Pub Date : 2024-08-29DOI: 10.3103/S1541308X24700250
A. E. Donets, V. I. Rogozhin, V. P. Bakhtin, A. B. Buleyko, A. G. Bykov, O. T. Loza, A. A. Ravaev
Probe measurements of plasma generated by the thermionic cathode of the axially symmetric plasma maser are performed. Emission spectra of this plasma maser are recorded in its operation mode of a noise amplifier in the frequency band from 3 to 16 GHz at the power level of ~50 MW. It is shown that violation of azimuthal plasma concentration homogeneity leads to broadening of the emission spectrum by 30 to 100% of the central frequency. A possibility is found for pulse-to-pulse electron control of the width of the plasma maser emission spectrum in addition to the electron control of the frequency.
{"title":"Dependence of Plasma Maser Emission Spectra on Azimuthal Plasma Concentration Inhomogeneity","authors":"A. E. Donets, V. I. Rogozhin, V. P. Bakhtin, A. B. Buleyko, A. G. Bykov, O. T. Loza, A. A. Ravaev","doi":"10.3103/S1541308X24700250","DOIUrl":"10.3103/S1541308X24700250","url":null,"abstract":"<p>Probe measurements of plasma generated by the thermionic cathode of the axially symmetric plasma maser are performed. Emission spectra of this plasma maser are recorded in its operation mode of a noise amplifier in the frequency band from 3 to 16 GHz at the power level of ~50 MW. It is shown that violation of azimuthal plasma concentration homogeneity leads to broadening of the emission spectrum by 30 to 100% of the central frequency. A possibility is found for pulse-to-pulse electron control of the width of the plasma maser emission spectrum in addition to the electron control of the frequency.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 4","pages":"268 - 272"},"PeriodicalIF":1.1,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142225173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-29DOI: 10.3103/S1541308X24700262
A. V. Gorbatova, A. M. Buryakov, P. Yu. Avdeev, E. D. Lebedeva, I. Yu. Pashen’kin, E. A. Karashtin, M. V. Sapozhnikov, E. D. Mishina
Properties of spintronic terahertz generators based on the IrMn/Co/WSe2 and Co/WSe2 structures grown on sapphire substrates are investigated. It is demonstrated that the optical energy of the pump pulse plays a critical role in coercivity control and in generation of terahertz radiation by a structure with an antiferromagnetic IrMn layer. Analysis of terahertz loops of magnetic hysteresis obtained for pump energies ranging from 0.35 to 3.85 mJ/cm2 has shown that laser-induced heating of IrMn up to temperatures above the blocking temperature is accompanied by an increase in spin injection from the Co layer into IrMn layer and a consequent increase in THz emission efficiency. The results show importance of further investigation of thermal laser-induced processes in antiferromagnetic-based spintronic emitters in the vicinity of critical temperatures, which is of great significance of further development of terahertz spintronic and photonic devices based on antiferromagnetic materials.
{"title":"Effect of Laser-Induced Heating of the Antiferromagnetic IrMn Layer on Generation of Terahertz Pulses in Co/WSe2-Based Spintronic Emitters","authors":"A. V. Gorbatova, A. M. Buryakov, P. Yu. Avdeev, E. D. Lebedeva, I. Yu. Pashen’kin, E. A. Karashtin, M. V. Sapozhnikov, E. D. Mishina","doi":"10.3103/S1541308X24700262","DOIUrl":"10.3103/S1541308X24700262","url":null,"abstract":"<p>Properties of spintronic terahertz generators based on the IrMn/Co/WSe<sub>2</sub> and Co/WSe<sub>2</sub> structures grown on sapphire substrates are investigated. It is demonstrated that the optical energy of the pump pulse plays a critical role in coercivity control and in generation of terahertz radiation by a structure with an antiferromagnetic IrMn layer. Analysis of terahertz loops of magnetic hysteresis obtained for pump energies ranging from 0.35 to 3.85 mJ/cm<sup>2</sup> has shown that laser-induced heating of IrMn up to temperatures above the blocking temperature is accompanied by an increase in spin injection from the Co layer into IrMn layer and a consequent increase in THz emission efficiency. The results show importance of further investigation of thermal laser-induced processes in antiferromagnetic-based spintronic emitters in the vicinity of critical temperatures, which is of great significance of further development of terahertz spintronic and photonic devices based on antiferromagnetic materials.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 4","pages":"273 - 279"},"PeriodicalIF":1.1,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142195654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X24700201
P. S. Ryzhikov, V. A. Makarov
Contributions of the terms related to the local and nonlocal nonlinear optical responses of a medium are determined in the expressions for the energy density, energy flux density, momentum density, and momentum flux density of the electromagnetic field at the self-focusing of elliptically polarized light in a nonabsorbing isotropic gyrotropic medium. It is shown that the contributions of the nonlinear optical response of the medium to the above quantities are maximal at the spatial points where during self-focusing of narrow elliptically polarized beams, radiation becomes linearly polarized, and they may be as large as one tenth of the contributions to the components of the Minkowski energy–momentum tensor of the electromagnetic field that are related to the linear local optical response of the medium to the external light field. Nonlocality of the optical response increases the components of the Minkowski energy–momentum tensor of the electromagnetic field in some regions of the space and decreases them in the rest of them due to the sign reversal of the degree of the self-focusing beam ellipticity.
