Metastable Configurations Research Articles

Chiral, Topological, and Knotted Colloids in Liquid Crystals

The geometric shape, symmetry, and topology of colloidal particles often allow for controlling colloidal phase behavior and physical properties of these soft matter systems. In liquid crystalline dispersions, colloidal particles with low symmetry and nontrivial topology of surface confinement are of particular interest, including surfaces shaped as handlebodies, spirals, knots, multi-component links, and so on. These types of colloidal surfaces induce topologically nontrivial three-dimensional director field configurations and topological defects. Director switching by electric fields, laser tweezing of defects, and local photo-thermal melting of the liquid crystal host medium promote transformations among many stable and metastable particle-induced director configurations that can be revealed by means of direct label-free three-dimensional nonlinear optical imaging. The interplay between topologies of colloidal surfaces, director fields, and defects is found to show a number of unexpected features, such as knotting and linking of line defects, often uniquely arising from the nonpolar nature of the nematic director field. This review article highlights fascinating examples of new physical behavior arising from the interplay of nematic molecular order and both chiral symmetry and topology of colloidal inclusions within the nematic host. Furthermore, the article concludes with a brief discussion of how these findings may lay the groundwork for new types of topology-dictated self-assembly in soft condensed matter leading to novel mesostructured composite materials, as well as for experimental insights into the pure-math aspects of low-dimensional topology.

Deformation, shape transformations, and stability of elastic rod loops within spherical confinement

Mechanical insight into the packing of slender objects within confinement is essential for understanding how polymers, filaments, or wires organize and rearrange in limited space. Here we combine theoretical modeling, numerical optimization, and experimental studies to reveal spherical packing behavior of thin elastic rod loops of homogeneous or inhomogeneous stiffness. Across varying loop lengths, a rich array of configurations including circle, saddle, figure-eight, and more intricate patterns are identified. A theoretical framework rooted in the local equilibrium of force and moment is proposed for the rod loop deformation, facilitating the determination of internal and contact forces experienced by the rods during deformation. For the confined homogeneous rod loops, their stable and metastable configurations are well described using proposed Euler rotation curves, which offer a concise and effective approach for configuration prediction. Moreover, formulated analysis on the stability and critical force for homogeneous rod loops on great circles of the spherical confinement are performed. For inhomogeneous rod loops with two segments of differing stiffness, the stiffer segment exhibits less deviation from the great circle, while the softer segment undergoes more pronounced deformation. These findings not only enhance our understanding of buckling and post-buckling phenomena but also offer insights into filament patterning within confining environments.

Flexible porous coordination polymer with multiple configurations for guest recognition and switchable CO2 sorption properties

Abstract Realizing multiple metastable configurations in a single porous coordination polymer has long been pursued to achieve switchable functionality. In this study, we reported multiple configurations in one porous coordination polymer material via the design of the adjustable intraframework π–π stacking moieties. We demonstrated that the porous coordination polymer can accommodate three different open pore phases depending on the type of solvent. Furthermore, this porous coordination polymer exhibits three distinct closed pore phases depending on the activation approaches, demonstrating different CO2 sorption properties.

Efficient high-throughput method utilizing neural network potentials to calculate interaction energies, validated by clean transfer experiment of CVD graphene with polymer mixtures

In this study, we designed a computational model involving energy decomposition using ground state energy minimized geometries resulting from a general-purpose neural network potential (ANI-1ccx). The numerical simulations show a distribution of energies, which indicate a two-fold reduction in interaction energy and polarity shift in electrostatic interaction, highlighting the computational novelty in exploring over a million metastable configurations. Experimentally, we validate our model by observing that using a mixture of two distinct polymers in the wet transfer process reduces transfer-induced doping and strain on transferred CVD graphene compared to the conventional single polymer wet transfer method, primarily due to decreased polymer contamination from the transfer process. This reduction is linked to the decreased interaction energy in the mixture of polymethyl methacrylate and angelica lactone polymer on graphene.

