Various Degrees Of Disorder Research Articles

Prediction of interface between regions of varying degrees of order or disorderness in intrinsically disordered proteins from dihedral angles

Intrinsically disordered proteins (IDPs) are proteins that do not form uniquely defined three-dimensional (3-D) structures. Experimental research on IDPs is difficult since they go against the traditional protein structure-function paradigm. Although there are several predictors of disorder based on amino acid sequences, but very limited based on the 3-D structures of proteins. Dihedral angles have a significant role in predicting protein structure because they establish a protein’s backbone, which, coupled with its side chain, establishes its overall shape. Here, we have carried out atomistic Molecular Dynamics (MD) simulations on four different proteins: one ordered protein (Monellin), two partially disordered proteins (p53-TAD and Amyloid beta (Aβ1-42) peptide), and one completely disordered protein (Histatin 5). The MD simulation trajectories for the corresponding four proteins were used to conduct dihedral angle (ϕ and ѱ) analysis. Then, the average dihedral angles for each of the residues were calculated and plotted against the residue index. We noticed steep rises or falls in the average ϕ value at certain locations in the plot. These sudden shifts in the average ϕ value reflect the interface between regions of varying degrees of order or disorderness in intrinsically disordered proteins. Using this method, the probable conformer of a protein with a higher degree of disorder can be found among the ensembles of structures sampled during the MD simulations. The results of our study offer new understandings on precisely identifying regions of various degrees of disorder in intrinsically disordered proteins. Communicated by Ramaswamy H. Sarma

Disorder within disordered regions of protein-free lipid bilayers.

Optical microscopy-based reports on protein-free lipid bilayers with heterogeneous compositions generally consider observed phase separations as thermodynamic endpoints; while MD simulations indicate kinetic characteristics of domain formations. Here, we study GUVs of POPC:DOPE (9:1) and POPC:DPPC (9:1), labeled with disordered-phase probe Liss-RhodPE (1/1000 w/w), using confocal imaging. In addition to confirming previously well-reported disorder and/or phase-separations in vesicular membranes of above compositions, we report the discovery of non-uniform probe distributions within disordered phases, indicating varying degrees of disorder (VDD) for the same vesicular membrane. We further examine dynamics of probe distributions in VDD regions of vesicular membranes. Regression analysis of time-dependent changes in average pixel intensities of probe molecules (avPIs) in different regions of interest (ROIs) allowed quantitative characterization of local (within ROIs) and global (overall vesicular membrane) motion of probe molecules within disordered phases. Optics-related artifacts (e.g., photobleaching, excitation and/or emission fluctuations) were ruled out by noting negligible variations in whole-vesicle avPIs with time. However, avPIs within certain ROIs showed considerable changes with time. In fact, in the same vesicular membrane, avPIs in different ROIs within disordered phases show (a) linear dependence on time (indicating diffusive motion), (b) dependence on square of time (indicating convective motion), and (c) other dependencies on time (e.g., logarithmic, exponential, power, 1/time etc.) - all clubbed together as non-diffusive-non-convective motions. Thus, we rigorously establish existence of further (at least three) levels of heterogeneity, based on dynamics of probe molecules, within disordered phases of protein-free lipid bilayers. Such heterogeneity has previously been ascribed only to biologically active membranes due to presence of membrane proteins. Interestingly, while diffusive motion may be linked to overall membrane viscosity, convective motion may be linked to concepts such as line-tension resulting from heterogeneous compositions.

Effect of environment and charge patterning on the dynamics of marginally disordered proteins.

