In numerical simulation of biomacromolecule, the issues of thermalization, i.e., equal distribution of energy over the degrees of freedom, occupy an important place. In this paper we consider some mechanisms of lattice thermalization: Chirikov resonances, wave turbulence and some others. We consider thermalization in a microcanonical ensemble when the system is isolated from external fields and the total energy is conserved. Although microcanonical ensembles are rarely used in practical calculations, however, the basic ideas about the thermalization mechanisms are obtained for these systems. The main attention is paid to the consideration of the lattices thermalization with Fermi-Pasta-Ulam-Tsingou potentials, since the main efforts to understand the basis of thermalization have been made precisely for lattices of this type. The role of solitons and breathers in thermalization is discussed.
{"title":"On The Thermalization of One-Dimensional Lattices. I. Microcanonical Ensemble","authors":"G.A. Vinogradov, V.D. Lakhno","doi":"10.17537/2024.19.248","DOIUrl":"https://doi.org/10.17537/2024.19.248","url":null,"abstract":"\u0000In numerical simulation of biomacromolecule, the issues of thermalization, i.e., equal distribution of energy over the degrees of freedom, occupy an important place. In this paper we consider some mechanisms of lattice thermalization: Chirikov resonances, wave turbulence and some others. We consider thermalization in a microcanonical ensemble when the system is isolated from external fields and the total energy is conserved. Although microcanonical ensembles are rarely used in practical calculations, however, the basic ideas about the thermalization mechanisms are obtained for these systems. The main attention is paid to the consideration of the lattices thermalization with Fermi-Pasta-Ulam-Tsingou potentials, since the main efforts to understand the basis of thermalization have been made precisely for lattices of this type. The role of solitons and breathers in thermalization is discussed.\u0000","PeriodicalId":509888,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"4 22","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141668294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nonlinear conformational distortions, such as, for example, locally unwound regions of the DNA double helix, named open states, are considered in this work as solitons moving in the potential field of this molecule. It is believed that open states play an important role in the processes of transcription, replication, denaturation, as well as in the transmission of structural changes and information along the DNA molecule. This work examines the problem of the movement of kink-like solitons (kinks) in the potential field of the pPF1 plasmid, the sequence of which includes the genes of the fluorescent proteins Egfp and mCherry, separated by a small intermediate region. The results of calculations of energy profiles of the main and complementary sequences of the plasmid, as well as 2D and 3D trajectories of kinks with a non-zero initial velocity are presented. It has been shown that two types of kinks can be activated in the pPF1 plasmid, which can be considered as two types of quasiparticles that have their own energy, mass, velocity and move in the potential field of the plasmid. It was found that the lowest energy required to form these kinks is observed in the intermediate region located between the fluorescent protein genes. It was shown that the nature of the motion of kinks does not depend on the value of their initial velocity. It was shown that there are threshold values of the torsion field, upon reaching which the behavior of kinks changes sharply: from damped oscillations within the intermediate region to forward motion and penetration into neighboring regions. These values have been calculated. It turned out that for the first kink moving in the main sequence potential field, the threshold value is 4.95×10–22 J, and for the second kink – 4.20 × 10–22 J.
非线性构象畸变，例如 DNA 双螺旋的局部解旋区域，被命名为开放态，在这项研究中被视为在该分子势场中运动的孤子。人们认为，开放态在 DNA 分子的转录、复制、变性以及结构变化和信息传递过程中发挥着重要作用。这项研究探讨了在 pPF1 质粒的势场中类似 "扭结 "的孤子（"kinks"）的运动问题，该质粒的序列包括荧光蛋白 Egfp 和 mCherry 的基因，中间有一小段间隔。本文介绍了质粒主序列和互补序列的能量曲线计算结果，以及初始速度不为零的扭结的二维和三维轨迹。研究表明，在 pPF1 质粒中可以激活两种类型的扭结，它们可以被视为两种类型的准粒子，具有各自的能量、质量和速度，并在质粒的势场中运动。研究发现，在位于荧光蛋白基因之间的中间区域，形成这些扭结所需的能量最低。研究表明，扭结运动的性质并不取决于其初始速度值。研究表明，扭结场存在阈值，达到阈值后，扭结的行为会发生急剧变化：从中间区域内的阻尼振荡变为向前运动并穿透邻近区域。这些数值已经计算出来。结果表明，在主序势场中运动的第一个扭结的阈值为 4.95×10-22 J，第二个扭结的阈值为 4.20×10-22 J。
