Short-range Interactions Research Articles

Non-hyperuniformity of Gibbs point processes with short-range interactions

Abstract We investigate the hyperuniformity of marked Gibbs point processes that have weak dependencies among distant points whilst the interactions of close points are kept arbitrary. Various stability and range assumptions are imposed on the Papangelou intensity in order to prove that the resulting point process is not hyperuniform. The scope of our results covers many frequently used models, including Gibbs point processes with a superstable, lower-regular, integrable pair potential, as well as the Widom–Rowlinson model with random radii and Gibbs point processes with interactions based on Voronoi tessellations and nearest-neighbour graphs.

Enhancement of adhesion strength in viscoelastic unsteady contacts

We present a general energy approach to study the unsteady adhesive contact of viscoelastic materials. Under the assumption of infinitely short-range adhesive interactions, we exploit the principle of virtual work to generalize Griffith’s local energy balance at contact edges to the case of a non-conservative (viscoelastic) material, subjected to a generic contact time–history. We apply the proposed energy balance criterion to study the approach–retraction motion of a rigid sphere in contact with a viscoelastic half-space. A strong interplay between adhesion and viscoelastic hysteretic losses is reported which can lead to strongly increased adhesion strength, depending on the loading history. Specifically, two different mechanisms are found to govern the increase of pull-off force during either approach–retraction cycles and approach – full relaxation – retraction tests. In the former case, hysteretic losses occurring close to the circular perimeter of the contact play a major role, significantly enhancing the energy release rate. In the latter case, instead, the pull-off enhancement mostly depends on the glassy response of the whole (bulk) material which, triggered by the fast retraction after relaxation, leads to a sort of ‘frozen’ state and results in a flat-punch-like detachment mechanism (i.e., constant contact area). In this case, the JKR theory of adhesive contact cannot be invoked to relate the observed pull-off force to the effective adhesion energy, i.e. the energy release rate G, and strongly overestimates it. Therefore, a rigorous mathematical procedure is also proposed to correctly calculate the energy release rate in viscoelastic dissipative contacts.

Inverse scattering for repulsive potential and strong singular interactions

In a previous work of 2014 on a quantum system governed by the repulsive Hamiltonian, the author proved uniqueness for short-range interactions described by a scattering operator consisting of regular and singular parts. In this paper, the singular part is assumed to have much stronger singularities and the same uniqueness theorem is proved. By applying the time-dependent method invented by Enss and Weder [J. Math. Phys. 36(8), 3902–3921 (1995)], the high-velocity limit for a wider class of the scattering operator with stronger singularities also uniquely determines the interactions of a multi-dimensional system.

A simplex path integral and a simplex renormalization group for high-order interactions *

Modern theories of phase transitions and scale invariance are rooted in path integral formulation and renormalization groups (RGs). Despite the applicability of these approaches in simple systems with only pairwise interactions, they are less effective in complex systems with undecomposable high-order interactions (i.e. interactions among arbitrary sets of units). To precisely characterize the universality of high-order interacting systems, we propose a simplex path integral and a simplex RG (SRG) as the generalizations of classic approaches to arbitrary high-order and heterogeneous interactions. We first formalize the trajectories of units governed by high-order interactions to define path integrals on corresponding simplices based on a high-order propagator. Then, we develop a method to integrate out short-range high-order interactions in the momentum space, accompanied by a coarse graining procedure functioning on the simplex structure generated by high-order interactions. The proposed SRG, equipped with a divide-and-conquer framework, can deal with the absence of ergodicity arising from the sparse distribution of high-order interactions and can renormalize a system with intertwined high-order interactions at the p-order according to its properties at the q-order ( p⩽q ). The associated scaling relation and its corollaries provide support to differentiate among scale-invariant, weakly scale-invariant, and scale-dependent systems across different orders. We validate our theory in multi-order scale-invariance verification, topological invariance discovery, organizational structure identification, and information bottleneck analysis. These experiments demonstrate the capability of our theory to identify intrinsic statistical and topological properties of high-order interacting systems during system reduction.

Effect of Ho3+ Substitution on Magnetic Properties of ZnCr2Se4.

