Orientation-dependent Interactions Research Articles

The Ordered Structures Formed by Janus-like Particles on a Triangular Lattice.

The formation of ordered structures by Janus-like particles, composed of two parts (A and B), with orientation-dependent interactions on a triangular lattice was studied using Monte Carlo methods. The assumed lattice model allows each particle to take on one of the six orientations. The interaction between the A parts of neighboring particles was assumed to be attractive, while the AB and BB interactions were assumed to be repulsive. Moreover, it was assumed that the interaction between a pair of neighboring particles depended on the degrees to which their AA, AB, and BB parts face each other. It was shown that several ordered phases of different densities and structures may appear, depending on the magnitudes of AB and BB interactions. In particular, we found several structures composed of small clusters consisting of three (OT), four (OR), and seven (S) particles, surrounded by empty sites, the lamellar phases (OL, OL1, and OL3), the structures with hexagonal symmetry (R3×3 and K), as well as the structures with more complex symmetry (R5×5 and LAD). Several phase diagrams were evaluated, which demonstrated that the stability regions of different ordered phases are primarily determined by the strengths of repulsive AB and BB interactions.

Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-causing mechanism

We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3'-untranslated region (3'-UTR) of SPINK1 as the cause of severe infantile isolated exocrine pancreatic insufficiency. Although we established that Alu_Ins leads to the complete loss of SPINK1 mRNA expression, the precise mechanisms remained elusive. Here, we aimed to elucidate these mechanisms through a hypothesis-driven approach. Initially, we speculated that, owing to its particular location, Alu_Ins could independently disrupt mRNA 3' end formation and/or affect other post-transcriptional processes such as nuclear export and translation. However, employing a 3'-UTR luciferase reporter assay, Alu_Ins was found to result in only an ∼50% reduction in luciferase activity compared to wild type, which is insufficient to account for the severe pancreatic deficiency in the Alu_Ins homozygote. We then postulated that double-stranded RNA (dsRNA) structures formed between Alu elements, an upstream mechanism regulating gene expression, might be responsible. Using RepeatMasker, we identified two Alu elements within SPINK1's third intron, both oriented oppositely to Alu_Ins. Through RNAfold predictions and full-length gene expression assays, we investigated orientation-dependent interactions between these Alu repeats. We provide compelling evidence to link the detrimental effect of Alu_Ins to extensive dsRNA structures formed between Alu_Ins and pre-existing intronic Alu sequences, including the restoration of SPINK1 mRNA expression by aligning all three Alu elements in the same orientation. Given the widespread presence of Alu elements in the human genome and the potential for new Alu insertions at almost any locus, our findings have important implications for detecting and interpreting Alu insertions in disease genes.

Asymmetry in Polymer-Solvent Interactions Yields Complex Thermoresponsive Behavior.

We introduce a lattice framework that incorporates elements of Flory-Huggins solution theory and the q-state Potts model to study the phase behavior of polymer solutions and single-chain conformational characteristics. Without empirically introducing temperature-dependent interaction parameters, standard Flory-Huggins theory describes systems that are either homogeneous across temperatures or exhibit upper critical solution temperatures. The proposed Flory-Huggins-Potts framework extends these capabilities by predicting lower critical solution temperatures, miscibility loops, and hourglass-shaped spinodal curves. We particularly show that including orientation-dependent interactions, specifically between monomer segments and solvent particles, is alone sufficient to observe such phase behavior. Signatures of emergent phase behavior are found in single-chain Monte Carlo simulations, which display heating- and cooling-induced coil-globule transitions linked to energy fluctuations. The framework also capably describes a range of experimental systems. Importantly, and by contrast to many prior theoretical approaches, the framework does not employ any temperature- or composition-dependent parameters. This work provides new insights regarding the microscopic physics that underpin complex thermoresponsive behavior in polymers.