Intrinsically disordered proteins (IDPs) and proteins with long intrinsically disordered regions (IDRs) compose a large fraction of the proteome in all domains of life. Despite an extensive body of literature on “ordinary” disordered proteins—ones with high charge to hydropathy ratio—disordered proteins with lower charge to hydropathy ratio remain underinvestigated. To what extent do such “borderline” proteins compactify or perhaps even fold under physiological conditions? In addition, how does the patterning of charged residues in the primary structure of these IDPs affect the three-dimensional structure? Here we aim to characterize three proteins with various degrees of disorder in vitro and in cell using a suite of biophysical techniques. Our results show that the chain dimensions of all three proteins are sensitive to temperature, ionic strength, and crowder concentration in vitro and inside cells, as predicted from analytical and computational models. Moreover, we observe cooperative collapse for two of the three proteins, reminiscent of folding transitions of globular proteins. We further show that charge decoration is the primary predictor of IDP chain dimensions and models that rely solely on the polymer net charge fail to capture the relative chain dimensions of the mutants of the IDPs in our study.

Disorder effects on the ballistic transport of gated phosphorene superlattices

In this paper, we carry out a theoretical study of the electronic ballistic transport in gated phosphorene superlattices. Our work is focused on the effects by the random introduction of structural disorder in the electrostatic potential barriers. Specifically, we consider various degrees of disorder in the width and height of the barriers. To explain the transport of the charge carriers (electrons and holes) in the armchair direction of phosphorene, we employ a low-energy two-band Hamiltonian derived from the tight-binding model. The transmission and conductance are calculated by the transfer matrix technique and the Landauer-B\"uttiker formalism, respectively. We have found that both types of disorder affect the transmission and conductance in different ways, and we also found distinct effects on the charge carriers. In general, the disorder significantly reduces the transmission as well as the peak zones associated with the tunneling effect. Particularly, for disorder in the width, the transmission miniband structure is greatly degraded, while for disorder in the height, the miniband structure is preserved. The variation in the width of the barriers interferes directly with the Fabry-P\'erot resonances of the propagating waves, while the variation in the height mainly reduces the magnitude of the transmission due to the dominance of evanescent waves. Consequently, the conductance loses its oscillatory characteristic and experiences flattening under the influence of disorder of the width, in contrast with the disorder of the height in which the oscillation prevails. Finally, we found that both types of disorder induce a redistribution of electron states. Specifically, the allowed energy bands are increased, and the occupation number as well as the accumulation of states are greatly reduced, which is in accordance with the effects of disorder observed in the transport properties.

Edge betweenness centrality as a failure predictor in network models of structurally disordered materials

Network theoretical measures such as geodesic edge betweenness centrality (GEBC) have been proposed as failure predictors in network models of load-driven materials failure. Edge betweenness centrality ranks which links are significant, based on the fraction of shortest paths that pass through the links between network nodes. We study GEBC as a failure predictor for two-dimensional fuse network models of load transmission in structurally disordered materials. We analyze the evolution of edge betweenness centrality in the run-up to failure and the correlation between GEBC and failure propensity for both hierarchical and non-hierarchical networks exhibiting various degrees of disorder. We observe a non trivial relationship between GEBC and failure propensity, which suggests that the idea of GEBC as a useful failure predictor needs to be strongly qualified.

An Ordered Alite Cement Clinker Phase (Ca3SiO5, aP162) from Flux Synthesis

AbstractCalcium silicates are the main components in cement clinkers. Alite, the nesosilicate or island silicate Ca3SiO5, also named C3S in cement chemistry notation, represents the main phase in Portland cement clinkers. Due to the metastability of Alite at room temperature, quenching from high temperatures is mandatory for phase preservation and impurities are important structure directing factors. Those two aspects result in a plethora of published polymorphs. Many Alite polymorphs described in the literature are characterized by various degrees of disorder within the Si−O substructure which is a direct consequence of afore mentioned features (i. e. quenching and presence of impurities). Here we report on the CaCl2‐flux mediated synthesis and structural characterization of an aP162 Alite featuring a fully‐ordered [SiO4] tetrahedron substructure. The orientation of the [SiO4] tetrahedron substructure is discussed based on the Nishi and Takéuchi nomenclature and is equivalent to the Golovastikov model reported in 1975. Rietveld analyses of a synthetic clinker and three commercial CEM I clinker substantiate that the aP162 model can successfully be applied for clinker phase analysis. Besides the structural characterization, quantum chemical band structure calculations based on Density Functional Theory methods illustrate the expected electrically isolating character of Ca3SiO5.

