Spontaneous Domain Formation Research Articles

Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study.

Amyloid-β (Aβ) peptides form assemblies that are pathological hallmarks of Alzheimer’s disease. Aβ oligomers are soluble, mobile, and toxic forms of the peptide that act in the extracellular space before assembling into protofibrils and fibrils. Therefore, oligomers play an important role in the mechanism of Alzheimer’s disease. Since it is difficult to determine by experiment the atomic structures of oligomers, which accumulate fast and are polymorphic, computer simulation is a useful tool to investigate elusive oligomers’ structures. In this work, we report extended all-atom molecular dynamics simulations, both canonical and replica exchange, of Aβ(1–42) trimer starting from two different initial conformations: (i) the pose produced by the best docking of a monomer aside of a dimer (simulation 1), representing oligomers freshly formed by assembling monomers, and (ii) a configuration extracted from an experimental mature fibril structure (simulation 2), representing settled oligomers in equilibrium with extended fibrils. We showed that in simulation 1, regions with small β-barrels are populated, indicating the chance of spontaneous formation of domains resembling channel-like structures. These structural domains are alternative to those more representative of mature fibrils (simulation 2), the latter showing a stable bundle of C-termini that is not sampled in simulation 1. Moreover, trimer of Aβ(1–42) can form internal pores that are large enough to be accessed by water molecules and Ca2+ ions.

Nonspecific characteristics of macromolecules create specific effects in living cells.

Recently, the important role of microphase separation in living cells has been attracting considerable interest in relation to cell organization and function. For example, many studies have focused on liquid-liquid phase separation (LLPS) as a very plausible mechanism for the presence of membraneless organelles. To confirm the role of phase separation in living cells, experimental studies on models and/or reconstructed systems are needed. In this short review, we discuss current paradigms of LLPS and provide some example "review data" to demonstrate particular points relating to the specific localization of biological macromolecules like DNAs and actin proteins with spontaneous domain formation in microdroplets emerging in an aqueous two-phase system (ATPS) (we use polyethylene glycol (PEG)/dextran (DEX)-a binary polymer solution). We also suggest that phase separation and transition may play basic roles in regulation of the biochemical reactivity of individual long genomic DNAs.

Spontaneous Domain Formation in Spherically Confined Elastic Filaments.

Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers.

Energy transfer mechanisms in a dipole chain: From energy equipartition to the formation of breathers.

We study the energy transfer in a classical dipole chain of N interacting rigid rotating dipoles. The underlying high-dimensional potential energy landscape is analyzed in particular by determining the equilibrium points and their stability in the common plane of rotation. Starting from the minimal energy configuration, the response of the chain to excitation of a single dipole is investigated. Using both the linearized and the exact Hamiltonian of the dipole chain, we detect an approximate excitation energy threshold between a weakly and a strongly nonlinear dynamics. In the weakly nonlinear regime, the chain approaches in the course of time the expected energy equipartition among the dipoles. For excitations of higher energy, strongly localized excitations appear whose trajectories in time are either periodic or irregular, relating to the well-known discrete or chaotic breathers, respectively. The phenomenon of spontaneous formation of domains of opposite polarization and phase locking is found to commonly accompany the time evolution of the chaotic breathers. Finally, the sensitivity of the dipole chain dynamics to the initial conditions is studied as a function of the initial excitation energy by computing a fast chaos indicator. The results of this study confirm the aforementioned approximate threshold value for the initial excitation energy, below which the dynamics of the dipole chain is regular and above which it is chaotic.

Spontaneous domain formation in disordered copolymers as a mechanism for chromosome structuring.

Motivated by the problem of domain formation in chromosomes, we studied a co-polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus introducing some quenched disorder in the system. Previous work has shown that in the case of regularly-spaced interacting monomers this chain can fold into structures characterized by multiple distinct domains of consecutive segments. In each domain, attractive interactions are balanced by the entropy cost of forming loops. We show by advanced replica-exchange simulations that adding disorder in the position of the interacting monomers further stabilizes these domains. The model suggests that the partitioning of the chain into well-defined domains of consecutive monomers is a spontaneous property of heteropolymers. In the case of chromosomes, evolution could have acted on the spacing of interacting monomers to modulate in a simple way the underlying domains for functional reasons.

Kibble-Zurek scalings of continuous magnetic phase transitions in spin-1 spin-orbit-coupled Bose-Einstein condensates

We investigate the universal dynamics of a continuous magnetic phase transition from a unmagnetized phase to a ferromagnetic phase in a spin-1 spin-orbit-coupled Bose-Einstein condensate. When the system approaches the critical point, the Landau critical velocity gradually decreases to zero and so the correlation length diverges. Therefore, during the slow passage through the critical point, ferromagnetic domains are spontaneously created according to the Kibble-Zurek mechanism. Through calculating the Bogoliubov excitations, we give the Landau critical velocity and the correlation length, from which we derive the Kibble-Zurek scalings. Furthermore, we numerically simulate the critical spatial-temporal dynamics of the bifurcation delay and spontaneous domain formation, and extract the universal scaling exponents. The numerical scalings extracted from the critical spatial-temporal dynamics are very consistent with the scalings derived from the correlation length.

