Journal of Biological Physics最新文献_第10页

Computational analysis of synergism in small networks with different logic 不同逻辑下小网络协同效应的计算分析

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-12-29 DOI: 10.1007/s10867-022-09620-0

Menghan Chen, Ruiqi Wang

{"title":"Computational analysis of synergism in small networks with different logic","authors":"Menghan Chen, Ruiqi Wang","doi":"10.1007/s10867-022-09620-0","DOIUrl":"10.1007/s10867-022-09620-0","url":null,"abstract":"<div><p>Cell fate decision processes are regulated by networks which contain different molecules and interactions. Different network topologies may exhibit synergistic or antagonistic effects on cellular functions. Here, we analyze six most common small networks with regulatory logic AND or OR, trying to clarify the relationship between network topologies and synergism (or antagonism) related to cell fate decisions. We systematically examine the contribution of both network topologies and regulatory logic to the cell fate synergism by bifurcation and combinatorial perturbation analysis. Initially, under a single set of parameters, the synergism of three types of networks with AND and OR logic is compared. Furthermore, to consider whether these results depend on the choices of parameter values, statistics on the synergism of five hundred parameter sets is performed. It is shown that the results are not sensitive to parameter variations, indicating that the synergy or antagonism mainly depends on the network topologies rather than the choices of parameter values. The results indicate that the topology with “Dual Inhibition” shows good synergism, while the topology with “Dual Promotion” or “Hybrid” shows antagonism. The results presented here may help us to design synergistic networks based on network structure and regulation combinations, which has promising implications for cell fate decisions and drug combinations.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 1","pages":"1 - 27"},"PeriodicalIF":1.8,"publicationDate":"2022-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09620-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5111799","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}

引用次数: 0

Clinical effects of 2-DG drug restraining SARS-CoV-2 infection: A fractional order optimal control study 2-DG药物抑制SARS-CoV-2感染的临床效果:分数阶最优对照研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-12-02 DOI: 10.1007/s10867-022-09617-9

Piu Samui, Jayanta Mondal, Bashir Ahmad, Amar Nath Chatterjee

{"title":"Clinical effects of 2-DG drug restraining SARS-CoV-2 infection: A fractional order optimal control study","authors":"Piu Samui, Jayanta Mondal, Bashir Ahmad, Amar Nath Chatterjee","doi":"10.1007/s10867-022-09617-9","DOIUrl":"10.1007/s10867-022-09617-9","url":null,"abstract":"<div><p>Fractional calculus is very convenient tool in modeling of an emergent infectious disease system comprising previous disease states, memory of disease patterns, profile of genetic variation etc. Significant complex behaviors of a disease system could be calibrated in a proficient manner through fractional order derivatives making the disease system more realistic than integer order model. In this study, a fractional order differential equation model is developed in micro level to gain perceptions regarding the effects of host immunological memory in dynamics of SARS-CoV-2 infection. Additionally, the possible optimal control of the infection with the help of an antiviral drug, viz. 2-DG, has been exemplified here. The fractional order optimal control would enable to employ the proper administration of the drug minimizing its systematic cost which will assist the health policy makers in generating better therapeutic measures against SARS-CoV-2 infection. Numerical simulations have advantages to visualize the dynamical effects of the immunological memory and optimal control inputs in the epidemic system.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 4","pages":"415 - 438"},"PeriodicalIF":1.8,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09617-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4074323","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}

引用次数: 3

Functionalization and Haemolytic analysis of pure superparamagnetic magnetite nanoparticle for hyperthermia application 用于热疗的纯超顺磁性纳米磁铁矿的功能化和溶血分析

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-25 DOI: 10.1007/s10867-022-09614-y

Hemalatha Kothandaraman, Alamelumangai Kaliyamoorthy, Arulmozhi Rajaram, Chandunika R. Kalaiselvan, Niroj Kumar Sahu, Parthipan Govindasamy, Muralidharan Rajaram

{"title":"Functionalization and Haemolytic analysis of pure superparamagnetic magnetite nanoparticle for hyperthermia application","authors":"Hemalatha Kothandaraman, Alamelumangai Kaliyamoorthy, Arulmozhi Rajaram, Chandunika R. Kalaiselvan, Niroj Kumar Sahu, Parthipan Govindasamy, Muralidharan Rajaram","doi":"10.1007/s10867-022-09614-y","DOIUrl":"10.1007/s10867-022-09614-y","url":null,"abstract":"<div><p>Superparamagnetic iron oxide nanoparticles (SPIONPs) are widely used in clinical research. The single domain nanoparticles are used in magnetic fluid hyperthermia (MFH) to treat cancer. When nanoparticles are exposed to an external magnetic field, it generates heat destroying tumour cells. SPIONPs have a large surface area, so the particles tend to aggregate, which leads to the destabilization of the colloidal system. To enhance the stability and biocompatibility of the nanomaterials, it is necessary to coat the surface with biocompatible material. Magnetite (Fe<sub>3</sub>O<sub>4</sub>) is a superparamagnetic nanoparticle (SPNPs) that was functionalized with oleic acid (OA) by sol–gel process using ethanol as the solvent. The oleic acid-coated magnetite (OA-Fe<sub>3</sub>O<sub>4</sub>) was characterized by X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), thermogravimetric analysis (TGA), UV–Visible diffuse reflectance spectroscopy (UV-DRS) and vibrating sample magnetometer (VSM). The haemolysis test has been used to investigate the haemocompatibility properties of nanomaterials. Hyperthermia study shows a high SAR value for the concentration of 1 mg/ml at the field of 600 Oe and frequency of 316 kHz. The OA coating enhanced the haemocompatibility of synthesized magnetite nanoparticles which can be used for magnetic fluid hyperthermia applications.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 4","pages":"383 - 397"},"PeriodicalIF":1.8,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09614-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4983430","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}