{"title":"Effect of the Contribution of the Local and Nonlocal Optical Response of an Isotropic Gyrotropic Medium on the Components of the Minkowski Energy–Momentum Tensor of the Electromagnetic Field of the Self-Focusing Beam","authors":"P. S. Ryzhikov, V. A. Makarov","doi":"10.3103/S1541308X24700201","DOIUrl":"10.3103/S1541308X24700201","url":null,"abstract":"<p>Contributions of the terms related to the local and nonlocal nonlinear optical responses of a medium are determined in the expressions for the energy density, energy flux density, momentum density, and momentum flux density of the electromagnetic field at the self-focusing of elliptically polarized light in a nonabsorbing isotropic gyrotropic medium. It is shown that the contributions of the nonlinear optical response of the medium to the above quantities are maximal at the spatial points where during self-focusing of narrow elliptically polarized beams, radiation becomes linearly polarized, and they may be as large as one tenth of the contributions to the components of the Minkowski energy–momentum tensor of the electromagnetic field that are related to the linear local optical response of the medium to the external light field. Nonlocality of the optical response increases the components of the Minkowski energy–momentum tensor of the electromagnetic field in some regions of the space and decreases them in the rest of them due to the sign reversal of the degree of the self-focusing beam ellipticity.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"227 - 231"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X24700213
E. A. Molkova, V. I. Pustovoi, I. V. Baimler, A. V. Simakin, D. E. Burmistrov, I. V. Gorudko, S. V. Gudkov
The influence of the solution acidity on the interaction between bovine serum albumin (BSA) molecules and gold nanoparticles in solutions has been investigated by absorbance spectroscopy, fluorescence spectroscopy, and dynamic light scattering (DLS). The influence of pH on the processes of aggregation–disaggregation of gold nanoparticles with BSA and without it and on the denaturation of protein solution is demonstrated. It is also shown that BSA molecules can stabilize gold nanoparticles at acidic pH values of 2.0–4.0. The data obtained can be useful for physiologists studying the influence of nanoparticles on different biological media of the body.
{"title":"Optical Study of the Influence of the Medium Acidity on the Interaction between Gold Nanoparticles and Bovine Serum Albumin in Aqueous Solution","authors":"E. A. Molkova, V. I. Pustovoi, I. V. Baimler, A. V. Simakin, D. E. Burmistrov, I. V. Gorudko, S. V. Gudkov","doi":"10.3103/S1541308X24700213","DOIUrl":"10.3103/S1541308X24700213","url":null,"abstract":"<p>The influence of the solution acidity on the interaction between bovine serum albumin (BSA) molecules and gold nanoparticles in solutions has been investigated by absorbance spectroscopy, fluorescence spectroscopy, and dynamic light scattering (DLS). The influence of pH on the processes of aggregation–disaggregation of gold nanoparticles with BSA and without it and on the denaturation of protein solution is demonstrated. It is also shown that BSA molecules can stabilize gold nanoparticles at acidic pH values of 2.0–4.0. The data obtained can be useful for physiologists studying the influence of nanoparticles on different biological media of the body.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"232 - 240"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X24700183
E. A. Zheligovskaya, G. A. Lyakhov
Structural mechanisms are developed for transitions between ices with either high or low density. Fractions of hydrogen bonds retained in the course of the transitions are calculated. Relative degrees of space filling by molecules of the considered ices are estimated. An assumption is formulated and partially substantiated that boundary exists between ice phases in the low-temperature region of the PvT phase diagram of ices. A new method for construction of PvTb diagrams of water is justified using the results of the structural analysis. The hydrogen bond concentration b serves as the second order parameter of phase transitions.
