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Keywords = reconstructions of quantum mechanics

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22 pages, 2487 KB  
Article
Integrating Molecular Biology and Cryptography: A DNA and RNA-Based Framework for Secure Data Encryption
by Muhammad Naeem Akhtar, Jawad Hussain Awan, Abdul Mateen Shahzaib Asad and Min Young Kim
Int. J. Mol. Sci. 2026, 27(10), 4522; https://doi.org/10.3390/ijms27104522 - 18 May 2026
Viewed by 242
Abstract
The rapid growth of digital communication and large-scale data exchange has increased the demand for advanced cryptographic techniques capable of resisting emerging computational threats. Conventional encryption methods primarily rely on mathematical complexity, which may become vulnerable with the advancement of high-performance computing and [...] Read more.
The rapid growth of digital communication and large-scale data exchange has increased the demand for advanced cryptographic techniques capable of resisting emerging computational threats. Conventional encryption methods primarily rely on mathematical complexity, which may become vulnerable with the advancement of high-performance computing and future quantum technologies. Biological molecules such as deoxyribonucleic acid (DNA) and RiboNucleic Acid (RNA) provide unique properties, including extremely high storage density, massive parallelism, and complex nucleotide structures that can inspire novel cryptographic mechanisms. This study proposes a bio-inspired cryptographic framework that integrates DNA encoding and RNA-based transformations to enhance data security. In the proposed framework, digital information is first converted into binary format and mapped to nucleotide sequences using a predefined encoding scheme. The encryption process incorporates multiple molecular transformations, including complementary base pairing, sequence permutation, and transcription-inspired DNA-to-RNA conversion to generate a highly randomized ciphertext. Decryption reverses these transformations to reconstruct the original plaintext. Security evaluation demonstrates that the proposed framework produces high entropy outputs, a substantially large key space, and enhanced resistance to statistical and brute-force attacks. The results indicate that DNA and RNA-inspired cryptographic systems can substantially enhance encryption complexity while maintaining reliable data recovery. This research highlights the potential of molecular cryptography as a promising interdisciplinary approach for future secure communication and biological data storage systems. Full article
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28 pages, 1515 KB  
Article
Q-DP-GAN: Improving EEG Data Privacy Through Quantum-Inspired Differential Privacy-Based GAN
by Shouvik Paul and Garima Bajwa
Cryptography 2026, 10(3), 31; https://doi.org/10.3390/cryptography10030031 - 11 May 2026
Viewed by 605
Abstract
Electroencephalography (EEG)-based brain–computer interface (BCI) systems pose significant privacy risks, as EEG data remain vulnerable to inference and reconstruction attacks. Conventional privacy-preserving techniques, including data anonymization, encryption, and perturbation, frequently compromise data utility or prove ineffective against advanced adversaries. To address these limitations [...] Read more.
Electroencephalography (EEG)-based brain–computer interface (BCI) systems pose significant privacy risks, as EEG data remain vulnerable to inference and reconstruction attacks. Conventional privacy-preserving techniques, including data anonymization, encryption, and perturbation, frequently compromise data utility or prove ineffective against advanced adversaries. To address these limitations and balance utility and privacy, we propose a quantum-inspired, differential privacy-based generative adversarial network (Q-DP-GAN). Unlike classical GANs, which lack adaptive privacy mechanisms during training, our method uses quantum-inspired stochasticity to dynamically calibrate noise and the privacy budget. The experimental results demonstrate that Q-DP-GAN is more robust to membership inference and reconstruction attacks than existing approaches. Evaluation on the widely used BCI Competition IV Datasets 2A and 2B indicates that our framework produces high-quality synthetic EEG data while maintaining utility and data confidentiality for BCI classification tasks. Full article
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23 pages, 3226 KB  
Article
A Detection and Recognition Method for Interference Signals Based on Radio Frequency Fingerprint Characteristics
by Yang Guo and Yuan Gao
Electronics 2026, 15(7), 1393; https://doi.org/10.3390/electronics15071393 - 27 Mar 2026
Viewed by 551
Abstract
With the advancement of 5G and the Internet of Things (IoT), traditional upper-layer authentication mechanisms are vulnerable to attacks, while quantum computing threatens cryptographic security. Radio frequency fingerprint identification (RFFI) offers a physical-layer solution by exploiting inherent hardware imperfections. However, in complex electromagnetic [...] Read more.