Disorder-driven two-dimensional quantum phase transitions in LixMoS2

Quantum phase transition (QPT) is the keystone in understanding the quantum state of matter. Here we report observation of QPT and its evolution in nanosheets of LixMoS2 with various degrees of disorder introduced by progressive thermal annealing. The material exhibits onset of superconducting transition at temperatures ranging between 3 and 6 K. We show that the angular dependence of the upper critical field is well described by Tinkham’s (2D) model. Finite-size scaling analysis reveals that the pristine samples with predominantly T/T′ phases exhibit magnetic-field driven superconductor-to-metal QPT. We further show that annealed samples with a higher content of 2H phase exhibit QPT with diverging critical exponents similar to the recently reported behaviours of highly crystalline 2D superconductors.

Study of the Dynamic Characteristics of BWE Based on Products, Difference With a Two-Stage Supply Chain

In previous studies, many researchers have achieved significant success in reducing the negative effects brought about by the bullwhip effect. In this article, the authors have established a supply chain that consists of one supplier and two retailers and has adopted a Cournot-Bertrand mixed duopoly model that successfully combines a nonlinear complexity dynamic system with the bullwhip effect. In order to partition systems with various degrees of disorder and take appropriate methods to refrain systems from falling into a chaos state, numerical simulation methods are conducted to find the stability range, bifurcation range and the chaos range. This article focuses on three different ranges that the authors analyze about the bullwhip effect and inventory variability. In the end, some practical suggestions on behavioral science management are made.

The order–disorder potential of the crystal structure of monohydrocalcite, CaCO3·H2O

Monohydrocalcite, CaCO3·H2O, forms a P31 structure composed of composite rods in which a spiral arrangement of Ca ions is accompanied by spiral arrangements of CO3 groups and of H2O molecules. The atom arrangement on the surface of the rods has rod symmetry P3121 whereas in the rod interior the atoms and atom groups have symmetry P31, which allows for two opposite orientations of a composite rod in respect to the [00.1] direction, connected with minimal change in the inter-rod bonding scheme. The ordered crystal structure contains both rod orientations in a complicated periodic arrangement but various degrees of disorder should occur, generating only small energy penalty.

Simulation of Temperature-Dependent Charge Transport in Organic Semiconductors with Various Degrees of Disorder.

Different trends in the temperature dependence of the mobility can be observed in organic semiconductors, which constitutes a serious challenge for theoretical approaches. In this work, we apply an atomistic bottom-up simulation for the calculation of temperature-dependent mobilities of a broad selection of materials, ranging from single crystal to amorphous solid. We evaluate how well the method is able to distinguish temperature dependences of different materials and how the findings relate to experimental observations. The applied method is able to cover the full range of temperature dependencies from activated transport in amorphous materials to band-like transport in crystals. In well-characterized materials, we find good agreement with the experiment and a band-like temperature dependence. In less-ordered materials, we find discrepancies from the experiment that indicated that experimentally studied materials possess a higher degree of disorder than do the simulated defect-free morphologies.

Jammed Particle Configurations and Dynamics in High-Density Lennard-Jones Binary Mixtures in Two Dimensions

We examine the changeover in the particle configurations and the dynamics in dense Lennard-Jones binary mixtures composed of small and large particles. By varying the composition at a low temperature, we realize crystal with defects, polycrystal with small grains, and glass with various degrees of disorder. In particular, we show configurations where small crystalline regions composed of the majority species are enclosed by percolated amorphous layers composed of the two species. We visualize the dynamics of configuration changes using the method of bond breakage and following the particle displacements. In quiescent jammed states, the dynamics is severely slowed down and is highly heterogeneous at any compositions. In shear, plastic deformations multiply occur in relatively fragile regions, growing into large-scale shear bands where the strain is highly localized. Such bands appear on short time scales and change on long time scales with finite life times.