摘要 为高密度或低密度冰之间的转变建立了结构机制。计算了过渡过程中保留的氢键比例。估算了所考虑的冰分子填充空间的相对程度。在冰的 PvT 相图的低温区域,冰相之间存在边界,这一假设已经提出并得到部分证实。利用结构分析结果证明了构建水 PvTb 相图的新方法。氢键浓度 b 是相变的二阶参数。
{"title":"Structural Mechanisms of Transitions between Ices with Different Densities—Features of Water Phase Diagrams","authors":"E. A. Zheligovskaya, G. A. Lyakhov","doi":"10.3103/S1541308X24700183","DOIUrl":"10.3103/S1541308X24700183","url":null,"abstract":"<p>Structural mechanisms are developed for transitions between ices with either high or low density. Fractions of hydrogen bonds retained in the course of the transitions are calculated. Relative degrees of space filling by molecules of the considered ices are estimated. An assumption is formulated and partially substantiated that boundary exists between ice phases in the low-temperature region of the <i>PvT</i> phase diagram of ices. A new method for construction of <i>PvTb</i> diagrams of water is justified using the results of the structural analysis. The hydrogen bond concentration <i>b</i> serves as the second order parameter of phase transitions.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"209 - 219"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X24700158
M. V. Kirov
A specific feature of regular water nanostructures, as well as extended ice, is residual entropy. The number of configurations with different arrangement of hydrogen atoms (protons) is immense. Of prime interest are the most stable proton configurations. The properties of the most unfavorable configurations of water clusters and other ice-like systems are generally beyond the attention of researchers. In this paper we present the results of studying the most weakly bound proton configurations of water nanostructures. The highly unusual spontaneous structural transformations of some weakly bound configurations are enumerated. Rather unexpectedly, one of these transformations demonstrated a pronounced ability of cubic water clusters to self-organization. The results of studying the processes of self-organization of water nanostructures from these clusters are presented. Similar behavior of the simplest system of cubic water clusters and very complex biopolymers is indicated; this similarity covers the high-level self-organization, specific type of molecular asymmetry, self-assembly of one-dimensional aperiodic crystals, and the letter code.
{"title":"Modeling of Self-Assembly of Water Nanostructures","authors":"M. V. Kirov","doi":"10.3103/S1541308X24700158","DOIUrl":"10.3103/S1541308X24700158","url":null,"abstract":"<p>A specific feature of regular water nanostructures, as well as extended ice, is residual entropy. The number of configurations with different arrangement of hydrogen atoms (protons) is immense. Of prime interest are the most stable proton configurations. The properties of the most unfavorable configurations of water clusters and other ice-like systems are generally beyond the attention of researchers. In this paper we present the results of studying the most weakly bound proton configurations of water nanostructures. The highly unusual spontaneous structural transformations of some weakly bound configurations are enumerated. Rather unexpectedly, one of these transformations demonstrated a pronounced ability of cubic water clusters to self-organization. The results of studying the processes of self-organization of water nanostructures from these clusters are presented. Similar behavior of the simplest system of cubic water clusters and very complex biopolymers is indicated; this similarity covers the high-level self-organization, specific type of molecular asymmetry, self-assembly of one-dimensional aperiodic crystals, and the letter code.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"190 - 195"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X24700134
N. V. Penkov, N. A. Penkova, V. A. Zhmurin, A. G. Pogorelov
Submicron heterogeneities (SMHs) spontaneously arising in aqueous solutions of adenosine triphosphate (ATP) are studied. Their size of about 100 nm is close to the size of SMHs earlier detected in other solutions. The SMHs have a ζ-potential of about –10 mV. It is one of their stability factors. It is shown that the tendency for ATP to form SMHs depends on the ionic composition. After removal of SMHs from the ATP solution by filtering they do not form for more than two hours in the presence of Ca2+, while when Ca2+ is absent or replaced with Mg2+, the SMHs form in less than 30 min. In some cases, fast formation of SMHs hampers their adequate investigation. Analysis of dielectric spectra of ATP solutions in the presence of Ca2+ before and after filering has shown that hydration of Ca·ATP complexes inside SMHs is manifested by lower binding of water molecules and smaller number of free water molecules as compared to hydration of Ca·ATP complexes not included in SMHs.