Water structural effects on DNA–DNA interactions and homologous recognition

Comprehending the principles underlying the interaction between DNA molecules in electrolyte solution is of crucial importance for understanding the phenomena of DNA condensation, recognition of homologous genes, and properties of DNA liquid crystals. Although DNA was considered in all its helical complexity over the last two decades, only a primitive, local, electrostatic model of the aqueous solution was considered. The forces acting between DNA molecules however must be influenced by the structure of the liquid separating them. In this paper we make a step towards unravelling earlier neglected effects of water structure on DNA–DNA interactions. We develop a model of DNA interaction accounting for the nonlocal dielectric response of water and of the electrolyte plasma dissolved in it. We focus particularly on the study of the dipolar overscreening effect, which leads to decaying oscillations of the electrostatic potential about DNA, and how it will affect electrostatic energy surfaces as a function of interaxial separation and mutual azimuthal orientation of the parallelly aligned interacting DNAs. We found that going beyond the classical electrostatic description of water (the so-called primitive model) reveals a complex oscillatory interaction surface in space, with many possible metastable configurations. These however vanish rapidly with smearing of the DNA charge distribution, due to dephasing of the oscillatory components of the interaction. This dephasing results in the suppression of oscillation amplitudes and leads to the dominance of non-oscillatory components in spatial dipolar correlations and the Debye screening. These dominant correlation patterns are shown to lead to a substantial enhancement of the difference between the interaction of homologous and nonhomologous DNA sequences, deepening and sharpening the homology recognition well.

Chemical Environment and Structural Variations in High Entropy Oxide Thin Film Probed with Electron Microscopy.

We employ analytical transmission electron microscopy (TEM) to correlate the structural and chemical environment variations within a stacked epitaxial thin film of the high entropy oxide (HEO) Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O (J14), with two layers grown at different substrate temperatures (500 and 200 °C) using pulsed laser deposition (PLD). Electron diffraction and atomically resolved STEM imaging reveal the difference in out-of-plane lattice parameters in the stacked thin film, which is further quantified on a larger scale using four-dimensional STEM (4D-STEM). In the layer deposited at a lower temperature, electron energy loss spectroscopy (EELS) mapping indicates drastic changes in the oxidation states and bonding environment for Co ions, and energy-dispersive X-ray spectroscopy (EDX) mapping detects more significant cation deficiency. Ab initio density functional theory (DFT) calculations validate that vacancies on the cation sublattice of J14 result in significant electronic and structural changes. The experimental and computational analyses indicate that low temperatures during film growth result in cation deficiency, an altered chemical environment, and reduced lattice parameters while maintaining a single phase. Our results demonstrate that the complex correlation of configurational entropy, kinetics, and thermodynamics can be utilized for accessing a range of metastable configurations in HEO materials without altering cation proportions, enabling further engineering of functional properties of HEO materials.

Comparative analysis of surface phase diagrams in aqueous environment: Implicit vs explicit solvation models.

Identifying the stable surface phases under a given electrochemical conditions serves as the basis for studying the atomistic mechanism of reactions at solid/water interfaces. In this work, we systematically compare the performance of the two main approaches that are used to capture the impact of an aqueous environment, implicit and explicit solvent, on surface energies and phase diagrams. As a model system, we consider the magnesium/water interface with (i) Ca substitution and (ii) proton and hydroxyl adsorption. We show that while the implicit solvent model is computationally very efficient, it suffers from two shortcomings. First, the choice of the implicit solvent parameters significantly influences the energy landscape in the vicinity of the surface. The default parameters benchmarked on solvation in water underestimate the energy of the dissolved Mg ion and lead to spontaneous dissolution of the surface atom, resulting in large differences in the surface energetics. Second, in systems containing a charged surface and a solvated ion, the implicit solvent model may not converge to the energetically stable ionic charge state but remain in a high-energy metastable configuration, representing the neutral charge state of the ion. When these two issues are addressed, surface phase diagrams that closely match the explicit water results can be obtained. This makes the implicit solvent model highly attractive as a computationally-efficient surrogate model to compute surface energies and phase diagrams.

