Low Temperature Physics最新文献_第7页

IR and Raman markers of the interactions between MoS2 and pyrimidine bases MoS2 与嘧啶碱相互作用的红外和拉曼标记

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-03-26 DOI: 10.1063/10.0024968

T. Piddubnyi, S. Stepanian, V. Karachevtsev, L. Adamowicz

{"title":"IR and Raman markers of the interactions between MoS2 and pyrimidine bases","authors":"T. Piddubnyi, S. Stepanian, V. Karachevtsev, L. Adamowicz","doi":"10.1063/10.0024968","DOIUrl":"https://doi.org/10.1063/10.0024968","url":null,"abstract":"Changes in vibrational spectra are among the most important manifestations of the interaction between transition metal dichalcogenides and nucleic acid bases (NAB). Infrared and Raman spectra were calculated using the DFT/M06-2X method for the most stable stacked and covalently bonded complexes of pyrimidine bases with MoS2. Obtained spectra were analyzed to determine the spectral markers of the interactions between the pyrimidine bases and MoS2. We found that interaction with MoS2 leads to significant changes in both frequencies and intensities of NAB vibrations. The correlation between the changes and interaction energies of the NAB molecules with MoS2 was demonstrated. In general, changes in the vibrational frequencies in complexes with covalent bonds are significantly greater than ones in stacked ones. For the bonded complexes, the most significant changes are observed for those fragments of the NAB molecules that are directly involved in the formation of the covalent bonds. Calculations predict the decrease of the IR intensity and Raman activities of the NAB molecules in the spectra of stacked complexes and their increase in the spectra of covalently bonded complexes.","PeriodicalId":18077,"journal":{"name":"Low Temperature Physics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140315640","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}

引用次数: 0

Which molecules can challenge density-functional tight-binding methods in evaluating the energies of conformers? investigation with machine-learning toolset 在评估构象能量时，哪些分子可以挑战密度函数紧密结合方法？利用机器学习工具集进行研究

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-03-26 DOI: 10.1063/10.0024962

Andrii Terets, Tymofii Nikolaienko

{"title":"Which molecules can challenge density-functional tight-binding methods in evaluating the energies of conformers? investigation with machine-learning toolset","authors":"Andrii Terets, Tymofii Nikolaienko","doi":"10.1063/10.0024962","DOIUrl":"https://doi.org/10.1063/10.0024962","url":null,"abstract":"Large organic molecules and biomolecules can adopt multiple conformations, with the occurrences determined by their relative energies. Identifying the energetically most favorable conformations is crucial, especially when interpreting spectroscopic experiments conducted under cryogenic conditions. When the effects of irregular surrounding medium, such as noble gas matrices, on the vibrational properties of molecules become important, semi-empirical (SE) quantum-chemical methods are often employed for computational simulations. Although SE methods are computationally more efficient than first-principle quantum-chemical methods, they can be inaccurate in determining the energies of conformers in some molecules while displaying good accuracy in others. In this study, we employ a combination of advanced machine learning techniques, such as graph neural networks, to identify molecules with the highest errors in the relative energies of conformers computed by the semi-empirical tight-binding method GFN1-xTB. The performance of three different machine learning models is assessed by comparing their predicted errors with the actual errors in conformer energies obtained via the GFN1-xTB method. We further applied the ensemble machine-learning model to a larger collection of molecules from the ChEMBL database and identified a set of molecules as being challenging for the GFN1-xTB method. These molecules hold potential for further improvement of the GFN1-xTB method, showcasing the capability of machine learning models in identifying molecules that can challenge its physical model.","PeriodicalId":18077,"journal":{"name":"Low Temperature Physics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140315543","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}

引用次数: 0

The interactions of antiviral drugs and a phosphonium fluorescent dye with proteins as revealed by a multiple ligand simultaneous docking 多配体同时对接揭示的抗病毒药物和鏻荧光染料与蛋白质的相互作用

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-03-26 DOI: 10.1063/10.0024961

O. A. Zhytniakivska, U. K. Tarabara, K. O. Vus, V. M. Trusova, G. P. Gorbenko

引用次数: 0

Clusteroluminogenic polymers: Applications in biology and medicine (Review article) 簇发光聚合物：生物学和医学中的应用（综述文章）

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-03-26 DOI: 10.1063/10.0024970

Tamara Sakhno, Dmytro Ivashchenko, Anatolii Semenov, Olena Ivashchenko, Yuriy Sakhno

引用次数: 0

Unusual bending patterns of spermidine3+ bound to DNA double helix 与 DNA 双螺旋结合的亚精胺 3+ 的异常弯曲模式

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-03-26 DOI: 10.1063/10.0024969

Sergiy Perepelytsya, Tudor Vasiliu, Aatto Laaksonen, Leon De Villiers Engelbrecht, Francesca Mocci