引用次数: 0

Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV SARS-CoV-2和SARS-CoV刺突蛋白疏水性谱的计算和比较研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-23 DOI: 10.1007/s10867-022-09615-x

Uma Shekhawat, Anindita Roy Chowdhury (Chakravarty)

引用次数: 2

A pilot study of ion current estimation by ANN from action potential waveforms 基于动作电位波形的人工神经网络估计离子电流的初步研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-14 DOI: 10.1007/s10867-022-09619-7

Sevgi Şengül Ayan, Selim Süleymanoğlu, Hasan Özdoğan

{"title":"A pilot study of ion current estimation by ANN from action potential waveforms","authors":"Sevgi Şengül Ayan, Selim Süleymanoğlu, Hasan Özdoğan","doi":"10.1007/s10867-022-09619-7","DOIUrl":"10.1007/s10867-022-09619-7","url":null,"abstract":"<div><p>Experiments using conventional experimental approaches to capture the dynamics of ion channels are not always feasible, and even when possible and feasible, some can be time-consuming. In this work, the ionic current–time dynamics during cardiac action potentials (APs) are predicted from a single AP waveform by means of artificial neural networks (ANNs). The data collection is accomplished by the use of a single-cell model to run electrophysiological simulations in order to identify ionic currents based on fluctuations in ion channel conductance. The relevant ionic currents, as well as the corresponding cardiac AP, are then calculated and fed into the ANN algorithm, which predicts the desired currents solely based on the AP curve. The validity of the proposed methodology for the Bayesian approach is demonstrated by the R (validation) scores obtained from training data, test data, and the entire data set. The Bayesian regularization’s (BR) strength and dependability are further supported by error values and the regression presentations, all of which are positive indicators. As a result of the high convergence between the simulated currents and the currents generated by including the efficacy of a developed Bayesian solver, it is possible to generate behavior of ionic currents during time for the desired AP waveform for any electrical excitable cell.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 4","pages":"461 - 475"},"PeriodicalIF":1.8,"publicationDate":"2022-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09619-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4585221","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}

引用次数: 0

Correction to: Non-extensitivity and criticality of atomic hydropathicity around a voltage-gated sodium channel’s pore: a modeling study 修正:电压门控钠通道孔周围原子亲水性的非广泛性和临界性:模型研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-12 DOI: 10.1007/s10867-022-09616-w

Markos N. Xenakis, Dimos Kapetis, Yang Yang, Jordi Heijman, Stephen G. Waxman, Giuseppe Lauria, Catharina G. Faber, Hubert J. Smeets, Patrick J. Lindsey, Ronald L. Westra

引用次数: 0

A dynamical model of combination therapy applied to glioma 胶质瘤联合治疗的动力学模型

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-11-11 DOI: 10.1007/s10867-022-09618-8

Handoko Handoko, Setyanto Tri Wahyudi, Ardian Arif Setyawan, Agus Kartono

{"title":"A dynamical model of combination therapy applied to glioma","authors":"Handoko Handoko, Setyanto Tri Wahyudi, Ardian Arif Setyawan, Agus Kartono","doi":"10.1007/s10867-022-09618-8","DOIUrl":"10.1007/s10867-022-09618-8","url":null,"abstract":"<div><p>Glioma is a human brain tumor that is very difficult to treat at an advanced stage. Studies of glioma biomarkers have shown that some markers are released into the bloodstream, so data from these markers indicate a decrease in the concentration of blood glucose and serum glucose in patients with glioma; these suggest an association between glucose and glioma. This decrease mechanism in glucose concentration can be described by the coupled ordinary differential equations of the early-stage glioma growth and interactions between glioma cells, immune cells, and glucose concentration. In this paper, we propose developing a new mathematical model to explain how glioma cells evolve and survive combination therapy between chemotherapy and oncolytic virotherapy, as an alternative to glioma treatment. In this study, three therapies were applied for analysis, that is, (1) chemotherapy, (2) virotherapy, and (3) a combination of chemotherapy and virotherapy. Virotherapy uses specialist viruses that only attack tumor cells. Based on the simulation results of the therapy carried out, we conclude that combination therapy can reduce the glioma cells significantly compared to the other two therapies. The simulation results of this combination therapy can be an alternative to glioma therapy.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 4","pages":"439 - 459"},"PeriodicalIF":1.8,"publicationDate":"2022-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09618-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4476301","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}

