Journal of Biological Physics最新文献

{"title":"Similarity analysis of bioconvection of unsteady nonhomogeneous hybrid nanofluids influenced by motile microorganisms.","authors":"Samah Mohamed Mabrouk, Mustafa Inc, Ahmed Saad Rashed, Ali Akgül","doi":"10.1007/s10867-023-09651-1","DOIUrl":"10.1007/s10867-023-09651-1","url":null,"abstract":"<p><p>Motile bacteria in hybrid nanofluids cause bioconvection. Bacillus cereus, Pseudomonas viscosa, Bacillus brevis, Salmonella typhimurium, and Pseudomonas fluorescens were used to evaluate their effect and dispersion in the hybrid nanofluid. Using similarity analysis, a two-phase model for mixed bioconvection magnetohydrodynamic flow was developed using hybrid nanoparticles of Al₂O₃ and Cu (Cu-Al₂O₃/water). The parametric investigation, covering the magnetic parameter, permeability coefficient, nanoparticle shape factor, temperature ratio, radiation parameter, nanoparticle fraction ratio, Brownian parameter, thermophoresis parameter, motile bacteria diffusivity, chemotaxis parameter, and Nusselt, Reynold, Prandtl, Sherwood numbers, as well as the number of motile microorganisms', showed significant outcomes. Velocity and shear stresses are sensitive to M, Pr, and [Formula: see text]. Magnetic, radiation, and chemotaxis factors impact bacterial density. The hybrid nanofluid velocity decreases when the magnetic parameter, M, Prandtl number Pr increases, while it increases with the increasing of porosity coefficient, [Formula: see text], and the hybrid nanoparticle ratio N_f. The temperature distribution decreases with the increasing of Prandtl number and N_f. Increasing temperature differential and bacterium diffusivity increases bacterial aggregation.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10864241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139518996","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":"Generic algebraic conditions for the occurrence of switch-like behavior of a chemical kinetic system of the hypoxia pathway.","authors":"Quentin Vanhaelen","doi":"10.1007/s10867-023-09647-x","DOIUrl":"10.1007/s10867-023-09647-x","url":null,"abstract":"<p><p>Weakly reversible chemical reaction networks with zero deficiency associated with mass-action kinetics admit, within each positive stoichiometric compatibility class, one positive steady state which is locally asymptotically stable and this irrespective of the values of the kinetics constants. Networks which do not enjoy these structural properties potentially exhibit more diverse dynamical behaviors. In this article, we consider a chemical reaction network associated with mass-action kinetics which is not weakly reversible and has a deficiency larger than one. The chemical reactions are at most bimolecular, but inflow and outflow reactions are present. Our results are as follows. We establish the existence of positive steady-state solutions and obtain their analytic expressions in the concentration space and in convex coordinates. We show that the system fulfills necessary conditions for a saddle-node and for a bifurcation into a saddle and a node. We apply a constructive approach to obtain a set of numerical values for the state variables and kinetic parameters, not reported previously, such that the reduced Jacobian is characterized by a zero eigenvalue with all other eigenvalues having negative real parts. The bifurcation diagram confirms the presence of the switch-like behavior.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10864246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138827587","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":"Base flipping mechanism and binding strength of methyl-damaged DNA during the interaction with AGT.","authors":"Rajendra Prasad Koirala, Narayan Prasad Adhikari","doi":"10.1007/s10867-023-09649-9","DOIUrl":"10.1007/s10867-023-09649-9","url":null,"abstract":"<p><p>Methyl damage to DNA bases is common in the cell nucleus. O6-alkylguanine-DNA alkyl transferase (AGT) may be a promising candidate for direct damage reversal in methylated DNA (mDNA) at the O6 point of the guanine. Indeed, atomic-level investigations in the contact region of AGT-DNA complex can provide an in-depth understanding of their binding mechanism, allowing to evaluate the silico-drug nature of AGT and its utility in removing methyl damage in DNA. In this study, molecular dynamics (MD) simulation was utilized to examine the flipping of methylated nucleotide, the binding mechanism between mDNA and AGT, and the comparison of binding strength prior and post methyl transfer to AGT. The study reveals that methylation at the O6 atom of guanine weakens the hydrogen bond (H-bond) between guanine and cytosine, permitting for the flipping of such nucleotide. The formation of a H-bond between the base pair of methylated nucleotide (i.e., cytosine) and the intercalated arginine of AGT also forces the nucleotide to rotate. Following that, electrostatics and van der Waals contacts as well as hydrogen bonding contribute to form the complex of DNA and protein. The stronger binding of AGT with DNA before methyl transfer creates the suitable condition to transfer methyl adduct from DNA to AGT.