Code for molecular dynamics simulation of two dimensional Mercedes-Benz water model

The Mercedes-Benz (MB) water model is a simple two-dimensional toy model of water that can reproduce many of the anomalous properties of water. Within the model, the water particles are represented as Lennard-Jones disks with explicitly added orientation-dependent interactions that mimic the formation of hydrogen bonds. Due to the simple implementation of the MB model in Monte Carlo simulations, it was mainly studied with Monte Carlo simulations in different ensembles. The implementation of the model in molecular dynamics simulations is not trivial. In this paper we present the code for molecular dynamics simulations. The structural and thermodynamic properties of the model were calculated using molecular dynamics and compared with data from Monte Carlo simulations to confirm that the molecular dynamics code works correctly. We also used molecular dynamics to calculate the dynamic properties of the model. The Fortran source code of our molecular dynamics simulation of the MB water model is provided.

On currents in the $O(n)$ loop model

Using methods from the conformal bootstrap, we study the properties of Noether currents in the critical O(n)O(n) loop model. We confirm that they do not give rise to a Kac-Moody algebra (for n≠ 2n≠2), a result expected from the underlying lack of unitarity. By studying four-point functions in detail, we fully determine the current-current OPEs, and thus obtain several structure constants with physical meaning. We find in particular that the terms :\!J\bar{J}\!::JJ‾: in the identity and adjoint channels vanish exactly, invalidating the argument made in [Nucl. Phys. B 419, 411 (1994)] that adding orientation-dependent interactions to the model should lead to continuously varying exponents in self-avoiding walks. We also determine the residue of the identity channel in the JJJJ two-point function, finding that it coincides both with the result of a transfer-matrix computation for an orientation-dependent correlation function in the lattice model, and with an earlier Coulomb gas computation of Cardy [Nucl. Phys. B 265, 409 (1986)]. This is, to our knowledge, one of the first instances where the Coulomb gas formalism and the bootstrap can be successfully compared.

A 3D multi-phase-field model for orientation-dependent complex crack interaction in fiber-reinforced composite laminates

We formulate a 3D multi-phase field model to simulate bulk and interfacial fracture in fiber-reinforced composites. The purpose of this study is to predict the complex crack interaction between the interlaminar and intralaminar fracture in FRPCs. For that, the discrete crack and the sharp interface are both smeared using the phase-field approach. A second-order anisotropic tensor is incorporated in the elastic as well as the fracture surface energy to promote direction-dependent crack growth. The interface constitutive behavior is represented by the uncoupled 3D traction–separation laws—in exponential and bi-linear form. The proposed model captures the complicated failure phenomena in FRPCs such as matrix damage, interfacial delamination, and their interactions for different configurations of lamina with different fiber orientations and fracture energies. This model’s capability is further illustrated to study the three common modes of fracture i.e. modes I, II, and III, in 3D FRPC laminates where the crack impinges on the interface. Finally, the obtained framework is validated by two benchmark problems including the mode I and mode II delamination test, and is compared against experimental data reported in the literature.

Thermodynamics perturbation theory for solvation of nonpolar solutes in rose model.

A simple model of water, called the rose model, is used in this work. The rose model is a very simple model that can provide insight into the anomalous properties of water. In the rose water model, the molecules are represented as two-dimensional Lennard-Jones disks with potentials for orientation-dependent pairwise interactions mimicking formations of hydrogen bonds. We have recently applied a Wertheim integral equationtheory (IET) and a thermodynamic perturbation theory (TPT) to the rose model in bulk. These analytical theories offer the advantage of being computationally less intensive than computer simulations by orders of magnitudes. Here we have applied the TPT to study the transfer of a nonpolar solute into rose water, the so-called hydrophobic effect. Similarly as in our previous work for bulk water, we have found that the theory reproduces the computer simulation results quite well at higher temperatures, while the theories predict the qualitative trends at low temperatures.

Molecular van der Waals Fluids in Cavity Quantum Electrodynamics.

Intermolecular van der Waals interactions are central to chemical and physical phenomena ranging from biomolecule binding to soft-matter phase transitions. In this work, we demonstrate that strong light-matter coupling can be used to control the thermodynamic properties of many-molecule systems. Our analyses reveal orientation dependent single molecule energies and interaction energies for van der Waals molecules. For example, we find intermolecular interactions that depend on the distance between the molecules R as R-3 and R0. Moreover, we employ ab initio cavity quantum electrodynamics calculations to develop machine-learning-based interaction potentials for molecules inside optical cavities. By simulating systems ranging from 12 H2 to 144 H2 molecules, we observe varying degrees of orientational order because of cavity-modified interactions, and we explain how quantum nuclear effects, light-matter coupling strengths, number of cavity modes, molecular anisotropies, and system size all impact the extent of orientational order.

