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Automatic classification of seizure and seizure-free EEG signals based on phase space reconstruction features J. Biol. Phys. (IF 1.8) Pub Date : 2024-03-11 Shervin Skaria, Sreelatha Karyaveetil Savithriamma
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Similarity analysis of bioconvection of unsteady nonhomogeneous hybrid nanofluids influenced by motile microorganisms J. Biol. Phys. (IF 1.8) Pub Date : 2024-01-23 Samah Mohamed Mabrouk, Mustafa Inc, Ahmed Saad Rashed, Ali Akgül
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Microrheological comparison of melanoma cells by atomic force microscopy J. Biol. Phys. (IF 1.8) Pub Date : 2024-01-19 M. Manuela Brás, Aureliana Sousa, Tânia B. Cruz, Jonas Michalewski, Marina Leite, Susana R. Sousa, Pedro L. Granja, Manfred Radmacher
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Roles of astrocytes and prions in Alzheimer’s disease: insights from mathematical modeling J. Biol. Phys. (IF 1.8) Pub Date : 2023-12-29 Mitali Maji, Subhas Khajanchi
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Base flipping mechanism and binding strength of methyl-damaged DNA during the interaction with AGT J. Biol. Phys. (IF 1.8) Pub Date : 2023-12-27
Abstract 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
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Generic algebraic conditions for the occurrence of switch-like behavior of a chemical kinetic system of the hypoxia pathway J. Biol. Phys. (IF 1.8) Pub Date : 2023-12-21
Abstract 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
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Structural insights into the pathogenicity of point mutations in human acyl-CoA dehydrogenase homotetramers J. Biol. Phys. (IF 1.8) Pub Date : 2023-12-16 Homa Faraji, Azadeh Ebrahim-Habibi
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Microfluidic technology for cell biology–related applications: a review J. Biol. Phys. (IF 1.8) Pub Date : 2023-12-06 Joydeb Mukherjee, Deepa Chaturvedi, Shlok Mishra, Ratnesh Jain, Prajakta Dandekar
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Ion currents through the voltage sensor domain of distinct families of proteins J. Biol. Phys. (IF 1.8) Pub Date : 2023-10-18 César Arcos-Hernández, Takuya Nishigaki
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High order sliding mode control for restoration of a population of predators in a Lotka-Volterra system J. Biol. Phys. (IF 1.8) Pub Date : 2023-10-06 Jesica A. Escobar, Ana Gabriela Gallardo-Hernandez, Marcos Angel Gonzalez-Olvera, Cristina Revilla-Monsalve, Debbie Hernandez, Ron Leder
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Impact of noise on the instability of spiral waves in stochastic 2D mathematical models of human atrial fibrillation J. Biol. Phys. (IF 1.8) Pub Date : 2023-10-04 Euijun Song
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Synchronization in STDP-driven memristive neural networks with time-varying topology J. Biol. Phys. (IF 1.8) Pub Date : 2023-09-01 Marius E. Yamakou, Mathieu Desroches, Serafim Rodrigues
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Suppression of beta oscillations by delayed feedback in a cortex-basal ganglia-thalamus-pedunculopontine nucleus neural loop model J. Biol. Phys. (IF 1.8) Pub Date : 2023-08-12 Yuqin Sun, Jiali Lü, Ye Zhou, Yingpeng Liu, Yuan Chai
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Thermal transport across membranes and the Kapitza length from photothermal microscopy J. Biol. Phys. (IF 1.8) Pub Date : 2023-07-21 Panagis D. Samolis, Michelle Y. Sander, Mi K. Hong, Shyamsunder Erramilli, Onuttom Narayan
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Identifying key factors in cell fate decisions by machine learning interpretable strategies J. Biol. Phys. (IF 1.8) Pub Date : 2023-07-17 Xinyu He, Ruoyu Tang, Jie Lou, Ruiqi Wang
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Numerical simulation of calcium dynamics dependent ATP degradation, IP3 and NADH production due to obesity in a hepatocyte cell J. Biol. Phys. (IF 1.8) Pub Date : 2023-07-06 Vedika Mishra, Neeru Adlakha
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Analysis of SARS-CoV-2 interactions with the Vero cell lines by scanning electron microscopy J. Biol. Phys. (IF 1.8) Pub Date : 2023-06-30 Zuzana Malá, Marek Vojta, Jan Loskot, Radek Sleha, Bruno Ježek, Josef Zelenka
