Journal of Biological Physics最新文献

{"title":"In silico simulation of the effect of hypoxia on MCF-7 cell cycle kinetics under fractionated radiotherapy","authors":"Adrian S. Remigio","doi":"10.1007/s10867-021-09580-x","DOIUrl":"10.1007/s10867-021-09580-x","url":null,"abstract":"<div><p>The treatment outcome of a given fractionated radiotherapy scheme is affected by oxygen tension and cell cycle kinetics of the tumor population. Numerous experimental studies have supported the variability of radiosensitivity with cell cycle phase. Oxygen modulates the radiosensitivity through hypoxia-inducible factor (HIF) stabilization and oxygen fixation hypothesis (OFH) mechanism. In this study, an existing mathematical model describing cell cycle kinetics was modified to include the oxygen-dependent G1/S transition rate and radiation inactivation rate. The radiation inactivation rate used was derived from the linear-quadratic (LQ) model with dependence on oxygen enhancement ratio (OER), while the oxygen-dependent correction for the G1/S phase transition was obtained from numerically solving the ODE system of cyclin D-HIF dynamics at different oxygen tensions. The corresponding cell cycle phase fractions of aerated MCF-7 tumor population, and the resulting growth curve obtained from numerically solving the developed mathematical model were found to be comparable to experimental data. Two breast radiotherapy fractionation schemes were investigated using the mathematical model. Results show that hypoxia causes the tumor to be more predominated by the tumor subpopulation in the G1 phase and decrease the fractional contribution of the more radioresistant tumor cells in the S phase. However, the advantage provided by hypoxia in terms of cell cycle phase distribution is largely offset by the radioresistance developed through OFH. The delayed proliferation caused by severe hypoxia slightly improves the radiotherapy efficacy compared to that with mild hypoxia for a high overall treatment duration as demonstrated in the 40-Gy fractionation scheme.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 3","pages":"301 - 321"},"PeriodicalIF":1.8,"publicationDate":"2021-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09580-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4705151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Double-diffusion convective biomimetic flow of nanofluid in a complex divergent porous wavy medium under magnetic effects","authors":"Khurram Javid,&nbsp;Mohsan Hassan,&nbsp;Dharmendra Tripathi,&nbsp;Salahuddin Khan,&nbsp;Elena Bobescu,&nbsp;Muhammad Mubashir Bhatti","doi":"10.1007/s10867-021-09583-8","DOIUrl":"10.1007/s10867-021-09583-8","url":null,"abstract":"<div><p>We explore the physical influence of magnetic field on double-diffusive convection in complex biomimetic (peristaltic) propulsion of nanofluid through a two-dimensional divergent channel. Additionally, porosity effects along with rheological properties of the fluid are also retained in the analysis. The mathematical model is developed by equations of continuity, momentum, energy, and mass concentration. First, scaling analysis is introduced to simplify the rheological equations in the wave frame of reference and then get the final form of equations after applying the low Reynolds number and lubrication approach. The obtained equations are solved analytically by using integration method. Physical interpretation of velocity, pressure gradient, pumping phenomena, trapping phenomena, heat, and mass transfer mechanisms are discussed in detail under magnetic and porous environment. The magnitude of velocity profile is reduced by increasing Grashof parameter. The bolus circulations disappeared from trapping phenomena for larger strength of magnetic and porosity medium. The magnitude of temperature profile and mass concentration are increasing by enhancing the Brownian motion parameter. This study can be productive in manufacturing non-uniform and divergent shapes of micro-lab-chip devices for thermal engineering, industrial, and medical technologies.