Browse Articles

Noise-induced synchronization in coupled quantum oscillators

We consider the quantum dynamics of a pair of coupled quantum oscillators coupled to a common correlated dissipative environment. The resulting equations of motion for both the operator moments and covariances can be integrated analytically using the Lyapunov equations. We find that for fully correlated and fully anti-correlated environments, the oscillators relax into a phase-synchronized state that persists for long-times when the two oscillators are nearly resonant and (essentially) forever if the two oscillators are in resonance. We identify an exceptional point that indicates the onset of broken symmetry between an unsynchronized and synchronized dynamical phase of the system as correlations within the environment are increased. We also show that the environmental noise correlation leads to quantum entanglement, and all the correlations between the two oscillators are purely quantum mechanical in origin. This work provides a robust mathematical foundation for understanding how long-lived exciton coherences can be linked to vibronic correlation effects.

Dynamic heterogeneity of short semi-crystalline polymer chains during recrystallization

The instant crystallization of semi-crystalline polymers has become possible following the recent advances in Fast Scanning Calorimetry (FSC) and enables us to make a bridge between the time scale available experimentally with those accessible with computer simulations. Although the FSC observations have provided new information on the crystallization kinetics and evolution of the crystals, the molecular details on the chain exchange events between the ordered and disordered domains of crystals have remained elusive. Using molecular dynamics simulations, we examined the detailed chain dynamics and thermodynamics of polyamide 6 (PA6) system under two heating treatments: (i) quenching PA6 melt deeply below the melting temperature Tm and (ii) annealing the resulting quenched system to a temperature close to Tm. We categorized the chains into mobile amorphous fraction (MAF) and rigid amorphous fraction (RAF), based on the length of consecutive chain’s bond angles in the trans state. In the deep quenched system close to the glass transition temperature Tg, the mobility of the MAF chains is strongly suppressed and they remain in the glassy state. However, upon rising the temperature close to melting temperature, the system undergoes recrystallization, leading to the coexistence of RAF and supercooled liquid MAF chains. The highly mobile unentangled MAF chains explore the interphase domains, and during the late-stage of crystallization, they are thermally translocated into the lamella by reducing the fold number of RAF chains. The chain mobility in the annealed system could potentially lead to improved biodegradation in semi-crystalline chains.

Electrostatic interactions in nucleosome and higher-order structures are regulated by protonation state of histone ionizable residue

The nucleosome serves as the fundamental unit of chromatin organization, with electrostatic interactions acting as the driving forces in the folding of nucleosomes into chromatin. Perturbations around physiological pH conditions can lead to changes in the protonation states of titratable histone residues, impacting nucleosome surface electrostatic potentials and interactions. However, the effects of proton uptake or release of histone ionizable groups on nucleosome–partner protein interactions and higher-order chromatin structures remain largely unexplored. Here, we conducted comprehensive analyses of histone titratable residue pKa values in various nucleosome contexts, utilizing 96 experimentally determined complex structures. We revealed that pH-induced changes in histone residue protonation states modulated nucleosome surface electrostatic potentials and significantly influenced nucleosome–partner protein interactions. Furthermore, we observed that proton uptake or release often accompanied nucleosome–partner protein interactions, facilitating their binding processes. In addition, our findings suggest that alterations in histone protonation can also regulate nucleosome self-association, thereby modulating the organization and dynamics of higher-order chromatin structure. This study advances our understanding of nucleosome–chromatin factor interactions and how chromatin organization is regulated at the molecular level.

Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence

Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the biological milieu. Studying such structural changes in membrane-embedded proteins and understanding the associated topological signatures in membrane leaflets, therefore, remain relatively unexplored. Herein, we first aim to estimate the free energy barrier and the minimum free energy path (MFEP) connecting the membrane-embedded fully and partially inserted states of the bacteriorhodopsin fragment. To achieve this, we have considered independent sets of simulations from membrane-mimicking and membrane-embedded environments, respectively. An autoencoder model is used to elicit state-distinguishable collective variables for the system utilizing membrane-mimicking simulations. Our in-house Expectation Maximized Molecular Dynamics algorithm is initially used to deduce the barrier height between the two membrane-embedded states. Next, we develop the Geometry Optimized Local Direction search as a post-processing algorithm to identify the MFEP and the corresponding peptide conformations from the autoencoder-projected trajectories. Finally, we apply a graph attention neural network (GAT) model to learn the membrane surface topology as a function of the associated peptide structure, supervised by the membrane-embedded simulations. The resultant GAT model is then utilized to predict the membrane leaflet topology for the peptide structures along MFEP, obtained from membrane-mimicking simulations. The combined framework is expected to be useful in capturing key phenomena accompanying folding transitions in membranes. We discuss opportunities and avenues for further development.

Evidence and origin of anomalous diffusion of Ag+ ion in amorphous silica: A molecular dynamics study with neural network interatomic potentials

The release of Ag+ ions into the environment through silica layers is a promising strategy for the development of anti-microbial surface coating devices. The aim of the present study is to provide some insight into the elementary mechanisms of diffusion of Ag+ ions through silica with the objective of proposing control strategies. Thanks to the development of interaction potentials based on neural networks, the diffusion processes were studied via molecular dynamics simulations. Silver diffusion was found to be anomalous and sub-diffusive, the origin of which could be attributed to deceleration and temporal anti-correlations. This sub-diffusion has been attributed primarily to the disordered nature of the silica matrix. Furthermore, it is magnified by the presence of coordination defects within the silica matrix. These defects, in particular the under-coordinated oxygen atoms, act as traps for Ag+ by forming O–Ag bonds, thereby limiting the jump length and retaining the ion for long duration. By comparison with existing diffusion models, the diffusion mechanism in the absence of defects appears to be of the fractional Brownian motion type, substantially modified by the presence of defects. Two possible approaches have emerged to tune the release of Ag+ ions through the silica layer: the monitoring of the number of defects and the opening/closing of diffusion paths via, e.g., a modification of the silica density.

Function domains and the universal matrix functional of multi-state density functional theory

On the basis of recent advancements in the Hamiltonian matrix density functional for multiple electronic eigenstates, this study delves into the mathematical foundation of the multistate density functional theory (MSDFT). We extend a number of physical concepts at the core of Kohn–Sham DFT, such as density representability, to the matrix density functional. In this work, we establish the existence of the universal matrix functional for many states as a proper generalization of the Lieb universal functional for the ground state. Consequently, the variation principle of MSDFT can be rigorously defined within an appropriate domain of matrix densities, thereby providing a solid framework for DFT of both the ground state and excited states. We further show that the analytical structure of the Hamiltonian matrix functional is considerably constrained by the subspace symmetry and invariance properties, requiring and ensuring that all elements of the Hamiltonian matrix functional are variationally optimized in a coherent manner until the Hamiltonian matrix within the subspace spanned by the lowest eigenstates is obtained. This work solidifies the theoretical foundation to treat multiple electronic states using density functional theory.

A century of quantum physics

Revealing correlation mechanisms through nonorthogonal multiconfiguration self-consistent field calculations

The presence of spin and spatial symmetry breaking upon variational optimization of mean-field wavefunctions is known to be an indicator of nondynamical electron correlation. However, a single mean-field wavefunction may not have sufficient flexibility to flag the correlated orbital space where there are multiple correlation mechanisms present. In such situations, there are multiple nearly degenerate self-consistent field solutions that describe different correlation mechanisms, but it is often not possible to know a priori when such situations will occur or if sufficient solutions have been obtained. In this work, we examine the role of spin and spatial symmetries of nonorthogonal multiconfigurational self-consistent field (NOMCSCF) calculations in revealing correlation mechanisms. We provide details of the theory for optimization of NOMCSCF wavefunctions with desired symmetries, establish which types of symmetries recover the most correlation energy when the symmetry constraints are relaxed, and discuss how the different-orbitals for different-configuration wavefunctions reveal the different correlation mechanisms present.