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In-phase and anti-phase bursting dynamics and synchronisation scenario in neural network by varying coupling phase J. Biol. Phys. (IF 1.8) Pub Date : 2023-05-17 Thazhathethil Remi, Pallimanhiyil Abdulraheem Subha
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Modified diffusive epidemic process on Apollonian networks J. Biol. Phys. (IF 1.8) Pub Date : 2023-04-29 David Alencar, Antonio Filho, Tayroni Alves, Gladstone Alves, Ronan Ferreira, Francisco Lima
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Evaluation of copper-induced biomolecular changes in different porin mutants of Escherichia coli W3110 by infrared spectroscopy J. Biol. Phys. (IF 1.8) Pub Date : 2023-04-03 Gulcin Cetin Kilicaslan, Rafig Gurbanov, Cihan Darcan
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Effect of strain rates on the mechanical response of whole muscle bundle J. Biol. Phys. (IF 1.8) Pub Date : 2023-04-03 Dat Trong Tran, Liren Tsai
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A biomechanical view of epigenetic tumor regulation J. Biol. Phys. (IF 1.8) Pub Date : 2023-04-01 Boyuan Zhao, Yonggang Lv
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Revisiting and redefining return rate for determination of the precise growth status of a species J. Biol. Phys. (IF 1.8) Pub Date : 2023-03-22 Ayan Paul, Neelakshi Chatterjee, Sabyasachi Bhattacharya
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Electrostatic effects on water-soluble fullerene derivatives interaction with cytochrome c and cytochrome c oxidase J. Biol. Phys. (IF 1.8) Pub Date : 2023-03-18 Darya A. Poletaeva, Raisa A. Kotelnikova, Irina I. Faingold, Olga A. Kraevaya, Pavel A. Troshin, Alexander I. Kotelnikov
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Probing the binding of morin with alpha-2-macroglobulin using multi-spectroscopic and molecular docking approach J. Biol. Phys. (IF 1.8) Pub Date : 2023-03-13 Sana Ansari, Mohammad Khalid Zia, Shamila Fatima, Haseeb Ahsan, Fahim H. Khan
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Neural waves and short-term memory in a neural net model J. Biol. Phys. (IF 1.8) Pub Date : 2023-03-02 Stephen Selesnick
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Cellular nitric oxide synthesis is affected by disorders in the interdependent $$Ca^{2+}$$ and $$IP_{3}$$ dynamics during cystic fibrosis disease J. Biol. Phys. (IF 1.8) Pub Date : 2023-02-22 Ankit B. Kothiya, Neeru Adlakha
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Bistability regulates TNFR2-mediated survival and death of T-regulatory cells J. Biol. Phys. (IF 1.8) Pub Date : 2023-02-13 Suvankar Halder, Samrat Chatterjee
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Adaptive behaviors of Drosophila larvae on slippery surfaces J. Biol. Phys. (IF 1.8) Pub Date : 2023-02-15 Li Guo, Yixuan Sun, Sijian Liu
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Exploring the interaction of myricetin with human alpha-2-macroglobulin: biophysical and in-silico analysis J. Biol. Phys. (IF 1.8) Pub Date : 2023-01-20 Sana Ansari, Haseeb Ahsan, Mohammad Khalid Zia, Mansour K. Gatasheh, Fahim H. Khan
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Determinant factors for residence time of kinesin motors at microtubule ends J. Biol. Phys. (IF 1.8) Pub Date : 2023-01-16 Ping Xie
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Energy-guided synapse coupling between neurons under noise J. Biol. Phys. (IF 1.8) Pub Date : 2023-01-14 Bo Hou, Jun Ma, Feifei Yang
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Computational analysis of synergism in small networks with different logic J. Biol. Phys. (IF 1.8) Pub Date : 2022-12-29 Menghan Chen, Ruiqi Wang
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Clinical effects of 2-DG drug restraining SARS-CoV-2 infection: A fractional order optimal control study J. Biol. Phys. (IF 1.8) Pub Date : 2022-12-02 Piu Samui, Jayanta Mondal, Bashir Ahmad, Amar Nath Chatterjee
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Functionalization and Haemolytic analysis of pure superparamagnetic magnetite nanoparticle for hyperthermia application J. Biol. Phys. (IF 1.8) Pub Date : 2022-11-25 Hemalatha Kothandaraman, Alamelumangai Kaliyamoorthy, Arulmozhi Rajaram, Chandunika R. Kalaiselvan, Niroj Kumar Sahu, Parthipan Govindasamy, Muralidharan Rajaram
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Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV J. Biol. Phys. (IF 1.8) Pub Date : 2022-11-23 Uma Shekhawat, Anindita Roy Chowdhury (Chakravarty)
