Moderate Attractive Interaction Research Articles

Sound Propagation in a Bose-Fermi Mixture: From Weak to Strong Interactions.

Particlelike excitations, or quasiparticles, emerging from interacting fermionic and bosonic quantum fields underlie many intriguing quantum phenomena in high energy and condensed matter systems. Computation of the properties of these excitations is frequently intractable in the strong interaction regime. Quantum degenerate Bose-Fermi mixtures offer promising prospects to elucidate the physics of such quasiparticles. In this work, we investigate phonon propagation in an atomic Bose-Einstein condensate immersed in a degenerate Fermi gas with interspecies scattering length a_{BF} tuned by a Feshbach resonance. We observe sound mode softening with moderate attractive interactions. For even greater attraction, surprisingly, stable sound propagation reemerges and persists across the resonance. The stability of phonons with resonant interactions opens up opportunities to investigate novel Bose-Fermi liquids and fermionic pairing in the strong interaction regime.

Study of the phase diagram of the Kitaev-Hubbard chain

We present a detailed study of the phase diagram of the Kitaev-Hubbard chain, that is the Kitaev chain in the presence of a nearest-neighbour density-density interaction, using both analytical techniques as well as DMRG. In the case of a moderate attractive interaction, the model has the same phases as the non-interacting chain, a trivial and a topological phase. For repulsive interactions, the phase diagram is more interesting. Apart from the previously observed topological, incommensurate and charge density wave phases, we identify the `excited state charge density wave' phase. In this phase, the ground state resembles an excited state of an ordinary charge density phase, but is lower in energy due to the frustrated nature of the model. We find that the dynamical critical exponent takes the value $z\simeq 1.8$. Interestingly, this phase only appears for even system sizes, and is sensitive to the chemical potential on the edges of the chain. For the topological phase, we present an argument that excludes the presence of a strong zero mode for a large part of the topological phase. For the remaining region, we study the time dependence of the edge magnetization (using the bosonic incarnation of the model). These results further expand the region where a strong zero mode does not occur.

Coil-helix-globule transition for self-attractive semiflexible ring chains

An off-lattice dynamics Monte Carlo method is used to study the conformations of self-attractive semiflexible ring chains. The conformations depend mainly on the bending energy b and the self-attractive interaction ε of ring chains, and perfect helical structures are found in self-attractive semiflexible ring chains with the moderate attractive interaction ε. Some monomers of the semiflexible ring chains wrap around the linearly aligned monomers and the size of helix is independent of chain length of ring chains. Coil-helix-globule transition occurs when the self-attractive interaction increases within semiflexibe ring chains, and the phase transition is attributed to the competition among the configurational entropy, the bending energy, and the self-attractive interaction. This study can help us understand the effects of topological constraints on the conformations and dynamical behaviors of polymer chains, and the importance of chain stiffness in biological systems and in the dynamics of DNA and protein folding.

Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity

Wrapping, crossover, and braiding of DNA are the motifs of fundamental interest in genome packaging, gene regulation, and enzyme recognition. This study explores elastic mechanisms for the selection of chirality in wrapping, crossover, and braiding of DNA based on a coarse-grained model. The DNA model consists of two elastic chains that mutually intertwine in a right-handed manner forming a double-stranded helix with the distinction between major and minor grooves. Although individual potential energy functions of the DNA model have no asymmetry in terms of left and right twist, the model as a whole exhibits an asymmetric propensity to writhe in the left direction upon bending due to the right-handed helical geometry. Monte Carlo simulations of this model suggest that DNA has a propensity to prefer left-handed wrapping around a spherical core particle and also around a uniform rod due to the asymmetric elastic coupling between bending and writhing. This result indicates an elastic origin of the uniform left-handed wrapping of DNA in nucleosomes and also has implications on the wrapping of double-stranded DNA around rod-like molecules. Monte Carlo simulations of the DNA model also suggest that two juxtaposed DNA molecules can braid each other spontaneously under moderate attractive interactions with the preference for left-handed braiding due to the asymmetric coupling between bending and writhing. This result suggests the importance of asymmetric elasticity in the selection of chirality in braiding of a pair of DNA molecules.

Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators.

Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long-distance regulatory interactions. The mechanistic basis for insulator activity and how it relates to enhancer action-at-a-distance remains unclear. Here we explore the idea that topological loops could simultaneously account for regulatory interactions of distal enhancers and the insulating activity of boundary elements. We show that while loop formation is not in itself sufficient to explain action at a distance, incorporating transient nonspecific and moderate attractive interactions between the chromatin fibers strongly enhances long-distance regulatory interactions and is sufficient to generate a euchromatin-like state. Under these same conditions, the subdivision of the loop into two topologically independent loops by insulators inhibits interdomain interactions. The underlying cause of this effect is a suppression of crossings in the contact map at intermediate distances. Thus our model simultaneously accounts for regulatory interactions at a distance and the insulator activity of boundary elements. This unified model of the regulatory roles of chromatin loops makes several testable predictions that could be confronted with in vitro experiments, as well as genomic chromatin conformation capture and fluorescent microscopic approaches.

