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Atomistic analysis of nematic phase transition in 4-cyano-4′-<i>n</i>-alkyl biphenyl liquid crystals: Sampling for the first-order phase transition and the free-energy decomposition
Molecular dynamics simulations were conducted using the generalized replica exchange method (gREM) on the 4-cyano-4′-n-alkyl biphenyl (nCB) system with n = 5, 6, 7, and 8, which exhibits a nematic–isotropic (NI) phase transition. Sampling near the phase transition temperature in systems undergoing first-order phase transitions, such as the NI phase transition, is demanding due to the substantial energy gap between the two phases. To address this, gREM, specifically designed for first-order phase transitions, was utilized to enhance sampling near the NI phase transition temperature. Free-energy calculations based on the energy representation (ER) theory were employed to characterize the NI phase transition. ER evaluates the insertion free energy of the nCB molecule for both nematic and isotropic phases, revealing a change in the temperature dependence across the NI phase transition. Further decomposition into energetic and entropic terms quantitatively shows the balance between these contributions at the NI phase transition temperature.
Shift of nanodroplet and nanocluster size distributions induced by dopant pick-up statistics
In pick-up experiments using nanodroplet and nanocluster beams, the size distribution of hosts carrying a specified number of dopants changes when the vapor density in the pick-up region is altered. This change, analyzed here, has quantitative consequences for the interpretation of data that are sensitive to host size, such as mass spectrometric, spectroscopic, and deflection measurements.
Potential distribution theory of alchemical transfer
We present an analytical description of the Alchemical Transfer Method (ATM) for molecular binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding free energy by mapping the bound and unbound states of the complex by translating the ligand coordinates. PDT relates the free energy and the probability densities of the perturbation energy along the alchemical path to the probability density at the initial state, which is the unbound state of the complex in the case of a binding process. Hence, the ATM probability density of the transfer energy at the unbound state is first related by a convolution operation of the probability densities for coupling the ligand to the solvent and coupling it to the solvated receptor—for which analytical descriptions are available—with parameters obtained from maximum likelihood analysis of data from double-decoupling alchemical calculations. PDT is then used to extend this analytical description along the alchemical transfer pathway. We tested the theory on the alchemical binding of five guests to the tetramethyl octa-acid host from the SAMPL8 benchmark set. In each case, the probability densities of the perturbation energy for transfer along the alchemical transfer pathway obtained from numerical calculations match those predicted from the theory and double-decoupling simulations. The work provides a solid theoretical foundation for alchemical transfer, offers physical insights on the form of the probability densities observed in alchemical transfer calculations, and confirms the conceptual and numerical equivalence between the alchemical transfer and double-decoupling processes.
Spontaneous formation of potential cascade enhances charge separation in PM6-Y6 organic photovoltaics
Mechanisms that enhance charge separation at donor–acceptor interfaces are the key to material design of non-fullerene electron acceptors for high-efficiency organic photovoltaics (OPV). Here, the energetics of charge separation at the PM6-Y6 donor–acceptor interface in the state-of-the-art OPV is analyzed on the basis of quantum mechanics/molecular mechanics calculations. The electron energy level in Y6 becomes lower with increasing distance from the interface with PM6 at which the crystallinity is lower than in the bulk region. Electrostatic interactions from the multipoles of Y6 stabilize the electron in the crystalline region. The PM6-ITIC donor–acceptor interface also exhibits a similar potential cascade owing to the quadruple of ITIC. The potential cascade destabilizes charge transfer states at the PM6-Y6 interface, thereby decreasing the potential barrier for charge separation. Charge delocalization on several molecules via transfer integral further decreases the barrier for charge separation.