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A pilot study of ion current estimation by ANN from action potential waveforms J. Biol. Phys. (IF 1.8) Pub Date : 2022-11-14 Sevgi Şengül Ayan, Selim Süleymanoğlu, Hasan Özdoğan
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A dynamical model of combination therapy applied to glioma J. Biol. Phys. (IF 1.8) Pub Date : 2022-11-11 Handoko Handoko, Setyanto Tri Wahyudi, Ardian Arif Setyawan, Agus Kartono
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Effect of detachment of motor protein from track on its transport J. Biol. Phys. (IF 1.8) Pub Date : 2022-10-03 Mohd Suhail Rizvi
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Fisetin decreases the duration of ictal-like discharges in mouse hippocampal slices J. Biol. Phys. (IF 1.8) Pub Date : 2022-08-10 Hilal Ozturk, Harun Basoglu, Nuri Yorulmaz, Selcen Aydin-Abidin, Ismail Abidin
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How to discern external acoustic waves in a piezoelectric neuron under noise? J. Biol. Phys. (IF 1.8) Pub Date : 2022-08-10 Ying Xie, Jun Ma
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Noise-induced collective dynamics in the small-world network of photosensitive neurons J. Biol. Phys. (IF 1.8) Pub Date : 2022-07-25 Fan Li, Xiaola Li, Liqing Ren
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Instantaneous maturity rate: a novel and compact characterization of biological growth curve models J. Biol. Phys. (IF 1.8) Pub Date : 2022-07-02 Biman Chakraborty, Amiya Ranjan Bhowmick, Joydev Chattopadhyay, Sabyasachi Bhattacharya
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Effect of Joule heating and entropy generation on multi-slip condition of peristaltic flow of Casson nanofluid in an asymmetric channel J. Biol. Phys. (IF 1.8) Pub Date : 2022-04-28 Asha Kotnurkar, Namrata Kallolikar
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“Flexible hinge” dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy J. Biol. Phys. (IF 1.8) Pub Date : 2022-04-22 Timour B. Ten, Viktoriya Zvoda, Manas K. Sarangi, Serguei V. Kuznetsov, Anjum Ansari
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Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model J. Biol. Phys. (IF 1.8) Pub Date : 2022-04-20 Ke Tang, Jorjethe Roca, Rong Chen, Anjum Ansari, Jie Liang
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Quantification of adaptive forces on SNP rs1010211 due to viral zoonotic pathogens J. Biol. Phys. (IF 1.8) Pub Date : 2022-04-15 Daniah Alsufyani, James Lindesay
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Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides J. Biol. Phys. (IF 1.8) Pub Date : 2022-04-14 Sergio A. Hassan, Peter J. Steinbach
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Interaction among bovine serum albumin (BSA) molecules in the presence of anions: a small-angle neutron scattering study J. Biol. Phys. (IF 1.8) Pub Date : 2022-04-13 Subhankar Pandit, Sarathi Kundu, Vinod K. Aswal
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Investigation of extracellular medium osmolality depending on zinc application and incubation time on A549 cancer cells J. Biol. Phys. (IF 1.8) Pub Date : 2022-03-24 Duygu Tarhan, Nural Pastaci Özsobaci, Dilek Düzgün Ergün, Alev Meltem Ercan
Changes in the osmolality of the extracellular medium (ECM) affect cell volume and cellular processes such as cell migration and proliferation. Not only may high concentrations of zinc (Zn) lead to cell death by apoptosis, but Zn is also a physiological suppressor of apoptosis. The aim of our study was to examine whether Zn and regulation of extracellular osmolality had an effect on the lung cancer
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A neurocomputational model for the processing of conflicting information in context-dependent decision tasks J. Biol. Phys. (IF 1.8) Pub Date : 2022-03-08 Francisco M. López, Andrés Pomi
Context-dependent computation is a relevant characteristic of neural systems, endowing them with the capacity of adaptively modifying behavioral responses and flexibly discriminating between relevant and irrelevant information in a stimulus. This ability is particularly highlighted in solving conflicting tasks. A long-standing problem in computational neuroscience, flexible routing of information,
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Study of β-lactam-based drug interaction with albumin protein using optical, sensing, and docking methods J. Biol. Phys. (IF 1.8) Pub Date : 2022-01-30 Hannaneh Monirinasab, Mostafa Zakariazadeh, Havva Kohestani, Morteza Kouhestani, Farzaneh Fathi
