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biophysics

1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability...

["Biochemistry","Biophysics","Drugs and Devices","Pharmacology"]
doi:10.7717/peerj.2299

The F1 sub-complex of ATP synthase is a biological nanomotor that converts the free energy of ATP hydrolysis into mechanical work with an astonishing efficiency of up to 100% (Kinosita et al., 2000). To probe the principal mechanics of the machine, I re-engineered...

["Biochemistry","Bioengineering","Biophysics","Synthetic Biology"]
doi:10.7717/peerj.2286
7 downloads
95 views

Bacteria surface charge derives its meaning from the cell’s environment; thus, there is no specific surface charge. Determining the surface charge of bacteria in its native environment requires measuring the proxy variable, zeta potential, using cells obtained...

["Bioengineering","Biophysics","Biotechnology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.2086v2
5 downloads
52 views

With increasing sophistication of instruments and techniques, in addition to the increment in intricacies, girth and complexities of the problems being addressed, simple methods (especially computational biology techniques) are being overlooked, replaced or phased...

["Bioinformatics","Biophysics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2296v1
12 downloads
103 views

We present a rationale and proposed approach to the modification and development of bind sites using their respective cognate ligands as template. This is in support of a plausible “instructive” role for the ligand and therefore its involvement in determination...

["Biochemistry","Bioengineering","Biophysics","Biotechnology","Mathematical Biology"]
doi:10.7287/peerj.preprints.2161v2
29 downloads
57 views

Flies use specialized photoreceptors R7 and R8 in the dorsal rim area (DRA) to detect skylight polarization. R7 and R8 form a tiered waveguide (rhabdom) with R7 on top, filtering light delivered to R8. We examine how the division of a given resource, rhabdom length,...

["Animal Behavior","Biophysics","Mathematical Biology","Neuroscience","Zoology"]
doi:10.7287/peerj.preprints.2192v1
48 downloads
452 views

Static properties of leaves with parallel venation, with particular emphasis on the genus EpipactisZinn, 1757 (Orchidaceae, Neottieae) have been modelled with coupled quasi-parallel elastic “beams.” The non-linear theory of strongly bended beams have been employed....

["Agricultural Science","Biophysics","Mathematical Biology","Plant Science"]
doi:10.7717/peerj.2165
22 downloads
80 views

Design and production of polypeptide/proteins with desired bind site properties involves utilization of the ligand of interest in selection of those bind sites that yield the desired properties from an assortment bind sites with different structures and properties....

["Biochemistry","Bioengineering","Biophysics","Biotechnology"]
doi:10.7287/peerj.preprints.2160v1
73 downloads
810 views

Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the...

["Biochemistry","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7717/peerj.2136
72 downloads
246 views

Metabolomic profiling is an increasingly important method for identifying potential biomarkers in cancer cells with a view towards improved diagnosis and treatment. Nuclear magnetic resonance (NMR) provides a potentially noninvasive means to accurately characterize...

["Biophysics","Metabolic Sciences"]
doi:10.7717/peerj.2104
386 downloads
478 views

History is often thought to be dull and boring – where large numbers of facts are memorized for passing exams. But the past informs the present and future, especially in delineating the context surrounding specific events that, in turn, help provide a deeper understanding...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.552v4
109 downloads
476 views

Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the...

["Biophysics","Pharmacology","Computational Science"]
doi:10.7717/peerj.2088
89 downloads
351 views

The PM6 semiempirical method and the dispersion and hydrogen bond-corrected PM6-D3H+ method are used together with the SMD and COSMO continuum solvation models to predict pKa values of pyridines, alcohols, phenols, benzoic acids, carboxylic acids, and phenols using...

["Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2075v1
603 downloads
431 views

The past influence the present and future; for example, in computational chemistry, simplifying assumptions and approximations important to problem solving in the pre-computing era remains relevant today in allowing simulation of larger systems with reasonable...

["Biochemistry","Bioengineering","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.365v2
30 downloads
142 views

1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability...

["Biochemistry","Biophysics"]
doi:10.7287/peerj.preprints.1989v2

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