Journal of Biological Physics最新文献_第4页

Phase gradient modulation of spiral waves in cortical circuits using the complex Ginzburg–Landau equation 用复金兹堡-朗道方程调制皮质电路中螺旋波的相位梯度。

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2026-01-20 DOI: 10.1007/s10867-025-09699-1

Sayge Urban, Jean-Philippe Thivierge

{"title":"Phase gradient modulation of spiral waves in cortical circuits using the complex Ginzburg–Landau equation","authors":"Sayge Urban, Jean-Philippe Thivierge","doi":"10.1007/s10867-025-09699-1","DOIUrl":"10.1007/s10867-025-09699-1","url":null,"abstract":"<div><p>Disinhibited brain networks exhibit various forms of spatiotemporal waves, including complex spiral waves that evolve around a fixed spatial locus. In experiments, spiral waves are observed to alter their direction of rotation over time, for instance producing a series of waves with clockwise cycles before switching to waves rotating counterclockwise, or vice-versa. To capture this effect, we developed a model based on the Complex Ginzburg–Landau equation (CGLE). By introducing a modulation in the phase gradient of the complex field that reflects global, time-dependent fluctuations in the surrounding environment, the model produced waves that alternated in their direction of rotation. The rate of alternations was directly proportional to the amplitude of phase modulation. Conditions were explored for the emergence of quasi-stationary frozen waves and noise-induced quenching of spiral waves. Overall, the modified CGLE model provides a candidate mechanism for the emergence of spiral waves where rotational directions are dynamically altered, yielding rich forms of activity that account for the spatiotemporal patterns observed in disinhibited brain circuits.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"52 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146008603","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}

引用次数: 0

Molecular docking and dynamic simulation of escherichia coli K-12 Elements as a Biosensor for Detecting 2,4,6-Trinitrotoluene (TNT) 大肠杆菌K-12元件检测2,4,6-三硝基甲苯（TNT）生物传感器的分子对接与动态模拟

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2026-01-03 DOI: 10.1007/s10867-025-09697-3

Nina Alexsandra, Zahra Silmi Muscifah, Arwansyah Arwansyah, Agus Kartono, Setyanto Tri Wahyudi

{"title":"Molecular docking and dynamic simulation of escherichia coli K-12 Elements as a Biosensor for Detecting 2,4,6-Trinitrotoluene (TNT)","authors":"Nina Alexsandra, Zahra Silmi Muscifah, Arwansyah Arwansyah, Agus Kartono, Setyanto Tri Wahyudi","doi":"10.1007/s10867-025-09697-3","DOIUrl":"10.1007/s10867-025-09697-3","url":null,"abstract":"<div><p>Trinitrotoluene (TNT) is widely used in military and industrial fields due to its strong explosive properties and chemical stability. However, its persistence in the environment and harmful effects on living organisms make it important to develop sensitive and selective detection methods. Previous research has identified the Escherichia coli genes yadG and aspC as promising components for TNT biosensors, based on their increased gene expression in response to TNT exposure. Although these findings are promising, it is still unclear whether the proteins produced from these genes directly interact with TNT at the molecular level. This study focuses on analyzing the binding interactions between TNT and the protein products of yadG and aspC using computational methods. Molecular docking showed that TNT binds more strongly to yadG (− 6.81 ± 0.02 kcal/mol) than to aspC (− 6.23 ± 0.00 kcal/mol). Further analysis using molecular dynamics simulations with MM-GBSA calculations confirmed that the yadG–TNT complex is more stable, with a binding free energy (ΔG) of − 23.58 kJ/mol, in line with fluorescence data that also indicated stronger binding to yadG. TNT binding to yadG involves aromatic residues (Tyr-106, His-153) and hydrophobic contacts (Ala-150), which may promote π–π stacking and suggest reduced water occupancy. These features highlight key principles for protein engineering and suggest a clear route from computational findings to biosensor development.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"52 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886974","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}

引用次数: 0

Difference in cell death response between mitomycin C and 5-fluorouracil treatment studied using quartz crystal microbalance combined with simultaneous monitoring of viable cells 石英晶体微天平联合活细胞同步监测研究丝裂霉素C与5-氟尿嘧啶处理细胞死亡反应的差异。

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-12-22 DOI: 10.1007/s10867-025-09695-5