Collective dynamic length increases monotonically in pinned and unpinned glass forming systems
The Random First-Order Transition (RFOT) theory predicts that transport proceeds by the cooperative movement of particles in domains, whose sizes increase as a liquid is compressed above a characteristic volume fraction, ϕd. The rounded dynamical transition around ϕd, which signals a crossover to activated transport, is accompanied by a growing correlation length that is predicted to diverge at the thermodynamic glass transition density (&gt;ϕd). Simulations and imaging experiments probed the single particle dynamics of mobile particles in response to pinning all the particles in a semi-infinite space or randomly pinning (RP) a fraction of particles in a liquid at equilibrium. The extracted dynamic length increases non-monotonically with a peak around ϕd, which not only depends on the pinning method but is also different from ϕd of the actual liquid. This finding is at variance with the results obtained using the small wavelength limit of a four-point structure factor for unpinned systems. To obtain a consistent picture of the growth of the dynamic length, one that is impervious to the use of RP, we introduce a multiparticle structure factor, Smpc(q,t), that probes collective dynamics. The collective dynamical length, calculated from the small wave vector limit of Smpc(q,t), increases monotonically as a function of the volume fraction in a glass-forming binary mixture of charged colloidal particles in both unpinned and pinned systems. This prediction, which also holds in the presence of added monovalent salt, may be validated using imaging experiments.
Time-reversal symmetry in RDMFT and pCCD with complex-valued orbitals
Reduced density matrix functional theory (RDMFT) and coupled cluster theory restricted to paired double excitations (pCCD) are emerging as efficient methodologies for accounting for the so-called non-dynamic electronic correlation effects. Up to now, molecular calculations have been performed with real-valued orbitals. However, before extending the applicability of these methodologies to extended systems, where Bloch states are employed, the subtleties of working with complex-valued orbitals and the consequences of imposing time-reversal symmetry must be carefully addressed. In this work, we describe the theoretical and practical implications of adopting time-reversal symmetry in RDMFT and pCCD when allowing for complex-valued orbital coefficients. The theoretical considerations primarily affect the optimization algorithms, while the practical implications raise fundamental questions about the stability of solutions. In particular, we find that complex solutions lower the energy when non-dynamic electronic correlation effects are pronounced. We present numerical examples to illustrate and discuss these instabilities and possible problems introduced by N-representability violations.
Cross-correlations in the fluctuation–dissipation relation influence barrier-crossing dynamics
The Generalized Langevin Equation has been successfully used to model and understand the conformational dynamics of molecules in solution. However, recent works have demonstrated that, in these kinds of applications, the usual fluctuation–dissipation relation connecting the statistics of the random force to the memory kernel could contain a cross-correlation term. In this work, we systematically explore the origins of this cross-correlation term and argue that it plays a role, particularly in the folding dynamics of biopolymers. Finally, we propose an approximation for the cross-correlation term within the usual fluctuation–dissipation relation.
ABFML: A problem-oriented package for rapidly creating, screening, and optimizing new machine learning force fields
Machine Learning Force Fields (MLFFs) require ongoing improvement and innovation to effectively address challenges across various domains. Developing MLFF models typically involves extensive screening, tuning, and iterative testing. However, existing packages based on a single mature descriptor or model are unsuitable for this process. Therefore, we developed a package named ABFML, based on PyTorch, which aims to promote MLFF innovation by providing developers with a rapid, efficient, and user-friendly tool for constructing, screening, and validating new force field models. Moreover, by leveraging standardized module operations and cutting-edge machine learning frameworks, developers can swiftly establish models. In addition, the platform can seamlessly transition to the graphics processing unit environments, enabling accelerated calculations and large-scale parallel simulations of molecular dynamics. In contrast to traditional from-scratch approaches for MLFF development, ABFML significantly lowers the barriers to developing force field models, thereby expediting innovation and application within the MLFF development domains.
