ray diffraction patterns as well as mechanical properties, such as the negative thermal expansion coefficient and the bulk modulus. In addition, different loadings of CO2 were introduced, and the associated self-diffusion coefficients and activation energies were investigated. The results show very good agreement with those of other experimental and theoretical investigations. This study provides detailed insights into the capability of semi-empirical DFTB-based molecular dynamics simulations of these challenging guest@host systems. Based on the comparison of the guest-guest pair distributions observed inside the MOF host and the corresponding gas-phase reference, a liquid-like structure of CO2 can be deduced upon storage in the host material.

Dimensionless parameter of structural ordering and excess entropy of metallic and tellurite glasses

Using a notion on the excess entropy of glass with respect to the counterpart crystal, we introduce a simple dimensionless order parameter ξ, which changes from ξ→0 to ξ→1. The former case corresponds to a strongly disordered liquid-like structure while the latter instance describes a highly ordered crystal-like glass. This approach is applied to 13 metallic and 2 tellurite glasses. We found that ξ is strongly sensitive to structural state and/or chemical composition. This parameter can be also used for a comparison of the order in glasses belonging to different classes and appears to represent a new way of structural order estimate. It is important that the ordering parameter ξ has a strong correlation with the glass-forming ability.

Assessment of the Quality Attributes of Oat β-glucan Fortified Reduced-Fat Goat Milk Yogurt Supported by Microfluidization.

In this study, goat milk blends (1.5% fat) fortified with 0%, 0.25%, and 0.50% oat β-glucan were coded as YC, Y1, and Y2 and MFYC, MFY1, and MFY2. Microfluidization was applied at 103.4 MPa pressure in a 100 µm-process chamber at one stage for MFYC, MFY1, and MFY2 prior to yogurt making. Phase separation occurred due to the casein-β-glucan interaction observed at the oat β-glucan ratio (≥0.25%) but was more distinct at 0.50%. Microfluidization solved the textural instability at all ratios of β-glucan; a creamy and less cohesive structure was maintained in all yogurt samples. Among the samples, Y2 and MFY2 were the least viscous (p < 0.05), and syneresis was the highest and the lowest for Y2 and MFY1, respectively (p < 0.01). Lightness (L*) decreased, and yellowness (b*) and greenness (a*) increased with oat β-glucan concentration (p < 0.01) and MFYC. MFY1 and MFY2 were brighter and less green (p < 0.05). Microfluidization enhanced sensory attributes and oat β-glucan suppressed the goaty and salty taste, but the cereal taste became more obvious with the increase in the oat β-glucan ratio. Y1 and MFY1 were generally acceptable, and Y2 was less (p < 0.01). A liquid-like structure was observed in Y2 and this affected the sensorial perception in Y2.

Structure of the Medium Formed in Heavy Ion Collisions

We investigate the structure of the medium formed in heavy ion collisions using three different models: the Color String Percolation Model (CSPM), the Core–Shell-Color String Percolation Model (CSCSPM), and the Color Glass Condensate (CGC) framework. We analyze the radial distribution function of the transverse representation of color flux tubes in each model to determine the medium’s structure. Our results indicate that the CSPM behaves as an ideal gas, while the CSCSPM exhibits a structural phase transition from a gas-like to a liquid-like structure. Additionally, our analysis of the CGC framework suggests that it produces systems that behave like non-ideal gases for AuAu central collisions at RHIC energies and liquid-like structures for PbPb central collisions at LHC energies.

Reduction of ice adhesion on nanostructured and nanoscale slippery surfaces

Ice nucleation and accretion on structural surfaces are sources of major safety and operational concerns in many industries including aviation and renewable energy. Common methods for tackling these are active ones such as heating, ultrasound, and chemicals or passive ones such as surface coatings. In this study, we explored the ice adhesion properties of slippery coated substrates by measuring the shear forces required to remove a glaze ice block on the coated substrates. Among the studied nanostructured and nanoscale surfaces [i.e., a superhydrophobic coating, a fluoropolymer coating, and a polydimethylsiloxane (PDMS) chain coating], the slippery omniphobic covalently attached liquid (SOCAL) surface with its flexible polymer brushes and liquid-like structure significantly reduced the ice adhesion on both glass and silicon surfaces. Further studies of the SOCAL coating on roughened substrates also demonstrated its low ice adhesion. The reduction in ice adhesion is attributed to the flexible nature of the brush-like structures of PDMS chains, allowing ice to detach easily.

Compression Induced Deformation Twinning Evolution in Liquid-Like Cu2Se.

For practical applications of copper selenide (Cu2Se) thermoelectric (TE) materials with liquid-like behavior, it is essential to determine the structure-property relations as a function of temperature. Here, we investigate β-Cu2Se structure evolution during uniaxial compression over the temperature range of 400-1000 K using molecular dynamics simulations. We find that at temperatures above 800 K, Cu2Se exhibits poor stability with breaking order that is described as a liquid-like or hybrid structure comprising a rigid Se sublattice and mobile Cu ions. A uniaxial load causes accumulated structural heterogeneity that is alleviated by diffusion-induced accommodation of local deformations. With increasing strain, the deformation mode changes into a combination of compression and shear, accompanied by restructuring in terms of twinning. Interestingly, in addition to a plastic behavior rarely found in inorganic semiconductors, we find that higher temperature promotes deformation twinning in liquid-like Cu2Se, showing the role of thermal instability, including Cu diffusion, in structural adaptation and mechanical modulation. These findings reveal the micromechanism of hybrid structural evolution as well as performance tuning through twinning, which provides a theoretical guide toward advanced Cu2Se TE materials design.