With the advancement of 5G and the Internet of Things (IoT), traditional upper-layer authentication mechanisms are vulnerable to attacks, while quantum computing threatens cryptographic security. Radio frequency fingerprint identification (RFFI) offers a physical-layer solution by exploiting inherent hardware imperfections. However, in complex electromagnetic environments, narrowband and especially agile interference (characterized by low power and narrow bandwidth) can severely distort fingerprint features, rendering conventional detection algorithms ineffective. To address this challenge, this paper proposes a novel interference detection framework tailored for Orthogonal Frequency Division Multiplexing (OFDM) systems. First, a signal transmission model incorporating non-ideal hardware characteristics (e.g., DC offset, I/Q imbalance) is established. Based on this model, we design an agile interference detection algorithm comprising two key components: (1) a time-series anomaly detection method that fuses multi-domain expert features (fractal, complexity, and high-order statistics) with machine learning, demonstrating superior performance over the traditional CME algorithm under narrowband interference, and (2) a progressive search segmental detection algorithm that, combined with reconstruction error features extracted by an autoencoder, effectively identifies low-power agile interference by appropriately trading-off computation time for detection sensitivity. Finally, an OFDM simulation platform is developed to validate the proposed methods. The results show that the segmental detection algorithm achieves reliable detection at a jammer-to-signal ratio (JSR) as low as −10 dB, significantly outperforming existing approaches and enhancing the robustness of RFFI in challenging interference environments. Full article
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47 pages, 4135 KB  
Article
Adaptive Compressed Sensing Differential Privacy Federated Learning Based on Orbital Spatiotemporal Characteristics in Space–Air–Ground Networks
by Weibang Li, Ling Li and Lidong Zhu
Sensors 2026, 26(6), 1874; https://doi.org/10.3390/s26061874 - 16 Mar 2026
Cited by 1 | Viewed by 538
Abstract
With the development of 6G communication technology, Space–Air–Ground Integrated Networks (SAGINs) have become critical infrastructure for global intelligent collaborative computing. However, federated learning deployment in SAGINs faces three severe challenges: the high dynamics of satellite orbital motion, node resource heterogeneity, and privacy vulnerabilities [...] Read more.
With the development of 6G communication technology, Space–Air–Ground Integrated Networks (SAGINs) have become critical infrastructure for global intelligent collaborative computing. However, federated learning deployment in SAGINs faces three severe challenges: the high dynamics of satellite orbital motion, node resource heterogeneity, and privacy vulnerabilities in data transmission. This paper proposes an adaptive compressed sensing differential privacy federated learning framework based on orbital spatiotemporal characteristics. First, we design orbital periodicity-driven time-varying sparse sensing matrices that dynamically adjust compression strategies according to satellite orbital positions, achieving intelligent communication efficiency optimization. Second, we propose an orbital predictability-based privacy budget temporal allocation mechanism and perform differential privacy noise injection in the compressed domain, establishing a compression–privacy joint optimization algorithm. Furthermore, we construct an energy–communication–privacy ternary collaborative mechanism that achieves multi-objective dynamic balance through model predictive control. Finally, we design reinforcement learning-based dynamic routing scheduling and hierarchical aggregation strategies to effectively handle the time-varying characteristics of network topology. Simulation experiments demonstrate that compared to existing methods, the proposed approach achieves 3–12% improvement in model accuracy and 30–50% enhancement in communication efficiency while maintaining differential privacy protection with dynamic privacy budget ε[0.1,10.0] and compression ratio ρ[0.2,0.8]. Unlike static compressed sensing approaches that ignore orbital periodicity, the proposed orbital-driven time-varying sensing matrices reduce reconstruction error by up to 19.4% compared to fixed-matrix baselines, validating the synergistic effectiveness of integrating orbital spatiotemporal characteristics with federated learning in 6G SAGIN deployments. The framework assumes reliable orbital propagation via SGP4/SDP4 models and does not account for Doppler frequency shifts or inter-satellite link handover delays; future extensions include scalability to mega-constellations and integration of quantum-resistant privacy mechanisms. Full article