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11413403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139039324","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":"Microrheological comparison of melanoma cells by atomic force microscopy.","authors":"M Manuela Brás, Aureliana Sousa, Tânia B Cruz, Jonas Michalewski, Marina Leite, Susana R Sousa, Pedro L Granja, Manfred Radmacher","doi":"10.1007/s10867-023-09648-w","DOIUrl":"10.1007/s10867-023-09648-w","url":null,"abstract":"<p><p>Melanoma is one of the most severe cancers due to its great potential to form metastasis. Recent studies showed the importance of mechanical property assessment in metastasis formation which depends on the cytoskeleton dynamics and cell migration. Although cells are considered purely elastic, they are viscoelastic entities. Microrheology atomic force microscopy (AFM) enables the assessment of elasticity and viscous properties, which are relevant to cell behavior regulation. The current work compares the mechanical properties of human neonatal primary melanocytes (HNPMs) with two melanoma cell lines (WM793B and 1205LU cells), using microrheology AFM. Immunocytochemistry of F-actin filaments and phosphorylated focal adhesion kinase (p-FAK) and cell migration assays were performed to understand the differences found in microrheology AFM regarding the tumor cell lines tested. AFM revealed that HNPMs and tumor cell lines had distinct mechanical properties. HNPMs were softer, less viscous, presenting a higher power-law than melanoma cells. Immunostaining showed that metastatic 1205LU cells expressed more p-FAK than WM793B cells. Melanoma cell migration assays showed that WM73B did not close the gap, in contrast to 1205LU cells, which closed the gap at the end of 23 h. These data seem to corroborate the high migratory behavior of 1205LU cells. Microrheology AFM applied to HNPMs and melanoma cells allowed the quantification of elasticity, viscous properties, glassy phase, and power-law properties, which have an impact in cell migration and metastasis formation. AFM study is important since it can be used as a biomarker of the different stages of the disease in melanoma.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10864228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139490462","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":"Roles of astrocytes and prions in Alzheimer’s disease: insights from mathematical modeling","authors":"Mitali Maji, Subhas Khajanchi","doi":"10.1007/s10867-023-09652-0","DOIUrl":"https://doi.org/10.1007/s10867-023-09652-0","url":null,"abstract":"<p>We present a mathematical model that explores the progression of Alzheimer’s disease, with a particular focus on the involvement of disease-related proteins and astrocytes. Our model consists of a coupled system of differential equations that delineates the dynamics of amyloid beta plaques, amyloid beta protein, tau protein, and astrocytes. Amyloid beta plaques can be considered fibrils that depend on both the plaque size and time. We change our mathematical model to a temporal system by applying an integration operation with respect to the plaque size. Theoretical analysis including existence, uniqueness, positivity, and boundedness is performed in our model. We extend our mathematical model by adding two populations, namely prion protein and amyloid beta-prion complex. We characterize the system dynamics by locating biologically feasible steady states and their local stability analysis for both models. The characterization of the proposed model can help inform in advancing our understanding of the development of Alzheimer’s disease as well as its complicated dynamics. We investigate the global stability analysis around the interior equilibrium point by constructing a suitable Lyapunov function. We validate our theoretical analysis with the aid of extensive numerical illustrations.