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biophysics

Sustained oscillations are frequently observed in biological systems consisting of a negative feedback loop, but a mathematical model with two ordinary differential equations (ODE) that has a negative feedback loop structure fails to produce sustained oscillations....

["Biophysics","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1272v1
64 downloads
223 views

Valveless, tubular pumps are widespread in the animal kingdom, but the mechanism by which these pumps generate fluid flow are often in dispute. Where the pumping mechanism of many organs was once described as peristalsis, other mechanisms, such as dynamic suction...

["Bioengineering","Biophysics","Computational Biology","Developmental Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.906v2
5 downloads
73 views

Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H+-assisted cleavage of the Hg–C bond of methylmercury...

["Biochemistry","Biophysics"]
doi:10.7717/peerj.1127
5 downloads
90 views

Electroencephalography (EEG) signals’ interpretation is based on waveform analysis, where meaningful information should emerge from a plethora of data. Nonetheless, the continuous increase in computational power and the development of new data processing algorithms...

["Bioengineering","Bioinformatics","Biophysics","Neuroscience","Neurology"]
doi:10.7287/peerj.preprints.1265v1
26 downloads
40 views

We show here that chicken gizzard caldesmon (CaD) and its C-terminal domain (residues 636-771, CaD136) are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136 and series of its single tryptophan mutants (W674A,...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.1261v1
10 downloads
16 views

This paper explores a possible underlying tenet of classical information-feed pathways (feedback and feedforward) as seen in metabolism and signaling in biological systems. We intend to determine whether information-feed pathways derive from spatial and temporal...

["Biochemistry","Bioengineering","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.1242v1
15 downloads
75 views

This work follows as a response to a problem posed in a previous work (Jeff-Eke, 2015b). Here we propose and explore a probable solution to the posed problem of how well a cellular system can tolerate random changes to the frequency of osmolytes infused into an...

["Biochemistry","Bioengineering","Biophysics","Cell Biology","Computational Biology"]
doi:10.7287/peerj.preprints.1187v2
21 downloads
115 views

This is a companion to A Gauge model for analysis of Biological systems. Here we reconcile the gauge model with a “real” system, which in this case is a unicellular system. We address effects of infusion of free osmolytes into an intracellular space of interest,...

["Biochemistry","Bioengineering","Biophysics","Cell Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1163v2
58 downloads
153 views

For this initial work, we shall focus on introducing a biological model for utilization [mainly] as a descriptive framework on which future analyses will be based. The model includes a definition of a biological systems as a composite of properties that occupy...

["Biophysics","Computational Biology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1148v3
43 downloads
193 views

Synaptic exocytosis requires the assembly of syntaxin 1A and SNAP-25 on the plasma membrane and synaptobrevin 2 (VAMP2) on the vesicular membrane to bridge the two opposite membranes. It is believed that the three SNARE proteins assemble in steps along the dynamic...

["Biochemistry","Biophysics","Microbiology","Neuroscience"]
doi:10.7717/peerj.1065
33 downloads
61 views

Prions are infectious proteins where the same protein may express distinct strains. The strains are enciphered by different misfolded conformations. Strain-like phenomena have also been reported in a number of other amyloid-forming proteins. One of the features...

["Biochemistry","Biophysics"]
doi:10.7287/peerj.preprints.1101v1
58 downloads
438 views

Complex systems may be mechanistically modelled by white-box modeling with using logical deterministic individual-based cellular automata. Mathematical models of complex systems are of three types: black-box (phenomenological), white-box (mechanistic, based on...

["Biophysics","Computational Biology","Ecology","Mathematical Biology","Computational Science"]
doi:10.7717/peerj.948
60 downloads
411 views

Due to alternative splicing, the human ACTN1 gene codes for three different transcripts of α-actinin; one isoform that is expressed only in the brain and two with a more general expression pattern. The sequence difference is located to the C-terminal domains and...

["Biochemistry","Biophysics"]
doi:10.7717/peerj.944
74 downloads
452 views

Background. Datasets consisting of synthetic neural data generated with quantifiable and controlled parameters are a valuable asset in the process of testing and validating directed functional connectivity metrics. Considering the recent debate in the neuroimaging...

["Biophysics","Neuroscience","Computational Science"]
doi:10.7717/peerj.923
59 downloads
252 views

Inducing cell death by heating targeted particles shows promise in cancer treatment. Here, we aim to demonstrate the feasibility of extending the use of this technique to treat and remove vascular deposits and thrombosis. We used induction heating of macrophages,...

["Bioengineering","Biophysics","Drugs and Devices","Translational Medicine"]
doi:10.7717/peerj.929

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