引用次数: 0

Effect of detachment of motor protein from track on its transport 运动蛋白脱离轨道对其运输的影响

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-10-03 DOI: 10.1007/s10867-022-09613-z

Mohd Suhail Rizvi

引用次数: 0

Fisetin decreases the duration of ictal-like discharges in mouse hippocampal slices 非瑟酮可减少小鼠海马切片中癫痫样放电的持续时间

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-08-10 DOI: 10.1007/s10867-022-09612-0

Hilal Ozturk, Harun Basoglu, Nuri Yorulmaz, Selcen Aydin-Abidin, Ismail Abidin

{"title":"Fisetin decreases the duration of ictal-like discharges in mouse hippocampal slices","authors":"Hilal Ozturk, Harun Basoglu, Nuri Yorulmaz, Selcen Aydin-Abidin, Ismail Abidin","doi":"10.1007/s10867-022-09612-0","DOIUrl":"10.1007/s10867-022-09612-0","url":null,"abstract":"<div><p>There is an increasing interest in the biological and therapeutic effects of fisetin, a natural phenolic compound. Fisetin has affinity on some neuronal targets and may have the potential to modulate neuronal activity. In this study the effects of acute application of fisetin on synchronized events were evaluated electro-physiologically. Besides, interaction of fisetin with closely related channels were investigated in silico. Acute horizontal hippocampal slices were obtained from 32- to 36-day-old C57BL/6 mice. Extracellular field potentials were recorded from CA3 region of the hippocampus. Bath application of 4 aminopyridine (4AP, 100 µM) initiated ictal- and interictal-like synchronized epileptiform discharges in the brain slices. Fifty micromolar fisetin was applied to the recording chamber during the epileptiform activity. The duration and frequencies of both ictal-like and interictal-like activities were calculated from the electrophysiological records. Molecular docking was performed to reveal interaction of fisetin on GABA-A, NMDA, AMPA receptors, and HCN2 channel, which are neuronal structures directly involved in recorded activity. Although fisetin does not affect basal neuronal activity in brain slice, it reduced the duration of ictal-like discharges significantly. Molecular docking results indicated that fisetin has no effect on GABA-A, NMDA, and AMPA receptors. However, fisetin binds to the (5JON) HCN2 channel strongly with the binding energy of −7.66 kcal/mol. Reduction on the duration of 4AP-induced ictal-like discharges can be explained as HCN channels can cause an inhibitory effect via enhancing M-type K + channels which increase K outward currents.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 3","pages":"355 - 368"},"PeriodicalIF":1.8,"publicationDate":"2022-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09612-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4413961","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}

引用次数: 2

How to discern external acoustic waves in a piezoelectric neuron under noise? 如何在噪声下辨别压电神经元中的外部声波？

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-08-10 DOI: 10.1007/s10867-022-09611-1

Ying Xie, Jun Ma

{"title":"How to discern external acoustic waves in a piezoelectric neuron under noise?","authors":"Ying Xie, Jun Ma","doi":"10.1007/s10867-022-09611-1","DOIUrl":"10.1007/s10867-022-09611-1","url":null,"abstract":"<div><p>Biological neurons keep sensitive to external stimuli and appropriate firing modes can be triggered to give effective response to external chemical and physical signals. A piezoelectric neural circuit can perceive external voice and nonlinear vibration by generating equivalent piezoelectric voltage, which can generate an equivalent trans-membrane current for inducing a variety of firing modes in the neural activities. Biological neurons can receive external stimuli from more ion channels and synapse synchronously, but the further encoding and priority in mode selection are competitive. In particular, noisy disturbance and electromagnetic radiation make it more difficult in signals identification and mode selection in the firing patterns of neurons driven by multi-channel signals. In this paper, two different periodic signals accompanied by noise are used to excite the piezoelectric neural circuit, and the signal processing in the piezoelectric neuron driven by acoustic waves under noise is reproduced and explained. The physical energy of the piezoelectric neural circuit and Hamilton energy in the neuron driven by mixed signals are calculated to explain the biophysical mechanism of auditory neuron when external stimuli are applied. It is found that the neuron prefers to respond to the external stimulus with higher physical energy and the signal which can increase the Hamilton energy of the neuron. For example, stronger inputs used to inject higher energy and it is detected and responded more sensitively. The involvement of noise is helpful to detect the external signal under stochastic resonance, and the additive noise changes the excitability of neuron as the external stimulus. The results indicate that energy controls the firing patterns and mode selection in neurons, and it provides clues to control the neural activities by injecting appropriate energy into the neurons and network.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 3","pages":"339 - 353"},"PeriodicalIF":1.8,"publicationDate":"2022-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09611-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4411131","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}

引用次数: 11