Computational Investigation
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2021 ◽  
Vol 17 (9) ◽  
pp. e1009446
Elzbieta Rembeza ◽  
Martin K. M. Engqvist

Only a small fraction of genes deposited to databases have been experimentally characterised. The majority of proteins have their function assigned automatically, which can result in erroneous annotations. The reliability of current annotations in public databases is largely unknown; experimental attempts to validate the accuracy within individual enzyme classes are lacking. In this study we performed an overview of functional annotations to the BRENDA enzyme database. We first applied a high-throughput experimental platform to verify functional annotations to an enzyme class of S-2-hydroxyacid oxidases (EC We chose 122 representative sequences of the class and screened them for their predicted function. Based on the experimental results, predicted domain architecture and similarity to previously characterised S-2-hydroxyacid oxidases, we inferred that at least 78% of sequences in the enzyme class are misannotated. We experimentally confirmed four alternative activities among the misannotated sequences and showed that misannotation in the enzyme class increased over time. Finally, we performed a computational analysis of annotations to all enzyme classes in the BRENDA database, and showed that nearly 18% of all sequences are annotated to an enzyme class while sharing no similarity or domain architecture to experimentally characterised representatives. We showed that even well-studied enzyme classes of industrial relevance are affected by the problem of functional misannotation.

2021 ◽  
Ciara G. McKenna ◽  
Ted J Vaughan

Polymer covered stents have demonstrated promising clinical outcomes with improved patency rates compared to traditional bare-metal stents, however little is known on the mechanical implication of stent covering. In the present work, a combined experimental-computational investigation was carried out to determine the role of a polymeric cover on the biomechanical performance of self-expanding laser-cut stents. Experimental bench top tests were conducted on bare and covered versions of a commercial stent to evaluate the radial, axial and bending response. In parallel, a computational framework with a novel covering strategy was developed that accurately predicts stent mechanical performance, and provides further insight into covered stent mechanics by considering different stent geometries and polymer materials. Results show that stent covering causes increased initial axial stiffness and substantial radial stiffening at small crimp diameters as the cover folds and self-contacts. It was also shown that use of a stiffer polymeric covering material caused significant alterations to the radial and axial response, highlighting the importance of considering the mechanical properties of the combined cover and stent.

Kevin M Scotland ◽  
Oliver K.L. Strong ◽  
Mark Parnis ◽  
Andrew James Vreugdenhil

The band gaps of three forms of polyaniline (PANI) are calculated using the DFT method with the B3LYP functional and SV(P) basis set. This marks the first time that the band gap for this polymer has been calculated using this DFT method. The calculations include an investigation of the effect of varying the benzoid-quinoid structural units, the effect of increasing oligomer length and the inclusion of Michael’s addition structures which could be residual in the polymer depending on the chosen synthetic method. All results were compared to the experimentally determined band gap of 1.5 eV as typically reported in the literature. A commonly used structural motif of alternating benzoid-quinoid units and a ratio of 0.5:0.5 benzoid: quinoid resulted in a computed band gap of 1.9 eV. Inclusion of one extra quinoid unit gave rise to a band gap of 1.3 eV. Incorporation of a Michael’s addition structure was found to dominate the band gap calculation, yielding a localized LUMO and a band gap of 1.3 eV that was insensitive to the polymer chain length and composition.

2021 ◽  
Eliot Woods ◽  
Alexandra Berl ◽  
Leanna Kantt ◽  
Christopher Eckdahl ◽  
Michael Wasielewski ◽  

π-Conjugated polymers can serve as active layers in flexible and lightweight electronics, and are conventionally synthesized by transition-metal-mediated polycondensation at elevated temperatures. We recently reported a photopolymerization of electron-deficient heteroaryl Grignard monomers that enables the catalyst-free synthesis of n-type π-conjugated polymers. Herein we provide an experimental and computational investigation of the mechanism of this photopolymerization. Spectroscopic studies performed <i>in situ</i> and after quenching reveal that the propagating species is a radical anion with halide end groups. DFT calculations for model oligomers suggest a Mg-templated S<sub>RN</sub>1-type coupling, in which Grignard monomer coordination to the radical anion chain avoids the formation of free sp<sup>2</sup> radicals and enables C–C bond formation with very low barriers. We find that light plays an unusual role in the reaction, photoexciting the radical anion chain to shift electron density to the termini and thus favor productive monomer binding.

