Short-range Attractive Interactions Research Articles

Adsorption of polyelectrolyte-like proteins to silica surfaces and the impact of pH on the response to ionic strength. A Monte Carlo simulation and ellipsometry study

HypothesisThe adsorbed amount of the polyelectrolyte-like protein histatin 5 on a silica surface depends on the pH and the ionic strength of the solution. Interestingly, an increase in ionic strength affects the adsorbed amount differently depending on the pH of the solution, as shown by ellipsometry measurements (Hyltegren, 2016). We have tested the hypothesis that the same (qualitative) trends can be found also from a coarse-grained model that takes all charge–charge interactions into account within the frameworks of Gouy–Chapman and Debye–Hückel theories. ExperimentsUsing the same coarse-grained model as in our previous Monte Carlo study of single protein adsorption (Hyltegren, 2016), simulations of systems with many histatin 5 molecules were performed and then compared with ellipsometry measurements. The strength of the short-ranged attractive interaction between the protein and the surface was varied. FindingsThe coarse-grained model does not qualitatively reproduce the pH-dependence of the experimentally observed trends in adsorbed amount as a function of ionic strength. However, the simulations cast light on the balance between electrostatic attraction between protein and surface and electrostatic repulsion between adsorbed proteins, the deficiencies of the Langmuir isotherm, and the implications of protein charge regulation in concentrated systems.

Clustering and melting in a wet granular monolayer

We investigate experimentally the collective behavior of a wet granular monolayer under vertical vibrations. The spherical particles are partially wet such that there are short-ranged attractive interactions between adjacent particles. As the vibration strength increases, clustering, reorganizing and melting regimes are identified subsequently through a characterization with the bond-orientational order parameters and the mean kinetic energy of the particles. The melting transition is found to be a continuous process starting from the defects inside the crystal.

Dipolar condensates with tilted dipoles in a pancake-shaped confinement

The effect of dipolar orientation with respect to the condensate plane on the mean-field dynamics of dipolar Bose-Einstein condensates in a pancake-shaped confinement is discussed. The stability of a quasi-two-dimensional condensate, with respect to the tilting angle, is found to be different from a two-dimensional layer of dipoles, indicating the relevance of the transverse extension while characterizing two-dimensional dipolar systems. An anisotropic excitation spectrum exhibiting a highly tunable, rotonlike minimum can arise entirely from the dipole-dipole interactions, by tilting the dipoles. At the magic angle and in the absence of contact interactions, the long-wavelength excitations are not phononlike and always unstable. The post-roton-instability dynamics, in contrast to phonon instability, in a uniform condensate, is featured by a transient, defect-free, stripe pattern, which eventually undergoes local collapses, and driving the condensate back into the stable regime can make them sustained for longer. Hopping between stripes has been observed before it melts into a uniform state in the presence of dissipation. Finally, we discuss a class of solutions, in which a quasi-two-dimensional condensate is self-trapped in one direction, as well as a regime of interaction parameters, including attractive short-range interactions, at which a two-dimensional anisotropic soliton can be stabilized, and we show that a chromium condensate with a relatively small number of atoms is well suited for this.

Cooperon condensation and intravalley pairing states in honeycomb Dirac systems

Motivated by recent developments in the experimental study of superconducting graphene and transition metal dichalcogenides, we investigate superconductivity of the Kane-Mele (KM) model with short-range attractive interactions on the two-dimensional honeycomb lattice. We show that intra-valley spin-triplet pairing arises from nearest-neighbor (NN) attractive interaction and the intrinsic spin-orbit coupling. We demonstrate this in two independent approaches: We study superconducting instability driven by condensation of Cooperons, which are in-gap bound states of two conduction electrons, within the $T$-matrix approximation and also study the superconducting ground state within the mean-field theory. We find that Cooperons with antiparallel spins condense at the $K$ and $K'$ points. This leads to the emergence of an intra-valley spin-triplet pairing state belonging to the irreducible representation A$_1$ of the point group $C_{6v}$. The fact that this pairing state has opposite chirality for $K$ and $K'$ identifies this state as a "helical" valley-triplet state, the valley-analog to the $^3$He-B phase in two dimension. Because of the finite center of mass momentum of Cooper pairs, the pair amplitude in NN bonds exhibits spatial modulation on the length scale of lattice constant, such that this pairing state may be viewed as a pair-density wave state. We find that the pair amplitude spontaneously breaks the translational symmetry and exhibits a $p$-Kekul\'e pattern. We also discuss the selection rule for pairing states focusing the characteristic band structure of the KM model and the Berry phase effects to the emergence of the intra-valley pairing state.