{"title":"Natural Submicron Heterogeneities in Aqueous Solutions of ATP","authors":"N. V. Penkov, N. A. Penkova, V. A. Zhmurin, A. G. Pogorelov","doi":"10.3103/S1541308X24700134","DOIUrl":"10.3103/S1541308X24700134","url":null,"abstract":"<p>Submicron heterogeneities (SMHs) spontaneously arising in aqueous solutions of adenosine triphosphate (ATP) are studied. Their size of about 100 nm is close to the size of SMHs earlier detected in other solutions. The SMHs have a ζ-potential of about –10 mV. It is one of their stability factors. It is shown that the tendency for ATP to form SMHs depends on the ionic composition. After removal of SMHs from the ATP solution by filtering they do not form for more than two hours in the presence of Ca<sup>2+</sup>, while when Ca<sup>2+</sup> is absent or replaced with Mg<sup>2+</sup>, the SMHs form in less than 30 min. In some cases, fast formation of SMHs hampers their adequate investigation. Analysis of dielectric spectra of ATP solutions in the presence of Ca<sup>2+</sup> before and after filering has shown that hydration of Ca·ATP complexes inside SMHs is manifested by lower binding of water molecules and smaller number of free water molecules as compared to hydration of Ca·ATP complexes not included in SMHs.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"178 - 186"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X24700146
I. V. Baimler, S. V. Gudkov, T. A. Matveeva, A. V. Simakin, I. A. Shcherbakov
The concentration of hydrogen peroxide and hydroxyl radicals in dependence of the intensity (strength) of water drop impact on a solid surface has been measured. The intensity was varied by changing the fall height from 1 to 4 m and the tilt angle of the surface onto which drops fell. It is shown that the content of hydrogen peroxide and hydroxyl radicals in solution increases after the drop impact on the solid surface. Apparently, the main mechanism of the observed effects is the generation of singlet oxygen and its further reduction.
{"title":"Generation of Reactive Oxygen Species during Water Drops Fall on a Solid Surface","authors":"I. V. Baimler, S. V. Gudkov, T. A. Matveeva, A. V. Simakin, I. A. Shcherbakov","doi":"10.3103/S1541308X24700146","DOIUrl":"10.3103/S1541308X24700146","url":null,"abstract":"<p>The concentration of hydrogen peroxide and hydroxyl radicals in dependence of the intensity (strength) of water drop impact on a solid surface has been measured. The intensity was varied by changing the fall height from 1 to 4 m and the tilt angle of the surface onto which drops fell. It is shown that the content of hydrogen peroxide and hydroxyl radicals in solution increases after the drop impact on the solid surface. Apparently, the main mechanism of the observed effects is the generation of singlet oxygen and its further reduction.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"187 - 189"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X2470016X
D. C. Kutov, A. V. Sulimov, V. B. Sulimov
Two solvent models, COSMO (old parametrization) and COSMO2 (new parametrization) are compared for a set of protein–ligand complexes in quantum quasi-docking, which is two-stage docking: positioning of a ligand in a target protein and calculation of binding enthalpy of the protein–ligand system using the PM7 quantum-chemical semiempirical method. In quantum quasi-docking, a wide spectrum of unique low-energy minima of the protein–ligand system is first found while employing the classical force field. Then energies of all these minima are recalculated within one of the continual models using the modern PM7 method with allowance for the solvent, and the global energy minimum is determined among the recalculated energies. The solution of the quantum quasi-docking problem is the position of the ligand in the protein corresponding to the global minimum of the protein–ligand system energy calculated by the quantum-chemical method with allowance for the solvent. Effectiveness of quantum quasi-docking is defined by the value (below 2 Å) of the root-mean-square deviation of ligand atoms from one another in two positions, namely, the position of the ligand in the protein corresponding to the calculated global energy minimum and the experimentally found crystallized position of the ligand with the protein. Comparison is performed for ten protein–ligand test complexes with well-defined structures taken from the Protein Data Bank, for which the ligand–protein binding enthalpy is measured and the positioning of the ligand in the protein is successful in quasi-docking within both solvent models used. In both methods, PM7 + COSMO and PM7 + COSMO2, a high correlation coefficient of the experimental and calculated ligand–protein binding enthalpy is obtained for both calculation techniques. Allowance for moveability of protein atoms in calculations of binding enthalpy leads to an increase in its negative values and to a slight decrease in the correlation coefficient of the experimental and calculated values. The role of hydrogen bonds between protein and ligand atoms is revealed: their contribution to binding enthalpy ranges from 14 to 24% for different complexes. The results indicate the way of implementing quantum docking so that the global minimum of the protein–ligand system energy calculated by the quantum-chemical technique is immediately obtained using the global optimization procedure.
