Frequency-Dependent Sternheimer Linear-Response Formalism for Strongly Coupled Light-Matter Systems.

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

In this work, we provide an overview of how well-established concepts in the fields of quantum chemistry and material sciences have to be adapted when the quantum nature of light becomes important in correlated matter-photon problems. We analyze model systems in optical cavities, where the matter-photon interaction is considered from the weak- to the strong-coupling limit and for individual photon modes as well as for the multimode case. We identify fundamental changes in Born-Oppenheimer surfaces, spectroscopic quantities, conical intersections, and efficiency for quantum control. We conclude by applying our recently developed quantum-electrodynamical density-functional theory to spontaneous emission and show how a straightforward approximation accurately describes the correlated electron-photon dynamics. This work paves the way to describe matter-photon interactions from first principles and addresses the emergence of new states of matter in chemistry and material science.

Analysis of a two dimensional molecular Berry phase system

In this work, we present an extremely efficient approach for a fast numerical evaluation of highly oscillatory spherical Bessel integrals occurring in the analytic expressions of the so-called molecular multi-center integrals over exponential type functions. The approach is based on the Slevinsky-Safouhi formulae for higher derivatives applied to spherical Bessel functions and on extrapolation methods combined with practical properties of sine and cosine functions. Recurrence relations are used for computing the approximations of the spherical Bessel integrals, allowing for a control of accuracy and the stability of the algorithm. The computer algebra system Maple was used in our development, mainly to prove the applicability of the extrapolation methods. Among molecular multi-center integrals, the three-center nuclear attraction and four-center two-electron Coulomb and exchange integrals are undoubtedly the most difficult ones to evaluate rapidly to a high pre-determined accuracy. These integrals are required for both density functional and ab initio calculations. Already for small molecules, many millions of them have to be computed. As the molecular system gets larger, the computation of these integrals becomes one of the most laborious and time consuming steps in molecular electronic structure calculation. Improvement of the computational methods of molecular integrals would be indispensable to a further development in computational studies of large molecular systems. Convergence properties are analyzed to show that the approach presented in this work is a valuable contribution to the existing literature on molecular integral calculations as well as on spherical Bessel integral calculations.

Most human diseases are complex multi-factorial diseases resulting from the combination of various genetic and environmental factors. In the KEGG database resource (http://www.genome.jp/kegg/), diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. Disease information is computerized in two forms: pathway maps and gene/molecule lists. The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. This database also captures knowledge about two types of molecular networks: the interaction network with target molecules, metabolizing enzymes, other drugs, etc. and the chemical structure transformation network in the history of drug development. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.

Typical experimental setups for molecular systems must deal with a certain coupling to the external environment, that is, the system is open and exchanges mass, momentum, and energy with its surroundings. Instead, standard molecular simulations are mostly performed using periodic boundary conditions with a constant number of molecules. In this review, we summarize major development of simulation methodologies, which, contrary to standard techniques, open up the boundaries of a molecular system and allow for exchange of energy and matter with the environment, in and out of equilibrium. In particular, we construct the review around the open boundary simulation approaches based on the Adaptive Resolution Scheme (AdResS), which seamlessly couples different levels of resolution in molecular simulations. Ideas and theoretical concepts used in its development lie at the crossroad of different fields and disciplines and open many different directions for future developments in molecular simulation. We examine progress related to theoretical as well as novel modeling approaches bridging length scales from quantum to the continuum description and report on their application in various molecular systems. The outlook of the review is dedicated to the perspective of how to further incorporate rigorous theoretical approaches such as the Bergmann–Lebowitz and Emch–Sewell models into the molecular simulation algorithms and stimulate further development of open boundary simulation methods and their application.

During recent decades it has become feasible to simulate the dynamics of molecular systems on a computer. The method of molecular dynamics (MD) solves Newton's equations of motion for a molecular system, which results in trajectories for all atoms in the system. From these atomic trajectories a variety of properties can be calculated. The aim of computer simulations of molecular systems is to compute macroscopic behavior from microscopic interactions. The main contributions a microscopic consideration can offer are (1) the understanding and (2) interpretation of experimental results, (3) semiquantitative estimates of experimental results, and (4) the capability to interpolate or extrapolate experimental data into regions that are only difficultly accessible in the laboratory. One of the two basic problems in the field of molecular modeling and simulation is how to efficiently search the vast configuration space which is spanned by all possible molecular conformations for the global low (free) energy regions which will be populated by a molecular system in thermal equilibrium. The other basic problem is the derivation of a sufficiently accurate interaction energy function or force field for the molecular system of interest. An important part of the art of computer simulation is to choose the unavoidable assumptions, approximations and simplifications of the molecular model and computational procedure such that their contributions to the overall inaccuracy are of comparable size, without affecting significantly the property of interest. Methodology and some practical applications of computer simulation in the field of (bio)chemistry will be reviewed.