Structure of Li 2MnO 3 with different degrees of defects

The synthesis and structural properties of the layered oxide Li 2MnO 3 have been studied in details. It represents a key for a better understanding of the complex structural evolutions pointed out in the materials like Li(Li,Ni,Mn,Co)O 2 when they are used as positive electrode materials in lithium-ion batteries. Li 2MnO 3 samples were prepared either via coprecipitation or via a two step solid state reaction followed by different annealing treatments. Using X-ray and electron diffraction in combination with diffraction data simulations, we show that in function of the synthesis conditions, Li 2MnO 3 is obtained with various degrees of disorder, along the c monoclinic direction, in the stacking of the ordered Li 1/3Mn 2/3 sheets within the cfc oxygen packing. We show that this disorder decreases when the synthesis temperature increases but the synthesis of a material free of stacking faults is not possible with these synthesis routes. Finally, the similarities between the evolutions pointed out in Li 2MnO 3 due to the synthesis conditions and those previously observed in the materials like Li(Li,Ni,Mn,Co)O 2 related to the evolution of the cations distribution in the slabs are underlined.

Nature of “Disorder” in the Ordered Double PerovskiteSr2FeMoO6

The degree of B/B;{'} alternate cation order is known to heavily influence the magnetic properties of A_{2}BB;{'}O_{6} double perovskites although the nature of such disorder has never been critically studied. Our detailed x-ray absorption fine structure studies in conjunction with synchrotron radiation x-ray diffraction experiments on polycrystalline Sr_{2}FeMoO_{6} samples with various degrees of disorder reveal that a very high degree of short range order is preserved even in samples with highly reduced long range chemical order. Based on these experimental results and with the help of detailed structural simulations, we are able to model the nature of the disorder in this important class of materials and discuss the consequent implications on its physical properties.

Ionically Conducting Two-Dimensional Heterostructures.

In the context of revealing interfacial effects on ion conduction, thin films are extremely worthwhile due to defined geometry. Of particular interest are heterostructures as they offer symmetric boundary conditions and a high density of hetero-interfaces. The recent progress in this field is reviewed. Materials classes under concern include halides and oxides, and refer to various degrees of disorder and different mobilities. Even though in its infancy, the field of ionic heterostructures is already characterized by a variety of results of fundamental importance and of technological relevance.

Vortex matter in Bi2Sr2CaCu2O8 with pointlike disorder

We investigate the effect of point-like disorder, introduced by irradiation with 2.3 MeV electrons, on the mixed state phase diagram of Bi2Sr2CaCu2O8 single crystals. We focus on the higher irradiation doses that produce a significant depression of the critical temperature Tc, to as low as 2/3 of the initial value. Surprisingly, the first order phase transition (FOT) of the vortex ensemble, from a crystal to the pancake vortex liquid, persists in those highly disordered samples. The second peak in the irreversible magnetization, observed at low temperatures, is equally observed after high irradiation doses, but at much lower magnetic fields. A simple scaling of the phase diagram for samples with various degrees of disorder is not possible, indicating that several fundamental parameters of the superconductor are affected. From the analysis of the angular dependence of the FOT, we deduce that the effective anisotropy factor increases after irradiation.