Strong Electro-Optic Effect and Spontaneous Domain Formation in Self-Assembled Peptide Structures.

Short peptides made from repeating units of phenylalanine self‐assemble into a remarkable variety of micro‐ and nanostructures including tubes, tapes, spheres, and fibrils. These bio‐organic structures are found to possess striking mechanical, electrical, and optical properties, which are rarely seen in organic materials, and are therefore shown useful for diverse applications including regenerative medicine, targeted drug delivery, and biocompatible fluorescent probes. Consequently, finding new optical properties in these materials can significantly advance their practical use, for example, by allowing new ways to visualize, manipulate, and utilize them in new, in vivo, sensing applications. Here, by leveraging a unique electro‐optic phase microscopy technique, combined with traditional structural analysis, it is measured in di‐ and triphenylalanine peptide structures a surprisingly large electro‐optic response of the same order as the best performing inorganic crystals. In addition, spontaneous domain formation is observed in triphenylalanine tapes, and the origin of their electro‐optic activity is unveiled to be related to a porous triclinic structure, with extensive antiparallel beta‐sheet arrangement. The strong electro‐optic response of these porous peptide structures with the capability of hosting guest molecules opens the door to create new biocompatible, environmental friendly functional materials for electro‐optic applications, including biomedical imaging, sensing, and optical manipulation.

Suppression of relative flow by multiple domains in two-component Bose-Einstein condensates

We investigate flow properties of immiscible Bose-Einstein condensates composed of two different Zeeman spin states of 87Rb. Spatially overlapping two condensates in the optical trap are prepared by application of a resonant radio frequency pulse, and then the magnetic field gradient is applied in order to produce the atomic flow. We find that the spontaneous multiple domain formation arising from the immiscible nature drastically changes the fluidity. The homogeneously overlapping condensates readily separate under the magnetic field gradient, and they form stable configuration composed of the two layers. In contrast, the relative flow between two condensates are largely suppressed in the case where the magnetic field gradient is applied after spontaneous domain formation.

Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid.

Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework combining solely these two ingredients, in order to characterize their joint effects. Specifically, we study a simple polymer physics computational model with weak ubiquitous short-ranged self attraction and stronger sparse bridging interactions. Combining theoretical arguments and simulations, we study the general phenomenology of polymer collapse induced by these dual contributions, in the case of regularly spaced bridging. Our results distinguish a regime of classical Flory-like coil-globule collapse dictated by the interplay of excluded volume and attractive energy and a switch-like collapse where bridging interactions compete with entropy loss terms from the looped arms of a star-like rosette. Additionally, we show that bridging can induce stable compartmentalized domains. In these configurations, different "cores" of bridging proteins are kept separated by star-like polymer loops in an entropically favorable multi-domain configuration, with a mechanism that parallels micellar polysoaps. Such compartmentalized domains are stable, and do not need any intra-specific interactions driving their segregation. Domains can be stable also in the presence of uniform attraction, as long as the uniform collapse is above its theta point.

Pseudospin dynamics of exciton-polariton patterns in a coherently driven semiconductor microcavity

The influence of the exciton spin on the formation and stability properties of periodic cavity polariton patterns is studied in a semiconductor microcavity operating in the strong-coupling regime. A linearly polarized optical beam excites polaritons formed by excitons with different spin orientations and left- and right-circularly polarized photons. The perturbation analysis of homogeneous solutions reveals a competition between these two spin states. The outcome of this competition is determined by the sign of the cross-phase modulation parameter. In particular, it is shown that linearly polarized patterns are preferred, if this parameter is positive. Otherwise, a spontaneous symmetry-breaking instability leads to the formation of transverse patterns with a spatial polarization asymmetry. In the regime of bistable homogeneous solutions we observe the spontaneous formation of domains framed by one-dimensional dark half solitons.

Universality in nonequilibrium condensation of exciton-polaritons

We investigate the process of condensation of exciton-polaritons in a one-dimensional nanowire, predicting spontaneous formation of domains of uncondensed excitons and condensed polaritons. We find that the system does not follow the standard Kibble-\ifmmode \dot{Z}\else \.{Z}\fi{}urek scenario of defect formation. Nevertheless, the universal scaling laws are still present if the critical exponents are replaced by their ``nonequilibrium'' counterparts related to the imaginary part of the time-dependent Bogoliubov spectrum.