Native point defects in HgCdTe infrared detector material: Identifying deep centers from first principles

We investigate the native point defects in the long-wavelength infrared (LWIR) detector material Hg0.75Cd0.25Te using a dielectric-dependent hybrid density functional combined with spin–orbit coupling. Characterizing these point defects is essential as they are responsible for intrinsic doping and nonradiative recombination centers in the detector material. The dielectric-dependent hybrid functional allows for an accurate description of the bandgap (Eg) for Hg1−xCdxTe (MCT) over the entire compositional range, a level of accuracy challenging with standard hybrid functionals. Our comprehensive examination of the native point defects confirms that cation vacancies VHg(Cd) are the primary sources of p-type conductivity in the LWIR material given their low defect formation energies and the presence of a shallow acceptor level (−/0) near the valence-band maximum. In addition to the shallow acceptor level, the cation vacancies exhibit a deep charge transition level (2−/−) situated near the midgap, characteristic of nonradiative recombination centers. Our results indicate that Hg interstitial could also be a deep center in the LWIR MCT through a metastable configuration under the Hg-rich growth conditions. While an isolated Te antisite does not show deep levels, the formation of VHg–TeHg defect complex introduces a deep acceptor level within the bandgap.

CO‐induzierte Dimer‐Dissoziation verursacht Gem‐Dicarbonyl‐Bildung auf einem Einzelatom‐Katalysator‐Modell

AbstractDie Fähigkeit, mehrere Reaktanten an derselben aktiven Stelle zu koordinieren ist eine wichtige Voraussetzung für die breite Anwendbarkeit der Einzelatom‐Katalyse. Modellkatalysatoren sind ideal, um den Zusammenhang zwischen der Geometrie der aktiven Stelle und der Bindung der Reaktanten zu untersuchen, da die Struktur der Einkristalloberflächen genau bestimmt werden kann. Die Adsorbate können mit Hilfe der Rastertunnelmikroskopie (STM) abgebildet werden; dadurch sind direkte Vergleiche mit der Dichtefunktionaltheorie möglich. In dieser Studie verfolgen wir mit Hilfe von STM‐Bildsequenzen einzelne Rh1‐Adatome und Rh2‐Dimere auf Fe3O4(001), während CO bei Raumtemperatur dosiert wird. Die CO‐Adsorption auf Rh1‐Adatomen führt ausschließlich zu stabilen Rh1CO‐Monocarbonylen, bei denen das Rh‐Atom die bevorzugte pseudo‐quadratisch planare Koordination erzielt. In geringem Maß bilden sich auch Rh1(CO)2 Gem‐Dicarbonyl‐Adsorbate; diese entstehen jedoch ausschließlich durch das Aufbrechen von Rh2 Dimeren; der Reaktionsweg führt über ein instabiles Rh2(CO)3 Zwischenprodukt. Unsere Ergebnisse veranschaulichen, wie Minderheitenspezies, die für (über die Probenfläche mittelnde) Spektroskopie‐Methoden unsichtbar sind, eine wichtige Rolle in katalytischen Systemen spielen können, und zeigen, dass die Zersetzung von Dimeren oder kleinen Clustern ein Weg sein kann, um reaktive, metastabile Konfigurationen in der Einzelatom‐Katalyse zu erzeugen.

CO-Induced Dimer Decay Responsible for Gem-Dicarbonyl Formation on a Model Single-Atom Catalyst.

The ability to coordinate multiple reactants at the same active site is important for the wide-spread applicability of single-atom catalysis. Model catalysts are ideal to investigate the link between active site geometry and reactant binding, because the structure of single-crystal surfaces can be precisely determined, the adsorbates imaged by scanning tunneling microscopy (STM), and direct comparisons made to density functional theory. In this study, we follow the evolution of Rh1 adatoms and minority Rh2 dimers on Fe3O4(001) during exposure to CO using time-lapse STM at room temperature. CO adsorption at Rh1 sites results exclusively in stable Rh1CO monocarbonyls, because the Rh atom adapts its coordination to create a stable pseudo-square planar environment. Rh1(CO)2 gem-dicarbonyl species are also observed, but these form exclusively through the breakup of Rh2 dimers via an unstable Rh2(CO)3 intermediate. Overall, our results illustrate how minority species invisible to area-averaging spectra can play an important role in catalytic systems, and show that the decomposition of dimers or small clusters can be an avenue to produce reactive, metastable configurations in single-atom catalysis.