Short-Range Electron Correlation Stabilizes Noncavity Solvation of the Hydrated Electron.

The hydrated electron, e-(aq), has often served as a model system to understand the influence of condensed-phase environments on electronic structure and dynamics. Despite over 50 years of study, however, the basic structure of e-(aq) is still the subject of controversy. In particular, the structure of e-(aq) was long assumed to be an electron localized within a solvent cavity, in a manner similar to halide solvation. Recently, however, we suggested that e-(aq) occupies a region of enhanced water density with little or no discernible cavity. The potential we developed was only subtly different from those that give rise to a cavity solvation motif, which suggests that the driving forces for noncavity solvation involve subtle electron-water attractive interactions at close distances. This leads to the question of how dispersion interactions are treated in simulations of the hydrated electron. Most dispersion potentials are ad hoc or are not designed to account for the type of close-contact electron-water overlap that might occur in the condensed phase, and where short-range dynamic electron correlation is important. To address this, in this paper we develop a procedure to calculate the potential energy surface between a single water molecule and an excess electron with high-level CCSD(T) electronic structure theory. By decomposing the electron-water potential into its constituent energetic contributions, we find that short-range electron correlation provides an attraction of comparable magnitude to the mean-field interactions between the electron and water. Furthermore, we find that by reoptimizing a popular cavity-forming one-electron model potential to better capture these attractive short-range interactions, the enhanced description of correlation predicts a noncavity e-(aq) with calculated properties in better agreement with experiment. Although much attention has been placed on the importance of long-range dispersion interactions in water cluster anions, our study reveals that largely unexplored short-range correlation effects are crucial in dictating the solvation structure of the condensed-phase hydrated electron.

Two-dimensional systems with competing interactions: dynamic properties of single particles and of clusters

Systems with short-range attractive and long-range repulsive interactions are able to form mesophases at sufficiently low temperatures. In two dimensions, such mesophases emerge as clusters, stripes or bubbles. Using extensive Monte Carlo simulations we investigate the static and the dynamic properties of such a cluster-forming system over a broad temperature range and for different densities. Via the static properties we analyse how ordering into close packed configurations sets in both at the level of the particles as well as at the level of the clusters. The dynamic properties provide information on how, at low temperature, the motion of individual particles is influenced by the dynamic slowing down of the clusters. Finally, we discuss the different diffusion mechanisms at play at low and intermediate densities.

Electrochemiluminescent (ECL) [Ru(bpy)3](2+)/PAMAM dendrimer reactions: coreactant effect and 5-fluorouracil/dendrimer complex formation.

Electrogenerated chemiluminescence (ECL) reactions between tris(2,2'-bipyridine)ruthenium(II) and PAMAM dendrimers of the full (G1.0) and half (G1.5) generations were carried out in an aqueous medium at pH 6.1 and 10.0. In the absence of 5-fluoro-1H,3H-pyrimidine-2,4-dione (5-fluorouracil, 5-Fu) (coreactant effect study), the ECL efficiency trends as a function of [G1.0] and [G1.5] at pH 6.1 and 10.0 revealed that PAMAM dendrimers are about 100 (G1.5, pH 6.1), 60 (G1.5, pH 10.0), 26 (G1.0, pH 10.0) and 13 (G1.0, pH 6.1) times more efficient as ECL coreactants than oxalate anion is. Moreover, ECL reactions were done in the presence of several solutions of 5-Fu at a fixed concentration of the G1.0 and G1.5 dendrimers at pH 6.1 and 10.0 (binding study). The ECL efficiency trends as a function of [5-Fu] highlighted a dendrimer/5-Fu binding. Therefore, one of the most remarkable and novel findings of this work is the potential of PAMAM dendrimers to be used as both sensors and biosensors in an aqueous medium in the presence of a suitable sensitizer. Redox potentials of the [Ru(bpy)3](3+/2+) couple were also determined in the absence and presence of 5-Fu at both pHs. In the absence of 5-Fu the positive or negative shift of redox potentials showed the influence of the repulsive or attractive electrostatic long-range and short-range interactions between the charged dendrimer surface and the oxidized and reduced forms of the couple. In the presence of 5-Fu the trends of redox potentials highlighted the existence of a charged dendrimer/5-Fu species. Graphical Abstract ECL emission for the [Ru(bpy)3](2+)/ G1.0 dendrimer reaction in the presence of the 5-Fu at pH 6.1.

