Solid-like Phases Research Articles

Interphase chromatin undergoes a local sol-gel transition upon cell differentiation.

Cell differentiation, the process by which stem cells become specialized, is associated with chromatin reorganization inside the cell nucleus. Here, we measure the chromatin distribution and dynamics in embryonic stem cells in vivo before and after differentiation into neurons. We find that undifferentiated chromatin is less compact, more homogeneous and more dynamic than differentiated chromatin. Further, we present a noninvasive experimental strategy that uses intrinsic chromatin dynamics, to measure chromatin rheology across a large range of timescales, and elucidates the viscoelastic nature of chromatin in live cells. Moreover, by spatially resolving the dynamics in different regions of the cell nucleus, our method reveals local rheology of the chromatin polymer in both euchromatin and heterochromatin states. The measured rheology reveals that undifferentiated chromatin behaves like a Maxwell fluid, while differentiated chromatin shows a coexistence of fluid-like (sol) and solid-like (gel) phases. Our data suggest that chromatin undergoes a local sol-gel transition upon cell differentiation, corresponding to the formation of the more dense and transcriptionally inactive heterochromatin [1]. This work was supported by the National Institutes of Health Grant R00-GM104152, the National Science Foundation (NSF) Grants CAREER PHY-1554880 and CMMI-1762506, New York University (NYU) MRSEC NSF Grant DMR-1420073 and NYU Whitehead Fellowship for Junior Faculty in Biomedical and Biological Sciences (to AZ). Eshghi I, Eaton JA and Zidovska A. Phys. Rev. Lett., 126, 228101 (2021).

Modulation of α-synuclein phase separation by biomolecules

Liquid-liquid phase separation (LLPS) is currently recognized as a common mechanism involved in the regulation of a number of cellular functions. On the other hand, aberrant phase separation has been linked to the biogenesis of several neurodegenerative disorders since many proteins that undergo LLPS are also found in pathological aggregates. The formation of mixed protein coacervates may constitute a risk factor in overlapping neuropathologies, such as Parkinson's (PD) and Alzheimer's (AD) diseases. In this work, we evaluated the homotypic and heterotypic phase behaviour of the PD-related protein α-synuclein (AS) in the presence of the biologically relevant molecules ATP, polyamines, and the AD-related protein Tau. We found that AS exhibits a low propensity to form homotypic liquid droplets, yet phase separates into liquid-like or solid-like phases depending on the interacting biomolecule. We further demonstrated the synergistic droplet formation of AS and Tau providing support for a mechanism in which mixed condensates might contribute to the biogenesis of AS/Tau pathologies.

Smoothed particle hydrodynamics for cohesive dense granular media

• An elastic–viscoplastic constitutive model for cohesive dense granular media is built. • Rheological model considering cohesion for liquid-like phase is put forward. • The solid-like phase and liquid-like phase are both modelled and simulated. • Smoothed particle hydrodynamics was first used for cohesive dense granular media. • Cohesive force plays an important role in granular pile collapse, flow and depositing. Dense granular media with cohesion exist widely in nature. A constitutive model that considers cohesion in terms of solid-like and liquid-like phases in dense granular media was designed in this study. In this new model, a linear elastic–plastic constitutive relationship based on the Drucker–Prager yield criterion affected by the parameters of cohesion was used to describe the solid-like phase. A viscoplastic constitutive model based on rheology, which also considers cohesion, was obtained through formula derivation for the liquid-like phase after plastic yielding. The conversion and transitional relationships from elastic to elastic-micro viscoplastic and then to complete elastic–viscoplastic were built. Smoothed particle hydrodynamics was adopted to solve the new model discretely, and the relationship between smoothed and actual particles and an approach employed to avoid particle aggregation caused by cohesion were illustrated. Several typical cases including the collapse of cohesive granular accumulation, collapse of dry and wet granular column, and flow of cohesive powder in a rotating drum were used for verification. A comparison between cohesive and dry granular flows and among numerical results, experimental results, and those of other numerical methods proved that the proposed model and algorithm are effective for simulating dense granular flow with cohesion; further, they provide a valid approach to describe issues of granular flow with veritable cohesion that exist in nature.