Systematic DFT Modeling van der Waals Heterostructures from a Complete Configurational Basis Applied to γ-PC/WS2.

Periodic boundary conditions in density functional theory (DFT)-based modeling of bilayer van der Waals heterostructures introduce an artificial lock to a metastable configuration. Depending on the initial supercell, geometric optimization may reach local energy minima at a fixed twist-angle in a restricted strain-space. In this work, an algorithm was introduced for generating a complete scope of ways to combine two monolayer unit cells into a common supercell. In its application to γ-PC/WS2, 18,123 bilayer supercells were derived, for which the constituting monolayers possessed isotropic strains, anisotropic strains, or intralayer shear strains. Based on analysis, 45 isotropically strained configurations were carefully chosen for optimization by DFT. Geometric and energetic features and band structures were revealed and compared, following the variations at different strains and twist-angles. As such, this case study brought to resolution the impacts of supercell construction on DFT's outcomes and the merits of in-depth screening of the different options. Repetitions and extensions to the demonstrated approach may be applied to characterize van der Waals heterostructures and derivatives in the future.

Qualitatively and Quantitatively Different Configurations of Nematic-Nanoparticle Mixtures.

We consider the influence of different nanoparticles or micrometre-scale colloidal objects, which we commonly refer to as particles, on liquid crystalline (LC) orientational order in essentially spatially homogeneous particle-LC mixtures. We first illustrate the effects of coupling a single particle with the surrounding nematic molecular field. A particle could either act as a "dilution", i.e., weakly distorting local effective orientational field, or as a source of strong distortions. In the strong anchoring limit, particles could effectively act as topological point defects, whose topological charge q depends on particle topology. The most common particles exhibit spherical topology and consequently act as q = 1 monopoles. Depending on the particle's geometry, these effective monopoles could locally induce either point-like or line-like defects in the surrounding LC host so that the total topological charge of the system equals zero. The resulting system's configuration is topologically equivalent to a crystal-like array of monopole defects with alternating topological charges. Such configurations could be trapped in metastable or stable configurations, where the history of the sample determines a configuration selection.

Persistent enhancement of exciton diffusivity in CsPbBr3 nanocrystal solids.

In semiconductors, exciton or charge carrier diffusivity is typically described as an inherent material property. Here, we show that the transport of excitons among CsPbBr3 perovskite nanocrystals (NCs) depends markedly on how recently those NCs were occupied by a previous exciton. Using transient photoluminescence microscopy, we observe a striking dependence of the apparent exciton diffusivity on excitation laser power that does not arise from nonlinear exciton-exciton interactions or thermal heating. We interpret our observations with a model in which excitons cause NCs to transition to a long-lived metastable configuration that markedly increases exciton transport. The exciton diffusivity observed here (>0.15 square centimeters per second) is considerably higher than that observed in other NC systems, revealing unusually strong excitonic coupling between NCs. The finding of a persistent enhancement in excitonic coupling may help explain other photophysical behaviors observed in CsPbBr3 NCs, such as superfluorescence, and inform the design of optoelectronic devices.

Persistent gravitational radiation from glitching pulsars – II. Updated scaling with vortex number

