Glassy, nonexponential relaxations in globular proteins are typically attributed to conformational behaviors that are missing from intrinsically disordered proteins. Yet, we show that single molecules of a disordered-protein construct display two signatures of glassy dynamics, logarithmic relaxations and a Kovacs memory effect, in response to changes in applied tension. We attribute this to the presence of multiple independent local structures in the chain, which we corroborate with a model that correctly predicts the force dependence of the relaxation. The mechanism established here likely applies to other disordered proteins.
Curvature-inducing proteins containing a Bin/Amphiphysin/Rvs domain often have intrinsically disordered domains. Recent experiments have shown that these disordered chains enhance curvature sensing and generation. Here, we report on the modification of protein-membrane interactions by disordered chains using meshless membrane simulations. The protein and bound membrane are modeled together as a chiral crescent protein rod with two excluded-volume chains. As the chain length increases, the repulsion between them reduces the cluster size of the proteins. It induces spindle-shaped vesicles and a …
The low-temperature thermal and transport properties of an unusual kind of crystal exhibiting minimal molecular positional and tilting disorder have been measured. The material, namely, low-dimensional, highly anisotropic pentachloronitrobenzene (PCNB) has a layered structure of rhombohedral parallel planes in which the molecules execute large-amplitude in-plane as well as concurrent out-of-plane librational motions. Our study reveals that low-temperature glassy anomalies can be found in a system with minimal disorder due to the freezing of (mostly in-plane) reorientational jumps of molecules …
From isolated polyelectrolytes to star-like assemblies: The role of sequence heterogeneity on the statistical structure of the intrinsically disordered Neurofilament-low tail domain
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP alpha-synuclein that include geometric, attractive hydrophobic, and screened electrostatic interactions and are calibrated to the inter-residue separations measured in recent smFRET experiments. We find that alpha-synuclein is disordered with conformational statistics that are intermediate between random walk and collapsed globule behavior. An advantage of cali…
Structural glasses formed by quenching a melt are known to host a population of low-energy quasilocalized (nonphononic) excitations whose frequencies $ω$ follow a universal $\sim\!ω^4$ distribution as $ω\!\to\!0$, independently of the glass formation history, the interparticle interaction potential or spatial dimension. Here, we show that the universal quartic law of nonphononic excitations also holds in disordered crystals featuring finite long-range order, which is absent in their glassy counterparts. We thus establish that the degree of universality of the quartic law extends beyond structu…
We report on a non-equilibrium phase of matter, the minimally disordered crystal phase, which we find exists between the maximally amorphous glasses and the ideal crystal. Even though these near crystals appear highly ordered, they display glassy and jamming features akin to those observed in amorphous solids. Structurally, they exhibit a power-law scaling in their probability distribution of weak forces and small interparticle gaps as well as a flat density of vibrational states. Dynamically, they display anomalous aging above a characteristic pressure. Quantitatively this disordered crystal …
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge to a finite value at T=0. The authors used an exact enumeration method to obtain all ground states for a given RNA sequence. Because of the exponential growing degeneracy, only sequences up to length L=256 could be studied. Here it is shown that, in contrast to the previous results, by going to much larger sizes as L=2000 the variance coverges towards zero,…
The human proteome is enriched in proteins that do not fold into a stable 3D structure. These intrinsically disordered proteins (IDPs) spontaneously fluctuate between a large number of configurations in their native form. Remarkably, the disorder does not lead to dysfunction as with denatured folded proteins. In fact, unlike denatured proteins, recent evidences strongly suggest that multiple biological functions stem from such structural plasticity. Here, focusing on the nanoscopic length-scale, we review the latest advances in IDP research and discuss some of the future directions in this hig…
Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical and cosmetic applications. Increasing demands for functional complexity have been met with challenges in biochemical engineering, driving researchers to innovate in the design of new amphiphiles. An emerging class of molecules, namely, peptide amphiphiles, combines key advantages and circumvents some of the disadvantages of conventional phospholipids and block-copolymers. Herein, we present new peptid…