Short-to-medium range atomic order of Zr-Cu metallic glasses under compression

Metallic glasses are amorphous solids, usually alloys, with liquid-like atomic structure involving short-range order characterized by clusters of atoms and medium-range order – a spatial arrangement of those clusters. Amorphous metals lack the translational symmetry of crystals, yet their atomic packing density is nearly as high as in crystalline materials. The packing density of metallic glasses can be further enhanced by external pressure, which forces the disordered structure to accommodate the load. In this work, we employ molecular dynamics simulations to follow variations of short-to-medium-range order of three binary Zr-Cu metallic glasses during hydrostatic compression from 0 to 100 GPa. Our study confirms the previously reported unusual contraction of Zr-Zr pairs. We suggest that the effect is related to the theoretically predicted step change of the electronic configuration of Zr atoms under compression. A common feature of the investigated systems is an increasing contribution of icosahedral order around Cu atoms which is accomplished by preferential straining of the mechanically soft Zr-Zr bonds. Our results reveal structural similarities of different alloys in the high-pressure regime and show that their topological short-to-medium-range order becomes composition-independent under compression. We conclude that the topology of short-to-medium-range order in Zr-Cu MGs under compression exhibits a universal, composition-independent character.

Quasi-water layer sandwiched between hexagonal ice and wall and its influences on the ice tensile stress.

The presence of a quasi-water/premelting layer at the interface between wall and ice when the temperature (T) is below the melting point was extensively observed in experiments. In this work, molecular dynamics simulations are performed to analyze the underlying physics of the quasi-water layer and the effects of the layer on the ice tensile stress. The results indicate that each molecule and its four nearest neighbours in the quasi-water layer representing an equilibrium structure gradually form a tetrahedral ice-like arrangement from an unstructured liquid-like structure along the direction away from the wall. The average density of the quasi-water layer is equal to or higher than the bulk density of water at T ≥ 240 K or T ≤ 240 K respectively, and reaches 1.155 g cm-3 at T = 210 K, suggesting a structural correlation with the high-density liquid phase of water. Depending on the temperature and wall wettability, the thickness of the quasi-water layer (Hq) ranges from ∼2 Å to ∼25 Å. For prescribed hydrophilic walls, Hq increases monotonically with temperature, and is almost proportional to(Tm - T)-1/3, where Tm is the melting temperature of ice. Hq keeps an almost constant value (2 Å) as the temperature increases and rises sharply after passing a threshold temperature of T ≈ 250 K. In the joint effects of the wall wettability and quasi-water layer's thickness, the ice tensile stress decreasing monotonically at a larger temperature shows an upward trend and then reduces to almost a constant value as the wall changes from a hydrophobic to a hydrophilic one. The results reveal the potential development of anti-icing/de-icing techniques by heating the wall or modifying its surface to increase Hq.

Uticaj različito umrežavanih polimernih veziva na reološka svojstva plastičnih eksploziva

Plastic Explosive Compositions consisting of HMX and liquid polyurethane binder were prepared in order to determine influence of differently cured polymeric binders on rheological properties of plastic explosives. First, a set of polymeric binders was prepared in polyaddition reaction between HTPB and IPDI, with varying NCO:OH ratio and examined through the standard and non-standard rheological tests on a dynamic rotational rheometer. Viscosity curves of polymeric binders show viscosity increase with NCO:OH ratio increase, as expected. Amplitude sweep tests reveal liquid-like structure of PEs, with structure strength increase with higher NCO:OH ratio of polymeric binder used, and limiting values of LVER vary from 10-3 to 10-2 strain. Results of creep test reveal that with increase of NCO:OH ratio of polymeric binder in PE zero-shear viscosity increase and viscous portion deformation decrease. Also, penetration decrease with increase of NCO:OH ratio. The obtained results indicate that initial rheology testing is crucial in plastic explosive formulation regarding their processability and physical properties.

Bifurcation phenomenon in molecular dynamics model of coalescence/sintering on the nanoscale

Using the isothermal molecular dynamics, coalescence/sintering of Au nanoparticles (NPs) was simulated. We have found that the solid NP sintering scenario is switched to the coalescence scenario not at the NP melting temperature T m exactly but at a lower temperature T 0 ≈ 0.9T m interpreted as the critical temperature corresponding to a coalescence/sintering bifurcation phenomenon: in the temperature range from T 0 – 2 K to T 0 + 2 K to the resulting (daughter) NPs of the same size can have either liquid-like or crystalline structure after coalescence/sintering at the same fixed temperature.

Destruction of hydrogen bonding and electrostatic interaction in soy hull polysaccharide: Effect on emulsion stability

Hydrogen bonding and electrostatic interactions play an important role in the microstructure of soy hull polysaccharide (SHPA) and the stability of corresponding emulsions. In this study, urea and NaCl were added in the preparation of samples, which could destroy these two noncovalent interactions, and they were labeled as SHPA-U and SHPA-N, respectively. The results show that more hydrogen bonding was generated along with the electrostatic shielding effect, which led to longer and branched polysaccharide chains of SHPA-N. However, the chain of SHPA-U was rough and fragmentary, which may be attributed to hydrogen bonding and protein regions destroyed by urea. Furthermore, the addition of NaCl and urea led to lower interfacial pressure, and the adsorption kinetics at the oil/water interface were significantly changed. In addition, all emulsions had a liquid-like structure, and both SHPA-N and SHPA-U emulsions had a bimodal size distribution. The relaxation time and line width of the 1H NMR analysis decreased with the addition of NaCl and urea, indicating the decreasing interaction between SHPA-N/SHPA-U and oil molecules. These phenomena were related to the coalescence and flocculation in these two emulsions. After 24 h of storage, the stability of the SHPA-N emulsion was superior to the others; this may be due to its higher viscosity. This study laid the foundation for further research on the mechanism of polysaccharide O/W emulsions stabilized by SHPA and other polysaccharides.