AIMS Biophysics最新文献

{"title":"A review of molecular biology detection methods for human adenovirus","authors":"N. Datta","doi":"10.3934/biophy.2023008","DOIUrl":"https://doi.org/10.3934/biophy.2023008","url":null,"abstract":"In humans particularly in children, adenovirus is one of the most common viruses that cause respiratory illnesses. Knowing how to detect adenovirus proficiently and rapidly will help reinforce surveillance of adenovirus infections, detect epidemic situations in real-time, and understand the trend of virus epidemics, which will allow effective actions to be taken quickly. The rapid detection of antiviral antibodies or viral antigens in clinical samples can be achieved by molecular diagnostic techniques like PCR, Real-Time PCR, LAMP, mPCR-RLB, PCR-ELISA, Tem-PCR, Gene Chip, and so on. Some of the molecular diagnostic methods are relatively economical, exceedingly sensitive and explicit. There are several commercially accessible molecular diagnostic techniques that enable their use in clinical laboratories all over the world. In this review, the principles, characteristics, and applications of molecular biology surveillance methods commonly used in labs and clinics for the detection of human adenoviruses are examined and highlighted.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185313","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}

{"title":"Similarity of epidemic spreading and information network connectivity mechanisms demonstrated by analysis of two probabilistic models","authors":"Into Almiala, Vesa Kuikka","doi":"10.3934/biophy.2023011","DOIUrl":"https://doi.org/10.3934/biophy.2023011","url":null,"abstract":"The modelling of epidemic spreading is essential in understanding the mechanisms of outbreaks and pandemics. Many models for different kinds of spreading have been proposed throughout the history of modelling, each suited for a specific scenario and parameters. On the other hand, models of information networks provide important tools for the analysis of the performance and reliability of such networks. We have previously presented a model for simulating the spreading of infectious disease throughout a social network and another one for simulating the connectivity of data traffic in an information network. We argue that these models are similar in that they produce equivalent results with appropriate parameters when run on the same network. We explain this by reasoning that the manners in which the models carry out their calculations, although devised from different assumptions, turn out to be equivalent. We also show empirical results of applying the models to calculate the spread of contagion and information connectivity on two complex networks suitable for the models. Based on the results, we calculate centrality metrics reflecting the outcome of the application, highlighting its important properties. We note that the centrality values obtained by running the epidemic model and the connectivity model turn out to be mutually equivalent, as predicted by their similar fashions of calculation. As the models were independently developed for their own applications, the equivalence in their calculation can not be explained by the models purposefully built similarly. Thus, not only are the two apparently completely separate areas of interest analysable with a single model but there appear to be inherent similarities in the mechanisms of epidemic spreading and determining network connectivity.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185437","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}

{"title":"Analysis of a fractional pollution model in a system of three interconnecting lakes","authors":"Y. N. Anjam, Mehmet Yavuz, Mati ur Rahman, Amna Batool","doi":"10.3934/biophy.2023014","DOIUrl":"https://doi.org/10.3934/biophy.2023014","url":null,"abstract":"Water pollution is a critical global concern that demands ongoing scrutiny and revision of water resource policies at all levels to safeguard a healthy living environment. In this study, we focus on examining the dynamics of a fractional-order model involving three interconnected lakes, utilizing the Caputo differential operator. The aim is to investigate the issue of lake pollution by analyzing a system of linear equations that represent the interconnecting waterways. To numerically solve the model, we employ two methods: The Laplace transform with the Adomian decomposition method (LADM) and the Homotopy perturbation method (HPM). We compare the obtained numerical solutions from both methods and present the results. The study encompasses three variations of the model: the periodic input model, the exponentially decaying input model, and the linear input model. MATLAB is employed to conduct numerical simulations for the proposed scheme, considering various fractional orders. The numerical results are further supported by informative graphical illustrations. Through simulation, we validate the suitability of the proposed model for addressing the issue at hand. The outcomes of this research contribute to the understanding and management of water pollution, aiding policymakers and researchers in formulating effective strategies for maintaining water quality and protecting our environment.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185518","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}