Generalized bond polarizability model for more accurate atomistic modeling of Raman spectra
Raman spectroscopy is an important tool for studying molecules, liquids and solids. While Raman spectra can be obtained theoretically from molecular dynamics (MD) simulations, this requires the calculation of electronic polarizability along the simulation trajectory. First-principles calculations of electronic polarizability are computationally expensive, motivating the development of atomistic models for the evaluation of the changes in the electronic polarizability with the changes in the atomic coordinates of the system. The bond polarizability model (BPM) is one of the oldest and simplest such atomistic models but cannot reproduce the effects of angular vibrations, leading to inaccurate modeling of Raman spectra. Here, we demonstrate that the generalization of BPM through the inclusion of terms for atom pairs that are traditionally considered to be not involved in bonding dramatically improves the accuracy of polarizability modeling and Raman spectra calculations. The generalized BPM (GBPM) reproduces the ab initio polarizability and Raman spectra for a range of tested molecules (SO2, H2S, H2O, NH3, CH4, CH3OH, and CH3CH2OH) with high accuracy and also shows significantly improved agreement with ab initio results for the more complex ferroelectric BaTiO3 systems. For liquid water, the anisotropic Raman spectrum derived from atomistic MD simulations using the GBPM evaluation of polarizability shows significantly improved agreement with the experimental spectrum compared to the spectrum derived using the BPM. Thus, the GBPM can be used for the modeling of Raman spectra using large-scale molecular dynamics and provides a good basis for the further development of atomistic polarizability models.
Toward an FPGA-based dedicated computer for molecular dynamics simulations
First steps toward a molecular dynamics (MD) implementation in a cluster of field-programmable gate arrays (FPGAs) are presented, reaching a simulation speed of a few microseconds/day. The nodes in this cluster are programmed into a mid-ranged FPGA (Artix 7 XC7A200T), interconnected as a 3D torus by fast optical links. The implemented MD algorithm is highly parallelized and highly pipelined internally. The FPGA cluster is freely scalable in terms of size, i.e., a larger MD system requires more nodes, however, without compromising simulation speed. The performance in terms of energy stability and simulation speed is analyzed. At present, the focus lies on the fast networking, while only minimal MD functionality has been implemented so far, i.e., Lennard-Jones interactions and a thermostat, which were needed to demonstrate the feasibility of the FPGA cluster to run multi-microsecond simulations. To that end, the nucleation of a super-cooled Lennard-Jones liquid is investigated by unbiased MD simulations, which is a difficult MD problem since a high nucleation barrier has to be overcome. Finally, the pathways toward a full MD implementation are outlined. The current implementation will be made available as an open-source development project.
Electronic-vibrational resonance damping time-dependent photosynthetic energy transfer acceleration revealed by 2D electronic spectroscopy
The effects of damping time of electronic-vibrational resonance modes on energy transfer in photosynthetic light-harvesting systems are examined. Using the hierarchical equations of motion (HEOM) method, we simulate the linear absorption and two-dimensional electronic spectra (2DES) for a dimer model based on bottleneck sites in the light-harvesting complex of photosystem II. A site-dependent spectral density is incorporated, with only the low-energy site being coupled to the resonance mode. Similar patterns are observed in linear absorption spectra and early time 2DES for various damping times, owing to the weak coupling strength. However, notable differences emerge in the dynamics of the high-energy diagonal and cross-peaks in the 2DES. It is found that the coupling of electronic-vibrational resonance modes accelerates the energy transfer process, with rates being increased as the damping time is extended, but the impact becomes negligible when the damping time exceeds a certain threshold. To evaluate the reliability of the perturbation method, the modified Redfield (MR) method is employed to simulate 2DES under the same conditions. The results from the MR method are aligned with those obtained from the HEOM method, but the MR method predicts faster dynamics.