{"title":"Trajectories of Solitons Movement in the Potential Field of pPF1 Plasmid with Non-Zero Initial Velocity","authors":"L. Yakushevich, L. Krasnobaeva","doi":"10.17537/2024.19.232","DOIUrl":"https://doi.org/10.17537/2024.19.232","url":null,"abstract":"\u0000Nonlinear conformational distortions, such as, for example, locally unwound regions of the DNA double helix, named open states, are considered in this work as solitons moving in the potential field of this molecule. It is believed that open states play an important role in the processes of transcription, replication, denaturation, as well as in the transmission of structural changes and information along the DNA molecule. This work examines the problem of the movement of kink-like solitons (kinks) in the potential field of the pPF1 plasmid, the sequence of which includes the genes of the fluorescent proteins Egfp and mCherry, separated by a small intermediate region. The results of calculations of energy profiles of the main and complementary sequences of the plasmid, as well as 2D and 3D trajectories of kinks with a non-zero initial velocity are presented. It has been shown that two types of kinks can be activated in the pPF1 plasmid, which can be considered as two types of quasiparticles that have their own energy, mass, velocity and move in the potential field of the plasmid. It was found that the lowest energy required to form these kinks is observed in the intermediate region located between the fluorescent protein genes. It was shown that the nature of the motion of kinks does not depend on the value of their initial velocity. It was shown that there are threshold values of the torsion field, upon reaching which the behavior of kinks changes sharply: from damped oscillations within the intermediate region to forward motion and penetration into neighboring regions. These values have been calculated. It turned out that for the first kink moving in the main sequence potential field, the threshold value is 4.95×10–22 J, and for the second kink – 4.20 × 10–22 J.\u0000","PeriodicalId":509888,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"317 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141686679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vitiligo involves the gradual disappearance of melanocytes, causing skin depigmentation. Long noncoding RNAs (lncRNAs), a type of noncoding RNA, are important for regulating inflammation and immunity. Despite this significance, there needs to be more published research on how lncRNAs are expressed in vitiligo cases and their potential roles in the biology of this skin condition. This study aims to elucidate the molecular landscape of vitiligo by analyzing gene expression profiles of vitiligo skin and normal skin. Two datasets, RNA-seq and microarray, were thoroughly investigated to identify differentially expressed (DE) genes and lncRNAs associated with vitiligo development. Functional enrichment analysis revealed biological processes and pathways influenced by dysregulated genes, highlighting intricate processes such as melanin biosynthesis and melanogenesis, shedding light on the complex regulatory networks involved in pigmentation and immune responses. Protein-protein interaction analysis highlighted significantly downregulated hub genes, including TYRP1, MLANA, MC1R, SLC45A2, PAX3, TYR, DCT, OCA2, PMEL, and SOX10, revealing significant functional relationships among identified hub genes within the network. RNA-seq data analysis uncovered DE-lncRNAs, emphasizing the regulatory role of lncRNAs in vitiligo. Moreover, the correlation analysis between the expression of lncRNAs and key genes associated with melanogenesis (OCA2, TYRP1, and PMEL) unveiled novel upregulated lncRNAs such as CRTC3-AS1, LCMT1-AS1, LINC02178 contributing to vitiligo development. Additionally, lncRNA-gene networks constructed based on key melanocyte-related genes provided insights into the molecular relationships relevant to vitiligo. Overall, this study offers a comprehensive understanding of vitiligo pathogenesis, identifying potential therapeutic targets and laying the foundation for future research in this critical area.
