Quantum Mechanics Research Articles

Quantum mechanics insights into melatonin and analogs binding to melatonin MT1 and MT2 receptors

Melatonin receptors MT1 and MT2 are G protein-coupled receptors that mediate the effects of melatonin, a hormone involved in circadian rhythms and other physiological functions. Understanding the molecular interactions between these receptors and their ligands is crucial for developing novel therapeutic agents. In this study, we used molecular docking, molecular dynamics simulations, and quantum mechanics calculation to investigate the binding modes and affinities of three ligands: melatonin (MLT), ramelteon (RMT), and 2-phenylmelatonin (2-PMT) with both receptors. Based on the results, we identified key amino acids that contributed to the receptor-ligand interactions, such as Gln181/194, Phe179/192, and Asn162/175, which are conserved in both receptors. Additionally, we described new meaningful interactions with Gly108/Gly121, Val111/Val124, and Val191/Val204. Our results provide insights into receptor-ligand recognition’s structural and energetic determinants and suggest potential strategies for designing more optimized molecules. This study enhances our understanding of receptor-ligand interactions and offers implications for future drug development.

Essential oils from fennel plants as valuable chemical products: gas chromatography–mass spectrometry, FTIR, quantum mechanical investigation, and antifungal activity

AbstractIn the present study, the biomass produced by fennel plants (Foeniculum vulgare Mill.) was converted to yield bioactive chemicals, and the hydrodistillation method was used to extract the essential oils (EOs) from both the leaves and the umbels. The antifungal activity of the EOs was tested using bioassay against the development of Fusarium oxysporum MW854649 and Alternaria solani MT279570. Molecular spectroscopic detection techniques were used to evaluate the EO products using gas chromatography–mass spectrometer (GC–MS) and Fourier transform infrared spectroscopy (FTIR). GC–MS equipped with single quadruple analyzers have been used to measure the electron ionization (EI) mass spectra of the primary constituents of fennel EOs at 70 eV. The main chemical compounds in the EO from leaves were anethole, estragole, D-limonene, trans-β-ocimene, and fenchone, with percentages of 37.94, 35.56, 17.46, 1.53, and 1.49%, respectively. The abundant compounds in the EO from umbels were estragole, anethole, D-limonene, fenchone, and γ-terpinene, with percentages of 51.18, 25.08, 12.22, 6.57, and 2.86%, respectively. EI mass spectral fragmentation of the major compounds D-limonene, estragole, anethole, and fenchone has been investigated. Umbels and leaf EOs at 5000 mg/L displayed the strongest suppression of fungal growth against A. solani, with values of 87.78% and 79.63%, respectively, compared to the positive control (94.44%). The EOs from umbels and leaves at 5000 mg/L showed the highest inhibition of fungal growth against F. oxysprium as compared to the positive control (94.44%), with values of 77.77% and 72.96%, respectively. All of the important ions—including a few distinctive fragment ions—have comprehensive fragmentation pathways defined. Based on EI, the main routes of fragmentation for the primary compounds have been identified. The existence of alkenes, aliphatic alcohols, ethers, carboxylic acids, ester compounds, alkanes, hydrogen-bonded alcohols, and phenols was demonstrated by the FTIR analysis of fennel EOs. On the other hand, the reactive behavior of the studied molecules has been investigated using two quantum mechanics method: the modified neglect of diatomic overlap (MNDO), a semi-empirical method, and the density functional theory (DFT)/B3LYP hybrid density functional method with the 6-311G (d, p) basis set in the ground state for gas phase. The optimum geometries have been obtained through the execution of computations and electrostatic potential. The obtained analytical and calculated results were then used to understand the activity of the studied EOs in further medical applications.

Black hole — wormhole transitions in two dimensional string theory

We study charged black hole and wormhole solutions of Type 0A/IIA string theory in two dimensions, by analysing their low energy equations of motion at leading order in α′. There is a competition between Euclidean wormholes and near extremal black holes in the thermodynamic ensemble. In a certain regime of phase space, the former can disassociate into the latter. Since such solutions are of string scale near the wormhole throat that takes an AdS2 form, there is a need for an exact worldsheet description. We discuss relevant WZW coset models which we argue will shed light on this problem. Finally, we present appropriate versions of the Type 0A/IIA matrix quantum mechanics models that are expected to describe these geometries.