Wave spectroscopy in a driven granular material

Driven granular media constitute model systems in out-of-equilibrium statistical physics. By assimilating the motions of granular particles to those of atoms, by analogy, one can obtain macroscopic equivalent of phase transitions. Here, we study fluid-like and crystal-like two-dimensional states in a driven granular material. In our experimental device, a tunable magnetic field induces and controls remote interactions between the granular particles. We use high-speed video recordings to analyse the velocity fluctuations of individual particles in stationary regime. Using statistical averaging, we find that the particles self-organize into collective excitations characterized by dispersion relations in the frequency-wavenumber space. These findings thus reveal that mechanical waves analogous to condensed matter phonons propagate in driven granular media. When the magnetic coupling is weak, the waves are longitudinal, as expected for a fluid-like phase. When the coupling is stronger, both longitudinal and transverse waves propagate, which is typically seen in solid-like phases. We model the dispersion relations using the spatial distribution of particles and their interaction potential. Finally, we infer the elastic parameters of the granular assembly from equivalent sound velocities, thus realizing the spectroscopy of a granular material.

Linear viscoelastic properties of the vertex model for epithelial tissues.

Epithelial tissues act as barriers and, therefore, must repair themselves, respond to environmental changes and grow without compromising their integrity. Consequently, they exhibit complex viscoelastic rheological behavior where constituent cells actively tune their mechanical properties to change the overall response of the tissue, e.g., from solid-like to fluid-like. Mesoscopic mechanical properties of epithelia are commonly modeled with the vertex model. While previous studies have predominantly focused on the rheological properties of the vertex model at long time scales, we systematically studied the full dynamic range by applying small oscillatory shear and bulk deformations in both solid-like and fluid-like phases for regular hexagonal and disordered cell configurations. We found that the shear and bulk responses in the fluid and solid phases can be described by standard spring-dashpot viscoelastic models. Furthermore, the solid-fluid transition can be tuned by applying pre-deformation to the system. Our study provides insights into the mechanisms by which epithelia can regulate their rich rheological behavior.

Dynamic response on a nanometer scale of binary phospholipid-cholesterol vesicles: Low-frequency Raman scattering insight.

Low-frequency Raman spectroscopy was used to study the dynamic response on a nanometer scale of aqueous suspensions of two-component lipid vesicles. Binary mixtures of saturated phospholipid (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) and cholesterol are interesting for possible coexistence of solidlike and liquid-ordered phases, while the phase coexistence was not reported for unsaturated phospholipid (1,2-dioleoyl-sn-glycero-3-phosphocholine, DOPC) and cholesterol mixtures. The DOPC-DPPC mixtures represent the well-documented case of coexisting domains of solidlike and liquid-disordered phases. These three series of lipid mixtures are studied here. A broad peak with the maximum in the range of 30-50cm^{-1} and a narrow peak near 10cm^{-1} are observed in the Raman susceptibility of the binary mixtures and attributed to the acousticlike vibrational density of states and layer modes, respectively. Parameters of the broad and narrow peaks are sensitive to lateral and conformational hydrocarbon chain ordering. It was also demonstrated that the low-frequency Raman susceptibility of multicomponent lipid bilayers allows one to determine the phase state of lipid bilayers and distinguish the homogeneous distribution of molecular complexes from coexisting domains with sizes above several nanometers. Thus, the low-frequency Raman spectroscopy provides unique information in studying phase coexistence in lipid bilayers.

A novel jamming phase diagram links tumor invasion to non-equilibrium phase separation

SummaryIt is well established that the early malignant tumor invades surrounding extracellular matrix (ECM) in a manner that depends upon material properties of constituent cells, surrounding ECM, and their interactions. Recent studies have established the capacity of the invading tumor spheroids to evolve into coexistent solid-like, fluid-like, and gas-like phases. Using breast cancer cell lines invading into engineered ECM, here we show that the spheroid interior develops spatial and temporal heterogeneities in material phase which, depending upon cell type and matrix density, ultimately result in a variety of phase separation patterns at the invasive front. Using a computational approach, we further show that these patterns are captured by a novel jamming phase diagram. We suggest that non-equilibrium phase separation based upon jamming and unjamming transitions may provide a unifying physical picture to describe cellular migratory dynamics within, and invasion from, a tumor.