Modest Protein−Crowder Attractive Interactions Can Counteract Enhancement of Protein Association by Intermolecular Excluded Volume Interactions

We study the effects of attractive interactions between spherical crowders and protein residues on the thermodynamics and structure of two weakly binding protein complexes: ubiquitin/UIM1 and cytochrome c/cytochrome c peroxidase. Systematic replica exchange Monte Carlo (REMC) simulations are performed over a range of attraction strengths and crowder packing fractions using a transferable coarse-grained protein binding model. We find that moderate attractive interactions (≈0.2 kcal/mol) between crowders and protein residues can destabilize protein association, and therefore counteract the stabilizing effect of excluded volume interactions. The destabilization of protein binding, as measured by an increase in binding free energy, increases with increasing crowder packing fraction. For a critical attraction strength value, which is found to be approximately independent of crowder packing fraction, the destabilization due to attractions is exactly canceled by the stabilization effect of excluded volume interactions. This results in a net zero change in binding free energy with respect to a crowder-free solution. Further, we find that attractive interactions between crowders and protein residues can favor transiently bound encounter complexes over the native specific complexes in the bound state. We propose a simple theoretical model based on the scaled particle theory augmented by a mean-field attraction term that can explain our simulation results semiquantitatively.

Protein Structural Conformation and Not Second Virial Coefficient Relates to Long-Term Irreversible Aggregation of a Monoclonal Antibody and Ovalbumin in Solution

The purpose of the study was to investigate the relationship of the second virial coefficient, B22, to the extent of irreversible protein aggregation upon storage. A monoclonal antibody and ovalbumin were incubated at 37 degrees C (3 months) under various solution conditions to monitor the extent of aggregation. The B22 values of these proteins were determined under similar solution conditions by a modified method of flow-mode static light scattering. The conformation of these proteins was studied using circular dichroism (CD) spectroscopy and second-derivative Fourier transform infrared spectroscopy. Both proteins readily aggregated at pH 4.0 (no aggregation observed at pH 7.4); the extent of aggregation varied with the ionic strength and the presence of cosolutes (sucrose, glycine, and Tween 80). Debye plots of the monoclonal antibody showed moderate attractive interactions at pH 7.4, whereas, at pH 4.0, nonlinear plots were obtained, indicating self-association. CD studies showed partially unfolded structure of antibody at pH 4.0 compared with that at pH 7.4. In the case of ovalbumin, similar B22 values were obtained in all solution conditions irrespective of whether the protein aggregated or not. CD studies of ovalbumin indicated the presence of a fraction of completely unfolded as well as partially unfolded species at pH 4.0 compared with that at pH 7.4. The formation of a structurally altered state is a must for irreversible aggregation to proceed. Because this aggregation-prone species could be an unfolded species present in a small fraction compared with that of the native state or it could be a partially unfolded state whose net interactions are not significantly different compared with those of the native state, yet the structural changes are sufficient to lead to long-term aggregation, it is unlikely that B22 will correlate with long-term aggregation.

Histone core slips along DNA and prefers positioning at the chain end.

We studied the stability and dynamics of a model of a nucleosome, the fundamental unit for the packing of long DNA in eukaryotes, using a Brownian dynamics simulation. For the proper folding of a stiff polymer on a core particle, moderate attractive interaction is shown to be essentially important, which explains the empirical experimental protocol for the reconstitution of nucleosomes. The effect of the chain end on the positioning of the core particle is examined and compared with the experimental data by atomic force microscopy measurement. It is also suggested that the core particle exhibits sliding motion along the chain as a manifestation of Brownian motion.

Dynamic light scattering study of precrystallizing ribonuclease solutions

The translational diffusion coefficient of bovine pancreatic ribonuclease A, a globular protein, has been measured by dynamic light scattering under various conditions related to the crystallization process. In all cases, a monomodal light scattering autocorrelation function was observed. The diffusion coefficient exhibited a linear dependence on protein concentration and an interaction parameter could be calculated. Attractive interactions were found to increase with salt concentration and to decrease with pH in the presence of salts. Finally, optimal crystallization conditions correspond to moderate attractive interactions.

Photoemission and high resolution electron energy loss spectroscopy study of CO/K/Cu(110)

Adsorption of CO on the Cu(110) surface modified with a low (near the work function minimum) potassium precoverage has been investigated by use of low energy electron diffraction, photoelectron spectroscopy based on synchrotron radiation, work function measurements (ΔΦ), and high resolution electron energy loss spectroscopy (HREELS). During potassium adsorption at 118 K the binding energy (BE) of the K 3p peak shifts −0.3 eV. For a thick potassium overlayer both a surface and a bulk K 3p peak, with a 0.9 eV difference in BE, are observed. The work function results at ΘK∼0.5 ML show after saturation with CO an increase of 1.11 eV. An electrostatic interaction energy between CO and K equal to 0.23 eV is determined. This energy indicates a moderate attractive interaction between CO and K. A CO overlayer on K/Cu(110) shows the 4σ satellite, the 4σ orbital, and the 5σ/1π joint feature. No observable change in the BE separation between the 4σ and the 5σ/1π band (3.1 eV) was found, thereby indicating a negligible CO–CO interaction. From the 4σ to the 5σ/1π intensity ratio (∼2) a weakening of the CO–metal binding with increasing CO coverage is deduced. In the HREEL spectrum, an intense feature at 1731 cm−1 besides the fundamental stretching frequency at 2030 cm−1 implies a substantial potassium induced weakening of the C–O bond.