Recent Advances in the Theory and Simulation of Model Colloidal Microphase Formers.

This mini-review synthesizes our understanding of the equilibrium behavior of particle-based models with short-range attractive and long-range repulsive (SALR) interactions. These models, which can form stable periodic microphases, aim to reproduce the essence of colloidal suspensions with competing interparticle interactions. Ordered structures, however, have yet to be obtained in experiments. In order to better understand the hurdles to periodic microphase assembly, marked theoretical and simulation advances have been made over the past few years. Here, we present recent progress in the study of microphases in models with SALR interactions using liquid-state theory and density-functional theory as well as numerical simulations. Combining these various approaches provides a description of periodic microphases, and gives insights into the rich phenomenology of the surrounding disordered regime. Ongoing research directions in the thermodynamics of models with SALR interactions are also presented.

Effects of confinement on pattern formation in two dimensional systems with competing interactions.

Template-assisted pattern formation in monolayers of particles with competing short-range attraction and long-range repulsion interactions (SALR) is studied by Monte Carlo simulations in a simple generic model [N. G. Almarza et al., J. Chem. Phys., 2014, 140, 164708]. We focus on densities corresponding to formation of parallel stripes of particles and on monolayers laterally confined between straight parallel walls. We analyze both the morphology of the developed structures and the thermodynamic functions for broad ranges of temperature T and the separation L2 between the walls. At low temperature stripes parallel to the boundaries appear, with some corrugation when the distance between the walls does not match the bulk periodicity of the striped structure. The stripes integrity, however, is rarely broken for any L2. This structural order is lost at T = TK(L2) depending on L2 according to a Kelvin-like equation. Above the Kelvin temperature TK(L2) many topological defects such as breaking or branching of the stripes appear, but a certain anisotropy in the orientation of the stripes persists. Finally, at high temperature and away from the walls, the system behaves as an isotropic fluid of elongated clusters of various lengths and with various numbers of branches. For L2 optimal for the stripe pattern the heat capacity as a function of temperature takes the maximum at T = TK(L2).

Langevin simulations of stripe forming systems with long-range isotropic competing interactions

We address the critical properties of the isotropic-nematic phase transition in stripe forming systems. We focus on isotropic models in which a short range attractive interaction competes with a long range repulsive interaction decaying as a power-law, paying particular attention to the cases in which this interaction is of dipolar or Coulomb types. Using Langevin dynamics simulations we show that these models belong to different universality classes. The numerical algorithms developed for each case are presented and discussed in detail. The obtained results are in agreement with recent theoretical predictions [1], according to which the orientational transition belongs to the Kosterlitz-Thouless universality class for dipolar systems, while it is of the second-order type for Coulomb systems.

Two-dimensional colloidal fluids exhibiting pattern formation.

Fluids with competing short range attraction and long range repulsive interactions between the particles can exhibit a variety of microphase separated structures. We develop a lattice-gas (generalised Ising) model and analyse the phase diagram using Monte Carlo computer simulations and also with density functional theory (DFT). The DFT predictions for the structures formed are in good agreement with the results from the simulations, which occur in the portion of the phase diagram where the theory predicts the uniform fluid to be linearly unstable. However, the mean-field DFT does not correctly describe the transitions between the different morphologies, which the simulations show to be analogous to micelle formation. We determine how the heat capacity varies as the model parameters are changed. There are peaks in the heat capacity at state points where the morphology changes occur. We also map the lattice model onto a continuum DFT that facilitates a simplification of the stability analysis of the uniform fluid.

Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide.

For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state over extended states and the paired helix bundle in the assembly of two helices. The energetic contributions of attractive protein-solvent interactions are separated into quasi-chemical components consisting of a short-range part arising from interactions with solvent in the first hydration shell and the remaining long-range part that is well described by a Gaussian. In the helix-coil transition, short-range attractive protein-solvent interactions outweigh hydrophobic hydration and favor the extended coil states. Analysis of enthalpic effects shows that it is the favorable hydration of the peptide backbone that favors the unfolded state. Protein intramolecular interactions favor the helix state and are decisive in favoring folding. In the pairing of two helices, the cavity contribution outweighs the short-range attractive protein-water interactions. However, long-range, protein-solvent attractive interactions can either enhance or reverse this trend depending on the mutual orientation of the helices. In helix-helix assembly, change in enthalpy arising from change in attractive protein-solvent interactions favors disassembly. In helix pairing as well, favorable protein intramolecular interactions are found to be as important as hydration effects. Overall, hydrophilic protein-solvent interactions and protein intramolecular interactions are found to play a significant role in the thermodynamics of folding and assembly in the system studied.