Inherent loss of parahydrogen-induced polarization for systems with magnetically equivalent nuclei in magnetic field cycling experiments

In the present work, we elucidate the inherent loss of net magnetization (⟨Iz⟩) in parahydrogen-induced polarization (PHIP) experiments with magnetic field cycling (MFC) for spin systems containing magnetically equivalent protons. The effects are shown for propane and diethyl ether as representative examples of potential hyperpolarized MRI contrast agents, but the findings of this work are equally applicable to other multispin systems in the liquid or gas phase. These results are relevant to both adiabatic longitudinal transport after dissociation engenders net alignment (ALTADENA) experiments (where 1H nuclei are polarized) and MFC protocols used to transfer parahydrogen spin order to a heteronucleus such as 13C. The investigated effects should be incorporated for a correct evaluation of both the maximum possible NMR signal enhancement and the pairwise selectivity, which are useful in the context of mechanistic studies in the field of catalytic hydrogenation. Among signal enhancement damping factors in ALTADENA, such as T1 relaxation and insufficient adiabaticity of a field sweep, the inherent loss of net magnetization in spin systems containing magnetically equivalent protons (especially in PHIP systems commonly used for mechanistic studies such as propene or propane) has not been thoroughly considered and needs to be clarified. The maximum possible net magnetization in ALTADENA for diethyl ether and propane was shown to be ∑|⟨Iiz⟩| ≈ 0.56 for diethyl ether and ∑|⟨Iiz⟩| ≈ 0.45 for propane, respectively. The inherent loss of net heteronuclear magnetization of the same order of magnitude with an increase in the number of magnetically equivalent protons was also demonstrated for AmMnX-type spin systems.

Protect yourself — and your data — with these cybersecurity tips

Revisiting the manganese dimer on the base of first-principles theory

Manganese is one of the most intriguing elements showing multiple magnetic phases. In order to shed some light on the complex behavior, the manganese dimer has been the focus of extensive interest in theoretical research. Various quantum techniques have been utilized to comprehend the characteristics of the Mn dimer. Several approaches and functionals have been employed that suggest that the ferromagnetic (FM) state is its lowest energy configuration. Nevertheless, these findings are inconsistent with the experimental results showing that Mn2 has an antiferromagnetic (AFM) Σg+1 configuration at an interatomic Mn–Mn distance of dMn–Mn = 3.40 Å. This work presents a comparative assessment of outcomes obtained through several levels of the exchange–correlation functional: generalized gradient approximation (GGA), meta-GGA, GGA+U, and the hybrid Heyd–Scuseria–Ernzerhof (HSE06), the Perdew–Burke–Ernzerhof 0, and the Becke, 3-parameter, Lee–Yang–Parr. The results of our investigation are discussed based on previous theoretical and experimental reports. We found that the best description is obtained with the hybrid HSE06 functional. The Mn2 has a FM coupling at short distances and the characteristic AFM Σg+1 state at dMn–Mn = 3.27 Å. Furthermore, we obtained a magnetic moment (μ) per Mn atom of μ = 4.527 μB, a stretching frequency of ω = 80 cm−1, and a binding energy of Eb = −195 meV, which is in good agreement with the experimental results.

A relativistic third-order algebraic diagrammatic construction theory for electron detachment, attachment, and excitation problems

We present the theory and implementation of a relativistic third-order algebraic diagrammatic construction [ADC(3)] method based on a four-component (4c) Dirac–Coulomb Hamiltonian for the calculation of ionization potentials (IPs), electron affinities (EAs), and excitation energies (EEs). Benchmarking calculations for IP, EA, and EE were performed on both atomic and molecular systems to assess the accuracy of the newly developed four-component relativistic ADC(3) method. The results show good agreement with the available experimental data. The Hermitian nature of the 4c-ADC(3) Hamiltonian, combined with the perturbative truncation of the wave function, offers significant computational advantages over the standard equation-of-motion coupled-cluster approach, particularly for property calculations. The method’s suitability for property calculations is further demonstrated by computing oscillator strengths and excited-state dipole moments for heavy elements.