Study of the regio- and enantioselectivity of the reactions of osmium tetroxide with allylic alcohols and allylic sulfonamides

The regioselectivities of the osmylation of geraniol, its derivatives and geranyl sulfonamides suggest the presence of a moderate attractive interaction between OsO 4 and the allylic groups bearing acidic protons. This allylic directing effect may be due to the development of a hydrogen bonding interaction between OsO 4 and the substrates during the osmylation process. The potential for a hydrogen bond can also have a substantial effect on the enantioselectivities of the osmium tetroxide catalyzed asymmetric dihydroxylation of allylic alcohols.

Properties of a single chain embedded into a polymer matrix of varied thermodynamic quality and density

AbstractThe properties (squared dimensions, anisotropy, numbers of intra‐ and intermolecular contacts) of a single five‐way cubic lattice chain embedded into an environment (matrix) of chains of the same length n = 50 were evaluated as a function of matrix volume fraction (matrix density) v and intermolecular interaction between the matrix polymer and the minority chain segments, characterized by a parameter ϕ. No convincing evidence was found for the occurrence of a coil‐globule transition in the range of matrix densities (v ≤ 0.7) and repulsive interactions between matrix and minority chain (ϕ ≤ 0.2) investigated. For moderate attractive interaction (ϕ ≈ −0.17) a compensation of the chaincompressing action of the matrix and the chain‐expanding interaction with the matrix was observed resulting in a zero‐dependence of the size and shape of the minority chain on matrix density. It further turned out that there are fixed relations among the various size and shape data irrespective of the specific combination of matrix density and thermodynamic interaction by which a particular polymer dimension is produced. These interrelations are fairly the same as those evaluated for isolated chains the size of which is varied by an intramolecular energy parameter ϕi.

Coadsorption of bismuth with electrocatalytic molecules: A study of formic acid oxidation on Pt(100)

Bismuth is an effective promoter in formic acid electrocatalysis on Pt(100), yet this system is problematic and the reaction mechanisms not well understood. We investigate this from a surface science perspective by studying Bi adsorption and coadsorption with CO, O2, H2O, and HCOOH on Pt(100) with low-energy electron diffraction (LEED) and thermal desorption spectroscopy (TDS). The ‘‘hex’’ reconstruction of clean Pt(100) is gradually and completely lifted by increasing Bi coverage up to 0.25 monolayer (ML); saturation coverage is 0.5 ML with a c(2×2) LEED pattern. Low coverages of Bi (below 0.25 ML) exhibit moderate attractive interactions, whereas repulsive interactions occur for higher coverages. The heat of adsorption for Bi in the limit of zero coverage is 380 kJ/mol. Bismuth is an effective site blocker for CO and O2 with each adatom blocking two CO molecules and two O atoms. Strangely, Bi is not hydrated by coadsorbed H2O and a Pt(100) surface with only 0.2 ML Bi is hydrophobic. Both clean and Bi-covered Pt(100) are inert to HCOOH; only molecular adsorption occurs below 220 K. Preadsorbed oxygen dramatically enhances HCOOH reaction, however, with complete oxidation to CO2 and H2O occurring at 300 K via the formate intermediate. The implications of these results towards electrocatalysis are discussed.

On the problem of potential shifts at glassy carbon electrodes: Part II. Voltammetric analysis of the surface interactions involved in the electrode processes of nitrobenzenes at freshly polished and electrochemically pretreated electrodes

The contribution of the heterogeneous (involving non-adsorbed solution species) and surface path (involving adsorbed species) to the electrode processes of aromatic nitro compounds has been studied as a function of the surface conditions of glassy carbon (GC-20) by linear sweep voltammetry (LSV) and cyclic voltammetry (CV). The influence of adsorption was negligible at the freshly polished electrodes. Oxidative electrochemical pretreatment led to the formation of active sites at which the adsorption of the reactant resulted in enhanced electron-transfer rates. The nature of the adsorption process and the characteristics of the electrode reaction in the adsorbed state were studied in detail for p-nitrotoluene. The adsorption followed the Frumkin isotherm with an interaction parameter of 1.2, indicating moderate attractive interactions between the adsorbed molecules. The rate constant for the adsorbed species was of the order of 10 5, higher than the apparent heterogeneous rate constant of p-nitrotoluene in the solution phase. The magnitude of the potential shift and the strength of adsorption varied with the relative position and electron-withdrawing power of the substituent in the aromatic ring of nitrobenzene. Free radical coupling was selectively catalysed at electrochemically pretreated electrodes.