Thermodynamics and rheology of droplet aggregation of water-in-crude oil emulsion systems

An emulsion may be classified as a colloidal system depending on the scale analyzed. State parameters (e.g.temperature, volume fraction and osmotic pressure) determine whether the system is regarded as in a liquid-like, liquid/solid-like or solid-like phase. The transition threshold between different phases has been separately observed from thermodynamic and rheological viewpoints. For the case in which the system is under free particle motion regime (van der Waals forces, Brownian motion, depletion, etc.), we obtained a relationship between the rheological behavior and the thermodynamic state. The thermodynamic analysis is based on the McMillan-Mayer theory, and binodal curves were determined with a perturbation theory. It was that liquid-like phases behave as Newtonian, while liquid/solid-like and solid-like phases possess a non-Newtonian rheological behavior. Water-in-crude oil emulsions were used in the experiments. We studied the effect of volume fraction (φ = 20% and 30%), temperature (T = 60°C, 40°C, 25°C), and mean size diameter (dp = 6.4 μm, 5.34 μm, and 4.22 μm). The transition line from the liquid-like to the liquid-solid phase moves with volume fraction, temperature, monolayer thickness and particle diameter, consistently with the rheology results.

Multiphase theory of granular media and particle simulation method for projectile penetration in sand beds

Studying projectile penetration in sand beds is of great significance for solving practical problems in the fields of weapon damage, consolidation of foundations, and mine explosions. In this study, a coupled model using the elastic-viscoplastic-kinetic constitutive relation and discrete particle dynamics was established to describe the multiple phases of sand-like materials, namely, the solid-like, liquid-like, gas-like, and inertial discrete phases. A linear elastic model was used to describe the solid-like phase; however, after the plastic yield point was reached, a viscoplastic constitutive model based on rheology was used to describe this liquid-like phase. When the volume fraction of the particles reduced to a certain value, the gas-like phase was described using the kinetic theory of granular flow; however, when the assumption of binary collisions was no longer satisfied, discrete particle dynamics was used to describe this inertial discrete phase. Smoothed discrete particle hydrodynamics coupled with the discrete element method was used to discretize our model based on established multiphase models of sand-like materials. Our new theoretical model and numerical method were used to simulate the high-speed penetration of spherical and slender projectiles in dry sand accumulation. A comparison with the results from experiments and other numerical methods shows that the new numerical method is suitable for describing the different motion states of sand-like materials owing to different projectile penetration velocities. Finally, the ricochet phenomenon of a conical projectile penetrating a sand bed was captured, which further verifies the applicability of our model for solving engineering problems.

Interphase Chromatin Undergoes a Local Sol-Gel Transition upon Cell Differentiation.

Cell differentiation, the process by which stem cells become specialized cells, is associated with chromatin reorganization inside the cell nucleus. Here, we measure the chromatin distribution and dynamics in embryonic stem cells invivo before and after differentiation. We find that undifferentiated chromatin is less compact, more homogeneous, and more dynamic than differentiated chromatin. Furthermore, we present a noninvasive rheological analysis using intrinsic chromatin dynamics, which reveals that undifferentiated chromatin behaves like a Maxwell fluid, while differentiated chromatin shows a coexistence of fluidlike (sol) and solidlike (gel) phases. Our data suggest that chromatin undergoes a local sol-gel transition upon cell differentiation, corresponding to the formation of the more dense and transcriptionally inactive heterochromatin.

Constitutive model for solid-like, liquid-like, and gas-like phases of granular media and their numerical implementation

Granular media, a macroscopic amorphous matter composed of mesoscopic discrete particles, exhibits different behaviour characteristics (e.g., solid-, liquid-, and gas-like phases) depending on the volume fraction and loading conditions. Therefore, it poses a significant challenge to three-phase modelling and analysis. In this study, a description of multiple phases in granular media is realised by establishing the transition criteria and parameter conversion relations between different phases, using the already established theories of the elastic-plastic constitutive relation in solid mechanics, the viscoplastic constitutive relation in rheology, and the kinetic theory of granular flow. The new model realises the coexistence of different phases and the conversions therebetween. Smoothed discrete particle hydrodynamics are introduced to discretise the new theoretical model, and the correspondence between the smoothed and actual particles for different phases and discrete formulas under different models are described in detail. Two typical cases are used for numerical tests: the collapse of one side of a three-dimensional granular column and the collapse and flow of a granular column on an inclined surface. The calculated morphology of granular flow, distributions of velocity vectors, scaling law of spreading range under different height-width ratios, and the transient characteristics of particle spreading all accord well with the experimental results. Furthermore, quasi-static, slow, fast, and other phases of particle motions are well captured. Thus, we verify the feasibility of the new model and method for the multiple-phase simulation of granular media.