Spontaneous shape changes in polymersomes via polymer/polymer segregation

We demonstrate that nanometre-sized polymer vesicles (polymersomes) assembled from two dissimilar diblock copolymers can undergo shape changes, driven by strong lateral polymer/polymer segregation within the membrane. The two particular block copolymers consisted of identical hydrophobic fragments to stimulate co-assembly, while their hydrophilic segments were either neutrally or negatively charged. It is hypothesized that demixing of the two types of polymer amphiphiles within the bilayer is caused by the different hydrophilic polymer fractions exhibiting intrinsically different interfacial curvatures upon self-assembly. Evidence for spontaneous domain formation came from dynamic light scattering analysis, electron microscopy and a fluorophore/quencher system. Given the vast amount of possible polymeric amphiphiles that can be co-assembled into hybrid aggregates, many more interesting and possibly biomedically relevant materials can be generated once inter-membrane phase separation becomes well-characterised and understood.

Two intertwined facets of adherent membranes: membrane roughness and correlations between ligand–receptors bonds

We study equilibrium fluctuations of adherent membranes by means of Langevin simulations in the case when the interaction of the membrane with the substrate is twofold: a non-specific homogeneous harmonic potential is placed at large distances, whereas discrete ligand–receptor interactions occur at short distances from the flat substrate. We analyze the correlations between neighboring ligand–receptor bonds in a regime of relatively strong membrane fluctuations. By comparison with the random distribution of bonds, we find that the correlations between the bonds are always positive, suggesting spontaneous formation of domains. The equilibrium roughness of the membrane is then determined by fluctuations in the number density of bonds within the domains. Furthermore, we show that the excess number of bonds arising due to correlations and the instantaneous roughness of the membrane both follow master curves that depend only on the instantaneous bond density and not on the intrinsic binding strength of the ligand–receptor pair. The master curves show identical trends, further corroborating the link between membrane roughness and bond correlations.

Polarization phenomena in resonantly pumped disordered semiconductor microcavities

We analyze the spatial distribution of the intensity of photoluminescence and its polarization in resonantly pumped semiconductor microcavities. The strong spin anisotropy of polariton-polariton interactions leads to the spontaneous formation of domains with strong circular polarization in real space under a uniformly polarized elliptical pump. These domains can serve as an experimental map of the disorder profile present in the system.

Dynamical Instability and Domain Formation in a Spin-1 Bose-Einstein Condensate

We interpret the recently observed spatial domain formation in spin-1 atomic condensates as a result of dynamical instability. Within the mean field theory, a homogeneous condensate is dynamically unstable (stable) for ferromagnetic (antiferromagnetic) atomic interactions. We find that this dynamical instability naturally leads to spontaneous domain formation as observed in several recent experiments for condensates with rather small numbers of atoms. For trapped condensates, our numerical simulations compare quantitatively to the experimental results, thus largely confirming the physical insight from our analysis of the homogeneous case.

Reversible Trilayer Formation at the Air−Water Interface from a Mixed Monolayer Containing a Cationic Lipid and an Anionic Porphyrin

The molecular organization of a cationic matrix (DOMA) as influenced by the presence of an anionic water-soluble porphyrin (TSPP), in the mixed monolayer, molar ratio TSPP/DOMA = 1:4, has been studied by π−A isotherms, the reflection spectra, BAM images, and imaging ellipsometry at the air−water interface. A reversible collapse of the mixed film at high surface pressures is observed. The formation of an aggregate of the porphyrin molecules under compression is inferred from the reflection spectra. BAM images show the spontaneous formation of domains at 35 mN/m that become bigger during the spontaneous dense process at constant surface pressure. The reversible character of that process was also observed by BAM. The evaluation of the reflection spectra as well as the area fraction of the domains and the surrounding dark regions have led us to consider a trilayer structure for the TSPP/DOMA domains emerging during the collapse process. By using imaging ellipsometry on selected regions of interest (few microns), the thicknesses of domains (ddom = 5.045 nm) and surrounding areas (ddark = 1.764 nm) were estimated. These thickness values are in good agreement with the trilayer architecture where the DOMA molecules have retained the TSPP molecules by electrostatic interactions.

Symmetry locking and commensurate vortex domain formation in periodic pinning arrays.

The spontaneous formation of domains of commensurate vortex patterns near rational fractional matching fields of a periodic pinning array has been investigated with high resolution scanning Hall probe microscopy. We show that domain formation is promoted due to the efficient incorporation of mismatched excess vortices and vacancies at the corners of domain walls, which outweighs the energetic cost of creating them. Molecular dynamics simulations with a generic pinning potential reveal that domains are formed only when vortex-vortex interactions are long range.