The Fano effect or Fano resonance with a characteristically asymmetric line shape originates from quantum interference between direct and indirect transition pathways in continuum-bound coupled systems, and is a ubiquitous phenomenon in atomic, molecular, nuclear and solid-state physics. In optical nanoscale structures, the Fano effect has wide-ranging applications that include optical filtering, sensing, all-optical switching, quantum interferometry and nonlinear optics, and this opens new avenues for photonic devices. The emergent area of ultracold atomic and molecular gases presents an ideal platform for studying Fano resonances, since the physical parameters of these gases can be extensively tuned with high precision using external fields. However, an experimental demonstration of the Fano effect in hybridized atom-molecular coupled systems has remained elusive. Here, we report on observations of the Fano effect in molecular spectra obtained by photoassociation near a d-wave Feshbach resonance. This effect occurs due to quantum interference in PA transitions involving the continuum of atom-atom scattering states, the underlying Feshbach and photoassociated excited bound molecular states. We measure the variation in atom loss rate with an external magnetic field close to the Feshbach resonance in the presence of PA laser, and thereby clearly demonstrate the Fano effect. Our results further reveal that the Fano effect has significant influence on spectral shifts. Based on Fano's method, we develop a theory that explains the observed experimental results relatively well. Our theoretical formulation takes into account quantum interference between or among multiple transition pathways and between inelastic channels. Our results present a novel method for tuning the collisional interaction strength with laser light using Fano resonance.

Machine learning interatomic potentials (MLIPs) enables molecular dynamics (MD) simulations with ab initio accuracy and has been applied to various fields of physical science. However, the performance and transferability of MLIPs are limited by insufficient labeled training data, which require expensive ab initio calculations to obtain the labels, especially for complex molecular systems. To address this challenge, we design a novel geometric structure learning paradigm that consists of two stages. We first generate a large quantity of 3D configurations of target molecular system with classical molecular dynamics simulations. Then, we propose geometry-enhanced self-supervised learning consisting of masking, denoising, and contrastive learning to better capture the topology and 3D 1 geometric information from the unlabeled 3D configurations. We evaluate our method on various benchmarks ranging from small molecule datasets to complex periodic molecular systems with more types of elements. The experimental results show that the proposed pre-training method can greatly enhance the accuracy of MLIPs with few extra computational costs and works well with different invariant or equivariant graph neural network architectures. Our method improves the generalization capability of MLIPs and helps to realize accurate MD simulations for complex molecular systems.

Computational materials science, as an intersection of theoretical physics, condensed matter physics and material science, its main tasks, in general, are firstly, research and calculate the physical and chemical properties for known materials. This would help us to better understand the microscopic mechanism of some material properties and open up new fields of applications. Secondly, computational design of new materials, that would help us to explore and design new materials to meet some proposed requirements. As we known, new material design and development is the basis of high-tech material and its device applications. The research history of computational materials science can actually be traced back to the mid 20s of last century. Immediately after the birth of quantum mechanics theory, many excellent theoretical works were applied to the study of physical properties of solid materials. In the early years of the computational materials science, it is mainly to adopt semi-empirical method. This is because the object being studied is a many-particle system which contains very large amounts of atoms and electrons. One cannot find the rigorous analytical solutions, but the empirical values of the measurable parameters are available, Therefore, in semi-empirical method, the number of experience parameters is at least as much as that of material types, hence, most studies are pointed only to the computing research category of physical properties. Until the mid 60s of last century, Hohenberg-Kohn (Hohenberg & Kohn. 1964) and Kohn-Sham (Kohn & Sham 1965) proposed the Density Functional Theory (DFT) and Local Density Approximation (LDA), to get rid of the semiempirical method restriction, and hence causing the birth of so-called ab initio or the first principles method that do not depend on experimental parameters. This method has now become a core technology of the computational material science, computational chemistry and computational condensed matter physics and is widely used. What is a First Principles for the physical world, no one seems to be specified clarify its meaning. Many physicists believe that the most precise description of atoms and smaller than the atomic system is the theory of quantum electrodynamics (QED). Therefore, QED is a theory called first principles of the micro world. In the field of condensed matter physics and materials science, within the framework of the density functional theory, if one do not consider the high-energy radiation correction, one needs only the electromagnetic theory, Schrodinger equation and/or Dirac equation and a few of parameters unrelated to specific

