Fundamental Physical Interactions Research Articles

Exploring protein-ligand binding affinity prediction with electron density-based geometric deep learning.

Rational structure-based drug design relies on accurate predictions of protein-ligand binding affinity from structural molecular information. Although deep learning-based methods for predicting binding affinity have shown promise in computational drug design, certain approaches have faced criticism for their potential to inadequately capture the fundamental physical interactions between ligands and their macromolecular targets or for being susceptible to dataset biases. Herein, we propose to include bond-critical points based on the electron density of a protein-ligand complex as a fundamental physical representation of protein-ligand interactions. Employing a geometric deep learning model, we explore the usefulness of these bond-critical points to predict absolute binding affinities of protein-ligand complexes, benchmark model performance against existing methods, and provide a critical analysis of this new approach. The models achieved root-mean-squared errors of 1.4-1.8 log units on the PDBbind dataset, and 1.0-1.7 log units on the PDE10A dataset, not indicating significant advantages over benchmark methods, and thus rendering the utility of electron density for deep learning models context-dependent. The relationship between intermolecular electron density and corresponding binding affinity was analyzed, and Pearson correlation coefficients r > 0.7 were obtained for several macromolecular targets.

Методичні особливості викладання природничих дисциплін засобами емерджентно-інтегративного підходу

The article is devoted to the search for the possibilities of implementing an emergent-integrative approach to the training of future teachers of natural sciences in the process of mastering the cycle of fundamental sciences: physics, astronomy, astrophysics, cosmology, cosmogony. The possibility of one of the variants of the system-integrative approach to the structuring and study of educational material about fundamental interactions in nature and the current state of the process of combining the physical theories that describe them is substantiated. As research methods, a comprehensive analysis of scientific and methodological sources was used, in which a unified approach to solving pedagogical problems is represented, and a synthesis of the relevant research results published in scientific and pedagogical publications, with the results of the author's work on their experimental implementation in educational practice. We practice teaching the integrative content of the material about fundamental interactions in nature consistently in the form of several stages. First, the nature of all fundamental interactions, their general characteristics, comparative data on the magnitude of numerical values, manifestation of fundamental interactions (forces) in physics, astronomy, chemistry, etc. are considered. The next stage consists in determining the influence of the change in the numerical values of the world constants on the evolution of the universe. After that, modern theories are considered at a qualitative level, which try to combine all fundamental interactions into a single system (scientific picture of the world). As a result of the conducted research, the possibilities of an integrative study of the material about fundamental interactions in nature and their quantum-statistical nature have been clarified. Their fundamentally opposite properties have been determined (long-range nature of gravitational and electromagnetic interactions and short-range – weak and strong), which in combination determine the structural unity and evolution of our universe, the possibility of the existence of a plurality of other universes, the property of inexhaustible «crushing» of matter into smaller and smaller particles, thereby confirming the dialectic of unity and the struggle of opposites.

Is the H Atom Surrounded by A Cloud of Virtual Quanta Due to the Lamb Shift?

The Lamb shift, one of the most fundamental interactions in atomic physics, arises from the interaction of H atoms with the electromagnetic fluctuations of the quantum vacuum. The energy shift has been computed in a variety of ways. The energy shift, as Feynman, Power, and Milonni demonstrated, equals the change in the vacuum energy in the volume containing the H atoms due to the change in the index of refraction arising from the presence of the H atoms. Using this result and a group theoretical calculation of the contribution to the Lamb shift from each frequency of the vacuum fluctuations, in this paper we obtain an expression for the region of the vacuum energy for each frequency ω around the H atom due to the Lamb shift. This same field plays an essential role in the van der Waals force. We show the ground state atom is surrounded by a region of positive vacuum energy that extends well beyond the atom for low frequencies. This region can be described as a steady state cloud of vacuum fluctuations. For energies E=ℏω less than 1 eV, where ℏ is the reduced Planck constant and ω is frequency, the radius of the positive energy region is shown to be approximately 14.4/E Å. For a vacuum fluctuation of wavelength, λ, the radius is (α/2π)λ, where α is the fine-structure constant. Thus, for long wavelengths, the region has macroscopic dimensions. The energy–time uncertainty relation predicts a maximum possible radius that is larger than the radius based on the radiative shift calculations by a factor of 1/4α.