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 4","pages":"477 - 498"},"PeriodicalIF":1.8,"publicationDate":"2021-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09583-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4665323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of the histology and stiffness of ventricles in Anura of different habitats","authors":"Megumi Ito,&nbsp;Yoshihiro Ujihara,&nbsp;Shukei Sugita,&nbsp;Masanori Nakamura","doi":"10.1007/s10867-021-09579-4","DOIUrl":"10.1007/s10867-021-09579-4","url":null,"abstract":"<div><p>Vertebrate hearts have undergone marked morphological and structural changes to adapt to different environments and lifestyles as part of the evolutionary process. Amphibians were the first vertebrates to migrate to land. Transition from aquatic to terrestrial environments required the ability to circulate blood against the force of gravity. In this study, we investigated the passive mechanical properties and histology of the ventricles of three species of Anura (frogs and toads) from different habitats, <i>Xenopus laevis</i> (aquatic), <i>Pelophylax nigromaculatus</i> (semiaquatic), and <i>Bufo japonicus formosus</i> (terrestrial). Pressure-loading tests demonstrated stiffer ventricles of <i>P. nigromaculatus</i> and <i>B. j. formosus</i> compared <i>X. laevis</i> ventricles. Histological analysis revealed a remarkable difference in the structure of cardiac tissue: thickening of the compact myocardium layer of <i>P. nigromaculatus</i> and <i>B. j. formosus</i> and enrichment of the collagen fibers of <i>B. j. formosus.</i> The amount of collagen fibers differed among the species, as quantitatively confirmed by second-harmonic generation light microscopy. No significant difference was observed in cardiomyocytes isolated from each animal, and the sarcomere length was almost the same. The results indicate that the ventricles of Anura stiffen during adaptation to life on land.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 3","pages":"287 - 300"},"PeriodicalIF":1.8,"publicationDate":"2021-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09579-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4557291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fitness landscapes for coupled map lattices","authors":"Noelle Driver,&nbsp;Michael Frame","doi":"10.1007/s10867-021-09577-6","DOIUrl":"10.1007/s10867-021-09577-6","url":null,"abstract":"<div><p>Our goal is to match some dynamical aspects of biological systems with that of networks of coupled logistic maps. With these networks we generate sequences of iterates, convert them to symbol sequences by coarse-graining, and count the number of times combinations of symbols occur. Comparison of this with the number of times these combinations occur in experimental data—a sequence of interbeat intervals for example—is a measure of the fitness of each network to describe the target data. The most fit networks provide a cartoon that suggests a decomposition of the experimental data into a component that may be produced by a simple dynamical subsystem, and a residual component, the result of detailed, particular characteristics of the system that generated the target data. In the space of all network parameters, each point corresponds to a particular network. We construct a fitness landscape when we assign a fitness to each point. Because the parameters are distributed continuously over their ranges, and because fitnesses are estimated numerically, any plot of the landscape involves a finite sample of parameter values. We’ll investigate how the local landscape geometry changes when the array of sample parameters is refined, and use the landscape geometry to explore complex relations between local fitness maxima.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 3","pages":"215 - 235"},"PeriodicalIF":1.8,"publicationDate":"2021-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09577-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4362643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spontaneous circulation of active microtubules confined by optical traps","authors":"Stephen E Martin,&nbsp;Matthew E Brunner,&nbsp;Joshua M Deutsch","doi":"10.1007/s10867-021-09578-5","DOIUrl":"10.1007/s10867-021-09578-5","url":null,"abstract":"<div><p>We propose an experiment to demonstrate spontaneous ordering and symmetry breaking of kinesin-driven microtubules confined to an optical trap. Calculations involving the feasibility of such an experiment are first performed which analyze the power needed to confine microtubules and address heating concerns. We then present the results of first-principles simulations of active microtubules confined in such a trap and analyze the types of motion observed by the microtubules as well as the velocity of the surrounding fluid, both near the trap and in the far-field. We find three distinct phases characterized by breaking of distinct symmetries and also analyze the power spectrum of the angular momenta of polymers to further quantify the differences between these phases. Under the correct conditions, microtubules were found to spontaneously align with one another and circle the trap in one direction.