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139064617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural insights into the pathogenicity of point mutations in human acyl-CoA dehydrogenase homotetramers","authors":"Homa Faraji, Azadeh Ebrahim-Habibi","doi":"10.1007/s10867-023-09650-2","DOIUrl":"https://doi.org/10.1007/s10867-023-09650-2","url":null,"abstract":"<p>Acyl-CoA dehydrogenase deficiency (ACAD) is an inherited and potentially fatal disorder with variable clinical symptoms. The relationship between pathogenicity and deleterious point mutations is investigated here in ACAD structures of short (SCAD) and medium-chain (MCAD) types. Structures and dynamic features of native and mutant forms of enzymes models were compared. A total of 2.88 µs molecular dynamics simulations were performed at four different temperatures. Total energy, RMSD, protein ligand interactions and affinity, RMSF measures, secondary structure changes, and important interactions were studied. Mutations in the three main domains of ACADs are pathogenic, while those located at linker turns are not. Mutations affect mostly tetramer formations, secondary structures, and many contacts and interactions. In R206H (MCAD mutant) which is experimentally known to cause a huge turnover decrease, the lack of a single H-bond between substrate and FAD was observed. Secondary structures showed temperature-dependent changes, and SCAD activity was found to be highly correlated to the enzyme helix 3–10 content. Finally, RMSF patterns pointed to one important loop that maintains the substrate close to the active site and is a cause of substrate wobbling upon mutation. Despite similar structure, function, and cellular location, SCAD and MCAD may have different optimum temperatures that are related to the structure taken at that specific temperature. In conclusion, new insight has been provided on the effect of various SCAD and MCAD pathogenic mutations on the structure and dynamical features of the enzymes.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138689022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ion currents through the voltage sensor domain of distinct families of proteins","authors":"César Arcos-Hernández,&nbsp;Takuya Nishigaki","doi":"10.1007/s10867-023-09645-z","DOIUrl":"10.1007/s10867-023-09645-z","url":null,"abstract":"<div><p>The membrane potential of a cell (V_m) regulates several physiological processes. The voltage sensor domain (VSD) is a region that confers voltage sensitivity to different types of transmembrane proteins such as the following: voltage-gated ion channels, the voltage-sensing phosphatase (Ci-VSP), and the sperm-specific Na⁺/H⁺ exchanger (sNHE). VSDs contain four transmembrane segments (S1–S4) and several positively charged amino acids in S4, which are essential for the voltage sensitivity of the protein. Generally, in response to changes of the V_m, the positive residues of S4 displace along the plasma membrane without generating ionic currents through this domain. However, some native (e.g., Hv1 channel) and mutants of VSDs produce ionic currents. These gating pore currents are usually observed in VSDs that lack one or more of the conserved positively charged amino acids in S4. The gating pore currents can also be induced by the isolation of a VSD from the rest of the protein domains. In this review, we summarize gating pore currents from all families of proteins with VSDs with classification into three cases: (1) pathological, (2) physiological, and (3) artificial currents. We reinforce the model in which the position of S4 that lacks the positively charged amino acid determines the voltage dependency of the gating pore current of all VSDs independent of protein families.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09645-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41231477","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":"High order sliding mode control for restoration of a population of predators in a Lotka-Volterra system","authors":"Jesica A. Escobar,&nbsp;Ana Gabriela Gallardo-Hernandez,&nbsp;Marcos Angel Gonzalez-Olvera,&nbsp;Cristina Revilla-Monsalve,&nbsp;Debbie Hernandez,&nbsp;Ron Leder","doi":"10.1007/s10867-023-09643-1","DOIUrl":"10.1007/s10867-023-09643-1","url":null,"abstract":"<div><p>Human-induced extinction and rapid ecological changes require the development of techniques that can help avoid extinction of endangered species. The most used strategy to avoid extinction is reintroduction of the endangered species, but only 31% of these attempts are successful and they require up to 15 years for their results to be evaluated. In this research, we propose a novel strategy that improves the chances of survival of endangered predators, like lynx, by controlling only the availability of prey. To simulate the prey-predator relationship we used a Lotka-Volterra model to analyze the effects of varying prey availability on the size of the predator population. We calculate the number of prey necessary to support the predator population using a high-order sliding mode control (HOSMC) that maintains the predator population at the desired level. In the wild, nature introduces significant and complex uncertainties that affect species’ survival. This complexity suggests that HOSMC is a good choice of controller because it is robust to variability and does not require