We observe non-monotonic aging and memory effects, two hallmarks of glassy dynamics, in two disordered mechanical systems: crumpled thin sheets and elastic foams. Under fixed compression, both systems exhibit monotonic non-exponential relaxation. However, when after a certain waiting time the compression is partially reduced, both systems exhibit a non-monotonic response: the normal force first increases over many minutes or even hours until reaching a peak value, and only then relaxation is resumed. The peak-time scales linearly with the waiting time, indicating that these systems retain long…
We report a thorough characterization of the glassy phases of mixtures of succinonitrile and glutaronitrile via dielectric spectroscopy and differential scanning calorimetry. This system is revealed to be one of the rare examples where both glassy states of matter, a structurally disordered supercooled liquid and an orientationally disordered plastic crystal, can be prepared in the same material. Both disordered states can be easily supercooled, finally arriving at a structural-glass or a glassy-crystal state. Detailed investigations using broadband dielectric spectroscopy enable a comparison …
Systems in which a short-ranged attraction and long-ranged repulsion compete are intrinsically frustrated, leading their structure and dynamics to be dominated either by mesoscopic order or by metastable disorder. Here we report the latter case in a colloidal system with long-ranged electrostatic repulsions and short-ranged depletion attractions. We find a variety of states exhibiting slow non-diffusive dynamics: a gel, a glassy state of clusters, and a state reminiscent of a Wigner glass. Varying the interactions, we find a continuous crossover between the Wigner and cluster glassy states, an…
In recent years, the paradigm of `soft glassy matter' has been used to describe diverse nonergodic materials exhibiting strong local disorder and slow mesoscopic rearrangement. As so far formulated, however, the resulting `soft glassy rheology' (SGR) model treats the shear stress in isolation, effectively `scalarizing' the stress and strain rate tensors. Here we offer generalizations of the SGR model that combine its nontrivial aging and yield properties with a tensorial structure that can be specifically adapted, for example, to the description of fluid film assemblies or disordered foams.
Liquid-liquid phase separation (LLPS) is an emerging and universal mechanism for intracellular biomolecule organization, particularly, via the formation of membraneless organelles (MOs). Intrinsically disordered proteins (IDPs) are the main constituents of MOs, wherein multivalent interactions and low-complexity domains (LCDs) drive LLPS. Using short oligopeptide derived from LCDs as 'stickers' and dextran backbones as 'spacers', we designed polymer-oligopeptide hybrids to mimic the multivalent FUS protein as represented by the 'stickers-and-spacers' model. We demonstrated that hybrids underwe…
Amorphous solids or glasses are known to exhibit stretched-exponential decay over broad time intervals in several of their macroscopic observables: intermediate scattering function, dielectric relaxation modulus, time-elastic modulus etc. This behaviour is prominent especially near the glass transition. In this Letter we show, on the example of dielectric relaxation, that stretched-exponential relaxation is intimately related to the peculiar lattice dynamics of glasses. By reformulating the Lorentz model of dielectric matter in a more general form, we express the dielectric response as a funct…
We determine the speed of a crystallisation (or more generally, a solidification) front as it advances into the uniform liquid phase after the system has been quenched into the crystalline region of the phase diagram. We calculate the front speed by assuming a dynamical density functional theory model for the system and applying a marginal stability criterion. Our results also apply to phase field crystal (PFC) models of solidification. As the solidification front advances into the unstable liquid phase, the density profile behind the advancing front develops density modulations and the wavele…
We show that ratchet effects can occur in a glassy media of interacting particles where there is no quenched substrate. We consider simulations of a disordered binary assembly of colloids in which only one species responds to a drive. We apply an asymmetric ac drive that would produce no net dc drift of an isolated overdamped particle. When interacting particles are present, the asymmetric ac drive produces a ratchet effect. A simple model captures many of the results from simulations, including flux reversals as a function of density and temperature.