A powder diffraction study of the phase transition in LaAlO3

The structure of LaAlO3 has been investigated around the phase transition at Tc ≈ 800 K by neutron powder diffraction in vacuum and by X-ray powder diffraction under nitrogen atmosphere as well as by a very high resolution synchrotron experiment in air. The results were analysed in frame of the Landau theory using the fluctuation-dissipation theorem to relate the susceptibility to the atomic displacement parameters. The room temperature structure is a rhombohedrally distorted perovskite structure, space group R-3c , which undergoes a transition to the ideal perovskite structure, space group Pm-3m , at high temperatures. The order parameter is a rotation of the O6-octahedron described by one x(O)-parameter. This parameter and the spontaneous strain (c/a-√6), as well as the relevant atomic displacement parameter Uop 11(O) in the order parameter system, show a critical behaviour in agreement with a second order phase transition. Although the critical exponents of the order parameter and strain show the expected coupling behaviour, there is a striking difference of the transition temperature: the metric becomes cubic roughly 30 K below the proper Tc. This is related to spontaneous formation of domains imposing the average cubic symmetry via internal stresses.

ORDERING AT SURFACES FROM ELASTIC AND ELECTROSTATIC INTERACTIONS

Elastic and electrostatic interactions can sometimes have a profound influence on surface morphology. Here, we review the conditions under which surface stress or surface dipole variations can give rise to spontaneous domain formation at surfaces, and focus especially on the case of the Si(100) surface. In principle, the anisotropy of the surface stress should cause the spontaneous formation of a striped domain structure on Si(100). In practice, the length scale for this domain structure turns out to be so large as to prevent its direct observation, although the influence of the elastic interactions has been observed indirectly in a variety of related experiments. It is now evident that by introducing Ge or B atoms, the conditions can be tuned in such a way that the spontaneous domain formation is strikingly observed. Because surface electrostatic dipolar interactions scale in the same way as elastic ones, it follows that similar effects can arise from these sources. We consider a simple model two-phase surface system with 1/r3 dipolar interactions, and find that the model exhibits spontaneous formation of two kinds of periodic domain structure. A striped domain structure is stable near half-filling, but as the area fraction is changed, a transition to a hexagonal lattice of almost-circular droplets occurs. The relation of this model to experimental surface systems, especially that of Langmuir layers at the water–air interface, will be discussed.

Syntheses, Structural Analyses, and Unusual Magnetic Properties of Ba2CoSi2O7 and BaCo2Si2O7

The compounds Ba2CoSi2O7, 1, and BaCo2Si2O7, 2, were obtained by heating mixtures of BaCO3, CoCO3, and SiO2 in the proper stoichiometries to 1300 °C for 48 h. Both materials were characterized by single-crystal X-ray diffraction and magnetization measurements on powder and partially oriented single crystals. Each cobalt ion in 1 is surrounded by four oxygen atoms derived from the [Si2O7]6- groups in the form of a distorted tetrahedron. The cobalt ions are bridged by O−Si−O and O−Si−O−Si−O groups from the [Si2O7]6- ions in an extended two-dimensional arrangement. The barium ions are arranged in layers that run parallel to the Co[Si2O7] layers. In 2 each cobalt ion is also surrounded by an arrangement of four oxygen atoms derived from the Si2O7 groups in a distorted tetrahedral shape. These tetrahedra are linked into chains through the sharing of one of the oxygen atoms from the Si2O7 groups. The CoO4 chains are crosslinked via O−Si−O−Si−O bridges from the Si2O7 groups. The barium ions occupy channels that run parallel to the crystallographic c-axis. Curie−Weiss behaviors and temperature independent paramagnetisms (TIP) coexist in the ranges 40−300 K and 100−300 K for 1 and 2, respectively. For both compounds the values of the Curie constant and TIP are consistent with tetrahedral Co(II) ions having three unpaired electrons. While compound 1 remains paramagnetic down to 5 K, 2 undergoes a transition into a state having a field-induced weak ferromagnetic response at Tc = 21 K. The weak ferromagnetic properties below Tc can be explained by spin canting and spontaneous domain formation. The canting angle is estimated to be about 5° at 5 K. Interestingly, 2 could represent the first example among the tetrahedral Co(II) compounds with the transition temperature (Tc = 21 K) being higher than the zero-field splitting of the 4A2 electronic ground state. Crystal data: for 1, formula Ba2CoSi2O7, a = 8.450(1) Å, b = 10.729(1) Å, c = 8.474(1) Å, β = 111.365(8)°, monoclinic, space group = C2/c, Z = 4; for 2, formula BaCo2Si2O7, a = 7.2131(6) Å, b = 12.781(1) Å, c = 13.762(1) Å, β = 90.299(8)°, monoclinic, space group = C2/c, Z = 8.