Direct Probing of a Large Spin–Orbit Coupling in the FeSe Superconducting Monolayer on STO

Spin-orbit coupling (SOC) is a fundamental physical interaction, which describes how the electrons' spin couples to their orbital motion. It is the source of a vast variety of fascinating phenomena in nanostructures. Although in most theoretical descriptions of high-temperature superconductivity SOC has been neglected, including this interaction can, in principle, revise the microscopic picture. Here by preforming energy-, momentum-, and spin-resolved spectroscopy experiments we demonstrate that while probing the dynamic charge response of the FeSe monolayer on strontium titanate, a prototype two-dimensional high-temperature superconductor using electrons, the scattering cross-section is spin dependent. We unravel the origin of the observed phenomenon and show that SOC in this two-dimensional superconductor is strong. We anticipate that such a strong SOC can have several consequences on the electronic structures and may compete with other pairing scenarios and be crucial for the mechanism of superconductivity.

The Significance of Generalized Gauge Transformation across Fundamental Interactions

The author of this paper has put forward a unified program of gauge field from the mathematical and physical picture of the principal associated bundles: thinking that our universe may have more fundamental interactions than the four fundamental interactions, and these basic interaction gauge fields are only the projection components to the base manifold, that is our universe, from a unified gauge potential or connection of the principal associated bundle manifold on the base manifold. These components can satisfy the transformation of gauge potential, and can even be transformed from one basic interaction gauge potential to another basic interaction gauge potential, and can be summarized into a unified equation, that is, the generalized gauge Equation (GGE), but the gauge potential or connection on the principal bundle is invariant, corresponding to the invariance of gauge transformation [1]. In this paper, we will continue to discuss this aspect concretely, and specifically construct a spatiotemporal model with the frame bundle as the principal bundle, and the tensor bundle as the associated bundle, so that the four fundamental interactions, especially the electromagnetic interaction and the gravitational interaction, can be reflected in the bottom manifold, that is, the regional distributions in our universe. Furthermore, this paper studies the existence of gauge transformation across basic interactions by establishing a model of gauge transformation of basic interaction field; it is found that the unified expression formula is GGE and the expression relation on the curvature of space-time. Therefore, the author discusses the feasibility of the generalized gauge transformation across the basic electromagnetic interaction and the basic gravitational interaction, and on this basis, specifically determines a method or way to find the generalized gauge transformation, so as to try to realize the last step of the “unification” of the four fundamental interactions in physics, that is, the “unification” of electromagnetism and gravity.

On the similarity of electromagnetic and gravitational fields

It is well known that gravitational quantities are in many ways similar to electromagnetic quantities. The masses that create a gravitational field are similar in this to electric charges. A gravitational static field, like an electrostatic field, is characterized by potential and intensity. Vortex and rotational movements of masses are often and quite justifiably compared with a magnetic field. According to existing concepts, there are four types of different fundamental physical interactions: strong, weak, electromagnetic and gravitational. Strong and weak interactions are manifested inside atomic nuclei and between elementary particles, electromagnetic – between charges, and gravitational acts between massive bodies, becoming the main one in the case of astronomical objects. The article presents a comparison of mechanical and gravitational quantities from the condition of their similarity to electromagnetic quantities. Visual systemically possible patterns involving field gravitational quantities similar to electromagnetic ones are given.

Creating a unified theory for the fundamental physical interactions

Creating a unified theory for the fundamental physical interactions

A review of design approaches for the implementation of low-frequency noise measurement systems.