{"title":"Comparison of COSMO Water Models in Quantum Quasi-Docking","authors":"D. C. Kutov, A. V. Sulimov, V. B. Sulimov","doi":"10.3103/S1541308X2470016X","DOIUrl":"10.3103/S1541308X2470016X","url":null,"abstract":"<p>Two solvent models, COSMO (old parametrization) and COSMO2 (new parametrization) are compared for a set of protein–ligand complexes in quantum quasi-docking, which is two-stage docking: positioning of a ligand in a target protein and calculation of binding enthalpy of the protein–ligand system using the PM7 quantum-chemical semiempirical method. In quantum quasi-docking, a wide spectrum of unique low-energy minima of the protein–ligand system is first found while employing the classical force field. Then energies of all these minima are recalculated within one of the continual models using the modern PM7 method with allowance for the solvent, and the global energy minimum is determined among the recalculated energies. The solution of the quantum quasi-docking problem is the position of the ligand in the protein corresponding to the global minimum of the protein–ligand system energy calculated by the quantum-chemical method with allowance for the solvent. Effectiveness of quantum quasi-docking is defined by the value (below 2 Å) of the root-mean-square deviation of ligand atoms from one another in two positions, namely, the position of the ligand in the protein corresponding to the calculated global energy minimum and the experimentally found crystallized position of the ligand with the protein. Comparison is performed for ten protein–ligand test complexes with well-defined structures taken from the Protein Data Bank, for which the ligand–protein binding enthalpy is measured and the positioning of the ligand in the protein is successful in quasi-docking within both solvent models used. In both methods, PM7 + COSMO and PM7 + COSMO2, a high correlation coefficient of the experimental and calculated ligand–protein binding enthalpy is obtained for both calculation techniques. Allowance for moveability of protein atoms in calculations of binding enthalpy leads to an increase in its negative values and to a slight decrease in the correlation coefficient of the experimental and calculated values. The role of hydrogen bonds between protein and ligand atoms is revealed: their contribution to binding enthalpy ranges from 14 to 24% for different complexes. The results indicate the way of implementing quantum docking so that the global minimum of the protein–ligand system energy calculated by the quantum-chemical technique is immediately obtained using the global optimization procedure.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"196 - 202"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-08DOI: 10.3103/S1541308X24700171
V. I. Kuzmin, A. A. Paramonov, D. L. Tytik, O. V. Souvorova
The possibility is considered of using asymmetric distributions to analyze emission/absorption spectra, which enables revealing the structure of polymodal spectra. A necessary condition for existence of the spectrum is a nonnegative relative increment of tis amplitude (emission/absorption intensity). The use of asymmetric distributions in spectrum shape simulation involves a certain type of differential equation, where the left-hand side is a relative amplitude increment and the right-hand side is the decreasing nonlinear function. As a result, a model is obtained, in which the signal amplitude increment is defined by classical results of statistical physics (L. Boltzmann, M Planck) and information theory (C. Shannon) that correspond to the limited growth model (Gompertz model). On the basis of the anamorphism of this model, relaxation parameters of the spectrum are determined, which are treated as objective characteristics of emission/absorption spectra. The result is illustrated by the analysis of the luminescence spectrum of deionized water.
{"title":"Method for Analysis of Asymmetric Spectra Based on the Information Entropy Model","authors":"V. I. Kuzmin, A. A. Paramonov, D. L. Tytik, O. V. Souvorova","doi":"10.3103/S1541308X24700171","DOIUrl":"10.3103/S1541308X24700171","url":null,"abstract":"<p>The possibility is considered of using asymmetric distributions to analyze emission/absorption spectra, which enables revealing the structure of polymodal spectra. A necessary condition for existence of the spectrum is a nonnegative relative increment of tis amplitude (emission/absorption intensity). The use of asymmetric distributions in spectrum shape simulation involves a certain type of differential equation, where the left-hand side is a relative amplitude increment and the right-hand side is the decreasing nonlinear function. As a result, a model is obtained, in which the signal amplitude increment is defined by classical results of statistical physics (L. Boltzmann, M Planck) and information theory (C. Shannon) that correspond to the limited growth model (Gompertz model). On the basis of the anamorphism of this model, relaxation parameters of the spectrum are determined, which are treated as objective characteristics of emission/absorption spectra. The result is illustrated by the analysis of the luminescence spectrum of deionized water.</p>","PeriodicalId":732,"journal":{"name":"Physics of Wave Phenomena","volume":"32 3","pages":"203 - 208"},"PeriodicalIF":1.1,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}