(This article belongs to the Section Communications)
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27 pages, 5794 KB  
Article
PARAFAC- and PCA-Resolved Excitation–Emission Matrix Fluorescence of Ultra-Fine Polyamide-Derived Carbon Quantum Dots for Mechanistic Microplastic Discrimination
by Christian Ebere Enyoh and Qingyue Wang
Micro 2026, 6(1), 15; https://doi.org/10.3390/micro6010015 - 12 Feb 2026
Cited by 1 | Viewed by 1107
Abstract
The rapid and selective discrimination of microplastics (MPs) is a critical analytical challenge, particularly as current carbon quantum dot (CQD)-based sensors often rely on single-wavelength “turn-on/off” or staining mechanisms that lack polymer-specific resolution. This work addresses these limitations by presenting a mechanism-driven fluorescence [...] Read more.
The rapid and selective discrimination of microplastics (MPs) is a critical analytical challenge, particularly as current carbon quantum dot (CQD)-based sensors often rely on single-wavelength “turn-on/off” or staining mechanisms that lack polymer-specific resolution. This work addresses these limitations by presenting a mechanism-driven fluorescence sensing platform using ultra-fine polyamide-derived carbon quantum dots (PACQDs; ~1.4 nm) to identify three prevalent MPs: polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET). Excitation–emission matrix (EEM) spectroscopy reveals polymer-specific photophysical responses: PAMPs and PPMPs induce fluorescence enhancement of 11.66% and 11.43%, respectively, whereas PETMPs cause net quenching (−4.61%) alongside a distinct, red-shifted emission band. Despite a common scatter-dominated peak at 290/308 nm, quantitative discrimination is achieved via integrated intensity and red/blue emission ratios (0.0137 for PAMPs, 0.0098 for PPMPs, and 0.0072 for PETMPs). Multivariate analysis reinforces this discrimination. Parallel factor analysis (PARAFAC) resolves the EEM data into three fluorescent components representing the intrinsic CQDs core and two interaction-induced surface states with a rank 3 model reducing the relative reconstruction error from 0.1625 to 0.1285. Principal component analysis (PCA) yields clear separation of the polymer classes, with the first two principal components capturing ~88% of the total spectral variance. ATR–FTIR spectroscopy provides direct molecular evidence for the underlying mechanisms: amide–amide coupling and interfacial rigidification for PAMPs; hydrophobic interaction without spectral shifts for PPMPs; and a synergistic interaction involving hydrogen bonding and π–π stacking for PETMPs. In particular, these polymer-specific fluorescence fingerprints are largely preserved in tap water, despite elevated background intensity and partial contrast attenuation, demonstrating the resilience of the EEM–chemometric approach under realistic matrix conditions. Collectively, the strong agreement between fluorescence metrics, multivariate signatures, and interfacial chemistry establishes a robust structure–property framework and positions PACQDs as a rapid, label-free, and matrix-tolerant platform for reliable microplastic discrimination in environmental analysis. Full article
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28 pages, 5314 KB  
Article
Quantum-Behaved Loser Reverse-Learning Differential Evolution Algorithm-Based Path Planning for Unmanned Aerial Vehicle
by Zhuoyun Chen, Xiangyin Zhang and Yao Lu
Actuators 2026, 15(2), 74; https://doi.org/10.3390/act15020074 - 26 Jan 2026
Viewed by 580
Abstract
This paper proposes the Quantum-behaved Loser Reverse-learning Differential Evolution (QLRDE) algorithm to address the inherent limitations of the standard Differential Evolution (DE) algorithm, including slow convergence speed and the premature stagnation in local optima. QLRDE incorporates three innovations: quantum-behaved mutation strategies suppress premature [...] Read more.