{"title":"Unusual bending patterns of spermidine3+ bound to DNA double helix","authors":"Sergiy Perepelytsya, Tudor Vasiliu, Aatto Laaksonen, Leon De Villiers Engelbrecht, Francesca Mocci","doi":"10.1063/10.0024969","DOIUrl":"https://doi.org/10.1063/10.0024969","url":null,"abstract":"Natural polyamines play a fundamental role in the cell cycle. Despite being recognized as the most abundant organic counterions of DNA in the cell nucleus, their interactions with DNA have not been fully characterized. In a recent work [S. Perepelytsya, T. Vasiliu, A. Laaksonen, L. Engelbrecht, G. Brancato, and F. Mocci, J. Molec. Liq.389, 122828 (2023)], we have shown how the interactions between spermidine3+ and the DNA double helix induce significant conformational variations in the polyamine molecule. Specifically, we found that DNA induces conformations that are not observed in solution. Following that study, we present here a detailed investigation of the most compact conformation of the polyamine, analyzing its connection to the interaction with the DNA duplex. The analysis reveals that anomalous bent conformations of the spermidine3+ molecule result from the interaction of all three amino groups of the polyamine with the DNA phosphate groups on the minor groove side of the double helix. The changes in dihedral angles of the bent spermidine3+ molecule can be explained in terms of conformational transformations of six- and seven-membered rings, analogous to cyclohexane and cycloheptane. The analysis of the position of spermidine3+ molecule along the DNA surface reveals a sequence specificity of this binding mode with a marked preference for the narrow minor groove of A-tracts. The formation of the anomalous bent conformations of spermidine3+ in the complex with the DNA double helix is expected to be of paramount importance in understanding the mechanisms underlying DNA’s biological function.","PeriodicalId":18077,"journal":{"name":"Low Temperature Physics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140315639","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}

引用次数: 0

The 8th International Conference “NANOBIOPHYSICS: Fundamental and Applied Aspects” (NBP–2023) Kyiv, Ukraine, October 3–6, 2023 第八届国际会议 "纳米生物物理：基础与应用方面"（NBP-2023），乌克兰基辅，2023 年 10 月 3-6 日

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-03-01 DOI: 10.1063/10.0024967

G. I. Dovbeshko, V. Karachevtsev

引用次数: 0

Dissociation of composite Abrikosov vortices in two-band superconductors in a strong rf field 强射频场下双带超导体中复合阿布里科索夫涡旋的解离

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-02-22 DOI: 10.1063/10.0024321

A. O. Pokusinskyi, A. L. Kasatkin

引用次数: 0

On the classification of degenerate equilibrium states of multisublattice SU(4) magnets with spin s = 3/2 关于自旋 s = 3/2 的多子晶格 SU(4) 磁体退化平衡态的分类

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-02-22 DOI: 10.1063/10.0024325

M. Yu. Kovalevsky

引用次数: 0

Magnetic properties of the frustrated Ising chain 受挫伊辛链的磁特性

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-02-22 DOI: 10.1063/10.0024328

D. V. Laptiev, O. O. Kryvchikov, Yu. V. Savin, V. V. Slavin

{"title":"Magnetic properties of the frustrated Ising chain","authors":"D. V. Laptiev, O. O. Kryvchikov, Yu. V. Savin, V. V. Slavin","doi":"10.1063/10.0024328","DOIUrl":"https://doi.org/10.1063/10.0024328","url":null,"abstract":"Using the Kramers–Wannier transfer matrix method, we studied several decorated Ising chains. The exact expressions for thermodynamic characteristics, including the ground state characteristics, were obtained. We considered several modeling chains with different signs and absolute values of exchange constants for the nearest- and the next-nearest neighbors. For these models, we calculated the magnetization curves. The critical values of magnetic fields and corresponding magnetization plateau parameters were obtained. Analytic expressions for the ground state entropy were obtained for the chains with different interaction constants. The dependencies of the number of states with minimum energy (the degeneration of the ground state) as the function of the number of particles were found. It was shown that these dependencies are expressed in terms of well-known numerical sequences, namely Lucas numbers and Pell numbers, which, in the limit of a large number of particles, are proportional to the powers of the golden and silver sections. Therefore, the ground state entropy (per particle) of the systems under consideration can be described in terms of these sections and, therefore, is nonzero.","PeriodicalId":18077,"journal":{"name":"Low Temperature Physics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139945927","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}

引用次数: 0

Structural studies of epoxy resin with impurities of carbon nanostructures 含有碳纳米结构杂质的环氧树脂的结构研究

IF 0.8 4区物理与天体物理

Low Temperature Physics Pub Date : 2024-02-22 DOI: 10.1063/10.0024329

D. E. Hurova, S. V. Cherednichenko, N. A. Aksenova, N. А. Vinnikov, А. V. Dolbin, N. N. Galtsov

引用次数: 0