Electronic noise has its roots in the fundamental physical interactions between matter and charged particles, carrying information about the phenomena that occur at the microscopic level. Therefore, Low-Frequency Noise Measurements (LFNM) are a well-established technique for the characterization of electron devices and materials and, compared to other techniques, they offer the advantage of being non-destructive and of providing a more detailed view of what happens in the matter during the manifestation of physical or chemical phenomena. For this reason, LFNM acquire particular importance in the modern technological era in which the introduction of new advanced materials requires in-depth and thorough characterization of the conduction phenomena. LFNM also find application in the field of sensors, as they allow to obtain more selective sensing systems even starting from conventional sensors. Performing meaningful noise measurements, however, requires that the background noise introduced by the measurement chain be much smaller than the noise to be detected and the instrumentation available on the market does not always meet the specifications required for reaching the ultimate sensitivity. Researchers willing to perform LFNM must often resort to the design of dedicated instrumentation in their own laboratories, but their cultural background does not necessarily include the ability to design, build, and test dedicated low noise instrumentation. In this review, we have tried to provide as much theoretical and practical guidelines as possible, so that even researchers with a limited background in electronic engineering can find useful information in developing or customizing low noise instrumentation.

The Higgs boson turns ten.

The discovery of the Higgs boson, ten years ago, was a milestone that opened the door to the study of a new sector of fundamental physical interactions. We review the role of the Higgs field in the Standard Model of particle physics and explain its impact on the world around us. We summarize the insights into Higgs physics revealed so far by ten years of work, discuss what remains to be determined and outline potential connections of the Higgs sector with unsolved mysteries of particle physics.

Modeling of the Lithium Calendering Process for Direct Contact Prelithiation of Lithium-Ion Batteries

The automotive industry’s rapid advancement and complex demands concerning energy storage capacities and service life require lithium-ion batteries with improved energy density and cycle life. There are several ways to improve these two performance indicators for battery cells, such as using innovative, high-capacity electrode materials or novel and improved processes within battery production. One approach is prelithiation, a method to compensate for the initial capacity losses occurring either during the cell formation or during battery operation through the addition of lithium during cell production. In the case of direct contact prelithiation, thin lithium foils with a thickness below 10 µm are necessary to ensure the safe and accurate execution of the prelithiation process. However, the commercial availability of free-standing lithium foils is limited to minimum thicknesses of down to only 20 µm. For this reason, the present work examines in detail the calendering process of lithium. As part of a comprehensive parameter study, the influences of lithium foil geometries, line load, and roller temperature on the deformation behavior of lithium during calendering are investigated. A suitable process model is developed to understand the processing and thickness reduction of lithium and the calendering of lithium foils for direct contact prelithiation. For this purpose, a model based on empirical and semi-analytical approaches using fundamental physical interactions during calendering and material properties is developed and is parameterized based on experimental investigations on a laboratory scale. The combination of empirical and analytical modeling allows predictions about lithium processing and their validity ranges. The modeling intends to enable upscaling of the process and a transferability of direct contact prelithiation to the production of lithium-ion batteries on an industrial scale. Finally, the developed model contributes to understanding metallic lithium processing and its use for direct contact prelithiation in a roll-to-roll process and enables transferability of direct contact prelithiation to the production of lithium-ion batteries.

Deciphering van der Waals interaction between polypropylene and carbonated fly ash from experimental and molecular simulation

Pollution emitted from power plants, including a considerable amount of fly ash (FA) and carbon dioxide (CO2), annually increases and is challenging from an environmentally friendly and sustainable point of view. To date, laboratory-scaled approaches cannot efficiently replace the FA-landfilling and mitigate the stress from CO2 emission. Here, a practically operatable fundamental work by combining carbonated FA (C-FA)—immobilizing CO2 in FA—and polypropylene (PP) matrix is reported and reveals abnormal mechanical and thermal features clarified by calculating van der Waals (vdW) interaction from an atomic scale. This is the first study wherein the interaction between instantaneous dipole moment-induced PP and fillers is simulated and examined. The vdW interactions at the (hetero)interfaces are –59.66, –82.30, and −224.39 kJ mol−1 Å−2 for PP, calcium oxide (CaO; before carbonation), and calcium carbonate (CaCO3; after carbonation), respectively, which provides concrete theoretical support for interesting findings such as the independence of tensile strength on filler loadings and “well-grown” interface-induced higher conductivity characteristics of the composites. Therefore, this work can offer practical solutions to mitigate pollution, provide a new perspective on fundamental physical interactions, and guide the development of practical next-generation composite materials.

