Pub Date : 2023-08-18DOI: 10.1142/s2737416523420103
Furkan Ozen
{"title":"Synthesis, Characterization and Calculations of Linear and Nonlinear Optical Properties of Acrylonitrile Substituted Spirocyclotriphosphazene Derivatives","authors":"Furkan Ozen","doi":"10.1142/s2737416523420103","DOIUrl":"https://doi.org/10.1142/s2737416523420103","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46789517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-18DOI: 10.1142/s2737416523500497
Sen Zhang, Yuhang Zhao, Zewen Chang
{"title":"Insights into molecular mechanism of nicotine addiction based on network pharmacology and molecular docking strategy","authors":"Sen Zhang, Yuhang Zhao, Zewen Chang","doi":"10.1142/s2737416523500497","DOIUrl":"https://doi.org/10.1142/s2737416523500497","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46807582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-10DOI: 10.1142/s2737416523420073
F. Mebarek‐Oudina, G. Dharmaiah, K. Balamurugan, A. I. Ismail, Hemlata Saxena
{"title":"The role of Quadratic-linearly Radiating Heat Source with Carreau Nanofluid and Exponential Space Dependent Past a Cone and a Wedge: A Medical Engineering Application and Renewable Energy","authors":"F. Mebarek‐Oudina, G. Dharmaiah, K. Balamurugan, A. I. Ismail, Hemlata Saxena","doi":"10.1142/s2737416523420073","DOIUrl":"https://doi.org/10.1142/s2737416523420073","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44357920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-10DOI: 10.1142/s2737416523500473
S. Reddy, Gunisetty Ramasekhar, S. Suneetha, Shaik Jakeer
{"title":"Entropy generation analysis on MHD of Ag+Cu/Blood tangent hyperbolic hybrid nanofluid flow over a porous plate","authors":"S. Reddy, Gunisetty Ramasekhar, S. Suneetha, Shaik Jakeer","doi":"10.1142/s2737416523500473","DOIUrl":"https://doi.org/10.1142/s2737416523500473","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48841644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-10DOI: 10.1142/s2737416523420085
Ramsha Ali, Sidra Nadeem, R. Khera, A. AlObaid, I. Warad, Mahmoud A. A. Ibrahim, Muhammad Waqas
{"title":"An approach towards low energy loss by end-capped modification of A2-D-A1-D-A2 type molecules for tuning the photovoltaic properties of organic solar cells","authors":"Ramsha Ali, Sidra Nadeem, R. Khera, A. AlObaid, I. Warad, Mahmoud A. A. Ibrahim, Muhammad Waqas","doi":"10.1142/s2737416523420085","DOIUrl":"https://doi.org/10.1142/s2737416523420085","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43240440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-10DOI: 10.1142/s2737416523500485
Yasmin Rahmati, Khosrow Khalifeh, Emran Heshmati
{"title":"Dynamic behavior and ligand binding properties of the wild type Deoxycytidine kinase and its characterized gemcitabine-resistant variant: A bioinformatics and computational study","authors":"Yasmin Rahmati, Khosrow Khalifeh, Emran Heshmati","doi":"10.1142/s2737416523500485","DOIUrl":"https://doi.org/10.1142/s2737416523500485","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46989722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-04DOI: 10.1142/s2737416523420061
Vipin Kumar, Prabhakar Chetti
{"title":"Effect of π-bridge in D–π–A architecture and Adsorption of Phenothiazine Dyes on TiO2 Nanocrystalline for Dye-Sensitized Solar Cells: A DFT Approach","authors":"Vipin Kumar, Prabhakar Chetti","doi":"10.1142/s2737416523420061","DOIUrl":"https://doi.org/10.1142/s2737416523420061","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43017183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-01Epub Date: 2023-06-08DOI: 10.1142/s2737416523500278
Xiaoqi Wei, Jiahui Chen, Guo-Wei Wei
Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has limitations, including its inability to handle heterogeneous information, such as multiple types of geometric objects; being qualitative rather than quantitative, e.g., counting a 5-member ring the same as a 6-member ring, and a failure to describe non-topological changes, such as homotopic changes in protein-protein binding. Persistent topological Laplacians (PTLs), such as persistent Laplacian and persistent sheaf Laplacian, were proposed to overcome the limitations of persistent homology. In this work, we examine the modeling and analysis power of PTLs in the study of the protein structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor binding domain (RBD). First, we employ PTLs to study how the RBD mutation-induced structural changes of RBD-angiotensin-converting enzyme 2 (ACE2) binding complexes are captured in the changes of spectra of the PTLs among SARS-CoV-2 variants. Additionally, we use PTLs to analyze the binding of RBD and ACE2-induced structural changes of various SARS-CoV-2 variants. Finally, we explore the impacts of computationally generated RBD structures on a topological deep learning paradigm and predictions of deep mutational scanning datasets for the SARS-CoV-2 Omicron BA.2 variant. Our results indicate that PTLs have advantages over persistent homology in analyzing protein structural changes and provide a powerful new TDA tool for data science.
{"title":"Persistent topological Laplacian analysis of SARS-CoV-2 variants.","authors":"Xiaoqi Wei, Jiahui Chen, Guo-Wei Wei","doi":"10.1142/s2737416523500278","DOIUrl":"10.1142/s2737416523500278","url":null,"abstract":"<p><p>Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has limitations, including its inability to handle heterogeneous information, such as multiple types of geometric objects; being qualitative rather than quantitative, e.g., counting a 5-member ring the same as a 6-member ring, and a failure to describe non-topological changes, such as homotopic changes in protein-protein binding. Persistent topological Laplacians (PTLs), such as persistent Laplacian and persistent sheaf Laplacian, were proposed to overcome the limitations of persistent homology. In this work, we examine the modeling and analysis power of PTLs in the study of the protein structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor binding domain (RBD). First, we employ PTLs to study how the RBD mutation-induced structural changes of RBD-angiotensin-converting enzyme 2 (ACE2) binding complexes are captured in the changes of spectra of the PTLs among SARS-CoV-2 variants. Additionally, we use PTLs to analyze the binding of RBD and ACE2-induced structural changes of various SARS-CoV-2 variants. Finally, we explore the impacts of computationally generated RBD structures on a topological deep learning paradigm and predictions of deep mutational scanning datasets for the SARS-CoV-2 Omicron BA.2 variant. Our results indicate that PTLs have advantages over persistent homology in analyzing protein structural changes and provide a powerful new TDA tool for data science.</p>","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":"22 5","pages":"569-587"},"PeriodicalIF":2.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569362/pdf/nihms-1888545.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41202808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号