{"title":"Mathematical modeling for solving fractional model cancer bosom malignant growth","authors":"Shaimaa A. M. Abdelmohsen, D. Sh. Mohamed, Haifa A. Alyousef, M. R. Gorji, Amr M. S. Mahdy","doi":"10.3934/biophy.2023018","DOIUrl":"https://doi.org/10.3934/biophy.2023018","url":null,"abstract":"<abstract> <p>In this essay, we have presented a fractional numerical model of breast cancer stages with cardiac outcomes. Five compartments were used to build the model, each of which represented a subpopulation of breast cancer patients. Variables A, B, C, D, and E each represent a certain subpopulation. They are levels 1 and 2 (A), level 3 (B), level 4 (C), disease-free (D) and cardiotoxic (E). We have demonstrated that the fractional model has a stable solution. We also discuss how to optimally control this model and numerically simulate the control problem. Using numerical simulations, we computed the results of the dissection. The model's compartment diagram has been completed. A predictor-corrector method has been used to manage the fractional derivatives and produce numerical solutions. The Caputo sense has been used to describe fractional derivatives. The results have been illustrated through numerical simulations. Furthermore, the numerical simulations show that the cancer breast malignant growth fractional order model is easier to model than the traditional integer-order model. To compute the results, we have used mathematical programming. We have made it clear that the numerical method that was applied in this publication to solve this model was not utilized by any other author before that, nor has this method been investigated in the past. Our investigation established this approach.</p> </abstract>","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135783571","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}

{"title":"Quantum mechanical aspects of cardiac arrhythmias: A mathematical model and pathophysiological implications","authors":"Mohammed I. A. Ismail, Abdallah Barjas Qaswal, Mo'ath Bani Ali, Anas Hamdan, Ahmad Alghrabli, Mohamad Harb, Dina Ibrahim, Mohammad Nayel Al-Jbour, Ibrahim Almobaiden, Khadija Alrowwad, Esra'a Jaibat, Mira Alrousan, Mohammad Banifawaz, Mohammed A. M. Aldrini, Aya Daikh, Nour Aldarawish, Ahmad Alabedallat, Ismail M. I. Ismail, Lou'i Al-Husinat","doi":"10.3934/biophy.2023024","DOIUrl":"https://doi.org/10.3934/biophy.2023024","url":null,"abstract":"<abstract> <p>Cardiac arrhythmias are serious myocardial electrical disturbances that affect the rate and rhythm of heartbeats. Despite the rapidly accumulating data about the pathophysiology and the treatment, new insights are required to improve the overall clinical outcome of patients with cardiac arrhythmias. Three major arrhythmogenic processes can contribute to the pathogenesis of cardiac arrhythmias; 1) enhanced automaticity, 2) afterdepolarization-triggered activity and 3) reentry circuits. The mathematical model of the quantum tunneling of ions is used to investigate these mechanisms from a quantum mechanical perspective. The mathematical model focuses on applying the principle of quantum tunneling to sodium and potassium ions. This implies that these ions have a non-zero probability of passing through the gate, which has an energy that is higher than the kinetic energy of ions. Our mathematical findings indicate that, under pathological conditions, which affect ion channels, the quantum tunneling of sodium and potassium ions is augmented. This augmentation creates a state of hyperexcitability that can explain the enhanced automaticity, after depolarizations that are associated with triggered activity and a reentry circuit. Our mathematical findings stipulate that the augmented and thermally assisted quantum tunneling of sodium and potassium ions can depolarize the membrane potential and trigger spontaneous action potentials, which may explain the automaticity and afterdepolarization. Furthermore, the quantum tunneling of potassium ions during an action potential can provide a new insight regarding the formation of a reentry circuit. Introducing these quantum mechanical aspects may improve our understanding of the pathophysiological mechanisms of cardiac arrhythmias and, thus, contribute to finding more effective anti-arrhythmic drugs.</p> </abstract>","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135800871","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}

{"title":"Characterizing pulsatile blood flow in a specific carotid bifurcation: insights into hemodynamics and rheology models","authors":"Boukedjane Mouloud, Bahi Lakhdar","doi":"10.3934/biophy.2023019","DOIUrl":"https://doi.org/10.3934/biophy.2023019","url":null,"abstract":"<abstract> <p>This study uses laminar and turbulent flow models to investigate the blood flow dynamics in a specific carotid bifurcation. Pulsatile boundary conditions and the rigid carotid artery wall are considered. Three viscosity models describe the non-Newtonian blood behavior. The Fluent solver and the finite volume method solve the equations. Results show a Poiseuille-like flow in the common carotid artery (CCA), unaffected by the flow regime, viscosity model, or boundary conditions. The branching zone exhibits a C-shaped stagnation zone with low velocity and wall shear stress due to the CCA widening and ICA/ECA curvature. Strong secondary flow is observed in the carotid sinus; the flow is directed towards the inner wall with higher velocity in the internal carotid artery. Discrepancies between viscosity models are pronounced in laminar flow, particularly with the natural boundary conditions. The non-Newtonian blood behavior is more apparent in the laminar flow of the external carotid artery, especially with the second set of boundary conditions.</p> </abstract>","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135556197","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}