A series of ZnCr2-xHoxSe4 microcrystalline spinels (where x = 0.05, 0.075, and 0.10) containing holmium ions in octahedral coordination were obtained by sintering of adequate reactants at high temperatures. The obtained doped materials were characterized by X-ray diffraction, Scanning Electron Microscopy, UV-Vis-NIR, molecular field approximation, and XPS spectroscopies. Their thermal properties were also investigated. The doping of the ZnCr2S4 matrix with paramagnetic Ho3+ ions with a content of not more than 0.1 and a screened 4f shell revealed a significant effect of orbital and Landau diamagnetism, a strong reduction in short-range ferromagnetic interactions, and a broadening and shift of the peak of the first critical field by simultaneous stabilization of the sharp peak in the second critical field. These results correlate well with FPLO calculations, which show that Cr sites have magnetic moments of 3.19 µB and Ho sites have significantly larger ones with a value of 3.95 µB. Zn has a negligible magnetic polarization of 0.02 µB, and Se induces a polarization of approximately -0.12 µB.

PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics.

PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.

Hierarchical Self-Aggregation of Multifunctional Steviol Glycosides in Aqueous Solutions.

Steviol glycosides (SGs) are a natural sweetener widely used in the food and beverage industry, but the low solubility and stability of SG aqueous solutions greatly limit their application performance, especially in liquid formulations. In this work, we explore the solubility behavior of rebaudioside A (Reb A) in water, a major component of SGs, with the aim of clarifying the underlying mechanisms of the solubility and stability constraints of SGs, as well as the impact on their multifunctional properties. We demonstrate for the first time that Reb A exhibits hierarchical self-assembly in solutions, forming spherical micelles first when the concentration exceeds its critical micelle concentration (5.071 mg/mL), which then further assemble into large rod-like aggregates. The formation of such large Reb A aggregates is mainly dominated by hydrogen bonding and short-range Coulomb interaction energy, thus leading to the low solubility and precipitation of Reb A solutions. Surprisingly, aggregated Reb A structures display significantly improved organoleptic properties, revealing that self-aggregation can be developed as a simple, efficient, and green strategy for improving the taste profile of SGs. Additionally, the self-aggregation of Reb A at high concentrations impairs active encapsulation and also affects its interfacial and emulsifying properties.

Ionic strength effect on the structure and dynamics of colloidal dispersions with weak attractive interactions

We present a macro- and microrheological study of the effect of ionic strength on the phase behavior, structure and flow properties of colloidal dispersions stabilized by short-range repulsive interactions inferred via co-polymerization of weak acid groups. We investigated the impact of ionic strength, by varying the concentration of natrium chloride (NaCl), on dispersions with only repulsive interactions, but also when additional attractive depletion forces are present due to added non-absorbent polymer, namely polyethyleneoxide (PEO). For dispersions with only repulsive electrosteric interactions, at low particle volume fractions (ϕ < 0.4), increasing ionic strength hardly affects the relative viscosity whereas at higher particle volume fractions, a decrease in viscosity is observed due to a reduced range of electrosteric repulsion between particles, corresponding to a reduction of the effective particle volume fraction ϕeff. For dispersions including attractive interactions, at volume fractions ϕ = 0.45 below the hard sphere freezing point (ϕc=0.5), independently of the ionic strength, the bulk viscosity increases monotonically with increasing PEO concentration due to the transition from a fluid to a fluid/crystalline and finally to a gel state. However, the increase in ionic strength shifts the concentrations of both phase transitions to lower polymer concentrations, indicating that in presence of salt a weaker attraction is required to induce these transitions. At ϕ=0.52, just above ϕc, for dispersions without added salt, broadening of the fluid-crystalline coexistence regime, due to added PEO, results in a viscosity minimum corresponding to different size and packing density of the crystalline regions as observed earlier in Weis et al. [1]. When salt is added, the initial state for dispersions without PEO is a fluid state due to the reduction of ϕeff and the addition of a small amount of PEO leads to an increase in bulk viscosity due to the formation of large crystals for dispersions containing 10 mM NaCl and a network of small, dense crystals of size ≈10 µm when 100 mM NaCl is added. At ϕ=0.54, a result similar to ϕ=0.52 is obtained for dispersions without added salt, whereas in presence of salt, we find that the fluid/crystalline coexistence regime narrows down as the range of electrosteric repulsion decreases and the addition of PEO results in gel formation and gels become more uniform with increasing attraction strength. These investigations demonstrate how superimposed short range electrosteric repulsion and weak depletion attraction affect microstructure and flow behavior of colloidal dispersions.

