Nearest-neighbor Interactions Research Articles

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

The homo-dodecameric ring-shaped trp RNA binding attenuation protein (TRAP) from Alkalihalobacillus halodurans (Aha) binds up to twelve tryptophan ligands (Trp) and becomes activated to bind a specific sequence in the 5’ leader region of the trp operon mRNA, thereby downregulating biosynthesis of Trp. Thermodynamic measurements of Trp binding have revealed a range of cooperative behavior for different TRAP variants, even if the averaged apparent affinities for Trp have been found to be similar. Proximity between the ligand binding sites, and the ligand-coupled disorder-to-order transition has implicated nearest-neighbor interactions in cooperativity. To establish a solid basis for describing nearest-neighbor cooperativity in TRAP, we engineered variants constructed with two subunits connected by a flexible linker (dTRAP). We mutated the binding sites of alternating protomers such that only every other site was competent for Trp binding (WT-Mut dTRAP). Ligand binding monitored by NMR, calorimetry, and native mass spectrometry revealed strong cooperativity in dTRAP containing adjacent binding-competent sites, but a severe binding defect when the wild-type sites were separated by mutated sites. Cryo-EM experiments of dTRAP in its ligand-free apo state, and both dTRAP and WT-Mut dTRAP in the presence of Trp, revealed progressive stabilization of loops that gate the Trp binding site and participate in RNA binding. These studies provide important insights into the thermodynamic and structural basis for the observed ligand binding cooperativity in TRAP. Such insights can be useful for understanding allosteric control networks and for the development of those with defined ligand sensitivity and regulatory control.

Monte Carlo Simulations of the Spin-3/2 Ashkin-Teller Model in the Presence of Two Competing Dynamics

This paper studies, by means of Monte Carlo simulations, an open ferromagnetic spin-3/2 Ashkin-Teller model defined on a square lattice. This model can be viewed as the superposition of two Ising models which are coupled by a four-spin interaction strength K4while in each Ising model, the nearest-neighbor interaction constant is K2. The model is here submitted to two stochastic dynamics that consist of two processes; the first one is the Glauber dynamics which simulates the contact of the system with a heat bath at temperature T and the second one is the Kawasaki dynamics which simulates the continuous energy flux into the system from an external source. The Glauber single-spin flip process happens with the probability p while the Kawasaki spin-exchange process between neighboring sites occurs with the probability q = 1− p. The temperature-dependence of the system magnetizations for fixed coupling constants and lattice anisotropy has been thoroughly investigated. Several thermodynamic phases and phase transitions have been obtained as well as multicritical points. When the Kawasaki dynamics becomes dominant, self-organized antiferromagnetic phases are generated. Several phase diagrams have been devised to illustrate model thermodynamic properties.

Compensation temperature of a three-sublattice ferrimagnetic Heisenberg model

Using the double-time Green’s function method in combination with the random phase approximation and Anderson–Callen approximation, we investigate the magnetic properties of the ferrimagnetic Heisenberg model on a decorated square lattice. The effects of nearest-neighbor interactions and single-ion anisotropy on the compensation temperature are explored. Our results indicate that the next-nearest-neighbor interaction and/or single-ion anisotropy are not a necessary condition of the appearance of compensation temperature. When considering only the nearest-neighbor interaction, the system can also exhibit a compensation temperature. By comparing the impact of the nearest-neighbor interaction and single-ion anisotropy on the sublattice magnetizations of the system, a general condition of the appearance of compensation temperature is claimed.

Chemical ordering and magnetism in face-centered cubic CrCoNi alloy

The impact of magnetism on chemical ordering in face-centered cubic CrCoNi medium entropy alloy is studied by a combination of ab initio simulations, machine learning potentials, and Monte Carlo simulations. Large magnetic energies are revealed for some mixed L12/L10 type ordered configurations, which are rooted in strong nearest-neighbor magnetic exchange interactions and chemical bonding among the constituent elements. There is a delicate interplay between magnetism and stability of MoPt2 and L12/L10 type of order, which may explain opposing experimental and theoretical findings.

Effects of Temperature and Random Forces in Phase Transformation of Multi-Stable Systems.