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 3","pages":"237 - 251"},"PeriodicalIF":1.8,"publicationDate":"2021-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09578-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4362644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A continuum mechanics model for the Fåhræus-Lindqvist effect","authors":"Angiolo Farina,&nbsp;Fabio Rosso,&nbsp;Antonio Fasano","doi":"10.1007/s10867-021-09575-8","DOIUrl":"10.1007/s10867-021-09575-8","url":null,"abstract":"<div><p>The decrease in apparent relative viscosity that occurs when blood is made to flow through a tube whose diameter is less than about 0.3 mm is a well-known and documented phenomenon in physiology, known as the Fåhræus-Lindqvist effect. However, since the historical work of Fåhræus and Lindqvist (Amer. J. Physiol. <b>96</b>(3): pp. 562–568, 1931), the underlying physical mechanism has remained enigmatic. A widely accepted qualitative explanation was provided by Haynes (Amer. J. Physiol. <b>198</b>, pp. 1193–1200, 1960) according to which blood flows in microvessels with a core-annulus structure, where the erythrocytes concentrate within a central core surrounded by a plasma layer. Although sustained by observations, this conjecture lacks a rigorous deduction from the basic principles of continuum dynamics. Moreover, relations aimed to reproduce the blood apparent relative viscosity, extensively used in micro-circulation, are all empirical and not derived from the analysis of the fluid mechanical phenomena involved. In this paper, we apply the recent results illustrated in Guadagni and Farina (Int. J. Nonlinear Mech. <b>126</b>, p. 103587, 2020), with the purpose of showing that Haynes’ conjecture, slightly corrected to make it more realistic, can be proved and can be used to reach a sound explanation of the Fåhræus-Lindqvist effect based on continuum mechanics. We propose a theoretical model for the blood apparent relative viscosity which is validated by matching not only the original experimental data reported by Fåhræus and Lindqvist (Amer. J. Physiol. <b>96</b>(3), pp. 562–568, 1931), but also those provided by several subsequent authors.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 3","pages":"253 - 270"},"PeriodicalIF":1.8,"publicationDate":"2021-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09575-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4125165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exciton transfer between LH1 antenna complex and photosynthetic reaction center dimer","authors":"Michal Pudlák,&nbsp;Richard Pinčák","doi":"10.1007/s10867-021-09576-7","DOIUrl":"10.1007/s10867-021-09576-7","url":null,"abstract":"<div><p>The exciton transfer between light-harvesting complex 1(LH1) and photosynthetic reaction center dimer is investigated theoretically. We assume a ring shape structure of the LH1 complex with dimer in the ring centre. The kinetic equations which describe the energy transfer between the antenna complex and reaction center dimer were derived. It was shown that the dimer does not act as a photon trap. There is a weak localization of the exciton on the dimer and there is relatively rapid back exciton transfer from dimer to antenna complex which depends on the number of the pigment molecules in the antenna ring. The relation between the rates of the exciton transfer from the antenna complex to dimer and back transfer from dimer to antenna complex has been derived.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 3","pages":"271 - 286"},"PeriodicalIF":1.8,"publicationDate":"2021-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09576-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4086231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinetic aspects of virus targeting by nanoparticles in vivo","authors":"Vladimir P. Zhdanov","doi":"10.1007/s10867-021-09570-z","DOIUrl":"10.1007/s10867-021-09570-z","url":null,"abstract":"<div><p>One of the suggested ways of the use of nanoparticles in virology implies their association with and subsequent deactivation of virions. The conditions determining the efficiency of this approach in vivo are now not clear. Herein, I propose the first kinetic model describing the corresponding processes and clarifying these conditions. My analysis indicates that nanoparticles can decrease concentration of infected cells by a factor of one order of magnitude, but this decrease itself (without feedback of the immune system) is insufficient for full eradication of infection. It can, however, induce delay in the progress of infection, and this delay can help to form sufficient feedback of the immune system.