An efficient strategy to boost photoelectrochemical water oxidation of g-C3N4 films modified with NiO as cocatalyst
Structural refinement and magnetic tuning in cobalt-substituted SrFe12O19 hexaferrite
In this study, we synthesize strontium hexaferrite (SrFe12O19, SrM) with transition metal substitution cobalt (SrFe12−xCoxO19, SrCoM) with weight percentage (x = 3%, 5%, and 7%) through a chemical co-precipitation approach. The hexaferrite phase (P63/mmc) along with a small amount of secondary phase identified as hematite (α-Fe2O3) and halite (NaCl) were found from the x-ray diffraction analysis. A three-phase Rietveld refinement using FullProf software was used to evaluate the average bond lengths and angles, offering important information on superexchange interactions’ impact inside the lattice. The magnetic ordering and crystal structure were also analyzed using neutron powder diffraction and the produced samples showed a ferrimagnetic arrangement at ambient temperature. The crystal structure, magnetic parameters, and maximal energy product (BH)max of the synthesized materials were found to be considerably affected by cobalt substitution: post-substitution, coercivity increases, while saturation magnetization and retentivity decrease. The present work emphasizes the potential of strontium hexaferrite and its cobalt-substituted derivatives as attractive magnetic materials for diverse magnetic applications.
Exploration and comparison of the effectiveness of swarm intelligence algorithm in early identification of cardiovascular disease
Defect-induced modification of electronic and optical properties of CeO2 unveiled by many-body Green’s function theory
We explore the impact of point defects, including oxygen vacancies (Ov), cerium interstitials (Ce-int), and hydroxyl groups (Hy), on the electronic and optical properties of bulk CeO2 using many-body Green’s function theory (GW method and Bethe–Salpeter equation). Although these three defects all produce occupied electronic levels near the conduction band minimum, they impose quite different effects. Ov and Ce-int induce strong peaks in the low-energy region of the imaginary part of the microscopic dielectric function, indicating stronger electronic screening compared to the pristine CeO2. This causes pronounced narrowing of the bandgap, e.g., by 0.8 eV in G0W0 and 1.6 eV in the eigenvalue self-consistent GW for Ov. Comparatively, Hy affects little electronic screening and bandgap at different levels of GW calculations. For the lowest several 4f orbitals, the exchange part of the self-energy (|Σx| &gt; 9 eV) in GW is much stronger than the correlation part (|Σc| &lt; 5 eV) for Ov and Ce-int, while |Σc| is much stronger than |Σx| instead for the pristine CeO2 and Hy. Quasiparticle weights in Ov and Ce-int decrease by a large quantity compared to the pristine CeO2. Consideration of Ov and Ce-int might to some extent relieve the discrepancy between the GW bandgap of the pristine CeO2 and the experimental gap. Ov and Ce-int could reduce the excitonic binding energy several times and result in optical absorption, which corresponds to the experiments.
Development of a new method for maintainability and downtime analysis of mining machinery
Resonance-enhanced multiphoton ionization detection of vibrationally excited O2
We report a rotationally resolved spectroscopic detection scheme for vibrationally excited molecular oxygen with high sensitivity. Two-color (2 + 1′) resonance-enhanced multiphoton ionization (REMPI) spectra of O2 hot bands were recorded for the first time via the 3dπ(v′=0)←X3Σg− (v″ = 1) Rydberg transitions. Spectroscopic constants and relative Franck–Condon factors were extracted and compared to simulations. This new access to quantum-state-resolved diagnostics of vibrationally excited O2 promises to shed light on the physical and chemical dynamics of many processes.
Advanced AI-driven detection of interproximal caries in bitewing radiographs using YOLOv8
Dispersion with fixed diagonal matrices: Exchange energy correction and an assessment of the Becke–Roussel exchange hole
An exchange-correction to the fixed diagonal matrices (FDM) method is introduced to improve accuracy when employing a single reference wavefunction. In addition, the performance of the Becke–Roussel exchange-hole in approximating the pair density-mediated integrals was explored. With the exchange-correction, the FDM procedure yields dispersion coefficients for closed-shell atoms on par with highly correlated methods when using only Hartree–Fock or Kohn–Sham pair density. Conversely, the Becke–Roussel exchange-hole results in an overestimation of the dispersion coefficients for closed-shell atoms; however, the performance of the Becke–Roussel model can be improved by scaling the multipole moment integrals by a fixed amount. For both the exchange–correction and the Becke–Roussel model, the FDM method continues to fail for open-shell atoms and ions by consistently underestimating the dispersion coefficients.