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5486
Etienne P. Hessou ◽  
Lucie A. Bédé ◽  
Hicham Jabraoui ◽  
Abderrahmane Semmeq ◽  
Michael Badawi ◽  

In this study, density functional theory (DFT) calculations have been performed to investigate the adsorption mechanisms of toluene and water onto various cationic forms of Y zeolite (LiY, NaY, KY, CsY, CuY and AgY). Our computational investigation revealed that toluene is mainly adsorbed via π–interactions on alkalis exchanged Y zeolites, where the adsorbed toluene moiety interacts with a single cation for all cases with the exception of CsY, where two cations can simultaneously contribute to the adsorption of the toluene, hence leading to the highest interaction observed among the series. Furthermore, we find that the interaction energies of toluene increase while moving down in the alkaline series where interaction energies are 87.8, 105.5, 97.8, and 114.4 kJ/mol for LiY, NaY, KY and CsY, respectively. For zeolites based on transition metals (CuY and AgY), our calculations reveal a different adsorption mode where only one cation interacts with toluene through two carbon atoms of the aromatic ring with interaction energies of 147.0 and 131.5 kJ/mol for CuY and AgY, respectively. More importantly, we show that water presents no inhibitory effect on the adsorption of toluene, where interaction energies of this latter were 10 kJ/mol (LiY) to 47 kJ/mol (CsY) higher than those of water. Our results point out that LiY would be less efficient for the toluene/water separation while CuY, AgY and CsY would be the ideal candidates for this application.

2021 ◽  
Vol 15 ◽  
Qian Zhang ◽  
Yi Zeng ◽  
Tielin Zhang ◽  
Taoyi Yang

Elucidating the multi-scale detailed differences between the human brain and other brains will help shed light on what makes us unique as a species. Computational models help link biochemical and anatomical properties to cognitive functions and predict key properties of the cortex. Here, we present a detailed human neocortex network, with all human neuron parameters derived from the newest Allen Brain human brain cell database. Compared with that of rodents, the human neural network maintains more complete and accurate information under the same graphic input. Unique membrane properties in human neocortical neurons enhance the human brain’s capacity for signal processing.

Soumya Mukherjee ◽  
Paritosh Mahata

CoVID-19 virus SARS-CoV-2 follows the endocytosis process to enter inside a cell to infect it. It is important to study the endocytosis of SARS-CoV-2 in cell membrane to prevent the pandemic of CoVID-19. In this paper we develop a finite element based computational model for endocytosis of SARS-CoV-2 in cell membrane and determine curvature generation on it during the process. The virus SARS-CoV-2 is modeled as a rigid spherical particle and cell membrane as an anisotropic elastic material, while its fluidic nature due to lipid exchange with infinite reservoir is preserved using suitable conditions. With the help of a contact pair created between the virus particle and cell membrane, endocytosis process is computationally studied and the curvature of membrane is evaluated as the time progresses during the endocytosis process. At the tip of the virus particle and half-radius distance from it, the membrane follows the curvature of virus very quickly. However, it takes more time for the membrane point located at a distance equal to the radius of the virus particle. This is compensated by the cytoplasmic peripheral proteins binding onto the inside surface of the cell membrane. The role of cytoplasmic peripheral BAR proteins is investigated by using a linear curvature-coupling model with protein concentrations. It is observed that F-BAR protein is more sensitive to the curvature of virus particle in comparison to the other BAR proteins. The sensitiveness deteriorates as the curvature is increased.

Henry C. London ◽  
Thomas J. Whittemore ◽  
Ariel G. Gale ◽  
Colin D. McMillen ◽  
David Y. Pritchett ◽  

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