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 2","pages":"95 - 101"},"PeriodicalIF":1.8,"publicationDate":"2021-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09570-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4088337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interaction of chloramphenicol with titin I27 probed using single-molecule force spectroscopy","authors":"Jyoti Yadav,&nbsp;Yashwant Kumar,&nbsp;Gayathri S. Singaraju,&nbsp;Shivprasad Patil","doi":"10.1007/s10867-021-09573-w","DOIUrl":"10.1007/s10867-021-09573-w","url":null,"abstract":"<div><p>Titin is a giant elastic protein which is responsible for passive muscle stiffness when muscle sarcomeres are stretched. Chloramphenicol, besides being a broad-spectrum antibiotic, also acts as a muscle relaxant. Therefore, it is important to study the interaction between titin I27 and chloramphenicol. We investigated the interaction of chloramphenicol with octamer of titin I27 using single-molecule force spectroscopy and fluorescence spectroscopy. The fluorescence data indicated that binding of chloramphenicol with I27 results in fluorescence quenching. Furthermore, it is observed that chloramphenicol binds to I27 at a particular concentration (<span>(sim )</span> 40 μM). Single-molecule force spectroscopy shows that, in the presence of 40 μM chloramphenicol concentration, the I27 monomers become mechanically stable, resulting in an increment of the unfolding force. The stability was further confirmed by chemical denaturation experiments on monomers of I27, which corroborate the evidence for enhanced mechanical stability at 40 μM drug concentration. The free energy of stabilization for I27 (wild type) was found to be 1.95 ± 0.93 kcal/mole and I27 with 40 μM drug was 3.25 ± 0.63 kcal/mole. The results show a direct effect of the broad-spectrum antibiotic chloramphenicol on the passive elasticity of muscle protein titin. The I27 is stabilized both mechanically and chemically by chloramphenicol.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 2","pages":"191 - 204"},"PeriodicalIF":1.8,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09573-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4036626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Local hemodynamic analysis after coronary stent implantation based on Euler-Lagrange method","authors":"Yuchen Wang,&nbsp;Jingmei Zhan,&nbsp;Weiguo Bian,&nbsp;Xiaoli Tang,&nbsp;Min Zeng","doi":"10.1007/s10867-021-09571-y","DOIUrl":"10.1007/s10867-021-09571-y","url":null,"abstract":"<div><p>Coronary stents are deployed to treat the coronary artery disease (CAD) by reopening stenotic regions in arteries to restore blood flow, but the risk of the in-stent restenosis (ISR) is high after stent implantation. One of the reasons is that stent implantation induces changes in local hemodynamic environment, so it is of vital importance to study the blood flow in stented arteries. Based on regarding the red blood cell (RBC) as a rigid solid particle and regarding the blood (including RBCs and plasma) as particle suspensions, a non-Newtonian particle suspensions model is proposed to simulate the realistic blood flow in this work. It considers the blood’s flow pattern and non-Newtonian characteristic, the blood cell-cell interactions, and the additional effects owing to the bi-concave shape and rotation of the RBC. Then, it is compared with other four common hemodynamic models (Newtonian single-phase flow model, Newtonian Eulerian two-phase flow model, non-Newtonian single-phase flow model, non-Newtonian Eulerian two-phase flow model), and the comparison results indicate that the models with the non-Newtonian characteristic are more suitable to describe the realistic blood flow. Afterwards, based on the non-Newtonian particle suspensions model, the local hemodynamic environment in stented arteries is investigated. The result shows that the stent strut protrusion into the flow stream would be likely to produce the flow stagnation zone. And the stent implantation can make the pressure gradient distribution uneven. Besides, the wall shear stress (WSS) of the region adjacent to every stent strut is lower than 0.5 Pa, and along the flow direction, the low-WSS zone near the strut behind is larger than that near the front strut. What’s more, in the regions near the struts in the proximal of the stent, the RBC particle stagnation zone is easy to be formed, and the erosion and deposition of RBCs are prone to occur. These hemodynamic analyses illustrate that the risk of ISR is high in the regions adjacent to the struts in the proximal and the distal ends of the stent when compared with struts in other positions of the stent. So the research can provide a suggestion on the stent design, which indicates that the strut structure in these positions of a stent should be optimized further.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"47 2","pages":"143 - 170"},"PeriodicalIF":1.8,"publicationDate":"2021-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09571-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5051170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}