The relation between elasticity and yielding is investigated in a model polymer solid by Molecular-Dynamics simulations. By changing the bending stiffness of the chain and the bond length, semicrystalline and disordered glassy polymers - both with bond disorder - as well as nematic glassy polymers with bond ordering are obtained. It is found that in systems with bond disorder the ratio Ty/G between the shear yield strength Ty and the shear modulus G is close to the universal value of the atomic metallic glasses. The increase of the local nematic order in glasses leads to the increase of the sh…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins, it loses much of its applicability when discussing intrinsically disordered proteins (IDPs). These peculiar proteins, whose tertiary structure constantly interconverts between a series of energetically favourable conformations, are the root of many current, pressing scientific mechanisms. Many biological processes that are still yet to be elucidated--the mec…
In order to understand the mechanisms for glassy dynamics in biological tissues and shed light on those in non-biological materials, we study the low-temperature disordered phase of 2D vertex-like models. Recently it has been noted that vertex models have quite unusual behavior in the zero-temperature limit, with rigidity transitions that are controlled by residual stresses and therefore exhibit very different scaling and phenomenology compared to particulate systems. Here we investigate the finite-temperature phase of two-dimensional Voronoi and Vertex models, and show that they have highly u…
Glasses and disordered materials are known to display anomalous features in the density of states, in the specific heat and in thermal transport. Nevertheless, in recent years, the question whether these properties are really anomalous (and peculiar of disordered systems) or rather more universal than previously thought, has emerged. New experimental and theoretical observations have questioned the origin of the boson peak and the linear in T specific heat exclusively from disorder and TLS. The same properties have been indeed observed in ordered or minimally disordered compounds and in incomm…
Quantifying mechanical disorder in solids, either disordered crystals or glassy solids, and understanding its range of variability are of prime importance, e.g.~for discovering structure-properties relations. The bounds on the degree of mechanical fluctuations in disordered solids and how those depend on solids formation history remain unknown. Here, we study a broadly applicable quantifier of mesoscopic mechanical disorder $χ$, defined via the dimensionless fluctuations of the shear modulus, over a wide variety of disordered computer solids and upon varying different control parameters. $χ$ i…
Recently introduced constitutive equations for the rheology of dense, disordered materials are investigated in the context of stick-slip experiments in boundary lubrication. The model is based on a generalization of the shear transformation zone (STZ) theory, in which plastic deformation is represented by a population of mesoscopic regions which may undergo non affine deformations in response to stress. The generalization we study phenomenologically incorporates the effects of aging and glassy relaxation. Under experimental conditions associated with typical transitions from stick-slip to stea…
We consider a phantom chain model of polymer with internal friction in a harmonic confinement and extend it to take care of effects of solvent quality following a mean field approach where an exponent $ν$ is introduced. The model termed as "Solvent Dependent Compacted Rouse with Internal Friction (SDCRIF)" is then used to calculate the reconfiguration time of a chain that relates to recent Förster resonance energy transfer (FRET) studies on folded and intrinsically disordered proteins (IDPs) and can account for the effects of solvent quality as well as the denaturant concentration on the recon…
Soil creeps imperceptibly downhill, but also fails catastrophically to create landslides. Despite the importance of these processes as hazards and in sculpting landscapes, there is no agreed upon model that captures the full range of behavior. Here we examine the granular origins of hillslope soil transport by Discrete Element Method simulations, and re-analysis of measurements in natural landscapes. We find creep for slopes below a critical gradient, where average particle velocity (sediment flux) increases exponentially with friction coefficient (gradient). At critical there is a continuous …
Intrinsically disordered proteins (IDPs) are typically low in nonpolar/hydrophobic but relatively high in polar, charged, and aromatic amino acid compositions. Some IDPs undergo liquid-liquid phase separation in the aqueous milieu of the living cell. The resulting phase with enhanced IDP concentration can function as a major component of membraneless organelles that, by creating their own IDP-rich microenvironments, stimulate critical biological functions. IDP phase behaviors are governed by their amino acid sequences. To make progress in understanding this sequence-phase relationship, we repo…