Protein microspheres as structuring agents in lipids: potential for reduction of total and saturated fat in food products.

Excess consumption of total and saturated fats is linked to the development of chronic diseases, such as obesity, heart disease, diabetes, and cancer. There is therefore considerable interest in the development of foods containing lower levels of total and saturated fats, but that still have the same desirable physicochemical and sensory characteristics as the original foods. Solid fats normally contribute a number of key functional attributes to foods due to their ability to form crystalline networks that alter texture (such as elasticity, plasticity, and spreadability) and appearance (such as opacity and creaminess). The aim of this review is to provide an overview and to discuss the potential applications of food proteins as fat structuring agents that may be able to offer some of the desirable attributes normally supplied by saturated and trans fats. Previous studies have shown that globular proteins (such as whey proteins) trapped inside water-in-oil emulsions form protein microspheres when they are thermally denatured, which leads to the creation of highly viscous or solid-like lipid phases, having higher rheological properties. These protein microspheres may therefore be useful for the development of reduced fat margarines and spreads with reduced level of saturated/trans-fat contents. © 2020 Society of Chemical Industry.

Phase separation in a two-dimensional binary colloidal mixture by quorum sensing activity.

We present results from Langevin dynamics simulations of a glassy active-passive mixture of soft-repulsive binary colloidal disks. Activity on the smaller particles is applied according to the quorum sensing scheme, in which a smaller particle will be active for a persistence time if its local nearest neighbors are equal to or greater than a certain threshold value. We start with a passive glassy state of the system and apply activity to the smaller particles, which shows a nonmonotonous glassy character of the active particles with the persistence time of the active force, from its passive limit (zero activity). On the other hand, passive particles of the active-passive mixture phase separate at the intermediate persistence time of the active force, resulting in the hexatic-liquid and solid-liquid phases. Thus, our system shows three regimes as active glass, phase separation, and active liquid, as the persistence time increases from its smaller values. We show that the solidlike and hexatic phases consisting of passive large particles are stable due to the smaller momentum transfer from active to passive particles, compared to the higher persistence time where the positional and orientational ordering vanishes. Our model is relevant to active biological systems, where glassy dynamics is present, e.g., bacterial cytoplasm, biological tissues, dense quorum sensing bacteria, and synthetic smart amorphous glasses.

Engineering medium-range order and polyamorphism in a nanostructured amorphous alloy

Like crystalline materials, the properties of amorphous materials can be tailored by tuning the local atomic-to-nanoscale structural configurations. Polyamorphism is evident by the coexistence of kinetically stabilized amorphous structures with tailorable short-to-medium-range orders, providing a viable means to engineer the degree of local order and heterogeneity. Here, we report experimental evidence of the coexistence of liquid-like and solid-like amorphous phases in a Ni82P18 amorphous alloy with enhanced thermal stability and plasticity prepared by pulsed electrodeposition. The two amorphous phases, of comparable volume fraction of ~50% each, have similar short-range order but are distinguished by packing at the medium-range length scale (>6 Å). Upon heating, a structure crossover at ~450 K was observed, where the liquid-like structure transforms to the solid-like structure, as evidenced by the enthalpy release and an anomalous contraction of atomic structure over the medium-range length scale, due to the metastable nature of the liquid-like structure.

Neural network potentials for dynamics and thermodynamics of gold nanoparticles.

For understanding the dynamical and thermodynamical properties of metal nanoparticles, one has to go beyond static and structural predictions of a nanoparticle. Accurate description of dynamical properties may be computationally intensive depending on the size of nanoparticle. Herein, we demonstrate the use of atomistic neural network potentials, obtained by fitting quantum mechanical data, for extensive molecular dynamics simulations of gold nanoparticles. The fitted potential was tested by performing global optimizations of size selected gold nanoparticles (Aun, 17 ≤ n ≤ 58). We performed molecular dynamics simulations in canonical (NVT) and microcanonical (NVE) ensembles on Au17, Au34, Au58 for a total simulation time of around 3 ns for each nanoparticle. Our study based on both NVT and NVE ensembles indicate that there is a dynamical coexistence of solid-like and liquid-like phases near melting transition. We estimate the probability at finite temperatures for set of isomers lying below 0.5 eV from the global minimum structure. In the case of Au17 and Au58, the properties can be estimated using global minimum structure at room temperature, while for Au34, global minimum structure is not a dominant structure even at low temperatures.