This paper proposes the Quantum-behaved Loser Reverse-learning Differential Evolution (QLRDE) algorithm to address the inherent limitations of the standard Differential Evolution (DE) algorithm, including slow convergence speed and the premature stagnation in local optima. QLRDE incorporates three innovations: quantum-behaved mutation strategies suppress premature convergence by leveraging quantum mechanics, the Loser Reverse-Learning Mechanism enhances diversity by reconstructing inferior individuals through opposition-based learning, and an adaptive parameter adjustment mechanism balances exploration and exploitation to improve robustness and convergence efficiency. Experimental evaluations on twelve benchmark functions confirm that QLRDE demonstrates better performance than existing algorithms in terms of search capability and convergence speed. Furthermore, QLRDE is employed for the 3D UAV path planning problem. QLRDE can generate B-Spline-based smooth flight paths and incorporate real-world constraints into the cost function. Simulation results confirm that QLRDE outperforms several competing algorithms with respect to path quality, computational efficiency, and robustness. Full article
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41 pages, 3913 KB  
Review
Advancing Bioconjugated Quantum Dots with Click Chemistry and Artificial Intelligence to Image and Treat Glioblastoma
by Pranav Kalaga and Swapan K. Ray
Cells 2026, 15(2), 185; https://doi.org/10.3390/cells15020185 - 19 Jan 2026
Cited by 2 | Viewed by 1721
Abstract
Glioblastoma (GB) is one of the most aggressive and invasive cancers. Current treatment protocols for GB include surgical resection, radiotherapy, and chemotherapy with temozolomide. However, despite these treatments, physicians still struggle to effectively image, diagnose, and treat GB. As such, patients frequently experience [...] Read more.
Glioblastoma (GB) is one of the most aggressive and invasive cancers. Current treatment protocols for GB include surgical resection, radiotherapy, and chemotherapy with temozolomide. However, despite these treatments, physicians still struggle to effectively image, diagnose, and treat GB. As such, patients frequently experience recurrence of GB, demanding innovative strategies for early detection and effective therapy. Bioconjugated quantum dots (QDs) have emerged as powerful nanoplatforms for precision imaging and targeted drug delivery due to their unique optical properties, tunable size, and surface versatility. Due to their extremely small size, QDs can cross the blood–brain barrier and be used for precision imaging of GB. This review explores the integration of QDs with click chemistry for robust bioconjugation, focusing on artificial intelligence (AI) to advance GB therapy, mechanistic insights into cellular uptake and signaling, and strategies for mitigating toxicity. Click chemistry enables site-specific and stable conjugation of targeting ligands, peptides, and therapeutic agents to QDs, enhancing selectivity and functionalization. Algorithms driven by AI may facilitate predictive modeling, image reconstruction, and personalized treatment planning, optimizing QD design and therapeutic outcomes. We discuss molecular mechanisms underlying interactions of QDs with GB, including receptor-mediated endocytosis and intracellular trafficking, which influence biodistribution and therapeutic efficacy. Use of QDs in photodynamic therapy, which uses reactive oxygen species to induce apoptotic cell death in GB cells, is an innovative therapy that is covered in this review. Finally, this review addresses concerns associated with the toxicity of metal-based QDs and highlights how QDs can be coupled with AI to develop new methods for precision imaging for detecting and treating GB for induction of apoptosis. By converging nanotechnology and computational intelligence, bioconjugated QDs represent a transformative platform for paving a safer path to smarter and more effective clinical interventions of GB. Full article
(This article belongs to the Special Issue Cell Death Mechanisms and Therapeutic Opportunities in Glioblastoma)
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19 pages, 3573 KB  
Article
Time-Dependent Theory of Electron Emission Perpendicular to Laser Polarization for Reconstruction of Attosecond Harmonic Beating by Interference of Multiphoton Transitions
by Matías L. Ocello, Sebastián D. López, Martín Barlari and Diego G. Arbó
Atoms 2025, 13(12), 99; https://doi.org/10.3390/atoms13120099 - 10 Dec 2025
Cited by 1 | Viewed by 737
Abstract
We present a time-dependent nonperturbative theory of the reconstruction of attosecond beating by interference of multiphoton transitions (RABBIT) for photoelectron emission from hydrogen atoms in the transverse direction relative to the laser polarization axis. Extending our recent semiclassical strong-field approximation (SFA) model developed [...] Read more.