ABSTRACT Superfluid vortices pinned to nuclear lattice sites or magnetic flux tubes in a neutron star evolve abruptly through a sequence of metastable spatial configurations, punctuated by unpinning avalanches associated with rotational glitches, as the stellar crust spins down electromagnetically. The metastable configurations are approximately but not exactly axisymmetric, causing the emission of persistent, quasimonochromatic, current quadrupole gravitational radiation. The characteristic gravitational wave strain h0 as a function of the spin frequency f and distance D from the Earth is bounded above by $h_0 = 1.2\substack{+1.3 \\ -0.9} \times 10^{-32} (f/30\,\,{\rm Hz})^{2.5} (D/1\,\,{\rm kpc})^{-1}$, corresponding to a Poissonian spatial configuration (equal probability per unit area, i.e. zero inter-vortex repulsion), and bounded below by $h_0 = 1.8\substack{+2.0 \\ -1.5} \times 10^{-50} (f/30\,\,{\rm Hz})^{1.5} (D/1\,\,{\rm kpc})^{-1}$, corresponding to a regular array (periodic separation, i.e. maximum inter-vortex repulsion). N-body point vortex simulations predict an intermediate scaling, $h_0 = 7.3\substack{+7.9 \\ -5.4} \times 10^{-42} (f/30\,\,{\rm Hz})^{1.9} (D/1\,\,{\rm kpc})^{-1}$, which reflects a balance between the randomizing but spatially correlated action of superfluid vortex avalanches and the regularizing action of inter-vortex repulsion. The scaling is calibrated by conducting simulations with Nv ≤ 5 × 103 vortices and extrapolated to the astrophysical regime Nv ∼ 1017(f/30 Hz). The scaling is provisional, pending future computational advances to raise Nv and include three-dimensional effects such as vortex tension and turbulence.

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.

Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.

3D Magnetization Textures: Toroidal Magnetic Hopfion Stability in Cylindrical Samples.

Topologically non-trivial magnetization configurations in ferromagnetic materials on the nanoscale, such as hopfions, skyrmions, and vortices, have attracted considerable attention of researchers during the last few years. In this article, by applying the theory of micromagnetism, I demonstrate that the toroidal hopfion magnetization configuration is a metastable state of a thick cylindrical ferromagnetic nanodot or a nanowire of a finite radius. The existence of this state is a result of the competition among exchange, magnetostatic, and magnetic anisotropy energies. The Dzyaloshinskii-Moriya exchange interaction and surface magnetic anisotropy are of second importance for the hopfion stabilization. The toroidal hopfion metastable magnetization configuration may be reached in the process of remagnetizing the sample by applying an external magnetic field along the cylindrical axis.

Solvent-polarity dependence of ultrafast excited-state dynamics of trans-4-nitrostilbene.

Ultrafast excited-state dynamics of the simplest nitrostilbenes, namely trans-4-nitrostilbene (t-NSB), was studied in solvents of various polarities with ultrafast broadband time-resolved fluorescence and transient absorption spectroscopies, and by quantum-chemical computations. The results revealed that the initially excited S1(ππ*) state deactivation dynamics is strongly influenced by the solvent polarity. Specifically, the t-NSB S1-state lifetime decreases by three orders of magnitude from ∼60 ps in high-polarity solvents to ∼60 fs in nonpolar solvents. The strong solvent-polarity dependence arises from the differences in dipole moments among the S1 and relevant states, including the major intersystem crossing (ISC) receiver triplet states, and therefore, the solvent polarity can modulate their relative energies and ISC rates. In nonpolar solvents, the sub-100 fs lifetime is due to a combination of efficient ISC and internal conversion. In medium-polarity solvents, the S1-state population decays via a competing ISC relaxation mechanism in a biphasic manner, and the ISC rates are found to obey the inverse energy gap law of the strong coupling case. In high-polarity solvents, the S1 state is stabilized to a much lower energy such that ISC becomes energetically infeasible, and the S1 state decays via barrier crossing along the torsion angle of the central ethylenic bond to the nonfluorescent perpendicular configuration. Regardless of the initial S1-state deactivation pathways in various solvents, the excited-state population is ultimately trapped in the metastable T1-state perpendicular configuration, at which a slower ISC occurs to bring the system to the ground state and bifurcate into either trans or cis form of NSB.

Atomic Charge Dependency of Spiropyran/Merocyanine Adsorption as a Precursor to Surface Isomerization Reactions.