Electric double layer in ionic liquids: A result of interplay between coupling effects and phase demixing

Ionic liquids (ILs) are appealing electrolytes for their favorable physicochemical properties. However, despite their longstanding use, understanding the capacitive behavior of ILs remains challenging. This is largely due to the formation of a nonconventional electric double layer (EDL) at the electrode-electrolyte interface. This study shows that the short-range Yukawa interactions, representing the large anisotropically charged ILs, demix IL to create a spontaneous surface charge separation, which is reinforced by the strongly coupled charge interaction. The properties of the condensed layer, the onset of charge separation, and the rise of overscreening and crowding critically depend on the asymmetry of Yukawa interactions. Published by the American Physical Society 2024

Modification of a ReaxFF potential at short range for energetic materials

The ReaxFF can describe the properties of energetic materials (EMs) at equilibrium state, but does not work properly in simulating high-energy particle irradiation process because of its weak short-range interaction. In this paper, a modification was made for such a potential by connecting Ziegler-Biersack-Littmark (ZBL) potential to ReaxFF-lg through comparing to Density Functional Theory (DFT) results to accurately describe short-range interactions. After modification, the newly fitted ReaxFF-lg/ZBL potential predicts better the equation of state for EMs In displacement cascade simulations, comparing to results from ab initio molecular dynamics (AIMD), ReaxFF-lg/ZBL presented the similar transferred energy from a primary knock-on atom to surrounding atoms, better than the original ReaxFF-lg potential. Further large-scale displacement cascade simulations indicated ReaxFF-lg/ZBL could be applied for cascade simulations with PKA energy from less than 1 keV to high energy (e.g. 35 keV) cases, which is suitable for effectively simulating high-energy displacement cascades in EMs using molecular dynamics method.

MacroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast

In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones, providing additional layers of structural and epigenetic regulation. Here, we systematically replace individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. We show that variants H2A.J, TsH2B, and H3.5 complement their respective replicative counterparts. However, macroH2A1 fails to complement, and its overexpression is toxic in yeast, negatively interacting with yeast's native histones and kinetochore genes. To isolate yeast with macroH2A1 chromatin, we uncouple the effects of its macro and histone fold domains, revealing that both domains suffice to override native nucleosome positioning. Furthermore, both uncoupled constructs of macroH2A1 exhibit lower nucleosome occupancy, decreased short-range chromatin interactions (<20 kb), disrupted centromeric clustering, and increased chromosome instability. Our observations demonstrate that lack of a canonical histone H2A dramatically alters chromatin organization in yeast, leading to genome instability and substantial fitness defects.

Theoretical study of short-range exchange interaction based on semiconductor dielectric function model toward time-dependent dielectric density functional theory

This study explores various models of semiconductor dielectric functions, with a specific emphasis on the large wavenumber spectrum and the derivation of the screened exchange interaction. Particularly, we discuss the short-range effect of the screened exchange potential. Our investigation reveals that the short-range effect originating from the high wavenumber spectrum is contingent upon the dielectric constant of the targeted system. To incorporate dielectric-dependent behaviors concerning the short-range aspect into the dielectric density functional theory (DFT) framework, we utilize the local Slater term and the Yukawa-type term, adjusting the ratio between these terms based on the dielectric constant. Additionally, we demonstrate the efficacy of the time-dependent dielectric DFT method in accurately characterizing the electronic structure of excited states in dyes and functional molecules. Several theoretical approaches have incorporated parameters dependent on the system to elucidate short-range exchange interactions. Our theoretical analysis and discussions will be useful for those studies.

Dynamics of Interacting Colloidal Particles Using the IIR Recursive Digital Filter Method

This paper focuses on the numerical study of spherical particle sedimentation, taking into account hydrodynamic interactions. Infinite impulse response (IIR) digital filters, specially tailored to solve the sedimentation dynamics, were used in the present study to numerically solve the coupled ordinary differential equations with the time-dependent coefficients of the problem. Hydrodynamic interactions are modeled using the Rotne–Prager–Yamakawa (RPY) approximation, to which a correction is made to better account for short-range interactions. In order to validate both the proposed numerical resolution method and the RPY correction, this paper begins with the study of two interacting spherical particle sedimentation methods. Comparisons with previously published analytical or numerical results confirm the relevance of the present approach.