We present a time-dependent nonperturbative theory of the reconstruction of attosecond beating by interference of multiphoton transitions (RABBIT) for photoelectron emission from hydrogen atoms in the transverse direction relative to the laser polarization axis. Extending our recent semiclassical strong-field approximation (SFA) model developed for parallel emission, we deduce analytical expressions for the transition amplitudes and demonstrate that the photoelectron probability distribution can be factorized into interhalf- and intrahalfcycle interference contributions, the latter modulating the intercycle pattern responsible for sideband formation. We identify the intrahalfcycle interference arising from trajectories released within the same half cycle as the mechanism governing attosecond phase delays in the perpendicular geometry. Our results reveal the suppression of even-order sidebands due to destructive interhalfcycle interference, leading to a characteristic spacing between adjacent peaks that doubles the standard spacing observed along the polarization axis. Comparisons with numerical calculations of the SFA and the ab initio solution of the time-dependent Schrödinger equation confirm the accuracy of the semiclassical description. This work provides a unified framework for understanding quantum interferences in attosecond chronoscopy, bridging the cases of parallel and perpendicular electron emission in RABBIT-like protocols. Full article
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57 pages, 640 KB  
Article
Geometric Origin of Quantum Waves from Finite Action
by Bin Li
Quantum Rep. 2025, 7(4), 61; https://doi.org/10.3390/quantum7040061 - 8 Dec 2025
Cited by 2 | Viewed by 1797
Abstract
Quantum mechanics postulates wave–particle duality and assigns amplitudes of the form eiS/, yet no existing formulation explains why physical observables depend only on the phase of the action. Here we show that if the quantum of action [...] Read more.
Quantum mechanics postulates wave–particle duality and assigns amplitudes of the form eiS/, yet no existing formulation explains why physical observables depend only on the phase of the action. Here we show that if the quantum of action geom is finite, the classical action manifold R becomes compact under the identification SS+2πgeom, yielding a U(1) action space on which only modular action is observable. Wave interference then follows as a geometric necessity: a finite action quantum forces physical amplitudes to live on a circle, while the classical limit arises when the modular spacing 2πgeom becomes negligible compared with macroscopic actions. We formulate this as a compact-action theorem. Chronon Field Theory (ChFT) provides the physical origin of geom: its causal field Φμ carries a quantized symplectic flux ω=geom, making Planck’s constant a geometric topological invariant rather than an imposed parameter. Within this medium, the Real–Now–Front (RNF) supplies a local reconstruction rule that reproduces the structure of the Feynman path integral, the Schrödinger evolution, the Born rule, and macroscopic definiteness as consequences of geometric compatibility rather than supplemental postulates. Phenomenologically, identifying the electron as the minimal chronon soliton—carrying the fundamental unit of symplectic flux—links its spin, charge, and stability to topological properties of the chronon field, yielding concrete experimental signatures. Thus the compact-action/RNF framework provides a unified geometric origin for quantum interference, measurement, and matter, together with falsifiable predictions of ChFT. Full article
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34 pages, 861 KB  
Article
Is Quantum Field Theory Necessarily “Quantum”?
by Ali Shojaei-Fard
Quantum Rep. 2025, 7(4), 53; https://doi.org/10.3390/quantum7040053 - 1 Nov 2025
Cited by 1 | Viewed by 1631
Abstract
The mathematical universe of the quantum topos, which is formulated on the basis of classical Boolean snapshots, delivers a neo-realist description of quantum mechanics that preserves realism. The main contribution of this article is developing formal objectivity in physical theories beyond quantum mechanics [...] Read more.