Coherence-mixedness trade-offs

Abstract Quantum coherence constitutes a foundational characteristic of quantum mechanics and is integral to emerging quantum resource theories. However, quantum coherence is severely restricted by environmental noise in general quantum processing, indicated by the loss of information of a quantum system. Such processing can be described by the trade-offs between the coherence and the mixedness. Based on the l2 norm coherence, conditional von Neumann entropy and Wigner-Yanase skew information, we derive basis-independent constraints on the attainable quantum coherence imposed by the mixedness of a quantum state, which generalize the prior basis-dependent relations, provide fundamental insights into the latent coherence resources present within arbitrary quantum systems that undergo decoherence and quantify the inherent limits on extractable coherence imposed by environmental noise.

Relational Quantum Mechanics: Ozawa’s Intersubjectivity Theorem as Justification of the Postulate on Internally Consistent Descriptions

The Ozawa’s intersubjectivity theorem (OIT) proved within quantum measurement theory supports the new postulate of relational quantum mechanics (RQM), the postulate on internally consistent descriptions. But from OIT viewpoint postulate’s formulation should be completed by the assumption of probability reproducibility. We remark that this postulate was proposed only recently to resolve the problem of intersubjectivity of information in RQM. In contrast to RQM for which OIT is a supporting theoretical statement, QBism is challenged by OIT.

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling.

Fully atomistic multiscale polarizable quantum mechanics (QM)/molecular mechanics (MM) approaches, combined with techniques to sample the solute-solvent phase space, constitute the most accurate method to compute spectral signals in aqueous solution. Conventional sampling strategies, such as classical molecular dynamics (MD), may encounter drawbacks when the conformational space is particularly complex, and transition barriers between conformers are high. This can lead to inaccurate sampling, which can potentially impact the accuracy of spectral calculations. For this reason, in this work, we compare classical MD with enhanced sampling techniques, i.e., replica exchange MD and metadynamics. In particular, we show how the different sampling techniques affect computed UV, electronic circular dichroism, nuclear magnetic resonance shielding, and optical rotatory dispersion of N-acetylproline-amide in aqueous solution. Such a system is a model peptide characterized by complex conformational variability. Calculated values suggest that spectral properties are influenced by solute conformers, relative population, and solvent effects; therefore, particular care needs to be paid for when choosing the sampling technique.

Strong Angular Oscillation of Rotationally Resolved Differential Cross Section in the H + HD → H2 + D Reaction at the Collision Energy of 2.07 eV: Evidence of Geometric Phase Effects.

Geometric phase (GP) effects in chemical reactions are subtle quantum phenomena that are challenging to identify. In this work, we report a joint experimental and theoretical study of the H + HD → H2 + D reaction at a collision energy of 2.07 eV, which is far below the energy of the conical intersection of 2.53 eV. The rotationally state-resolved differential cross sections were measured by a crossed-beam experiment with the scheme of D-atom Rydberg tagging time-of-flight detection. Experimental angular distributions of three rotational states of H2 products exhibit notable variation near the backward scattering direction. Time-dependent quantum mechanics calculations (TDQMs) were carried out at the same collision energy, with and without the inclusion of GP. The experimental angular distributions are in good agreement with TDQM results with the inclusion of GP but do not agree with TDQM results without the inclusion of GP. This work demonstrates the existence of GP effects at energy far below the conical intersection.