Multi-stable behavior at the microscopic length-scale is fundamental for phase transformation phenomena observed in many materials. These phenomena can be driven not only by external mechanical forces but are also crucially influenced by disorder and thermal fluctuations. Disorder, arising from structural defects or fluctuations in external stimuli, disrupts the homogeneity of the material and can significantly alter the system's response, often leading to the suppression of cooperativity in the phase transition. Temperature can further introduce novel effects, modifying energy barriers and transition rates. The study of the effects of fluctuations requires the use of a framework that naturally incorporates the interaction of the system with the environment, such as Statistical Mechanics to account for the role of temperature. In the case of complex phenomena induced by disorder, advanced methods such as the replica method (to derive analytical formulas) or refined numerical methods based, for instance, on Monte Carlo techniques, may be needed. In particular, employing models that incorporate the main features of the physical system under investigation and allow for analytical results that can be compared with experimental data is of paramount importance for describing many realistic physical phenomena, which are often studied while neglecting the critical effect of randomness or by utilizing numerical techniques. Additionally, it is fundamental to efficiently derive the macroscopic material behavior from microscale properties, rather than relying solely on phenomenological approaches. In this perspective, we focus on a paradigmatic model that includes both nearest-neighbor interactions with multi-stable (elastic) energy terms and linear long-range interactions, capable of ensuring the presence of an ordered phase. Specifically, to study the effect of environmental noise on the control of the system, we include random fluctuation in external forces. We numerically analyze, on a small-size system, how the interplay of temperature and disorder can significantly alter the system's phase transition behavior. Moreover, by mapping the model onto a modified version of the Random Field Ising Model, we utilize the replica method approach in the thermodynamic limit to justify the numerical results through analytical insights.

Techniques for learning sparse Pauli-Lindblad noise models

Error-mitigation techniques such as probabilistic error cancellation and zero-noise extrapolation benefit from accurate noise models. The sparse Pauli-Lindblad noise model is one of the most successful models for those applications. In existing implementations, the model decomposes into a series of simple Pauli channels with one- and two-local terms that follow the qubit topology. While the model has been shown to accurately capture the noise in contemporary superconducting quantum processors for error mitigation, it is important to consider higher-weight terms and effects beyond nearest-neighbor interactions. For such extended models to remain practical, however, we need to ensure that they can be learned efficiently. In this work we present new techniques that accomplish exactly this. We introduce twirling based on Pauli rotations, which enables us to automatically generate single-qubit learning correction sequences and reduce the number of unique fidelities that need to be learned. In addition, we propose a basis-selection strategy that leverages graph coloring and uniform covering arrays to minimize the number of learning bases. Taken together, these techniques ensure that the learning of the extended noise models remains efficient, despite their increased complexity.

Synthesis of Sr6LuAl(BO3)6:Sm3+ Red Phosphor with Excellent Thermal Stability and Its Application in w-LEDs.

In this study, a series of Sr6LuAl(BO3)6:Sm3+ red phosphors were successfully prepared with a high-temperature solid-phase technology. The Rietveld refinement analysis of the X-ray diffraction (XRD) diffraction patterns indicated that the as-prepared phosphors belong to the R3¯ space group of the hexagonal crystal system. Under 404 nm near-ultraviolet excitation, the Sr6LuAl(BO3)6:Sm3+ phosphor exhibits narrowband emission within the range of 550 to 750 nm. The primary emission peak is observed at a wavelength of 599 nm, corresponding to 6H5/2 → 4F7/2. The optimum doping concentration of the Sr6LuAl(BO3)6:xSm3+ phosphor is 10 mol%. Nearest-neighbor ion interaction is the mechanism of concentration quenching. The synthesized phosphors demonstrate exceptional thermal stability, with a high quenching temperature (T0.5 > 480 K). Furthermore, the assembled white light-emitting diode (w-LED) device exhibits a low color temperature (5464 K), an excellent color rendering index (Ra = 95.6), and CIE coordinates (0.333, 0.336) close to those of standard white light. Collectively, these results suggest the enormous potential of Sr6LuAl(BO3)6:Sm3+ phosphors for applications in w-LEDs.

Exactly Solvable Inhomogeneous Fermion Systems

Abstract 15 exactly solvable inhomogeneous (spinless) fermion systems on 1D lattices are constructed explicitly based on the discrete orthogonal polynomials of the Askey scheme, e.g. Krawtchouk, Hahn, Racah, Meixner, and q-Racah polynomials. The Schrödinger and Heisenberg equations are solved explicitly, as the entire set of the eigenvalues and eigenstates are known explicitly. The ground-state two-point correlation functions are derived explicitly. The multipoint correlation functions are obtained by Wick’s theorem. 15 corresponding exactly solvable XX spin systems are also displayed. They all have nearest-neighbor interactions. The exact solvability of the Schrödinger equation means that the corresponding Fokker–Planck equation is also exactly solvable. This leads to 15 exactly solvable birth and death fermions and 15 birth and death spin models. These provide plenty of material for calculating interesting quantities, e.g. entanglement entropy, etc.