{"title":"Scientific advances in complex systems of biophysical interest","authors":"Salvatore Magazù, M. T. Caccamo","doi":"10.3934/biophy.2023015","DOIUrl":"https://doi.org/10.3934/biophy.2023015","url":null,"abstract":"<jats:p xml:lang=\"fr\" />","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185525","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}

{"title":"Relationship between the major parameters of warm-blooded organisms' life activity and the properties of aqueous salt solutions","authors":"Anatoliy I. Fisenko, Oleksii V. Khorolskyi, Nikolay P. Malomuzh, Artur A. Guslisty","doi":"10.3934/biophy.2023022","DOIUrl":"https://doi.org/10.3934/biophy.2023022","url":null,"abstract":"<abstract> <p>We are devoted to the physical analysis of the habitat area of warm-blooded organisms – humans and many mammals. For this purpose, the establishment of equilibrium distribution of carbon dioxide in aqueous solutions of salts in contact with atmospheric air starting from some time is investigated. More precisely, the relaxation time of carbon dioxide, as a function of temperature and pH, is investigated. It is found that the pH-relaxation time <italic>τ_S</italic> is a very nontrivial function of temperature, pH values, and NaCl salt concentration. It was assumed that the minimum value of pH relaxation time corresponds to the optimal rate of physical processes in living matter. Using this selection principle and our experimental data, we have shown that the optimal temperature for human and mammalian life activity is close to <italic>T_o</italic> ≈ 37 °C. The lower and upper temperature limits for their possible activity are close to <italic>T_l</italic> ≈ 30 °C and <italic>T_u</italic> ≈ 42 °C, respectively. The optimal value of <italic>pH</italic>_o, determined by the same selection principle, also becomes true if supplemented by the influence of albumin and other proteins.</p> </abstract>","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"86 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135651038","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}

{"title":"Predicting factors and top gene identification for survival data of breast cancer","authors":"Sarada Ghosh, Guruprasad Samanta, Manuel De la Sen","doi":"10.3934/biophy.2023006","DOIUrl":"https://doi.org/10.3934/biophy.2023006","url":null,"abstract":"For high-throughput research with biological data-sets generated sequentially or by transcriptional micro-arrays, proteomics or other means, analytic techniques that address their high dimensional aspects remain desirable. The computation part basically predicts the tendency towards mortality due to breast cancer (BC) by using several classification methods, i.e., Logistic Regression (LR), Random Forest (RF), Support Vector Machine (SVM), Linear Discriminant Analysis (LDA) and Decision Tree (DT), and compared the models' performances. We proceed with the RF method since it provides better results than any other underlying models based on accuracy. We have also demonstrated some traditional and competing risk models, illustrated the models with real data analysis, depicted their curves' natures and also compared their fits using prediction error curves and the concordance index. Furthermore, two different survival splitting rules are used by using separate Random Survival Forest (RSF) methods and also constructing the ranking of risk factors due to breast cancer. The results show that high-level grade and diameter are the most important predictors for mortality progression in the presence of competing events of death, and lymph nodes, age and angiography are other vital criteria for this purpose. We have also implemented RSF backward selection criteria, which enables top gene selection related to mortality progression due to breast cancer. This method identifies c-MYB, CDCA7, NUSAP1, BIRC5, ANGPTL4, JAG1, IL6ST, and remaining genes that are mainly responsible for mortality progression due to breast cancer. In this work, R software is used to obtain and evaluate the results.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185302","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}

{"title":"On the dimensionless model of the transcription bubble dynamics","authors":"L. Krasnobaeva, L. Yakushevich","doi":"10.3934/biophy.2023013","DOIUrl":"https://doi.org/10.3934/biophy.2023013","url":null,"abstract":"The dynamics of transcription bubbles is modeled using a system of nonlinear differential equations, the one-soliton solutions of which (kinks), are interpreted as a mathematical images of transcription bubbles. These equations contain a lot of DNA dynamic parameters, including the moments of inertia of nitrous bases, distances between base pairs, distances from the centers of mass of bases to sugar-phosphate chains, rigidity of the sugar-phosphate backbone, and interactions between bases within pairs. However, estimates of the parameter values are often difficult, and it is not convenient or simple to operate with such multi-parameter systems. One of the ways to reduce the number of the DNA dynamic parameters is to transform the model equations to a dimensionless form. In this work, we construct a dimensionless DNA model and apply it to study transcription bubbles dynamics. We show that transformation to a dimensionless form really leads to a decrease in the number of the model parameters and really simplifies the analysis of model equations and their solutions.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185453","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}