Hao Long, Tomoyasu Sugiyama, Hiroshi Muramatsu

{"title":"Difference in cell death response between mitomycin C and 5-fluorouracil treatment studied using quartz crystal microbalance combined with simultaneous monitoring of viable cells","authors":"Hao Long, Tomoyasu Sugiyama, Hiroshi Muramatsu","doi":"10.1007/s10867-025-09695-5","DOIUrl":"10.1007/s10867-025-09695-5","url":null,"abstract":"<div><p>A quartz crystal microbalance (QCM) can be used to evaluate the physical properties of cells exposed to anticancer drugs. Mass-sensing techniques on electrodes detect subtle changes in adherent cells during drug treatment, providing insights into physiological, biochemical, and morphological events from a physical perspective. Although these methods have been established in many studies using living cells, their drug responses remain associated with cell viability. This study aimed to measure QCM response by simultaneously monitoring non-viable cell images. Treatment with mitomycin C (MMC) caused the resonant frequency to shift from a decrease to an increase, followed by a delayed rise in the proportion of non-viable cells. By contrast, treatment with 5-fluorouracil (5-FU) produced minimal frequency changes, accompanied by a shorter delay before cell death was observed. The fitting data to the model equations of the cumulative log-normal distribution curve showed a clear difference in parameter values between MMC and 5-FU, indicating distinct cell death processes. These results demonstrate that QCM-based monitoring of physical properties provides complementary information on drug responses and may serve as a useful tool in anticancer drug development.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"52 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145808827","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}

引用次数: 0

Observing grazing behavior transitions in Cafeteria roenbergensis with video-rate two-photon microscopy 用视频速率双光子显微镜观察roenbergensis自助餐厅放牧行为的转变

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-12-17 DOI: 10.1007/s10867-025-09696-4

Arifur Rahaman, Martin Chacon, Yuejiao Xian, Chuan Xiao, Chunqiang Li

{"title":"Observing grazing behavior transitions in Cafeteria roenbergensis with video-rate two-photon microscopy","authors":"Arifur Rahaman, Martin Chacon, Yuejiao Xian, Chuan Xiao, Chunqiang Li","doi":"10.1007/s10867-025-09696-4","DOIUrl":"10.1007/s10867-025-09696-4","url":null,"abstract":"<p>Grazing behavior of free-living aquatic heterotrophic nanoflagellates (HNFs) on bacteria plays a central role in shaping microbial community structure and driving nutrient cycling. However, direct observation of these predator–prey interactions has been limited by the rapid motility of flagellates and the transient nature of their encounters. To overcome these challenges, this study presents a novel application of video-rate two-photon fluorescence microscopy for high-resolution, real-time imaging of fast-moving microorganisms. Using the HNF <i>Cafeteria roenbergensis</i> as a model system, we investigate dynamic grazing interactions between fluorescently stained bacteria and the flagellates detected via their intrinsic cellular autofluorescence. This two-photon microscope combined with real-time imaging capability enables continuous observation of the full grazing sequence: contact, capture, ingestion, and digestion, at single-cell resolution. Quantitative analyses across varying prey concentration reveal phase-specific durations and saturation behavior in grazing activities. Furthermore, real-time tracking uncovers a previously unobserved transition in grazing dynamics across two feeding behaviors of flagellates from starved to fed states in motile flagellates. This technique provides a powerful new tool to study rapid microbial interactions in situ and can be broadly applicable to diverse microbe-microbe systems. With the integration of targeted fluorescent molecular probes, this technique offers significant potential to elucidate mechanical and biochemical processes underlying microbial feeding and communication.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"52 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145766242","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}

引用次数: 0

Structure-based discovery and molecular dynamics evaluation of dihydrorobinetin as a potential anti-osteoclastogenic RANKL inhibitor in rheumatoid arthritis 基于结构的发现和分子动力学评价：二氢宾素是类风湿关节炎中潜在的抗破骨细胞RANKL抑制剂。

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-11-19 DOI: 10.1007/s10867-025-09694-6