Random polyampholytes (PAs) contain positively and negatively charged monomers that are distributed randomly along the polymer chain. The interaction between charges is assumed to be given by the Debye-Huckel potential. We show that the size of the PA is determined by an interplay between electrostatic interactions, giving rise to the polyelectrolyte (PE) effect due to net charge per monomer ($σ$), and an effective attractive PA interaction due to charge fluctuations, $δσ$. The interplay between these terms gives rise to non-monotonic dependence of the radius of gyration, $R_g$ on the inverse …
We summarize current developments in the investigation of glassy matter using nonlinear dielectric spectroscopy. This work also provides a brief introduction into the phenomenology of the linear dielectric response of glass-forming materials and discusses the main mechanisms that can give rise to nonlinear dielectric response in this material class. Here we mainly concentrate on measurements of the conventional dielectric permittivity at high fields and the higher-order susceptibilities characterizing the 3-omega and 5-omega components of the dielectric response as performed in our group. Typi…
We study two dimensional frustrated but non-disordered systems applying a replica approach to a stripe forming model with competing interactions. The phenomenology of the model is representative of several well known systems, like high-Tc superconductors and ultrathin ferromagnetic films, which have been the subject of intense research. We establish the existence of a glass transition to a non-ergodic regime accompanied by an exponential number of long lived metastable states, responsible for slow dynamics and non-equilibrium effects.
Biomolecular condensates, physically underpinned to a significant extent by liquid-liquid phase separation (LLPS), are now widely recognized by numerous experimental studies to be of fundamental biological, biomedical, and biophysical importance. In the face of experimental discoveries, analytical formulations emerged as a powerful yet tractable tool in recent theoretical investigations of the role of LLPS in the assembly and dissociation of these condensates. The pertinent LLPS often involves, though not exclusively, intrinsically disordered proteins engaging in multivalent interactions that …
The emergence of glassy dynamics and the glass transition in dense disordered systems is still not fully understood theoretically. Mode-coupling theory (MCT) has shown to be effective in describing some of the non-trivial features of glass formation, but it cannot explain the full glassy phenomenology due to the strong approximations on which it is based. Generalized mode-coupling theory (GMCT) is a hierarchical extension of the theory, which is able to outclass MCT by carefully describing the dynamics of higher order correlations in its generalized framework. Unfortunately, the theory has so …
Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted multiple-chain simulations of the N-terminal intrinsically disordered region (IDR) of DEAD-box helicase Ddx4, as a test case, to assess the roles of electrostatic, hydrophobic, cation-$π$, and aromatic interactions in amino acid sequence-dependent LLPS. We evaluated 3 residue-residue interaction schemes with a shared electrostatic potential. Neither a common hydrophobicity scheme nor one augmented with arginine/lysine-ar…
Recent years have seen a rapid increase of interest in dense active materials, which, in the disordered state, share striking similarities with conventional passive glass-forming matter. For such passive glassy materials, it is well established (at least in three dimensions) that the details of the microscopic dynamics, e.g., Newtonian or Brownian, do not influence the long-time glassy behavior. Here we investigate whether this still holds true in the non-equilibrium active case by considering two simple and widely used active particle models, i.e., active Ornstein-Uhlenbeck particles (AOUPs) …
Mechanical response of a simple DNA nanostar hydrogel: symptoms of disorder and glassy emergence of solidity
Institut Néel-CNRS/UGA-Grenoble INP（内尔研究所）；LIMMS-CNRS/Institute of Industrial Science-The University of Tokyo（理化学研究所-东京大学工业科学研究所）；LIP-CNRS/ENS Lyon（里昂高等师范学校）；Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière（里昂第一大学）
The dynamics of a tracer particle in a glassy matrix of obstacles displays slow complex transport as the free volume approaches a critical value and the void space falls apart. We investigate the emerging subdiffusive motion of the test particle by extensive molecular dynamics simulations and characterize the spatio-temporal transport in terms of two-time correlation functions, including the time-dependent diffusion coefficient as well as the wavenumber-dependent intermediate scattering function. We rationalize our findings within the framework of critical phenomena and compare our data to a d…