{"title":"A Bioinformatics Analysis for Unveiling Novel Long Non-Coding RNAs and their Regulatory Impact on Key Genes Associated with Vitiligo","authors":"Safa Sadeq Fayez, Ahmed AbdulJabbar Suleiman","doi":"10.17537/2024.19.155","DOIUrl":"https://doi.org/10.17537/2024.19.155","url":null,"abstract":"\u0000 Vitiligo involves the gradual disappearance of melanocytes, causing skin depigmentation. Long noncoding RNAs (lncRNAs), a type of noncoding RNA, are important for regulating inflammation and immunity. Despite this significance, there needs to be more published research on how lncRNAs are expressed in vitiligo cases and their potential roles in the biology of this skin condition. This study aims to elucidate the molecular landscape of vitiligo by analyzing gene expression profiles of vitiligo skin and normal skin. Two datasets, RNA-seq and microarray, were thoroughly investigated to identify differentially expressed (DE) genes and lncRNAs associated with vitiligo development. Functional enrichment analysis revealed biological processes and pathways influenced by dysregulated genes, highlighting intricate processes such as melanin biosynthesis and melanogenesis, shedding light on the complex regulatory networks involved in pigmentation and immune responses. Protein-protein interaction analysis highlighted significantly downregulated hub genes, including TYRP1, MLANA, MC1R, SLC45A2, PAX3, TYR, DCT, OCA2, PMEL, and SOX10, revealing significant functional relationships among identified hub genes within the network. RNA-seq data analysis uncovered DE-lncRNAs, emphasizing the regulatory role of lncRNAs in vitiligo. Moreover, the correlation analysis between the expression of lncRNAs and key genes associated with melanogenesis (OCA2, TYRP1, and PMEL) unveiled novel upregulated lncRNAs such as CRTC3-AS1, LCMT1-AS1, LINC02178 contributing to vitiligo development. Additionally, lncRNA-gene networks constructed based on key melanocyte-related genes provided insights into the molecular relationships relevant to vitiligo. Overall, this study offers a comprehensive understanding of vitiligo pathogenesis, identifying potential therapeutic targets and laying the foundation for future research in this critical area.\u0000","PeriodicalId":509888,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141053937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The possibility of representation in a dynamic model of the three types of SARS-CoV-2 infection: asymptomatic, pre-symptomatic and symptomatic is studied. Furthermore, a compartmental model was proposed, with a branching of asymptomatic cases into pre-symptomatic and actually asymptomatic cases. Verification of the proposed model using data from the first wave of COVID-19 in St. Petersburg and the proportion of actually asymptomatic cases among all asymptomatic cases demonstrated adequate model behavior. The contribution of pre-symptomatic cases to the total number of symptomatic cases was studied. The need to account for the high proportion of asymptomatic carriers in strict quarantine was identified.
{"title":"Mathematical Modeling Of the Spread of COVID-19, Taking Into Account the Distribution of Asymptomatic Cases between Actually Asymptomatic and Pre-Symptomatic Cases","authors":"I. Kolesin, E. Zhitkova","doi":"10.17537/2024.19.52","DOIUrl":"https://doi.org/10.17537/2024.19.52","url":null,"abstract":"\u0000 The possibility of representation in a dynamic model of the three types of SARS-CoV-2 infection: asymptomatic, pre-symptomatic and symptomatic is studied. Furthermore, a compartmental model was proposed, with a branching of asymptomatic cases into pre-symptomatic and actually asymptomatic cases. Verification of the proposed model using data from the first wave of COVID-19 in St. Petersburg and the proportion of actually asymptomatic cases among all asymptomatic cases demonstrated adequate model behavior. The contribution of pre-symptomatic cases to the total number of symptomatic cases was studied. The need to account for the high proportion of asymptomatic carriers in strict quarantine was identified.\u0000","PeriodicalId":509888,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":" 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140222057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A universal methodological approach has been developed that allows solving the problem of differentiating closely related species using raw NGS sequencing data. The method is based on the use of single nucleotide polymorphisms (SNPs). This approach is universal; it can be used in the bioinformatic analysis of sequencing results, regardless of the biological species under study. The approach we developed is based on automating the process of searching for nucleotide sequences flanking the desired allele. The search is carried out on the researcher's personal computer, does not require expensive equipment, the Python v.3.10 programming language and the Jupyter Notebook software development environment are free and publicly available. The methodological approach for in silico genotyping is implemented in the form of the GENIS software. Within the framework of this work, the program was tested on files with the results of genome sequencing of animals of the genus Sus. Revealed polymorphisms for the differentiation of pigs of the Duroc breed.
{"title":"GENIS – methodological approach for in silico genotyping (validation on Sus scrofa sequencing)","authors":"V.N. Kipen, E. V. Snytkov","doi":"10.17537/2024.19.36","DOIUrl":"https://doi.org/10.17537/2024.19.36","url":null,"abstract":"\u0000 A universal methodological approach has been developed that allows solving the problem of differentiating closely related species using raw NGS sequencing data. The method is based on the use of single nucleotide polymorphisms (SNPs). This approach is universal; it can be used in the bioinformatic analysis of sequencing results, regardless of the biological species under study. The approach we developed is based on automating the process of searching for nucleotide sequences flanking the desired allele. The search is carried out on the researcher's personal computer, does not require expensive equipment, the Python v.3.10 programming language and the Jupyter Notebook software development environment are free and publicly available. The methodological approach for in silico genotyping is implemented in the form of the GENIS software. Within the framework of this work, the program was tested on files with the results of genome sequencing of animals of the genus Sus. Revealed polymorphisms for the differentiation of pigs of the Duroc breed.\u0000","PeriodicalId":509888,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"32 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140081387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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