Devi Soorya Narayana S., Vino Sundararajan

{"title":"Structure-based discovery and molecular dynamics evaluation of dihydrorobinetin as a potential anti-osteoclastogenic RANKL inhibitor in rheumatoid arthritis","authors":"Devi Soorya Narayana S., Vino Sundararajan","doi":"10.1007/s10867-025-09694-6","DOIUrl":"10.1007/s10867-025-09694-6","url":null,"abstract":"<div><p>Rheumatoid arthritis (RA) is a chronic inflammatory disease that destroys joints, and in vitro and in vivo studies have confirmed the significant role of osteoclasts in bone degradation associated with this disease. The receptor activator of nuclear factor-kappa B ligand (RANKL) is associated with osteoclast differentiation and bone degradation in RA. The present study investigated the inhibitory effects of phytocompounds against RANKL. Virtual screening of 10,100 phytochemicals retrieved from the IMPPAT database was performed using AutoDock Vina to identify the top 10 compounds with the best binding scores. The top ten compounds were filtered using the ADME property to identify the most promising lead compound. The lead compound was furthermore analyzed using a 1-µs molecular dynamics simulation with GROMACS to understand the stability of the complex in the system. MM-PBSA was employed for binding energy calculations, and additional post-simulation analyses, including principal component analysis, free energy landscape plotting, and VMD visualization, were performed. Dihydrorobinetin was the most promising inhibitor of the RANKL protein after filtration via ADMET analysis, with a strong binding affinity of − 8.8 kcal/mol, forming four hydrogen bonds. The 1-µs simulation revealed stable binding of dihydrorobinetin with RANKL, and the binding energy calculations performed via the MM-PBSA method showed favorable binding and stability of the complex. This study provides interesting insights into the therapeutic potential of dihydrorobinetin by inducing conformational changes in RANKL to treat bone destruction in RA, laying the groundwork for further experimental validation to confirm its efficacy and clinical potential.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"51 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145547525","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}

引用次数: 0

Time dispersion analysis of features as a tool for investigating plant electrophysiology: A case study using moderate magnetic field in bean plants 时间色散特征分析作为研究植物电生理的工具：以中等磁场在豆类植物中的应用为例

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-11-14 DOI: 10.1007/s10867-025-09692-8

Thiago Francisco de Carvalho Oliveira, Ádrya Vanessa Lira Costa, Douglas Antônio Posso, Gabriela Niemeyer Reissig, Gustavo Maia Souza

{"title":"Time dispersion analysis of features as a tool for investigating plant electrophysiology: A case study using moderate magnetic field in bean plants","authors":"Thiago Francisco de Carvalho Oliveira, Ádrya Vanessa Lira Costa, Douglas Antônio Posso, Gabriela Niemeyer Reissig, Gustavo Maia Souza","doi":"10.1007/s10867-025-09692-8","DOIUrl":"10.1007/s10867-025-09692-8","url":null,"abstract":"<div><p>Electrophysiological signals in plants, which are a part of the plant electrome, are essential for mediating responses to environmental stimuli but exhibit complex, non-linear dynamics that challenge conventional analyses. Here, we introduce the time dispersion analysis of features (TDAF), a novel method that preserves temporal integrity by assessing the dispersion of signal features over time by segmenting time series and evaluating the temporal evolution of extracted features. Unlike traditional methods, such as moving averages or stationarity-based models, that summarize the signal or lose temporal information, TDAF analyzes the evolution of features over time, maintaining their dynamic structure. We applied TDAF to investigate the effects of a moderate static magnetic field (~ 0.4 mT) on the electrome of common bean plants (<i>Phaseolus vulgaris</i> L.). Signals from 30 plants were recorded before and during magnetic field exposure, generating time series with 225,000 points each. Features such as approximate entropy (ApEn), detrended fluctuation analysis (DFA), fast Fourier transform (FFT), power spectral density (PSD), and average band power (ABP) were analyzed. Our results suggest that magnetic field exposure tends to reduce signal amplitude but preserves the structural complexity and temporal patterns of the electrome, indicating modulation without loss of information processing capacity. TDAF proved effective for detecting subtle physiological changes and offers a valuable tool for advancing plant electrophysiology, bioelectromagnetic research, and studies involving complex and long-duration biological signals.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"51 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145510418","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}

引用次数: 0

Dependency of cellular behavior of collective migration on the substrate stiffness and cluster size 集体迁移的细胞行为对基质刚度和簇大小的依赖性。

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-11-04 DOI: 10.1007/s10867-025-09690-w