The Movement of Efimov States in 2n Halo Nucleus: probing the roles of mass asymmetry and short range of interaction

This brief communication presents the results of our work to study the movement of Efimov states in 2-neutron halo nuclei. We discuss the emergence and evolution of Efimov states in to resonances beyond the two-body (n-Core) breakup threshold and also the movement of the Efimov state in a 2-neutron halo nucleus to the region of the so called, Thomas Collapse. We especially, probe the roles of mass asymmetry of the three-body system (n-n-core) and the short range of the n-core interaction in the movement of the Efimov states. The analysis has been carried out within the framework of a three-body model, assuming two-body, non-local, separable potentials for the binary sub-systems, namely, the n-n and n-core systems. The primary motivation has been to scan the parameter space of the range parameter and determine the value(s) for which the system can support the Efimov states. The analysis shows that the value of the range parameter $\beta$ = 5.2$\alpha$ ( $\alpha$ being the energy parameter given in terms of the deuteron binding energy ) produces the realistic three-body binding energy for $^{20}$C and also generates the excited Efimov states. However, as the value of $\beta$ is increased corresponding to decrease in the range of the two-body (n-core) interaction the ground and excited state binding energies increase drastically. In other words, as the range of the two-body interaction tends to zero the system enters the Thomas Collapse region away from the Efimov region.

An integrated DEM code for tracing the entire regolith mass movement on asteroids

ABSTRACT This paper presents a general strategy for tracking the scale-span movement process of asteroid regolith materials. It achieves the tracking of the mass movement on the asteroid at a realistic scale, under conditions of high-resolution asteroid surface topography (submeter level) and actual regolith particle sizes. To overcome the memory exponential expansion caused by the enlarged computational domain, we improved the conventional cell-linked list method so that it can be applied to arbitrarily large computational domains around asteroids. An efficient contact detection algorithm for particles and polyhedral shape models of asteroids is presented, which avoids traversing all surface triangles and thus allows us to model high-resolution surface topography. A parallel algorithm based on Compute Unified Device Architecture for the gravitational field of the asteroid is presented. Leveraging heterogeneous computing features, further architectural optimization overlaps computations of the long-range and short-range interactions, resulting in an approaching doubling of computational efficiency compared to the code lacking architectural optimizations. Using the above strategy, a specific high-fidelity discrete element method code that integrates key mechanical models, including the irregular gravitational field, the interparticle and particle-surface interactions, and the coupled dynamics between the particles and the asteroid, is developed to track the asteroid regolith mass movement. As tests, we simulated the landslide of a sand pile on the asteroid’s surface during spin-up. The simulation results demonstrate that the code can track the mass movement of the regolith particles on the surface of the asteroid from local landslides to mass leakage with good accuracy.

"Core-Shell" Wave Function Modulation in Organic Narrowband Emitters.

Efficient red-green-blue primary luminescence with an extraordinarily narrow band and durability is crucial for advanced display applications. Recently, the emergence of multiple-resonance (MR) from short-range atomic interactions has been shown to induce extremely narrow spectral widths in pure organic emitters. However, achieving wide-range color tuning without compromising color purity remains a persistent challenge for MR emitters. Herein, the concept of electronic donor/acceptor "core-shell" modulation is proposed within a boron/nitrogen (B/N) MR skeleton, enabling the rational utilization of intramolecular charge transfer to facilitate wavelength shift. The dense B atoms localized at the center of the molecule effectively compress the electron density and stabilize the lowest unoccupied molecular orbital wave function. This electron-withdrawing core is embedded with peripheral electron-donating atoms. Consequently, doping a single B atom into a deep-blue MR framework led to a profound bathochromic shift from 447 to 624 nm (∼0.8 eV) while maintaining a narrow spectral width of 0.10 eV in this pure-red emitter. Notably, organic light-emitting diodes assisted by thermally activated delayed fluorescence molecules achieved superb electroluminescent stability, with an LT99 (99% of the initial luminance) exceeding 400 h at an initial luminance of 1000 cd m-2, approaching commercial-level performance without the assistance of phosphors.

Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins

Euchromatin is an accessible phase of genetic material containing genes that encode proteins with increased expression levels. The structure of euchromatin in vitro has been described as a 30-nm fiber formed from ordered nucleosome arrays. However, recent advances in microscopy have revealed an in vivo euchromatin architecture that is much more disordered, characterized by variable-length linker DNA and sporadic nucleosome clusters. In this work, we develop a theoretical model to elucidate factors contributing to the disordered in vivo architecture of euchromatin. We begin by developing a 1D model of nucleosome positioning that captures the interactions between bound epigenetic reader proteins to predict the distribution of DNA linker lengths between adjacent nucleosomes. We then use the predicted linker lengths to construct 3D chromatin configurations consistent with the physical properties of DNA within the nucleosome array, and we evaluate the distribution of nucleosome cluster sizes in those configurations. Our model reproduces experimental cluster-size distributions, which are dramatically influenced by the local pattern of epigenetic marks and the concentration of reader proteins. Based on our model, we attribute the disordered arrangement of euchromatin to the heterogeneous binding of reader proteins and subsequent short-range interactions between bound reader proteins on adjacent nucleosomes. By replicating experimental results with our physics-based model, we propose a mechanism for euchromatin organization in the nucleus that impacts gene regulation and the maintenance of epigenetic marks.