Realization of Supersymmetry and Its Spontaneous Breaking in Quantum Hall Edges

Supersymmetry (SUSY) relating bosons and fermions plays an important role in unifying different fundamental interactions in particle physics. Since no superpartners of elementary particles have been observed, SUSY, if present, must be broken at low-energy. This makes it important to understand how SUSY is realized and broken, and study their consequences. We show that an N=(1,0) SUSY, arguably the simplest type, can be realized at the edge of the Moore-Read quantum Hall state. Depending on the absence or presence of edge reconstruction, both SUSY-preserving and SUSY broken phases can be realized in the same system, allowing for their unified description. The significance of the gapless fermionic Goldstino mode in the SUSY broken phase is discussed.

One-Electron Transfer in Reactions of Stable Organic Radicals with Oxygen

Mechanisms of oxidation of stable organic radicals with molecular oxygen are based on a fundamental physical interaction, namely Coulomb interaction. Provided that there is certain structural correspondence between the oxygen molecule and radical center of the substrate, one-electron transfer occurs in the reaction system via the tunneling effect. The electronic structure of unstable triradical generated in the reaction system as a result of one-electron transfer undergoes reorganization into energetically more favorable monoradical structure.

Einstein’s Geometrical versus Feynman’s Quantum-Field Approaches to Gravity Physics: Testing by Modern Multimessenger Astronomy

Modern multimessenger astronomy delivers unique opportunity for performing crucial observations that allow for testing the physics of the gravitational interaction. These tests include detection of gravitational waves by advanced LIGO-Virgo antennas, Event Horizon Telescope observations of central relativistic compact objects (RCO) in active galactic nuclei (AGN), X-ray spectroscopic observations of Fe Kα line in AGN, Galactic X-ray sources measurement of masses and radiuses of neutron stars, quark stars, and other RCO. A very important task of observational cosmology is to perform large surveys of galactic distances independent on cosmological redshifts for testing the nature of the Hubble law and peculiar velocities. Forthcoming multimessenger astronomy, while using such facilities as advanced LIGO-Virgo, Event Horizon Telescope (EHT), ALMA, WALLABY, JWST, EUCLID, and THESEUS, can elucidate the relation between Einstein’s geometrical and Feynman’s quantum-field approaches to gravity physics and deliver a new possibilities for unification of gravitation with other fundamental quantum physical interactions.

Engineered Nanomaterials for Sustainable Oil Separation and Recovery

AbstractIn this review, we focus on engineered nanomaterials (NMs) offering economic and environmental sustainability in oil extraction. We introduce underlying issues in oil recovery and separation and discuss fundamental physical and chemical interactions in typical oil‐water‐solid systems that guide the design of NMs. In recovery, the NMs change rock wettability, permeability, or sweep fluid properties to attain optimal resource use and minimal environmental impact. Applied NMs include nanosurfactants, silica core‐shell structures, nano‐encapsulated acids, and nanofluids. While for separation, the NMs use mechanisms of adsorption, filtration, or dispersion to improve separation performance in industrial or aquatic oil spill settings. The NMs include iron oxide nanoparticles, graphene Joule‐heating sponges, superhydrophilic poly(vinylidene fluoride) membranes, and amphiphilic Janus silicon dioxide nanoparticles. Albeit the NMs exhibit impressive performance in sustainable oil extraction, a technological gap remains between the lab‐scale demonstrations and practical field deployment. We conclude with a perspective on bridging this gap.

Program of Fundamental-Interaction Research for the Ultracold-Neutron Source at the the WWR-M Reactor

The use of ultracold neutrons opens unique possibilities for studying fundamental interactions in particles physics. Searches for the neutron electric dipole moment are aimed at testing models of CP violation. A precise measurement of the neutron lifetime is of paramount importance for cosmology and astrophysics. Considerable advances in these realms can be made with the aid of a new ultracold-neutron (UCN) supersource presently under construction at Petersburg Nuclear Physics Institute. With this source, it would be possible to obtain an UCN density approximately 100 times as high as that at currently the best UCN source at the high-flux reactor of the Institute Laue–Langevin (ILL, Grenoble, France). To date, the design and basic elements of the source have been prepared, tests of a full-scale source model have been performed, and the research program has been developed. It is planned to improve accuracy in measuring the neutron electric dipole moment by one order of magnitude to a level of 10−27 to 10−28e cm. This is of crucial importance for particle physics. The accuracy in measuring the neutron lifetime can also be improved by one order of magnitude. Finally, experiments that would seek neutron–antineutron oscillations by employing ultracold neutrons will become possible upon reaching an UCN density of 103 to 104 cm−3. The current status of the source and the proposed research program are discussed.