Model-free distributed state estimation with local measurements.

In this paper, the state estimation problem of physical plants with unknown system dynamic is revisited from the perspective of limited output information measurement, which corresponds to those with characteristics of high-dimensional, wide-area coverage and scatter. Given this fact, a network of sensors are used to carry out the measurement with each one accessing only partial outputs of the targeted systems and a novel model-free state estimation approach, named distributed stochastic variational inference state estimation, is proposed. The key idea of this method is to compensate for the impacts of local output measurements by adding nearest-neighbor rule-based information interaction among estimators to complete the state estimation. It finds from the numerical experiments that the proposed method has clear advantages in both estimation accuracy and speed, and it also provides guidance on how to improve the efficiency of state estimation under local measurements.

Generalized hydrodynamics and approach to generalized Gibbs equilibrium for a classical harmonic chain

Abstract We study the evolution of a classical harmonic chain with nearest-neighbor interactions starting from domain wall initial conditions. The initial state is taken to be either a product of two Gibbs ensembles (GEs) with unequal temperatures on the two halves of the chain or a product of two generalized Gibbs ensembles (GGEs) with different parameters in the two halves. For this system, we construct the Wigner function and demonstrate that its evolution defines the generalized hydrodynamics (GHD) describing the evolution of the conserved quantities. We solve the GHD for both finite and infinite chains and compute the evolution of conserved densities and currents. For a finite chain with fixed boundaries, we show that these quantities relax as ∼ 1 / t to their respective steady-state values given by the final expected GE or GGE state, depending on the initial conditions. Exact expressions for the Lagrange multipliers of the final expected GGE state are obtained in terms of the steady-state densities. In the case of an infinite chain, we find that the conserved densities and currents at any finite time exhibit ballistic scaling while, at infinite time, any finite segment of the system can be described by a current-carrying non-equilibrium steady state (NESS). We compute the scaling functions analytically and show that the relaxation to the NESS occurs as ∼ 1 / t for the densities and as ∼ 1 / t 2 for the currents. We compare the analytical results from hydrodynamics with those from exact microscopic numerics and find excellent agreement.

Chemical Design of Spin Frustration to Realize Topological Spin Glasses.

Patterning spins to generate collective behavior is at the core of condensed matter physics. Physicists develop techniques, including the fabrication of magnetic nanostructures and precision layering of materials specifically to engender frustrated lattices. As chemists, we can access such exotic materials through targeted chemical synthesis and create new lattice types by chemical design. Here, we introduce a new approach to induce magnetic frustration on a modified honeycomb lattice through a competition of alternating antiferromagnetic (AFM) and ferromagnetic (FM) nearest-neighbor interactions. By subtly modulating these two types of interactions through facile synthetic modifications, we created two systems: (1) a topological spin glass and (2) a frustrated spin-canted magnet with low-temperature exchange bias. To design this unconventional magnetic lattice, we used a metal-organic framework (MOF) platform, Ni3(pymca)3X3 (NipymcaX where pymca = pyrimidine-2-carboxylato and X = Cl, Br). We isolated two MOFs, NipymcaCl and NipymcaBr, featuring canted Ni2+-based moments. Despite this similarity, differences in the single-ion anisotropies of the Ni2+ spins result in distinct magnetic properties for each material. NipymcaCl is a topological spin glass, while NipymcaBr is a rare frustrated magnet with low-temperature exchange bias. Density functional theory calculations and Monte Carlo simulations on the NipymcaX lattice support the presence of magnetic frustration as a result of alternating AFM and FM interactions. Our calculations enabled us to determine the ground-state spin configuration and the distribution of spin-spin correlations relative to paradigmatic kagomé and triangular lattices. This modified honeycomb lattice is similar to the electronic Kekulé-O phase in graphene and provides a highly tunable platform to realize unconventional spin physics.