This computational study investigates the adsorption of various spiropyran and merocyanine isomers on a NaCl substrate using a combination of density functional theory (DFT) and molecular mechanics (MM) calculations. Four different charge methods were used to determine the partial atomic charges for the adsorbate molecules, including Mulliken population analysis and three electrostatic potential (ESP) methods (Merz-Kollman, ChelpG, and Hu-Lu-Yang), while three different force fields (AMBER 3, CHARMM 27, and MM+) were employed for the MM calculations. The results show that the various DFT charge methods produced similar outcomes for the molecules' partial atomic charges, with some exceptions for individual atoms and methods. Additionally, it was found that the ESP charge methods were more sensitive to the conformer orientation than the Mulliken approach. The adsorption behavior of merocyanine conformers with the central bond in trans orientation (T-conformers) was similar for various configurations, with the molecule adsorbing mostly flat with its aromatic rings almost parallel to the substrate. However, C-conformers (with their central bond in cis orientation) and spiropyran isomers exhibited inconsistent adsorption behavior, mostly because only some of the aromatic rings contributed to the adsorption behavior. Due to additional van der Waals interactions of more aromatic rings, the adsorption energies for T-conformers are consistently 0.2-0.3 eV higher than for C-conformers and for spiropyran. The study found that the adsorption geometries and energies of stable T-conformers were independent of the partial atomic charge scheme and force field used, and C-conformers show parameter-dependent behavior upon adsorption, leading to metastable configurations. These findings indicate viable pathways during the spiropyran-merocyanine isomerization reactions. Therefore, the results provide initial insights into the possibility of switching spiropyran isomers into merocyanine isomers and vice versa after adsorption onto substrates.

Metastable atomic-ordered configurations for Al1/2Ga1/2N predicted by Monte-Carlo method based on first-principles calculations

Metastability of Al n /12Ga1−n/12N (n= 2–10: integer) with the 1–2 monolayer (ML) in-plane configuration towards the c [0001] direction has been demonstrated recently. To theoretically explain the existence of these metastable structures, relatively large calculation cells are needed. However, previous calculations were limited to the use of small calculation cell sizes to estimate the local potential depth (Δσ) of ordered Al1/2Ga1/2N models. In this work, we were able to evaluate large calculation cells based on the interaction energies between proximate Al atoms (δE Al–Al) in AlGaN alloys. To do this, δE Al–Al values were estimated by first-principles calculations (FPCs) using a (5a 1 × 5a 2 × 5c) cell. Next, a survey of the possible ordered configurations using various large calculation cell models was performed using the estimated δE Al–Al values and the Monte-Carlo method. Then, various Δσ values were estimated by FPCs and compared with the configurations previously reported by other research groups. We found that the ordered configuration obtained from the (4a 1 × 2a 2 × 1c) calculation cell (C 42) has the lowest Δσ of −9.3 meV/cation and exhibited an in-plane configuration at the c(0001) plane having (–Al–Al–Ga–Ga–) and (–Al–Ga–) sequence arrangements observed along the planes. Hence, we found consistencies between the morphology obtained from experiment and the shape of the primitive cell based on our numerical calculations.

Molecular Mechanisms behind Conformational Transitions of the Influenza Virus Hemagglutinin Membrane Anchor.

Membrane fusion is a fundamental process that is exploited by enveloped viruses to enter host cells. In the case of the influenza virus, fusion is facilitated by the trimeric viral hemagglutinin protein (HA). So far, major focus has been put on its N-terminal fusion peptides, which are directly responsible for fusion initiation. A growing body of evidence points also to a significant functional role of the HA C-terminal domain, which however remains incompletely understood. Our computational study aimed to elucidate the structural and functional interdependencies within the HA C-terminal region encompassing the transmembrane domain (TMD) and the cytoplasmic tail (CT). In particular, we were interested in the conformational shift of the TMD in response to varying cholesterol concentration in the viral membrane and in its modulation by the presence of CT. Using free-energy calculations based on atomistic molecular dynamics simulations, we characterized transitions between straight and tilted metastable TMD configurations under varying conditions. We found that the presence of CT is essential for achieving a stable, highly tilted TMD configuration. As we demonstrate, such a configuration of HA membrane anchor likely supports the tilting motion of its ectodomain, which needs to be executed during membrane fusion. This finding highlights the functional role of, so far, the relatively overlooked CT region.