Hierarchy of anomalies in the simple rose model of water

The density, diffusion, and structural anomalies of the simple two-dimensional model of water were determined by Monte Carlo simulations. The rose model was used which is a very simple model for explaining the origin of water properties. Rose water molecules are modelled as two-dimensional Lennard-Jones disks with rose potentials for orientation dependent pairwise interactions mimicking formations of hydrogen bonds. The model can be seen also as a variance of silica-like models. Two parameters of potential in this work were selected in a way that (1) the model exhibits similar properties to Mercedes-Benz (MB) water model; and (2) that the model has real-like properties of water. Beside the known thermodynamic anomaly for the model we also found diffusion and structural anomalies. The orientational order parameters were calculated and maximum encountered for three and six-fold symmetry. For the MB parametrization, the anomalies occur in hierarchy order, which is a slight variation of the hierarchy order in real water. The diffusion anomaly region is the innermost in the hierarchy while for water it is the density anomaly region. In case of real water parametrization the most inner is the structural anomaly.

Simple rose model of water in constant electric field.

A simple two-dimensional statistical mechanical water model, called the rose model, was used in this work. We studied how a homogeneous constant electric field affects the properties of water. The rose model is a very simple model that helps explain the anomalous properties of water. Rose water molecules are represented as two-dimensional Lennard-Jones disks with potentials for orientation-dependent pairwise interactions mimicking formations of hydrogen bonds. The original model is modified by addition of charges for interaction with the electric field. We studied what kind of influence the electric field strength has on the model's properties. To determine the structure and thermodynamics of the rose model under the influence of the electric field we used Monte Carlo simulations. Under the influence of a weak electric field the anomalous properties and phase transitions of the water do not change. On the other hand, the strong fields shift the phase transition points as well as the position of the density maximum.

Orientation-Dependent Interaction between the Magnetic Plasmons in Gold Nanocups and the Excitons in WS2 Monolayer and Multilayer.

The integration of two-dimensional transition metal dichalcogenides with plasmonic nanostructures is extremely attractive for the investigation of the resonance coupling between plasmons and excitons, which offers a framework for the study of cavity quantum electrodynamics and is of great potential for exploring diverse quantum technologies. Herein we report on the coupling between the magnetic plasmons supported by individual asymmetric Au nanocups and the excitons in WS2 monolayer and multilayer. Resonance coupling with the strength varying from weak to strong regimes is realized by adjusting the orientation of the individual Au nanocups on WS2 monolayer. Different energy detunings between the magnetic plasmons and the excitons are achieved by varying the size of the Au nanocup. The Rabi splitting energies extracted at zero detuning are up to 106 meV. The anticrossing feature is observed in the measured scattering spectra and simulated absorption spectra, which indicates that the resonance coupling between the magnetic plasmons in the Au nanocup and the excitons in WS2 monolayer enters the strongly coupled regime. A dependence of the coupling strength on the layer number is further observed when the Au nanocups are coupled with WS2 multilayer. Our study suggests a promising approach toward the realization of different coupling regimes in a simple hybrid system made of individual Au nanocups and two-dimensional materials.

Orientation-Dependent Image Dipole Interaction for the Tuning of the Excitonic Properties of CdSe Nanoplatelets

The fundamental characteristics of semiconductor nanoplatelets (NPLs) have been intensively studied with a view to their use in various optoelectronic devices. In particular, the assembly of highly anisotropic NPLs into stacks allows their optical properties to be easily controlled. Here, we systematically investigate the radiative decay processes of NPL assemblies for two distinct configurations, face-down and edge-up, and find a new way of manipulating their excitonic properties by introducing metamaterial structures. While the exciton lifetime for face-down NPLs is not strongly affected by the metamaterials, a significant reduction in the exciton lifetime for edge-up NPLs is observed. We account for this interesting result in terms of orientation-dependent image dipole interactions by showing that the net transition dipole moments for the two NPL configurations can be affected inversely by metamaterials. These results will facilitate the development of optoelectronic applications requiring the active manipulation of exciton lifetimes.