Pairing correlation of the kagome-lattice Hubbard model with the nearest-neighbor interaction

Abstract A recently discovered family of kagome lattice materials, AV3Sb5 (A = K,Rb,Cs), has attracted great interest, especially in the debate over their dominant superconducting pairing symmetry. To explore this issue, we study the superconducting pairing behavior within the kagome-lattice Hubbard model through the constrained path Monte Carlo method. It is found that doping around the Dirac point generates a dominant next-nearest-neighbor-d pairing symmetry driven by on-site Coulomb interaction U. However, when considering the nearest-neighbor interaction V, it may induce nearest-neighbor-p pairing to become the preferred pairing symmetry. Our results provide useful information to identify the dominant superconducting pairing symmetry in the AV3Sb5 family.

Amplitude-dependent group velocity transformations in nonlinear lattices with nonlocal coupling

Mass-spring lattices with weak stiffness nonlinearity undergo shifts in their band structure as a function of wave amplitude. Prior studies have characterized these shifts using perturbation techniques to derive small corrections to linear band structures. While lattice systems with nearest neighbor interactions are typically studied, growing attention is surrounding the effect of non-local elastic coupling. In this work, we report dramatic amplitude-dependentdispersion shifting in nonlinear lattices with nonlocal coupling. We demonstrate that nonlocal interactions with weak cubic stiffness have a profound impact on the amplitude-dependent group velocity of plane waves. Using a multiple scales perturbation technique, we obtain closed-form corrections to band structures that exhibit significant changes in sign and magnitude of group velocity compared to their linear counterparts. Analytical results are validated through direct numerical integration of the lattice equations of motion. [Work supported by the Office of Naval Research.]

Signatures of spin-liquid-like state and spin-phonon coupling in square lattice Sr2CuTe0.5W0.5O6

A spin-liquid state can be induced by uncompensated interactions in the spin lattice due to disorder or randomness in exchange pathways. Sr2CuTeO6 and Sr2CuWO6 are square-lattice antiferromagnetic double perovskites (A2BB′O6) with dominant nearest-neighbor (Néel-type) and next-nearest neighbor (Columnar-type) magnetic interactions, respectively. Random distribution of these interactions in a system has been theoretically predicted to be a way to induce the spin-liquid state. Here, we have synthesized a spin-liquid candidate Sr2CuTe0.5W0.5O6 with B′-site mixing of its parent systems (Sr2CuTeO6 and Sr2CuWO6) to explore the phonon properties and their correlations with the liquid-like magnetic interactions. Our measurements reveal the presence of a broad continuum in the Raman spectrum of Sr2CuTe0.5W0.5O6, instead of the well-defined spin-wave excitations (magnon) observed in the parent systems. Observation of continuum feature in the Raman spectrum in conjunction with the lack of long-range magnetic order provide the signatures of liquid-like correlations. On the other hand, phonon anomalies are observed below the short-ranged magnetic ordering temperature indicating the onset of spin-phonon coupling.

Signatures of the attractive interaction in spin spectra of one-dimensional cuprate chains

Identifying the minimal model for cuprates is crucial for explaining the high-Tc pairing mechanism. Recent photoemission experiments have suggested a significant near-neighbor attractive interaction V in cuprate chains, favoring pairing instability. To determine its strength, we systematically investigate the dynamical spin structure factors S(q,ω) using the density matrix renormalization group. Our analysis quantitatively reveals a notable softening in the two-spinon continuum, particularly evident in the intense spectrum at large momentum. This softening is primarily driven by the renormalization of the superexchange interaction, as determined by a comparison with the slave-boson theory. We also demonstrate the feasibility of detecting this spectral shift in thin-film samples using resonant inelastic x-ray scattering. Therefore, this provides a distinctive fingerprint for the attractive interaction, motivating future experiments to unveil essential ingredients in cuprates. Published by the American Physical Society 2024

Condensate formation in a chiral lattice gas

Abstract We investigate the formation of condensates in a binary lattice gas in the presence of chiral interactions. These interactions differ between a given microscopic configuration and its mirror image. We consider a two dimensional lattice gas with nearest-neighbour interactions to which we add interactions involving favoured local structures that are chiral. We focus on favoured local structures that have the shape of the letter L and explore condensate formation through simulations and analytical calculations. At low temperature, this model can exhibit four different phases that are characterised by different periodic tiling patterns, depending on the strength of interactions and the chemical potential. When particle numbers are conserved, some of these phases can coexist. We analyse the structure and surface tension of interfaces between coexisting phases and determine the shapes of minimal free energy of crystalline condensates. We show that these shapes can be quadrilaterals or octagons of different orientation and symmetry.

Theoretical Investigations and Comparisons of the Amorphous Structures of Adamantane-like Cluster Materials Utilizing Molecular Dynamics Simulations.