Daily briefing: Jurassic mammals had dark fur

Langevin integration for isothermal–isobaric condition with a large time step

We propose an accurate method for evaluating temperature and pressure in Langevin integration, based on the approach by Leimkuhler and Matthews (J. Chem. Phys. 138, 174102). This method improves the quality of configuration space than other Langevin dynamics methods. However, it encounters issues in pressure evaluation due to inaccuracies in momentum space. In particular, the conventional approach for calculating kinetic temperature using the full-time step momentum introduces errors proportional to the square of the time step (Δt2), leading to unreliable results when employing a large time step under isothermal–isobaric conditions. By calculating kinetic energy using the half-time step momentum in pressure evaluation, we can reduce the numerical errors. We performed molecular dynamics (MD) simulations using our refined pressure evaluation and improved accuracy and stability in the isothermal–isobaric MD simulations even with a long time step (Δt = 5 fs).

‘My career is over’: Columbia University scientists hit hard by Trump team’s cuts

Attaining high accuracy for charge-transfer excitations in non-covalent complexes at second-order perturbation cost: The importance of state-specific self-consistency

Intermolecular charge-transfer (xCT) excited states important for various practical applications are challenging for many standard computational methods. It is highly desirable to have an affordable method that can treat xCT states accurately. In the present work, we extend our self-consistent perturbation methods, named one-body second-order Møller–Plesset and its spin-opposite scaling variant (O2BMP2), for excited states without additional costs to the ground state. We then assessed their performance for the prediction of xCT excitation energies. Thanks to self-consistency, our methods yield small errors relative to high-level coupled cluster methods and outperform other same scaling (N5) methods, such as CC2 and ADC(2). In particular, O2BMP2, whose scaling can be reduced to N4, can even reach the accuracy of CC3 (N7) with errors less than 0.1 eV. This method is thus highly promising for treating xCT states in large compounds vital for applications.

Your lab pollutes: here’s how to stop it

Quantum electrodynamic corrections for molecules: Vacuum polarization and electron self-energy in a two-component relativistic framework

Vacuum polarization (VP) and electron self-energy (SE) are implemented and evaluated as quantum electrodynamic (QED) corrections in a (quasi-relativistic) two-component zeroth order regular approximation (ZORA) framework. For VP, the Uehling potential is considered, and for SE, the effective potentials proposed by Flambaum and Ginges as well as the one proposed by Pyykkö and Zhao. QED contributions to ionization energies of various atoms and group 2 monofluorides, group 1 and 11 valence orbital energies, 2P1/2 ← 2S1/2 and 2P3/2 ← 2S1/2 transition energies of Li-, Na-, and Cu-like ions of nuclear charge Z = 10, 20, …, 90 as well as Π1/2 ← Σ1/2 and Π3/2 ← Σ1/2 transition energies of BaF and RaF are presented. Furthermore, perturbative and self-consistent treatments of QED corrections are compared for Kohn–Sham orbital energies of gold. It is demonstrated that QED corrections can be obtained in a two-component ZORA framework efficiently and in excellent agreement with corresponding four-component results.

Meta-analysis of heat-induced changes in cardiac function from over 400 laboratory-based heat exposure studies

Enhancing reaction efficiency in photochemical organic synthesis by controlling the dynamic effects of excitons

Donor–acceptor (D–A) molecules are key motifs in electron transfer processes. Recently, significant progress has been made in the development of organic synthetic reactions that utilize D–A molecules as photoredox catalysts. In these electron-transfer reactions, preventing undesired back-electron transfer and achieving efficient conversion is essential. In this Perspective, we introduce two examples in which the dynamic effects of excitons derived from catalyst molecules are controlled through precise molecular design.