The Lattice Model of Particles with Orientation-Dependent Interactions at Solid Surfaces: Wetting Scenarios.

Wetting phenomena in a lattice model of particles having two chemically different halves (A and B) and being in contact with solid substrates have been studied with Monte Carlo methods. The energy of the interaction between a pair of neighboring particles has been assumed to depend on the degree to which the AA, AB and BB regions face each other. In this work, we have assumed that uAA=-1.0 and considered three series of systems with uAB=uBB, uAB=0 and uBB=0. The phase behavior of bulk systems has been determined. In particular, it has been shown that at sufficiently low temperatures the bulk systems order into the superantiferromagnetic (SAF) phase, or into the antiferromagnetic (AF) phase, depending on the magnitudes of AA, AB and BB interaction energies, uAA, uAB and uBB. The SAF structure occurs whenever ϵ=uAA+uBB-2uAB is lower than zero and the AF structure is stable when ϵ is greater than zero. The wetting behavior has been demonstrated to depend strongly on the structure of the bulk condensed phase, the interactions between fluid particles and the strength of the surface potential. In all series, we have found the dewetting transition, resulting from the limited stability of different ordered structures of surface phases. However, in the systems that exhibit the gas-liquid transition in the bulk, the reentrant wetting transition has been observed at sufficiently high temperatures. The mechanism of dewetting and reentrant wetting transitions has been determined. Moreover, we have also demonstrated, how the dewetting transition in the series with uAB=0 is affected by the wall selectivity, i.e., when the interaction between the parts A and B of fluid particles and the solid is different.

Liquid-vapour coexistence line and percolation line of rose water model

Monte Carlo simulations and Wertheim’s thermodynamic perturbation theory (TPT) are used to predict the phase diagram and percolation curve for the simple two-dimensional rose model of water. In the rose model of water, the water molecules are modelled as two-dimensional Lennard-Jones disks, with additional rose potentials for orientation dependent pairwise interactions that mimic formation of hydrogen bonds. Modifying both the shape and range of a 3-petal rose function, it was constructed an efficient and dynamical mimic of the 2D Mercedes Benz (MB) water model and experimental water. The liquid part of the phase space is explored using grand canonical Monte Carlo simulations and two versions of Wertheim’s TPT for associative fluids. We find that the theory reproduces well the physical properties of hot water but is less successful at capturing the more structured hydrogen bonding that occurs in cold water. In addition to reporting the phase diagram and percolation curve of the model, it is shown that the improved TPT predicts the phase diagram rather well, while the standard one predicts a phase transition at lower temperatures. For the percolation line, both versions have problems predicting the correct position of the line at high temperatures.

Statistical-mechanical liquid theories reproduce anomalous thermodynamic properties of explicit two-dimensional water models.

We have developed an analytical theory for a simple model of liquid water. We apply Wertheim's thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the rose model, which is among the simplest models of water. The particles interact through rose potentials for orientation dependent pairwise interactions. Modifying both the shape and range of a three-petal rose function, we construct an efficient and dynamical mimic of the two-dimensional (2D) Mercedes-Benz (MB) water model. The particles in 2D MB are 2D Lennard-Jones disks with three hydrogen bonding arms arranged symmetrically, resembling the Mercedes-Benz logo. Both models qualitatively predict both the anomalous properties of pure water and the anomalous solvation thermodynamics of nonpolar molecules. The IET is based on the orientationally averaged version of the Ornstein-Zernike equation. This is one of the main approximations in the present work. IET correctly predicts the pair correlation functions at high temperatures. Both TPT and IET are in semi-quantitative agreement with the Monte Carlo values of the molar volume, isothermal compressibility, thermal expansion coefficient, and heat capacity. A major advantage of these theories is that they require orders of magnitude less computer time than the Monte Carlo simulations.

DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation.

An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.