prior knowledge of system parameters. These parameters can also be time varying. The output measurement required by the HOSMC is the number of predators. It can be obtained using continuous monitoring of environmental DNA that measures the number of lynxes and prey in a specific geographic area. The controller efficiency in the presence of these parametric uncertainties was demonstrated with a numerical simulation, where random perturbations were forced in all four model parameters at each simulation step, and the controller provides the specific prey input that will maintain the predator population. The simulation demonstrates how HOSMC can increase and maintain an endangered population (lynx) in just 21–26 months by regulating the food supply (hares), with an acceptable maximal steady-state error of 3%.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09643-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41100996","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":"Impact of noise on the instability of spiral waves in stochastic 2D mathematical models of human atrial fibrillation","authors":"Euijun Song","doi":"10.1007/s10867-023-09644-0","DOIUrl":"10.1007/s10867-023-09644-0","url":null,"abstract":"<div><p>Sustained spiral waves, also known as rotors, are pivotal mechanisms in persistent atrial fibrillation (AF). Stochasticity is inevitable in nonlinear biological systems such as the heart; however, it is unclear how noise affects the instability of spiral waves in human AF. This study presents a stochastic two-dimensional mathematical model of human AF and explores how Gaussian white noise affects the instability of spiral waves. In homogeneous tissue models, Gaussian white noise may lead to spiral-wave meandering and wavefront break-up. As the noise intensity increases, the spatial dispersion of phase singularity (PS) points increases. This finding indicates the potential AF-protective effects of cardiac system stochasticity by destabilizing the rotors. By contrast, Gaussian white noise is unlikely to affect the spiral-wave instability in the presence of localized scar or fibrosis regions. The PS points are located at the boundary or inside the scar/fibrosis regions. Localized scar or fibrosis may play a pivotal role in stabilizing spiral waves regardless of the presence of noise. This study suggests that fibrosis and scars are essential for stabilizing the rotors in stochastic mathematical models of AF. Further patient-derived realistic modeling studies are required to confirm the role of scar/fibrosis in AF pathophysiology.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41105024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synchronization in STDP-driven memristive neural networks with time-varying topology","authors":"Marius E. Yamakou,&nbsp;Mathieu Desroches,&nbsp;Serafim Rodrigues","doi":"10.1007/s10867-023-09642-2","DOIUrl":"10.1007/s10867-023-09642-2","url":null,"abstract":"<div><p>Synchronization is a widespread phenomenon in the brain. Despite numerous studies, the specific parameter configurations of the synaptic network structure and learning rules needed to achieve robust and enduring synchronization in neurons driven by spike-timing-dependent plasticity (STDP) and temporal networks subject to homeostatic structural plasticity (HSP) rules remain unclear. Here, we bridge this gap by determining the configurations required to achieve high and stable degrees of complete synchronization (CS) and phase synchronization (PS) in time-varying small-world and random neural networks driven by STDP and HSP. In particular, we found that decreasing <i>P</i> (which enhances the strengthening effect of STDP on the average synaptic weight) and increasing <i>F</i> (which speeds up the swapping rate of synapses between neurons) always lead to higher and more stable degrees of CS and PS in small-world and random networks, provided that the network parameters such as the synaptic time delay <span>(tau _c)</span>, the average degree <span>(langle k rangle)</span>, and the rewiring probability <span>(beta)</span> have some appropriate values. When <span>(tau _c)</span>, <span>(langle k rangle)</span>, and <span>(beta)</span> are not fixed at these appropriate values, the degree and stability of CS and PS may increase or decrease when <i>F</i> increases, depending on the network topology. It is also found that the time delay <span>(tau _c)</span> can induce intermittent CS and PS whose occurrence is independent <i>F</i>. Our results could have applications in designing neuromorphic circuits for optimal information processing and transmission via synchronization phenomena.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09642-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10130496","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}