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Biological computation: hearts and flytraps J. Biol. Phys. (IF 1.8) Pub Date : 2022-01-28 Kay L. Kirkpatrick
The original computers were people using algorithms to get mathematical results such as rocket trajectories. After the invention of the digital computer, brains have been widely understood through analogies with computers and now artificial neural networks, which have strengths and drawbacks. We define and examine a new kind of computation better adapted to biological systems, called biological computation
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The effects of temperature on the dynamics of the biological neural network J. Biol. Phys. (IF 1.8) Pub Date : 2022-01-21 Mohammad B Jabbari, Mahdi Rezaei Karamati
The nerve cells are responsible for transmitting messages through the action potential, which generates electrical stimulation. One of the methods and tools of electrical stimulation is infrared neural stimulation (INS). Since the mechanism of INS is based on electromagnetic radiation, it explains how a neuron is stimulated by the heat distribution which is generated by the laser. The present study
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Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model J. Biol. Phys. (IF 1.8) Pub Date : 2022-01-09 Xun Chen, Wei Lu, Min-Yeh Tsai, Shikai Jin, Peter G. Wolynes
Heme is an active center in many proteins. Here we explore computationally the role of heme in protein folding and protein structure. We model heme proteins using a hybrid model employing the AWSEM Hamiltonian, a coarse-grained forcefield for the protein chain along with AMBER, an all-atom forcefield for the heme. We carefully designed transferable force fields that model the interactions between the
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Pushing the limits of luminescence thermometry: probing the temperature of proteins in cells J. Biol. Phys. (IF 1.8) Pub Date : 2022-01-07 Maciel, Glauco S.
Proteins are involved in numerous cellular activities such as transport and catalysis. Misfolding during biosynthesis and malfunctioning as a molecular machine may lead to physiological disorders and metabolic problems. Protein folding and mechanical work may be viewed as thermodynamic energetically favorable processes in which stochastic nonequilibrium intermediate states may be present with conditions
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The identifiability of gene regulatory networks: the role of observation data J. Biol. Phys. (IF 1.8) Pub Date : 2022-01-06 Huang, Xiao-Na, Shi, Wen-Jia, Zhou, Zuo, Zhang, Xue-Jun
Identifying gene regulatory networks (GRN) from observation data is significant to understand biological systems. Conventional studies focus on improving the performance of identification algorithms. However, besides algorithm performance, the GRN identification is strongly depended on the observation data. In this work, for three GRN S-system models, three observation data collection schemes are used
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Correction to: Predictive landscapes hidden beneath biological cellular automata. J. Biol. Phys. (IF 1.8) Pub Date : 2022-03-01 Lars Koopmans,Hyun Youk
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Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems J. Biol. Phys. (IF 1.8) Pub Date : 2021-11-25 Wang, Jin
We give a review on the landscape theory of the equilibrium biological systems and landscape-flux theory of the nonequilibrium biological systems as the global driving force. The emergences of the behaviors, the associated thermodynamics in terms of the entropy and free energy and dynamics in terms of the rate and paths have been quantitatively demonstrated. The hierarchical organization structures
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Shape transformations of red blood cells in the capillary and their possible connections to oxygen transportation J. Biol. Phys. (IF 1.8) Pub Date : 2021-11-19 Wang, Caiqun, Li, Jianfeng, Zhao, Liutao, Qian, Ping
In this work, a series of numerical simulations have been performed to obtain the steady shapes of red blood cells under a shear force field in the capillary. Two possible classes of steady shapes, the axisymmetric parachute and the non-axisymmetric parachute, are found. If we assume that oxygen diffusion across the red cell membrane is mediated by membrane curvature, it is found that the non-axisymmetric