Cavity optomechanical systems have become a topic of great interest in recent years, and the coupled-cavity model is also a classic theoretical framework. This paper aims to construct a coupledcavity optomechanical system to study induced transparency, Fano resonance, and fast-slow light effects in such a system. By transferring phenomena typically studied in a single optical cavity to a coupled-cavity system, we analyze specific phenomena detected in optical and microwave cavities, such as transmission and absorption spectra, to investigate induced transparency. We also examine Fano resonance in the model by varying detuning, and study fast-slow light effects through group velocity. This paper first constructs the corresponding physical model, as shown in Figure 1. Based on the theoretical model, a reasonable Hamiltonian is proposed. By introducing appropriate dissipation and fluctuation noise terms, the Langevin equations of motion are derived. Next, the Langevin equations are linearized, and the resonant terms are retained to obtain <i>O</i><sub>+</sub> . The amplitude of the field modes is then derived using the input-output relations. Following the experimental data from referenced literature, a numerical simulation program is implemented in Mathematica. By substituting the relevant parameters and performing calculations, the results are obtained through simulation. For the first time, the interactions among photons, magnons, microwaves, and phonons— as well as the interplay between photons in the two cavities—are investigated in a coupled cavity optomagnomechanical system. Electromagnetically induced transparency (EIT), Fano resonance, and fast-slow light effects are studied in this coupled-cavity optomagnomechanical framework. Phenomena typically examined in a single optical cavity are extended to the coupled-cavity system, with specific observations analyzed separately in the optical and microwave cavities. When <i>δ</i>=<i>ω</i><i><sub>b</sub></i>, the absorption spectrum splits, and the absorption peak decreases from its maximum to its minimum. This phenomenon arises from the disruption of quantum interference effects. The resonance condition suppresses the generation of Fano resonance. At the resonant frequency <i>ω</i><i><sub>0</sub></i>, the group delay is greater than zero, indicating slow-light propagation, and this effect is enhanced with increasing coupling strength. Additionally, a group delay of τ is achieved. Meanwhile, on either side of the resonant frequency, the group delay peaks exhibit a decreasing positive value and an increasing negative value, respectively, signifying a gradual weakening of the slow-light effect and a corresponding enhancement of the fast-light effect. This paper investigates the MIT, MMIT, and OMIT windows in a coupled-cavity optomagnomechanical (OMM) system under a strong control field and weak probe field. The MMIT phenomenon is observed through nonlinear phonon-magnon interactions. Additionally, the photon-magnon interaction in the microwave cavity leads to MIT, while OMIT is achieved via the radiation pressure interaction between photons and nonlinear phonons in the optical cavity. The frequency of the probe field is tuned to interact with both the microwave and optical cavities. When the probe field couples with the microwave cavity, its absorption at the resonant frequency is significantly suppressed under optomechanical coupling, resulting in a pronounced optical switching effect on transmission. We analyze the asymmetric Fano resonance phenomenon, which reflects the existence of quantum interference mechanisms within the system and influences the fast- and slow-light conversion processes. Furthermore, by selecting appropriate coupling parameters, not only can the fast- and slow-light effects be enhanced, but dynamic switching between them can also be achieved.

A new mechanism for realizing negative permeability with a three-level ladder-type atomic (or molecular) system at microwave frequency is suggested. The explicit expressions for the magnetic permeability of both steady and transient cases are presented. Compared with the previous schemes to realize negative permeability within the framework of classical electromagnetic theory, the most remarkable feature in the present mechanism is that it can realize the isotropic material with negative permeability. Such a permeability can be controllably manipulated by external coupling fields and could lead to potential applications in quantum optical devices.

This paper presents an O(N) algorithm and its preliminary computer simulation results for virtual prototyping of molecular systems with a simple chain structure. The algorithm is based on proper integration between an internal coordinate method (ICM) and a multibody molecular model. ICM method makes the use of recursive relations possible between two adjacent subsets within a molecular system. The multibody molecular model takes the benefits of freezing degrees of freedom of some lightly excited high frequency bonds. Because these high frequency bonds would force the use of very small integration step sizes, which severely limits the time scales for virtual prototyping of dynamics of molecular conformation over long periods of time. Thus a new multiscale model and efficient algorithm is produced to increase computational efficiency for virtual prototyping of dynamical behaviors of molecular confirmation. This paper will be initially directed towards introduction of the new model and algorithm. Then attention will be turned to the implementation of the algorithm at macro scale, which can be used to demonstrate the validity of the procedure and algorithm. Final focus will be turned to the implementation of the algorithm to a simple molecular chain at micro scale. The algorithm gives an O(N) computational performance for formation/solution of equations of motion for a molecular chain system.

Continuous advancements in DNA nanotechnology have resulted in innovative information security strategies utilizing biomolecular-based encryption mechanisms to achieve effective protection and reliable storage. However, existing molecular encryption schemes are limited in their practical expansion due to their focus on the precise design and strict management of the key itself while neglecting the impact of complex environments, causing them to suffer from insufficient concealment and poor adaptability to complex access control scenarios. Here, we propose a pH-regulated camouflage strategy that significantly enhances the encryption concealment of molecular systems. Using pH-regulated logical operation transformations, we establish a switchable cascaded logic operation strategy that implements a two-layer DNA molecular firewall access control system. By integrating two distinct camouflage rules, the system constructs four differentiated access modes. This design effectively prevents unauthorized access, conceals true input addresses, and deceives potential attackers, thereby ensuring internal information security. This approach provides a simple method for the design and management of molecular systems and is expected to be applied in fields such as information security and environmental monitoring.

An analytical procedure to evaluate electronic integrals for molecular quantum mechanical calculations