Cluster materials of the composition AdR4 (Ad = adamantane, R = organic substituent) and [(RT)4E6] (R = organic substituent; T = Si, Ge, Sn; and E = S, Se, Te) exhibit directional white light emission or produce second harmonics when irradiated with a continuous wave infrared laser source. The nature of the nonlinear optical properties correlates with the macroscopic structures of the cluster materials. The desired white light emission predominantly occurs in amorphous materials. It is therefore crucial to understand the geometric structures of the materials and the order within the materials. Here, we investigate the geometric structures of 12 different adamantane-like cluster materials by molecular dynamics simulations using a nonperiodic particle approach. The comparison of the calculated structure factors for two cluster materials with the corresponding experimental data obtained from diffraction and EXAFS measurements shows very good agreement. Our computations revealed that, on the one hand, larger, more flexible core structures (Ad < {Si4S6} < {Ge4S6} < {Sn4S6}) tend to lead to amorphous solids. On the other hand, larger substituents (methyl < phenyl < naphthyl) lead to more defined nearest neighbor interactions, with a tendency toward crystalline solids. Overall, our results show that a beginning order in the material results from a combination of the degree of flexibility of the core structure and the variation of the nearest neighbor interaction determined by the substituents.

A statistical-physics approach for codon usage optimisation

The concept of “codon optimisation” involves adjusting the coding sequence of a target protein to account for the inherent codon preferences of a host species and maximise protein expression in that species. However, there is still a lack of consensus on the most effective approach to achieve optimal results. Existing methods typically depend on heuristic combinations of different variables, leaving the user with the final choice of the sequence hit. In this study, we propose a new statistical-physics model for codon optimisation. This model, called the Nearest-Neighbour interaction (NN) model, links the probability of any given codon sequence to the “interactions” between neighbouring codons. We used the model to design codon sequences for different proteins of interest, and we compared our sequences with the predictions of some commercial tools. In order to assess the importance of the pair interactions, we additionally compared the NN model with a simpler method (Ind) that disregards interactions. It was observed that the NN method yielded similar Codon Adaptation Index (CAI) values to those obtained by other commercial algorithms, despite the fact that CAI was not explicitly considered in the algorithm. By utilising both the NN and Ind methods to optimise the reporter protein luciferase, and then analysing the translation performance in human cell lines and in a mouse model, we found that the NN approach yielded the highest protein expression in vivo. Consequently, we propose that the NN model may prove advantageous in biotechnological applications, such as heterologous protein expression or mRNA-based therapies.

One dimensional lattice fluid mixture with nearest neighbour interactions

We present an exact derivation of the free energy functional of a fluid mixture of hard rods with arbitrary sizes on a one-dimensional lattice. Our approach is based on the Wertheim cluster theory which consists of mapping a system with finite range interactions to the system with pure hard-core interaction but with modified activities. We show that the free energy functional has the same form as the fundamental measure functional. The interactions part of the free energy has two contributions, one from the one-particle cavity restricted to the hard rod or hard-sphere diameter and a second from the two-particle cavity which includes the finite range of the interaction. In the limit of a one-component system, our results reduce to the one derived using the Markov chain approach. For vanishing interactions, the density functionals coincide exactly with the previously derived for the mixture of hard rods with pure hard-core interaction.

Enhancing quantum utility: Simulating large-scale quantum spin chains on superconducting quantum computers

We present the quantum simulation of the frustrated quantum spin-12 antiferromagnetic Heisenberg spin chain with competing nearest-neighbor (J1) and next-nearest-neighbor (J2) exchange interactions in the real superconducting quantum computer with qubits ranging up to 100. In particular, we implement the Hamiltonian with the next-nearest neighbor exchange interaction in conjunction with the nearest-neighbor interaction on IBM's superconducting quantum computer and carry out the time evolution of the spin chain by employing the first-order Trotterization. Furthermore, our implementation of the second-order Trotterization for the isotropic Heisenberg spin chain, involving only nearest-neighbor exchange interaction, enables precise measurement of the expectation values of staggered magnetization observable across a range of up to 100 qubits. Notably, in both cases, our approach results in a constant circuit depth in each Trotter step, independent of the number of qubits. Our demonstration of the accurate measurement of expectation values for the large-scale quantum system using superconducting quantum computers designates the quantum utility of these devices for investigating various properties of many-body quantum systems. This will be a stepping stone to achieving the quantum advantage over classical ones in simulating quantum systems before the fault tolerance quantum era. Published by the American Physical Society 2024