Beyond the Quantum Membrane Paradigm: A Philosophical Analysis of the Structure of Black Holes in Full QG

This paper presents a philosophical analysis of the structure of black holes, focusing on the event horizon and its fundamental status. While black holes have been at the centre of countless paradoxes arising from the attempt to merge quantum mechanics and general relativity, recent experimental discoveries have emphasised their importance as objects for the development of Quantum Gravity. In particular, the statistical mechanical underpinning of black hole thermodynamics has been a central research topic. The Quantum Membrane Paradigm, proposed by Wallace (Stud Hist Philos Sci Part B 66:103-117, 2019), posits a real membrane made of black hole microstates at the black hole horizon to provide a statistical mechanical understanding of black hole thermodynamics from an exterior observer’s point of view. However, we argue that the Quantum Membrane Paradigm is limited to low-energy Quantum Gravity and needs to be modified to avoid reference to geometric notions, such as the event horizon, which presumably do not make sense in the non-spatiotemporal context of full Quantum Gravity. Our proposal relies on the central dogma of black hole physics. It considers recent developments, such as replica wormholes and entanglement wedge reconstruction, to provide a new framework for understanding the nature of black hole horizons in full Quantum Gravity.

Order-N calculations for thermoelectric power factor based on linear response theory.

We present an order-N quantum transport calculation methodology to evaluate thermoelectric transport coefficients, such as electric conductivity and Seebeck coefficient. Different from a conventional method using the electric conductivity spectrum, it obtains the coefficients directly from the correlation function between heat and electric current based on linear response theory. As an example, we apply the methodology to a two-dimensional square-lattice model with static disorder and confirm that the calculated results are consistent with those obtained by the conventional method. The proposed methodology provides an effective approach to evaluate the thermoelectric performance of micron-scale materials based on quantum mechanics from an atomistic viewpoint.&#xD.

MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery.

Large language models have greatly enhanced our ability to understand biology and chemistry, yet robust methods for structure-based drug discovery, quantum chemistry and structural biology are still sparse. Precise biomolecule-ligand interaction datasets are urgently needed for large language models. To address this, we present MISATO, a dataset that combines quantum mechanical properties of small molecules and associated molecular dynamics simulations of ~20,000 experimental protein-ligand complexes with extensive validation of experimental data. Starting from the existing experimental structures, semi-empirical quantum mechanics was used to systematically refine these structures. A large collection of molecular dynamics traces of protein-ligand complexes in explicit water is included, accumulating over 170 μs. We give examples of machine learning (ML) baseline models proving an improvement of accuracy by employing our data. An easy entry point for ML experts is provided to enable the next generation of drug discovery artificial intelligence models.

Computational Insights into Cyclodextrin Inclusion Complexes with the Organophosphorus Flame Retardant DOPO

Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, we report a systematic study on the inclusion complexes of natural CDs (α-, β-, and γ-CD) with a representative OPFR of DOPO using computational methods of molecular docking, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations. The binding modes and energetics of host:guest inclusion complexes were analyzed in details. α-CD was not able to form a complete inclusion complex with DOPO, and the center of mass distance host:guest distance amounted to 4–5 Å. β-CD and γ-CD allowed for a deep insertion of DOPO into their hydrophobic cavities, and DOPO was able to frequently change its orientation within the γ-CD cavity. The energy decomposition analysis based on the dispersion-corrected density functional theory (sobEDAw) indicated that electrostatic, orbital, and dispersion contributions favored host:guest complexation, while the exchange–repulsion term showed the opposite. This work provides an in-depth understanding of using CD inclusion complexes in OPFRs formulations.

Spooky action at a distance? A two-phase study into learners’ views of quantum entanglement

Quantum entanglement is a challenging concept within the field of physics education, often eluding a full grasp by both educators and learners alike. In this paper, we report findings from a two-phase empirical study into the views of entanglement held by pre-service physics teachers and physics students from various universities. In the first phase, we utilized a questionnaire consisting of open-ended questions which was completed by 31 pre-service physics teachers. The study participants’ ideas were explored using qualitative content analysis which led to the creation of rating scale items used in study phase 2. These items were administered to a broader cohort including 73 physics university students in order to capture the learners’ agreement or disagreement with the questionnaire statements, and hence, helped to validate and substantiate the in-depth insights from study phase 1. Key findings revealed widespread accurate notions, like the need to consider the entire system when examining entangled states. However, less elaborated views were also identified, including ideas such as that measurements of entangled states always show perfect (anti-)correlation. Another striking observation was the confusion between quantum entanglement and superposition. In the case of quantum teleportation, many participants seemed to have a basic grasp of the concept, although a number of misconceptions were apparent, notably the idea that quantum entanglement enables faster-than-light communication. Practically, the findings can assist educators in anticipating and addressing widespread (mis-)conceptions, paving the way for more effective instruction in quantum mechanics and its real-world applications, such as quantum cryptography and computing.