Research of fundamental interactions with use of ultracold neutrons

Use of ultracold neutrons (UCN) gives unique opportunities of a research of fundamental interactions in physics of elementary particles. Search of the electric dipole moment of a neutron (EDM) aims to test models of CP violation. Precise measurement of neutron lifetime is extremely important for cosmology and astrophysics. Considerable progress in these questions can be reached due to supersource of ultracold neutrons on the basis of superfluid helium which is under construction now in PNPI NRC KI. This source will allow us to increase density of ultracold neutrons approximately by 100 times in respect to the best UCN source at high flux reactor of Institute Laue-Langevin (Grenoble, France). Now the project and basic elements of the source are prepared, full-scale model of the source is tested, the scientific program is developed. Increase in accuracy of neutron EDM measurements by order of magnitude, down to level 10-27 -10-28 e cm is planned. It is highly important for physics of elementary particles. Accuracy of measurement of neutron lifetime can be increased by order of magnitude also. At last, at achievement of UCN density ∼ 103 – 104 cm-3, the experiment search for a neutron-antineutron oscillations using UCN will be possible. The present status of the project and its scientific program will be discussed.

Precision Muonium Spectroscopy

The muonium atom is the purely leptonic bound state of a positive muon and an electron. It has a lifetime of 2.2 µs. The absence of any known internal structure provides for precision experiments to test fundamental physics theories and to determine accurate values of fundamental constants. In particular ground state hyperfine structure transitions can be measured by microwave spectroscopy to deliver the muon magnetic moment. The frequency of the 1s–2s transition in the hydrogen-like atom can be determined with laser spectroscopy to obtain the muon mass. With such measurements fundamental physical interactions, in particular quantum electrodynamics, can also be tested at highest precision. The results are important input parameters for experiments on the muon magnetic anomaly. The simplicity of the atom enables further precise experiments, such as a search for muonium–antimuonium conversion for testing charged lepton number conservation and searches for possible antigravity of muons and dark matter.

Deterministic nonclassicality from thermal states

Coupling an oscillator to a single two-level system is one of the most fundamental interactions in quantum physics. We report on a dynamical effect during which a thermal state of an oscillator is unconditionally transformed to a highly nonclassical state with negative Wigner function values by mere absorbtion by a single uncontrolled two-level system. This complements the traditional test of Rabi oscillations and it serves as a simply measurable witness that the process in question is highly nonclassical. The process is experimentally feasible with possible experimental implementation in a number of experimental platforms with intrinsic Jaynes-Cummings interaction and it has the potential of enabling deterministic generation of nonclassical quantum states.

Neutron Reflectivity as a Tool for Physics-Based Studies of Model Bacterial Membranes.

The principles of neutron reflectivity and its application as a tool to provide structural information at the (sub-) molecular unit length scale from models for bacterial membranes are described. The model membranes can take the form of a monolayer for a single leaflet spread at the air/water interface, or bilayers of increasing complexity at the solid/liquid interface. Solid-supported bilayers constrain the bilayer to 2D but can be used to characterize interactions with antimicrobial peptides and benchmark high throughput lab-based techniques. Floating bilayers allow for membrane fluctuations, making the phase behaviour more representative of native membranes. Bilayers of varying levels of compositional accuracy can now be constructed, facilitating studies with aims that range from characterizing the fundamental physical interactions, through to the characterization of accurate mimetics for the inner and outer membranes of Gram-negative bacteria. Studies of the interactions of antimicrobial peptides with monolayer and bilayer models for the inner and outer membranes have revealed information about the molecular control of the outer membrane permeability, and the mode of interaction of antimicrobials with both inner and outer membranes.