Preprints (not yet peer-reviewed)

65 downloads
201 views

This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones play first, could correspond to metastasis of cancer. Moreover, playing white stones on the second...

["Bioinformatics","Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.3434v1
244 downloads
1,385 views

Exposure to non-ionizing radiation used in wireless communication remains a contentious topic in the public mind - while the overwhelming scientific evidence to date suggests that microwave and radio frequencies used in modern communications are safe, public apprehension...

["Biophysics","Environmental Sciences","Cognitive Disorders","Oncology","Science and Medical Education"]
doi:10.7287/peerj.preprints.3355v1
154 downloads
520 views

Microbes often live in dense, dynamic, multi-species communities whose architecture and function are intimately intertwined. Imaging these complex, three-dimensional ensembles presents considerable technical challenges, however. In this review, I describe light...

["Biophysics","Microbiology"]
doi:10.7287/peerj.preprints.3135v2
39 downloads
137 views

1,4-dihydropyridines (1,4-DHP) possess important biochemical and pharmacological properties, including antioxidant and antimutagenic activities. Interaction of some 1,4-DHP with DNA was recently reported. AV-153-Na, an antimutagenic and DNA-repair-enhancing compound...

["Biophysics","Drugs and Devices"]
doi:10.7287/peerj.preprints.3317v1
51 downloads
121 views

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to...

["Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.3306v1
25 downloads
87 views

Scale transcends multiple levels of biological and physical organization, and is the critical factor that determines success of any scientific investigation. Specifically, the scale at which a question is posed plays a crucial role in influencing the type of experiments...

["Biochemistry","Bioengineering","Biophysics","Biotechnology","Cell Biology"]
doi:10.7287/peerj.preprints.3261v1
1,220 downloads
2,318 views

Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy parameter for bacterial cell surface charge. Nonspecific adsorption of ions or polyelectrolytes onto the cell surface, however, alters the value and polarity of the measured...

["Bioengineering","Biophysics","Biotechnology","Environmental Sciences","Microbiology"]
doi:10.7287/peerj.preprints.110v7
63 downloads
166 views

The osmotic pressure of chondroitin sulfate glycosaminoglycans (CS-GAGs) in a simulated physiological environment of articular cartilage is thoroughly examined in silico using full atomistic models. The effects of chemical and physical properties were investigated...

["Biochemistry","Biophysics","Computational Biology","Anatomy and Physiology","Rheumatology"]
doi:10.7287/peerj.preprints.3063v1
38 downloads
303 views

A complete understanding of the feeding structures is fundamental in order to study how animals survive. Some birds use long and protrusible tongues as the main tool to collect their central caloric source (e.g. woodpeckers and nectarivores). Hummingbirds are the...

["Biophysics","Zoology","Anatomy and Physiology"]
doi:10.7287/peerj.preprints.2986v1
411 downloads
541 views

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for...

["Biochemistry","Bioinformatics","Biophysics","Pharmacology","Computational Science"]
doi:10.7287/peerj.preprints.2857v2
71 downloads
195 views

Membrane proteins are the most medicinally important yet to be fully exploited pharmaceutical targets. Here druggability analyses are conducted on three different membrane proteins, namely, the human P2Y12 receptor, glycoprotein-41 that mediates the HIV-1 virus...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2868v1
37 downloads
227 views

The importance of histidine tautomerism for an accurate drug/protein structure determination and their relevance for the interaction between biological systems is recognized. Consequently, here we used a recently introduced method to determine the pKa values of...

["Bioinformatics","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2816v1
41 downloads
255 views

Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, 3-dimensional molecular structure analysis of P-type ATPases...

["Biochemistry","Bioinformatics","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2812v1
28 downloads
191 views

It is now widely accepted that oligomers consisting of Aβ peptide are the cytotoxic species contributing mostly to the development of Alzheimer’s disease. Aβ peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP)....

["Biophysics","Biotechnology","Cell Biology","Molecular Biology","Neuroscience"]
doi:10.7287/peerj.preprints.2804v1
70 downloads
217 views

Without exception, modern hypotheses explaining the origin of eukaryotes assume evolution from two (or more) distinct prokaryotes. Almost all prokaryotic cell membranes possess a chemiosmosis system, whereas eukaryotic cell membranes have lost that ability. Nevertheless,...

["Biophysics","Evolutionary Studies"]
doi:10.7287/peerj.preprints.2802v1
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