Anomalous structural transition of confined hard squares.

Structural transitions are examined in quasi-one-dimensional systems of freely rotating hard squares, which are confined between two parallel walls. We find two competing phases: one is a fluid where the squares have two sides parallel to the walls, while the second one is a solidlike structure with a zigzag arrangement of the squares. Using transfer matrix method we show that the configuration space consists of subspaces of fluidlike and solidlike phases, which are connected with low probability microstates of mixed structures. The existence of these connecting states makes the thermodynamic quantities continuous and precludes the possibility of a true phase transition. However, thermodynamic functions indicate strong tendency for the phase transition and our replica exchange Monte Carlo simulation study detects several important markers of the first order phase transition. The distinction of a phase transition from a structural change is practically impossible with simulations and experiments in such systems like the confined hard squares.

Universal scaling of dielectric response of various liquid crystals and glass-forming liquids

We present a new generalized scaling relationship accounting both for the real and imaginary parts of the complex permittivity data. The generalized scaling procedure has been successfully used for various relaxation processes in liquid crystals (4-bromobenzylidene-4′-pentyloxyaniline, 4-bromobenzylidene-4′-hexyloxyaniline, 4′-butyl-4-(2-methylbutoxy)-azoxybenzene, 4-ethyl-4′-octylazoxybenzene), and in glass-forming liquids (glycerol, propylene carbonate, salol, cresolphthalein-dimethylether). As it is shown, one obtains common master-curve for liquid-like phases (isotropic liquid, cholesteric, nematic, smectic A), solid-like phases (smectic B, conformationally disorder crystal) and supercooled liquid phase.

On the continuum modeling of dense granular flow in high shear granulation

This article addresses the subject of continuum modeling of dense granular flows with an application in high shear granulation. The possible use of continuum models and their ability to reproduce correct dynamics of such flows has been a subject of debate for a long time in the literature, and no consensus has been achieved so far. In this paper, we examine and compare two ways for making it possible to study dense granular flows in a continuum framework: the one that considers the stress tensor of a particulate phase as a sum of frictional and kinetic-collisional terms and the one that is based on modification of transport coefficients of the kinetic theory of granular flow. The latter framework is based on an analogy with molecular systems and how they behave at the phase transition from a liquid to a crystalline state. We show here that the formulation proposed in this work is able to correctly capture the phase transition and coexistence of solid-like and fluid-like phases in dense granular flows. This is in contrast to the model with added friction where the stress-strain dependence is shown to give a qualitatively different behavior compared to experimental data.

Microwave spectroscopic observation of distinct electron solid phases in wide quantum wells

In high magnetic fields, two-dimensional electron systems can form a number of phases in which interelectron repulsion plays the central role, since the kinetic energy is frozen out by Landau quantization. These phases include the well-known liquids of the fractional quantum Hall effect, as well as solid phases with broken spatial symmetry and crystalline order. Solids can occur at the low Landau-filling termination of the fractional quantum Hall effect series but also within integer quantum Hall effects. Here we present microwave spectroscopy studies of wide quantum wells that clearly reveal two distinct solid phases, hidden within what in d.c. transport would be the zero diagonal conductivity of an integer quantum-Hall-effect state. Explanation of these solids is not possible with the simple picture of a Wigner solid of ordinary (quasi) electrons or holes.

Glass-like dynamics in the cell and in cellular collectives.

Prominent fluctuations, heterogeneity, and cooperativity dominate the dynamics of the cytoskeleton as well as the dynamics of the cellular collective. Such systems are out of equilibrium, disordered, and remain poorly understood. To explain these findings, we consider a unifying mechanistic rubric that imagines these systems as comprising phases of soft condensed matter in proximity to a glass or jamming transition, with associated transitions between solid-like versus liquid-like phases. At the scale of the cytoskeleton, data suggest that intermittent dynamics, kinetic arrest, and dynamic heterogeneity represent mesoscale features of glassy protein-protein interactions that link underlying biochemical events to integrative cellular behaviors such as crawling, contraction, and remodeling. At the scale of the multicellular collective, jamming has the potential to unify diverse biological factors that previously had been considered mostly as acting separately and independently. Although a quantitative relationship between intra- and intercellular dynamics is still lacking, glassy dynamics and jamming offer insights linking the mechanobiology of cell to human physiology and pathophysiology.