PointGAT: A Quantum Chemical Property Prediction Model Integrating Graph Attention and 3D Geometry.

Predicting quantum chemical properties is a fundamental challenge for computational chemistry. While the development of graph neural networks has advanced molecular representation learning and property prediction, their performance could be further enhanced by incorporating three-dimensional (3D) structural geometry into two-dimensional (2D) molecular graph representation. In this study, we introduce the PointGAT model for quantum molecular property prediction, which integrates 3D molecular coordinates with graph-attention modeling. Comparison with other current models in molecular prediction tasks showed that PointGAT could provide higher predictive accuracy in various benchmark data sets from MoleculeNet, including ESOL, FreeSolv, Lipop, HIV, and 6 out of 12 tasks of the QM9 data set. To further examine PointGAT prediction of quantum mechanical (QM) energies, we constructed a C10 data set comprising 11,841 charged and chiral carbocation intermediates with QM energies calculated at the DM21/6-31G*//B3LYP/6-31G* levels. Notably, PointGAT achieved an R2 value of 0.950 and an MAE of 1.616 kcal/mol, outperforming even the best-performing graph neural network model with a reduction of 0.216 kcal/mol in MAE and an improvement of 0.050 in R2. Additional ablation studies indicated that incorporating molecular geometry into the model resulted in markedly higher predictive accuracy, reducing the MAE value from 1.802 to 1.616 kcal/mol. Moreover, visualization of PointGAT atomic attention weights suggested its predictions were interpretable. Findings in this study support the application of PointGAT as a powerful and versatile tool for quantum chemical property prediction that can facilitate high-accuracy modeling for fundamental exploration of chemical space as well as drug design and molecular engineering.

Quantum physics: A better model to understand consciousness-related brain functions

With the development of quantum mechanics, it is applied to different fields, including biology. As intricate as human brains, quantum physics is replacing classical physics in explaining consciousness-related brain functions. The bilayer phospholipid membrane enables neurons in the brain to store and protect quantum information, and the abundance of 1/2-spin phosphorous creates potential for quantum entanglement that allows information to transfer along long distances and process consciousness. Scientists have used Schrdinger's cat thought experiment to explain how the uncertain and superimposed states in quantum physics can be applied to our decision-making behavior with conditions of "Yes" or "No." Scientists also conducted experiments to witness the quantum entanglement of particles in the brain. The observation of the phenomenon broke the pre-assumption that quantum entanglement is too fragile to occur in the chaotic environment in human brains, and it allows the possibility of ongoing conscious processing there. To further understand the decision-making mechanism, physicists should also integrate the knowledge in neuroscience, psychology, sociology, and other interdisciplinary subjects.

Quantum work: Reconciling quantum mechanics and thermodynamics

It has been claimed that no protocol for measuring quantum work can satisfy standard physical principles, casting doubts on the compatibility between quantum mechanics, thermodynamics, and the classical limit. In this Letter, we present a solution for this incompatibility. We demonstrate that the standard formulation of these principles fails to address the classical limit properly. By proposing changes in this direction, we prove that all the essential principles can be satisfied when work is defined as a quantum observable, reconciling quantum work statistics and thermodynamics. Published by the American Physical Society 2024

An algebraic formulation of nonassociative quantum mechanics

Abstract We develop a version of quantum mechanics that can handle nonassociative algebras of observables and which reduces to standard quantum theory in the traditional associative setting. Our algebraic approach is naturally probabilistic and is based on using the universal enveloping algebra of a general nonassociative algebra to introduce a generalized notion of associative composition product. We formulate properties of states together with notions of trace, and use them to develop GNS constructions. We describe Heisenberg and Schrödinger pictures of completely positive dynamics, and we illustrate our formalism on the explicit examples of finite-dimensional matrix Jordan algebras as well as the octonion algebra.