Orientation-dependent electrostatic interaction between inverse patchy colloids

ABSTRACT An inverse patchy colloid (IPC) refers to a particle having patches that are mutually repulsive while the bare particle–patch interactions are attractive. We model a system of charged IPCs with a single patch using Debye-Hückel theory. We derive the full analytical expression for the effective interaction energy for a pair of IPCs as a function of inter-particle separation and particle orientations. The model is applicable for various patch coverage, ionic strengths and dielectric permittivity of the medium. Approximate solutions are derived under high screening limit and the results are compared with the full solution. The model can be used in molecular simulations such as Monte Carlo simulations to accurately describe the interaction between a pair of IPCs for a given experimental conditions.

Understanding crystallographic orientation, microstructure and mechanical properties dependent interaction between recrystallization and phase transformation of a Fe–Al–Mn–Mo–C dual-phase steel

The competition mechanism of ferritic recrystallization and austenitic transformation, nucleation and growth kinetics of different crystallographic orientation components during intercritical annealing of a cold-rolling Fe–Al–Mn–Mo–C deep drawing dual-phase steel were investigated by a series of continuous annealing simulation experiments. The experiments provided an insight into the microstructural characteristics and mechanical behaviors that were caused from the interaction of primary recrystallization and phase transformation. The results show that the promoting effect of austenite transformation is greater than that of ferrite recrystallization with the increase of temperature in the two-phase region, and an appropriate soaking time is contributed to the formation and development of {111} oriented grains. Austenite formation affects morphology and size of the microstructure owing to inhibiting ferrite recrystallization and growth. From these that experimental data of the observed temperature or time-dependent mechanical properties can be interpreted. An excellent comprehensive properties with tensile strength of 480 MPa and plastic strain ratio (r value) of 1.15 can be obtained at annealing temperature of 880 °C for 300 s.

Lattice Model of Multilayer Adsorption of Particles with Orientation Dependent Interactions at Solid Surfaces.

A simple lattice model has been used to study the formation of multilayer films by fluids with orientation-dependent interactions on solid surfaces. The particles, composed of two halves (A and B) were allowed to take on one of six different orientations. The interaction between a pair of differently oriented neighboring particles was assumed to depend on the degrees to which their A and B parts overlap. Here, we have assumed that the AA interaction was strongly attractive, the AB interaction was set to zero, while the BB interaction was varied between 0 and . The ground state properties of the model have been determined for the systems being in contact with non-selective and selective walls over the entire range of BB interaction energies between 0 and . It has been demonstrated that the structure of multilayer films depends on the strengths of surface potential felt by differently oriented particles and the interaction between the B halves of fluid particles. Finite temperature behavior has been studied by Monte Carlo simulation methods. It has been shown that the bulk phase phase diagram is qualitatively independent of the BB interaction energy, and has the swan neck shape, since the high stability of the dense ordered phase suppresses the possibility of the formation of disordered liquid-like phase. Only one class of non-uniform systems with the BB interaction set to zero has been considered. The results have been found to be consistent with the predictions stemming form the ground state considerations. In particular, we have found that a complete wetting occurs at any temperature, down to zero. Furthermore, the sequences of layering transitions, and the structure of multilayer films, have been found to be the same as observed in the ground state.

Creep behaviour of two-phase lamellar TiAl: Crystal plasticity modelling and analysis

Two-phase (α2Ti3Al+γTiAl) fully lamellar TiAl alloys show highly anisotropic creep behaviour. Depending on lamellar orientations, locally in the TiAl phases hard and easy deformation modes are active, which significantly influence the creep behaviour at a global scale. To obtain comprehensive understanding how the locally activated crystallographic deformation modes influence the macroscopic creep behaviour, a crystal plasticity (CP) model with modified hardening behaviour is proposed in this work. For this purpose, a softening parameter is introduced in the model that phenomenologically describes the threshold stresses for material softening depending on pile-up dislocation lengths during creep deformation. The model allows us to interpret the cause of creep anisotropy at macro-scale deformation based on the orientation dependent activation and interactions of slip systems at the TiAl phases. Comprehensive study was performed to validate the model and to predict creep parameters under different temperature and stress loading conditions. Comparing the experimental data with simulation results, we found that the proposed CP model captures creep behaviour in primary, secondary, and tertiary regime for all the lamellar orientations with good accuracy. This model can be further used for investigating microstructure-sensitive creep behaviour of a wide range of TiAl alloys.