Hydrogen-annealing modulated magnetocaloric effect and critical behavior of Weyl semimetallic Co3Sn2S2

Modulating the electron interaction and magnetic domains is an essential strategy to evoke novel physical properties, both for fundamental research and for related magnetic applications. The emerging annealing process attracted attention due to its capability of tuning the magnetic performance, but it has been rarely studied. Herein, we conducted hydrogen annealing on the Weyl semimetallic Co3Sn2S2 and investigated the magnetic interaction, critical behavior, and magnetocaloric effect (MCE). Hydrogen-annealed Co3Sn2S2 (HA-Co3Sn2S2) exhibits a distinct anisotropy-dependent magnetic behavior, where a typical second-order transition with an easy magnetization process is observed under H//c. However, a frustrated magnetic state composed of ferromagnetic (FM), antiferromagnetic (AFM), and/or spin glass phases is observed when H//ab. Critical analyses illustrate that the ground state of HA-Co3Sn2S2 lies between the 3D-Ising model and the Mean-filed model, indicating the presence of both long-range and short-range magnetic interactions in the system. Additionally, we found that HA-Co3Sn2S2 exhibits an enhanced saturation magnetization (Ms) and magnetic refrigeration capacity, both showing anisotropic dependence, compared to the pristine Co3Sn2S2. Our work develops hydrogen annealing to modulate electron coupling and magnetic domains, paving the way for further studies of anisotropic magnetic behavior and applications in magnetic refrigeration.

Spatial Chromosome Organization and Adaptation of Escherichia coli under Heat Stress.

The spatial organization of bacterial chromosomes is crucial for cellular functions. It remains unclear how bacterial chromosomes adapt to high-temperature stress. This study delves into the 3D genome architecture and transcriptomic responses of Escherichia coli under heat-stress conditions to unravel the intricate interplay between the chromosome structure and environmental cues. By examining the role of macrodomains, chromosome interaction domains (CIDs), and nucleoid-associated proteins (NAPs), this work unveils the dynamic changes in chromosome conformation and gene expression patterns induced by high-temperature stress. It was observed that, under heat stress, the short-range interaction frequency of the chromosomes decreased, while the long-range interaction frequency of the Ter macrodomain increased. Furthermore, two metrics, namely, Global Compactness (GC) and Local Compactness (LC), were devised to measure and compare the compactness of the chromosomes based on their 3D structure models. The findings in this work shed light on the molecular mechanisms underlying thermal adaptation and chromosomal organization in bacterial cells, offering valuable insights into the complex inter-relationships between environmental stimuli and genomic responses.

Effect of Solvent Composition on Non-DLVO Forces and Oriented Attachment of Zinc Oxide Nanoparticles.

Oriented attachment (OA) occurs when nanoparticles in solution align their crystallographic axes prior to colliding and subsequently fuse into single crystals. Traditional colloidal theories such as DLVO provide a framework for evaluating OA but fail to capture key particle interactions due to the atomistic details of both the crystal structure and the interfacial solution structure. Using zinc oxide as a model system, we investigated the effect of the solvent on short-ranged and long-ranged particle interactions and the resulting OA mechanism. In situ TEM imaging showed that ZnO nanocrystals in toluene undergo long-range attraction comparable to 1kT at separations of 10 nm and 3kT near particle contact. These observations were rationalized by considering non-DLVO interactions, namely, dipole-dipole forces and torques between the polar ZnO nanocrystals. Langevin dynamics simulations showed stronger interactions in toluene compared to methanol solvents, consistent with the experimental results. Concurrently, we performed atomic force microscopy measurements using ZnO-coated probes for the short-ranged interaction. Our data are relevant to another type of non-DLVO interaction, namely, the repulsive solvation force. Specifically, the solvation force was stronger in water compared to ethanol and methanol, due to the stronger hydrogen bonding and denser packing of water molecules at the interface. Our results highlight the importance of non-DLVO forces in a general framework for understanding and predicting particle aggregation and attachment.