Does Quantum Mechanics Require “Conspiracy”?

Quantum states containing records of incompatible outcomes of quantum measurements are valid states in the tensor-product Hilbert space. Since they contain false records, they conflict with the Born rule and with our observations. I show that excluding them requires a fine-tuning to an extremely restricted subspace of the Hilbert space that seems “conspiratorial”, in the sense that (1) it seems to depend on future events that involve records (including measurement settings) and on the dynamical law (normally thought to be independent of the initial conditions), and (2) it violates Statistical Independence, even when it is valid in the context of Bell’s theorem. To solve the puzzle, I build a model in which, by changing the dynamical law, the same initial conditions can lead to different histories in which the validity of records is relative to the new dynamical law. This relative validity of the records may restore causality, but the initial conditions still must depend, at least partially, on the dynamical law. While violations of Statistical Independence are often seen as non-scientific, they turn out to be needed to ensure the validity of records and our own memories and, by this, of science itself. A Past Hypothesis is needed to ensure the existence of records and turns out to require violations of Statistical Independence. It is not excluded that its explanation, still unknown, ensures such violations in the way needed by local interpretations of quantum mechanics. I suggest that an as-yet unknown law or superselection rule may restrict the full tensor-product Hilbert space to the very special subspace required by the validity of records and the Past Hypothesis.

On the construction of various soliton solutions of two space-time fractional nonlinear models

Abstract In this article, we investigate a couple of nonlinear fractional models of eminent interests subsequently the conformable derivative sense is used to designate the fractional order derivatives. The given structures are transformed into nonlinear ordinary differential equations of integer order, and the extended simple equation technique is then employed to solve the resulting equations. Initially, the nonlinear space time fractional Klein–Gordon equation is considered emerging from quantum and classical relativistic mechanics, which have application in plasma physics, dispersive wave phenomena, quantum field theory, and optical fibres. Later, the (2 + 1)-dimensional time fractional Zoomeron equation is analysed which is convenient to explore the innovative phenomena related to boomerons and trappons. As a result, various new soliton solutions are successfully established. The reported results offer a key implementation for analysing the soliton solutions of nonlinear fractional models which are extremely encouraging arising in the recent era of science and engineering. The 3D simulations have been carried out to demonstrate dynamics of the various soliton solutions for a given set of parameters.

Perspective: Probing elasto-quantum materials with X-ray techniques and in situ anisotropic strain.

Anisotropic lattice deformation plays an important role in the quantum mechanics of solid state physics. The possibility of mediating the competition and cooperation among different order parameters by applying in situ strain/stress on quantum materials has led to discoveries of a variety of elasto-quantum effects on emergent phenomena. It has become increasingly critical to have the capability of combining the in situ strain tuning with X-ray techniques, especially those based on synchrotrons, to probe the microscopic elasto-responses of the lattice, spin, charge, and orbital degrees of freedom. Herein, we briefly review the recent studies that embarked on utilizing elasto-X-ray characterizations on representative material systems and demonstrated the emerging opportunities enabled by this method. With that, we further discuss the promising prospect in this rising area of quantum materials research and the bright future of elasto-X-ray techniques.&#xD.

Copper(II) coordination to the intrinsically disordered region of SARS-CoV-2 Nsp1

The intrinsically disordered C-terminal peptide region of severe acute respiratory syndrome coronavirus 2 nonstructural protein-1 (Nsp1-CT) inhibits host protein synthesis by blocking messenger RNA (mRNA) access to the 40S ribosome entrance tunnel. Aqueous copper(II) ions bind to the disordered peptide with micromolar affinity, creating a possible strategy to restore protein synthesis during host infection. Electron paramagnetic resonance (EPR) and tryptophan fluorescence measurements on a 10-residue model of the disordered protein region (Nsp1-CT 10 ), combined with advanced quantum mechanics calculations, suggest that the peptide binds to copper(II) as a multidentate ligand. Two optimized computational models of the copper(II)-peptide complexes were derived: One corresponding to pH 6.5 and the other describing the complex at pH 7.5 to 8.5. Simulated EPR spectra based on the calculated model structures are in good agreement with experimental spectra.