Minoo Alavi, Mohammad Tafazzoli-Shadpour, Ehsan Mohammadi, Mehrdad Saviz

{"title":"Dependency of cellular behavior of collective migration on the substrate stiffness and cluster size","authors":"Minoo Alavi, Mohammad Tafazzoli-Shadpour, Ehsan Mohammadi, Mehrdad Saviz","doi":"10.1007/s10867-025-09690-w","DOIUrl":"10.1007/s10867-025-09690-w","url":null,"abstract":"<div><p>Collective migration is a crucial mechanism guiding cell movement in developmental processes and disease progression. Understanding the migration behavior of cell clusters is key to advancing our knowledge of morphogenesis, wound healing, and collective cancer invasion. Despite the understanding of the response of single cells to environmental physical cues, the collective behavior of cells in response to different levels of extracellular matrix stiffness is yet to be fully understood. Here, we present a quantitative investigation into how substrate stiffness and cell cluster size modulate the collective behavior and migration dynamics of NIH 3T3 fibroblasts. With the variation of PDMS and curing agent concentrations, two contrasting soft and stiff substrates with different stiffness were developed. Using a combination of atomic force microscopy (AFM) to precisely characterize substrate elastic moduli and time-lapse microscopy for tracking migration parameters, we demonstrate that substrate mechanics and cluster geometry synergistically govern collective behavior. Fibroblast migratory characteristics were greatly improved with increased stiffness and cluster size. Large clusters on stiff substrates exhibited greater circularity (~ 0.8), migration distance, displacement (135.6 µm), directionality (0.81), and velocity (24 µm/h) compared to single cells and small clusters on soft and stiff substrates. Moreover, detailed analysis of cytoskeletal reorganization via actin staining revealed the mechanotransductive pathways that convert physical cues into migratory behavior. These findings provide important insights into how substrate stiffness influences collective cell migration, offering potential applications in elucidating the mechanisms of morphogenesis and the dynamics of collective cell invasion during tumor progression.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"51 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145443588","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}

引用次数: 0

The role of fractional-order dynamics in understanding Escherichia coli resistance to carbapenem antibiotics 分数级动力学在了解大肠杆菌对碳青霉烯类抗生素耐药性中的作用。

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-11-04 DOI: 10.1007/s10867-025-09693-7

David Amilo, Bilgen Kaymakamzade, Emine Unal Evren, Cemile Bagkur

引用次数: 0

Minimization of greenhouse effects by optimal plankton feeding: a simulation-based study 通过最佳浮游生物摄食使温室效应最小化：一项基于模拟的研究。

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-09-24 DOI: 10.1007/s10867-025-09691-9

Resat Ozgur Doruk

引用次数: 0

An effective framework to study signal transmission due to non-homogeneous extracellular space in neuron 一个研究神经元胞外空间非均匀性导致的信号传递的有效框架

IF 2.2 4区生物学

Journal of Biological Physics Pub Date : 2025-08-20 DOI: 10.1007/s10867-025-09689-3

Biswajit Das, Satyabrat Malla Bujar Baruah, Soumik Roy, Dhruba Kumar Bhattacharyya

{"title":"An effective framework to study signal transmission due to non-homogeneous extracellular space in neuron","authors":"Biswajit Das, Satyabrat Malla Bujar Baruah, Soumik Roy, Dhruba Kumar Bhattacharyya","doi":"10.1007/s10867-025-09689-3","DOIUrl":"10.1007/s10867-025-09689-3","url":null,"abstract":"<div><p>Nerve conduction velocity studies are essential to understanding neurological disorders like ALS, Guillain-Barré syndrome, Charcot-Marie-Tooth disease, carpal tunnel syndrome, sciatic nerve disorders, and multiple sclerosis, which are marked by slowed signal conduction. Various ions in the extracellular space (ECS) and the nerve fiber regulate signal propagation, making it crucial to analyze ECS’s impact on signal transmission. This study examines how a non-homogeneous extracellular space affects nerve conduction velocity using a modified cable model that incorporates ECS parameters such as its diameter and resistance. The results suggest that a non-homogeneous extracellular space significantly impacts the conduction velocity of propagating signals, leading to variations in the conduction velocity, signal delays, phase shifts, and resonance. The model has been thoroughly examined using various combinations of electrophysiological parameters of the ECS and nerve fibers to simulate a wide range of biological conditions, and the simulated results have been consistent and align with the existing findings.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"51 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144880794","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}

引用次数: 0