A Cluster Expansion Approach to the Heilmann–Lieb Liquid Crystal Model

A monomer-dimer model with a short-range attractive interaction favoring colinear dimers is considered on the lattice $\mathbb{Z}^2$. Although our choice of the chemical potentials results in more horizontal than vertical dimers, the horizontal dimers have no long-range traslational order - in agreement with the Heilmann-Lieb conjecture.

Assessment of the Protein-Protein Interactions in a Highly Concentrated Antibody Solution by Using Raman Spectroscopy.

To investigate the protein-protein interactions of a highly concentrated antibody solution that could cause oligomerization or aggregation and to develop a better understanding of the optimization of drug formulations. In this study, we used Raman spectroscopy to investigate the structure and interactions of a highly concentrated antibody solution over a wide range of concentrations (10-200mg/mL) with the aid of a multivariate analysis. Our analysis of the amide I band, I 856 /I 830 of Tyr, and the relative intensity at 1004cm(-1) of the Phe and OH stretching region at around 3000cm(-1) showed that across this wide range of concentrations, the secondary structure of the IgG molecules did not change; however, short-range attractive interactions around the Tyr and Phe residues occurred as the distance between the IgG molecules decreased with increasing concentration. Analysis of the OH stretching region at around 3000cm(-1) showed that these short-range attractive interactions correlated with the amount of hydrated water around the IgG molecules. Our data show that Raman spectroscopy can provide valuable information of the protein-protein interactions based on conformational approaches to support conventional colloidal approaches, especially for analyses of highly concentrated solutions.

Emergent Devil's Staircase without Particle-Hole Symmetry in Rydberg Quantum Gases with Competing Attractive and Repulsive Interactions.

The devil's staircase is a fractal structure that characterizes the ground state of one-dimensional classical lattice gases with long-range repulsive convex interactions. Its plateaus mark regions of stability for specific filling fractions which are controlled by a chemical potential. Typically, such a staircase has an explicit particle-hole symmetry; i.e., the staircase at more than half filling can be trivially extracted from the one at less than half filling by exchanging the roles of holes and particles. Here, we introduce a quantum spin chain with competing short-range attractive and long-range repulsive interactions, i.e., a nonconvex potential. In the classical limit the ground state features generalized Wigner crystals that--depending on the filling fraction--are composed of either dimer particles or dimer holes, which results in an emergent complete devil's staircase without explicit particle-hole symmetry of the underlying microscopic model. In our system the particle-hole symmetry is lifted due to the fact that the staircase is controlled through a two-body interaction rather than a one-body chemical potential. The introduction of quantum fluctuations through a transverse field melts the staircase and ultimately makes the system enter a paramagnetic phase. For intermediate transverse field strengths, however, we identify a region where the density-density correlations suggest the emergence of quasi-long-range order. We discuss how this physics can be explored with Rydberg-dressed atoms held in a lattice.

Phase diagram and the pseudogap state in a linear chiral homopolymer model.

The phase structure of a single self-interacting homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the chain in the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence of a short-range attractive interaction between monomers, at various ambient temperature values. In the high-temperature limit the homopolymer chain is in the self-avoiding random walk phase. At very low temperatures two different phases are possible: When short-range attractive interactions dominate over chirality, the chain collapses into a space-filling conformation. But when the attractive interactions weaken, there is a low-temperature unfolding transition and the chain becomes like a straight rod. Between the high- and low-temperature limits, several intermediate states are observed, including the θ regime and pseudogap state, which is a novel form of phase state in the context of polymer chains. Applications to polymers and proteins, in particular collagen, are suggested.

Pressure, compressibility, and contact of the two-dimensional attractive fermi gas.

