Preprints (not yet peer-reviewed)

25 downloads
126 views

This document is my attempt at distilling some of the information in two papers published by Anthony Nicholls (J. Comput. Aided Mol. Des. 2014, 28, 887; ibid 2016, 30, 103). Anthony also very kindly provided some new equations, not found in the papers, in response...

["Biophysics","Computational Biology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.2693v1
1 download
59 views

Coral reefs are dynamic systems whose composition is highly influenced by unpredictable biotic and abiotic factors. Understanding the spatial scale at which long-term predictions of reef composition can be made will be crucial for guiding conservation efforts....

["Biophysics","Ecology","Marine Biology"]
doi:10.7287/peerj.preprints.2687v1
12 downloads
105 views

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification...

["Biochemistry","Biophysics","Computational Biology","Molecular Biology"]
doi:10.7287/peerj.preprints.2680v1
106 downloads
381 views

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48...

["Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.2564v2
44 downloads
190 views

Background: Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the ablation techniques of electrolytic ablation with cryosurgery. The goal of this study is to examine the hypothesis that electrolysis can take place in...

["Bioengineering","Biophysics","Oncology","Surgery and Surgical Specialties"]
doi:10.7287/peerj.preprints.2474v2
83 downloads
68 views

Background: Electrolytic ablation and electroporation based ablation are minimally invasive, non-thermal surgical technologies that employ electrical currents and electric fields to ablate undesirable cells in a volume of tissue. In this study we explore the attributes...

["Bioengineering","Biophysics","Oncology","Pathology","Histology"]
doi:10.7287/peerj.preprints.2549v1
34 downloads
241 views

The accurate prediction of protein chemical shifts using quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show...

["Biophysics"]
doi:10.7287/peerj.preprints.2476v1
467 downloads
618 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.552v5
857 downloads
1,526 views

Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy parameter for bacteria 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.110v5
737 downloads
585 views

The past influences the present and future; for example, in computation chemistry, simplifying assumptions and approximations important in the pre-computing era remains relevant today in allowing simulation of larger systems with reasonable amount of computer time....

["Biochemistry","Bioengineering","Biophysics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.365v3
26 downloads
175 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
72 downloads
88 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
18 downloads
153 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
82 downloads
154 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
60 downloads
122 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
What is a PeerJ Preprint?

A PeerJ Preprint is a draft of an article, abstract, or poster that has not yet been peer-reviewed for formal publication. Submit a draft, incomplete, or final version of your work for free.

Submissions today can be approved by Editorial Staff and online in 24 hours.

Establish precedent. Solicit feedback. Publish updates.

Top subject areas - Preprints

Top subject areas - People

View all subject areas