Density of states in structurally disordered 1D chains of atoms

A one-dimensional potential, V(x), assumed to be a sum of δ-Dirac peaks at atom positions is considered. Disorder is introduced by more or less irregular arrangements of atoms’ positions. Alternatively, a binary alloy is considered to be made up of two different potentials of atoms randomly distributed on a regular lattice. Disorder parameters are used to describe the degree of disorder in the system, and the density of states, ρ(E)’ is discussed for various sets of the model parameters and various degrees of disorder. In a limit case of a one-dimensional crystal, analytical results of the Kronig–Penney model serve as a test for computer simulations based on counting zeros of the wave function at a given energy. Simulations have been carried out for both amorphous and chemical disorders, for chains of up to N=10000 atoms. The results are discussed in terms of how the density of states is modified by a change in the order parameter, leading for example to the disappearance of the band gap, new localized states emerging, or smearing off and/or shifting of the band edges.

Surface structures of approximant phases in the Al-Pd-Mn system

We present a study of the surface of the ${\ensuremath{\xi}}^{\ensuremath{'}}$-Al-Pd-Mn approximant phase based upon scanning tunneling microscopy and low-energy electron diffraction. Several structures are observed on two different samples grown either by the Bridgman technique or by a self-flux method, and which contain various degrees of disorder. We also describe some other complex crystalline phases that are sometimes observed on the fivefold surface of Al-Pd-Mn quasicrystalline samples after the sputter-annealing cleaning process under ultrahigh vacuum conditions. This includes the T approximant phase resulting from surface decomposition after a high-temperature annealing.

Solution-mediated phase transformation of anhydrous to dihydrate carbamazepine and the effect of lattice disorder

This paper describes the kinetics of the solution-mediated phase transformation of the anhydrous monoclinic polymorph of carbamazepine (CBZ(A)) to the dihydrate crystal form (CBZ(D)). Monitoring both solution concentration and solid phase composition identified the steps and mechanisms that control the kinetic processes, and regulate the concentration of drug achieved during dissolution of the metastable solid phase, CBZ(A). The results show that the kinetics and the rate-controlling step for the transformation depend on grinding and storage conditions of CBZ(A). Grinding CBZ(A) shortened the transformation times and changed the rate-controlling step from crystallization of CBZ(D) to dissolution of CBZ(A). Grinding may cause various degrees of disorder in the form of lattice defects and/or amorphous regions. These disordered regions promote the anhydrous to dihydrate transformation by facilitating the surface nucleation of CBZ(D) on freshly ground CBZ(A) and on amorphous CBZ. The concentration-time profiles revealed aging effects on the solution-mediated transformation of ground CBZ(A) that were undetectable by diffraction and thermal analysis. These results have significant consequences on the concentration-time profiles of active pharmaceutical ingredients during dissolution of metastable solid phases, crystalline or amorphous.

Numerical Studies of Shot Noise in 3D Disordered Systems

Shot noise power in 3D disordered conductors has been studied by means of numerical simulations. The Anderson model of disordered conductor, Green's function technique and Fisher-Lee relations have been employed to calculate the transmission matrix t, its eigenvalues T n , the conductance G = Tr(tt + ) and the shot noise power S = Tr(t + t) - Tr(t + t) 2 for various degrees of disorder. To explain the results of simulations, Nazarov's microscopic theory describing the correction to the distribution of transmission eigenvalues has been applied. It was found that the crossover from the ballistic to the diffusive region is well described by the relation obtained by random matrix theory. In the weakly localized regime the correction to the shot noise power is different from the 1D result. Namely, S = G/3 + 0.209. At the localization-delocalization transition we have observed S ≅ 0.57G.

Acoustic measurements of crystalline aluminum and of an aluminum alloy (Al 5056)

We present vibrating reed experiments of aluminum with various degrees of disorder at a measuring frequency of 2.5 kHz and in the temperature range between 30 mK and 300 K . Evidence for the existence of ‘glass-like’ two-level tunneling systems is only observed for a poly-crystalline sample. The internal friction Q −1 of a single crystal is almost temperature independent between 30 mK and 1 K and has a maximum around 7 K which we attribute to the thermally activated motion of dislocations. Q −1 of our Al 5056 specimen is more than an order of magnitude smaller than that of the aluminum single crystal.