The mathematical universe of the quantum topos, which is formulated on the basis of classical Boolean snapshots, delivers a neo-realist description of quantum mechanics that preserves realism. The main contribution of this article is developing formal objectivity in physical theories beyond quantum mechanics in the topos-theory approach. It will be shown that neo-realist responses to non-perturbative structures of quantum field theory do not preserve realism. In this regard, the method of Feynman graphons is applied to reframe the task of describing objectivity in quantum field theory in terms of replacing the standard Hilbert-space/operator-algebra ontology with a new context category built from a certain family of topological Hopf subalgebras of the topological Hopf algebra of renormalization as algebraic/combinatorial data tied to non-perturbative structures. This topological-Hopf-algebra ontology, which is independent of instrumentalist probabilities, enables us to reconstruct gauge field theories on the basis of the mathematical universe of the non-perturbative topos. The non-Boolean logic of the non-perturbative topos cannot be recovered by classical Boolean snapshots, which is in contrast to the quantum-topos reformulation of quantum mechanics. The article formulates a universal version of the non-perturbative topos to show that quantum field theory is a globally and locally neo-realist theory which can be reconstructed independent of the standard Hilbert-space/operator-algebra ontology. Formal objectivity of the universal non-perturbative topos offers a new route to build objective semantics for non-perturbative structures. Full article
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30 pages, 1181 KB  
Article
Three-Space as a Quantum Hyperlayer in 1+3 Dimensions: A Case Study in Quantum Space and Time
by Marek Czachor
Entropy 2025, 27(6), 549; https://doi.org/10.3390/e27060549 - 23 May 2025
Viewed by 1107
Abstract
We discuss a formalism where a universe is identified with the support of a wave function propagating through space–time. The dynamics is of a squeezing type, with shrinking in time and expanding in space. As opposed to classical cosmology, the resulting universe is [...] Read more.
We discuss a formalism where a universe is identified with the support of a wave function propagating through space–time. The dynamics is of a squeezing type, with shrinking in time and expanding in space. As opposed to classical cosmology, the resulting universe is not a spacelike section of some space–time but a hyperlayer of a finite timelike width, a set which is not a three-dimensional submanifold of space–time. The universe is in superposition of different localizations in both space and time so that x0=ct has the same formal status of a position operator as the remaining three coordinates. We test the formalism on the example of a universe that contains a single harmonic oscillator, a generalization of the curvature-dependent Cariñena–Rañada–Santander (CRS) model. As opposed to the original CRS formulation, here, the curvature is not a parameter but a quantum observable, a function of the world-position operator. It is shown that asymptotically, for large values of the invariant evolution parameter τ, one reconstructs the standard quantum results, with one modification: The effective (renormalized) mass of the oscillator decreases with τ. The effect does not seem to be a peculiarity of harmonic oscillators, so one may speculate that masses of distant elementary quantum systems are greater than the values known from our quantum mechanical measurements. Full article
(This article belongs to the Section Time)
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12 pages, 256 KB  
Article
Mutual Compatibility/Incompatibility of Quasi-Hermitian Quantum Observables
by Miloslav Znojil
Symmetry 2025, 17(5), 708; https://doi.org/10.3390/sym17050708 - 5 May 2025
Viewed by 891
Abstract
In the framework of quasi-Hermitian quantum mechanics, the eligible operators of observables may be non-Hermitian, AjAj, j=1,2,,K. In principle, the standard probabilistic interpretation of the theory can be [...] Read more.