Using abinitio lattice methods, we calculate the finite temperature thermodynamics of homogeneous two-dimensional spin-1/2 fermions with attractive short-range interactions. We present results for the density, pressure, compressibility, and quantum anomaly (i.e., Tan's contact) for a wide range of temperatures (mostly above the superfluid phase, including the pseudogap regime) and coupling strengths, focusing on the unpolarized case. Within our statistical and systematic uncertainties, our prediction for the density equation of state differs quantitatively from the prediction by Luttinger-Ward theory in the strongly coupled region of parameter space, but otherwise agrees well with it. We also compare our calculations with the second- and third-order virial expansion, with which they are in excellent agreement in the low-fugacity regime.

Effect of self-propulsion on equilibrium clustering.

In equilibrium, colloidal suspensions governed by short-range attractive and long-range repulsive interactions form thermodynamically stable clusters. Using Brownian dynamics computer simulations, we investigate how this equilibrium clustering is affected when such particles are self-propelled. We find that the clustering process is stable under self-propulsion. For the range of interaction parameters studied and at low particle density, the cluster size increases with the speed of self-propulsion (activity) and for higher activity the cluster size decreases, showing a nonmonotonic variation of cluster size with activity. This clustering behavior is distinct from the pure kinetic (or motility-induced) clustering of self-propelling particles which is observed at significantly higher activities and densities. We present an equilibrium model incorporating the effect of activity as activity-induced attraction and repulsion by imposing that the strength of these interactions depend on activity superlinearly. The model explains the cluster size dependence of activity obtained from simulations semiquantitatively. Our predictions are verifiable in experiments on interacting synthetic colloidal microswimmers.

Hybrid Matter-Wave-Microwave Solitons Produced by the Local-Field Effect.

It was recently found that the electric local-field effect (LFE) can lead to a strong coupling of atomic Bose-Einstein condensates (BECs) to off-resonant optical fields. We demonstrate that the magnetic LFE gives rise to a previously unexplored mechanism for coupling a (pseudo-) spinor BEC or fermion gas to microwaves (MWs). We present a theory for the magnetic LFE and find that it gives rise to a short-range attractive interaction between two components of the (pseudo) spinor, and a long-range interaction between them. The latter interaction, resulting from deformation of the magnetic field, is locally repulsive but globally attractive, in sharp contrast with its counterpart for the optical LFE, produced by phase modulation of the electric field. Our analytical results, confirmed by the numerical computations, show that the long-range interaction gives rise to modulational instability of the spatially uniform state, and it creates stable ground states in the form of hybrid matter-wave-microwave solitons (which seem like one-dimensional magnetic monopoles), with a size much smaller than the MW wavelength, even in the presence of arbitrarily strong contact intercomponent repulsion. The setting is somewhat similar to exciton-polaritonic condensates in semiconductor microcavities. The release of matter waves from the soliton may be used for the realization of an atom laser. The analysis also applies to molecular BECs with rotational states coupled by the electric MW field.

Gamma crystallins of the human eye lens

BackgroundProtein crystallins co me in three types (α, β and γ) and are found predominantly in the eye, and particularly in the lens, where they are packed into a compact, plastic, elastic, and transparent globule of proper refractive power range that aids in focusing incoming light on to the retina. Of these, the γ-crystallins are found largely in the nuclear region of the lens at very high concentrations (>400mg/ml). The connection between their structure and inter-molecular interactions and lens transparency is an issue of particular interest. Scope of reviewWe review the origin and phylogeny of the gamma crystallins, their special structure involving the use of Greek key supersecondary structural motif, and how they aid in offering the appropriate refractive index gradient, intermolecular short range attractive interactions (aiding in packing them into a transparent ball), the role that several of the constituent amino acid residues play in this process, the thermodynamic and kinetic stability and how even single point mutations can upset this delicate balance and lead to intermolecular aggregation, forming light-scattering particles which compromise transparency. We cite several examples of this, and illustrate this by cloning, expressing, isolating and comparing the properties of the mutant protein S39C of human γS-crystallin (associated with congenital cataract-microcornea), with those of the wild type molecule. In addition, we note that human γ-crystallins are also present in other parts of the eye (e.g., retina), where their functions are yet to be understood. Major conclusionsThere are several ‘crucial’ residues in and around the Greek key motifs which are essential to maintain the compact architecture of the crystallin molecules. We find that a mutation that replaces even one of these residues can lead to reduction in solubility, formation of light-scattering particles and loss of transparency in the molecular assembly. General significanceSuch a molecular understanding of the process helps us construct the continuum of genotype–molecular structural phenotype–clinical (pathological) phenotype. This article is part of a Special Issue entitled Crystallin Biochemistry in Health and Disease.