In the framework of quasi-Hermitian quantum mechanics, the eligible operators of observables may be non-Hermitian, AjAj, j=1,2,,K. In principle, the standard probabilistic interpretation of the theory can be re-established via a reconstruction of physical inner-product metric ΘI, guaranteeing the quasi-Hermiticity AjΘ=ΘAj. The task is easy at K=1 because there are many eligible metrics Θ=Θ(A1). In our paper, the next case with K=2 is analyzed. The criteria of the existence of a shared metric, Θ=Θ(A1,A2), are presented and discussed. Full article
(This article belongs to the Special Issue Quantum Gravity and Cosmology: Exploring the Astroparticle Interface)
24 pages, 1747 KB  
Review
Application of Density Functional Theory to Molecular Engineering of Pharmaceutical Formulations
by Haoyue Guan, Huimin Sun and Xia Zhao
Int. J. Mol. Sci. 2025, 26(7), 3262; https://doi.org/10.3390/ijms26073262 - 1 Apr 2025
Cited by 78 | Viewed by 10720
Abstract
This review systematically examines the pivotal applications of the Density Functional Theory (DFT) in drug formulation design, emphasizing its capability to elucidate molecular interaction mechanisms through quantum mechanical calculations. By solving the Kohn–Sham equations with precision up to 0.1 kcal/mol, DFT enables accurate [...] Read more.
This review systematically examines the pivotal applications of the Density Functional Theory (DFT) in drug formulation design, emphasizing its capability to elucidate molecular interaction mechanisms through quantum mechanical calculations. By solving the Kohn–Sham equations with precision up to 0.1 kcal/mol, DFT enables accurate electronic structure reconstruction, providing theoretical guidance for optimizing drug–excipient composite systems. In solid dosage forms, DFT clarifies the electronic driving forces governing active pharmaceutical ingredient (API)–excipient co-crystallization, predicting reactive sites and guiding stability-oriented co-crystal design. For nanodelivery systems, DFT optimizes carrier surface charge distribution through van der Waals interactions and π-π stacking energy calculations, thereby enhancing targeting efficiency. Furthermore, DFT combined with solvation models (e.g., COSMO) quantitatively evaluates polar environmental effects on drug release kinetics, delivering critical thermodynamic parameters (e.g., ΔG) for controlled-release formulation development. Notably, DFT-driven co-crystal thermodynamic analysis and pH-responsive release mechanism modeling substantially reduce experimental validation cycles. While DFT faces challenges in dynamic simulations of complex solvent environments, its integration with molecular mechanics and multiscale frameworks has achieved computational breakthroughs. This work offers interdisciplinary methodology support for accelerating data-driven formulation design. Full article
(This article belongs to the Section Molecular Informatics)
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17 pages, 283 KB  
Article
What Is Ontic and What Is Epistemic in the Quantum Mechanics of Spin?
by Ariel Caticha
Entropy 2025, 27(3), 315; https://doi.org/10.3390/e27030315 - 18 Mar 2025
Viewed by 1253
Abstract
Entropic Dynamics (ED) provides a framework that allows the reconstruction of the formalism of quantum mechanics by insisting on ontological and epistemic clarity and adopting entropic methods and information geometry. Our present goal is to extend the ED framework to account for spin. [...] Read more.
Entropic Dynamics (ED) provides a framework that allows the reconstruction of the formalism of quantum mechanics by insisting on ontological and epistemic clarity and adopting entropic methods and information geometry. Our present goal is to extend the ED framework to account for spin. The result is a realist ψ-epistemic model in which the ontology consists of a particle described by a definite position plus a discrete variable that describes Pauli’s peculiar two-valuedness. The resulting dynamics of probabilities is, as might be expected, described by the Pauli equation. What may be unexpected is that the generators of transformations—Hamiltonians and angular momenta, including spin, are all granted clear epistemic status. To the old question, ‘what is spinning?’ ED provides a crisp answer: nothing is spinning. Full article
(This article belongs to the Special Issue Maximum Entropy Principle and Applications)
11 pages, 6719 KB  
Article
Activation of Cryptochrome 4 from Atlantic Herring
by Anders Frederiksen, Mandus Aldag, Ilia A. Solov’yov and Luca Gerhards
Biology 2024, 13(4), 262; https://doi.org/10.3390/biology13040262 - 15 Apr 2024
Cited by 4 | Viewed by 4403
Abstract
Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate [...] Read more.
Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor. Full article
(This article belongs to the Special Issue The Rules of Life Rethought: Latest Progress in Quantum Biology)
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