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2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Samane Khoshbakht ◽  
Majid Mokhtari ◽  
Sayyed Sajjad Moravveji ◽  
Sadegh Azimzadeh Jamalkandi ◽  
Ali Masoudi-Nejad

Abstract Background Elucidating the dynamic topological changes across different stages of breast cancer, called stage re-wiring, could lead to identifying key latent regulatory signatures involved in cancer progression. Such dynamic regulators and their functions are mostly unknown. Here, we reconstructed differential co-expression networks for four stages of breast cancer to assess the dynamic patterns of cancer progression. A new computational approach was applied to identify stage-specific subnetworks for each stage. Next, prognostic traits of genes and the efficiency of stage-related groups were evaluated and validated, using the Log-Rank test, SVM classifier, and sample clustering. Furthermore, by conducting the stepwise VIF-feature selection method, a Cox-PH model was developed to predict patients’ risk. Finally, the re-wiring network for prognostic signatures was reconstructed and assessed across stages to detect gain/loss, positive/negative interactions as well as rewired-hub nodes contributing to dynamic cancer progression. Results After having implemented our new approach, we could identify four stage-specific core biological pathways. We could also detect an essential non-coding RNA, AC025034.1, which is not the only antisense to ATP2B1 (cell proliferation regulator), but also revealed a statistically significant stage-descending pattern; Moreover, AC025034.1 revealed both a dynamic topological pattern across stages and prognostic trait. We also identified a high-performance Overall-Survival-Risk model, including 12 re-wired genes to predict patients’ risk (c-index = 0.89). Finally, breast cancer-specific prognostic biomarkers of LINC01612, AC092142.1, and AC008969.1 were identified. Conclusions In summary new scoring method highlighted stage-specific core pathways for early-to-late progressions. Moreover, detecting the significant re-wired hub nodes indicated stage-associated traits, which reflects the importance of such regulators from different perspectives.


2022 ◽  
Author(s):  
Mitchell Benton ◽  
Mercede Furr ◽  
Vivek Govind Kumar ◽  
Feng Gao ◽  
Colin D Heyes ◽  
...  

The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Nuclear-encoded LHCPs are synthesized in the cytoplasm then imported into the chloroplast. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54, a 54 kDa subunit homologous to the universally conserved GTPase in cytosolic SRP pathways. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. However, the high flexibility and structural dynamics of cpSRP43 is yet unexplained by current crystal structures of cpSRP43. This is due, in part, to the fact that free full length cpSRP43 is so flexible that it is unable to crystalize. In this study, we explore the structural stability of cpSRP43 under different conditions using various biophysical techniques and find that this protein is concurrently highly stable and flexible. This conclusion is interesting considering that stable proteins typically possess a non-dynamic structure. Molecular dynamics (MD) simulations which correlated with data from biophysical experimentation were used to explain the basis of the extraordinary stability of cpSRP43. This combination of biophysical data and microsecond-level MD simulations allows us to obtain a detailed perspective of the conformational landscape of these proteins.


2022 ◽  
Vol 12 (2) ◽  
pp. 752
Author(s):  
Mehedi Hasan ◽  
Stephane Redonnet ◽  
Andras Hernadi

With regard to the current needs for greener aviation, this study focuses on a novel concept of Box-Wing Aircraft (BWA). Labelled SmartLiner (BWA/SL), this conceptual aircraft comes as a triplane comprising backward and forward swept wings. The aerodynamic performance and structural characteristics of this BWA/SL aircraft are here explored through numerical simulation, using Computational Fluid Dynamics (CFD) and Fluid-Structure Interaction (FSI). The computational approach is first validated using NASA’s Common Research Model (CRM) aircraft, which is then taken as a reference solution against which to compare the aero-structural merits of the BWA/SL concept. Results show that, although its design is still preliminary and lacks optimization, the BWA/SL aircraft exhibits very decent aerodynamic performance, with higher lifting capacities and a reasonable lift-to-drag ratio. Moreover, thanks to the closed frame of its peculiar planform, it demonstrates superior structural characteristics, including under extreme loading scenarios. Based on this preliminary analysis and considering the room left for its further optimization, this conceptual aircraft thus appears as a potentially promising alternative for the development of more environmentally friendly airliners.


Crystals ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 90
Author(s):  
Emiliano Laudadio ◽  
Pierluigi Stipa ◽  
Luca Pierantoni ◽  
Davide Mencarelli

Background: Hafnium Dioxide (HfO2) represents a hopeful material for gate dielectric thin films in the field of semiconductor integrated circuits. For HfO2, several crystal structures are possible, with different properties which can be difficult to describe in detail from an experimental point of view. In this study, a detailed computational approach has been shown to present a complete analysis of four HfO2 polymorphs, outlining the intrinsic properties of each phase on the basis of atomistic displacements. Methods: Density functional theory (DFT) based methods have been used to accurately describe the chemical physical properties of the polymorphs. Corrective Hubbard (U) semi-empirical terms have been added to exchange correlation energy in order to better reproduce the excited-state properties of HfO2 polymorphs. Results: the monoclinic phase resulted in the lowest cohesive energy, while the orthorhombic showed peculiar properties due to its intrinsic ferroelectric behavior. DFT + U methods showed the different responses of the four polymorphs to an applied field, and the orthorhombic phase was the least likely to undergo point defects as oxygen vacancies. Conclusions: The obtained results give a deeper insight into the differences in excited states phenomena in relation to each specific HfO2 polymorph.


Author(s):  
E.I. Fatullaev ◽  
V.V. Bezrodnyi ◽  
I.M. Neelov

Biocompatible peptide dendrimers and dendrigrafts have useful properties for application in biomedicine. In previous papers the computational approach for study lysine dendrimers and dendrigrafts as well as their complexes with various medical peptides was used. In this paper the comparison of complex formation between molecules of therapeutic AEDG tetrapeptide and novel K2R peptide dendrimer or DG2 dendrigraft of near the same size and charge was fulfilled. The systems consisting of 16 therapeutic AEDG tetrapeptide molecules and one dendrimer or one dendrigraft were studied by molecular dynamics simulation. Full atomic models of these molecules in water with explicit counterions were used for this goal. First of all, the process of complex formation was studied. It was obtained that peptide molecules were attracted by both branched molecules and were quickly adsorbed by them. Times of complexes formation as well as size, anisotropy and structure of each complex were calculated. It was demonstrated that both K2R dendrimer and DG2 dendrigraft are effective for complexation of these peptide molecules but new dendrimer complex is more stable than dendrigraft complex because it has almost twice more hydrogen bonds with peptide molecules and 33% more ion pairs with their charged groups.


2022 ◽  
Author(s):  
Said Mikki

A new computational approach to quantum antennas based on first principle open stochastic quantum dynamics.<div><br></div><div>We develop a general computational approach for the analysis and design of quantum antenna systems comprised of coupled quantum dot arrays interacting with external fields and producing quantum radiation. The method is based on using the GKSL master equation to model quantum dissipation and decoherence. The density operator of a coupled two-level quantum dot (qbit) array, excited by classical external signals with variable amplitude and phase, is evolved in time using a quantum Liouville-like equation (the master equation). We illustrate the method in a numerical example where it is shown that manipulating the phase excitations of individual quantum dots may significantly enhance the directive radiation properties of the quantum dot antenna system<br></div>


Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 380
Author(s):  
Oluwakemi Ebenezer ◽  
Nkululeko Damoyi ◽  
Maryam A. Jordaan ◽  
Michael Shapi

The RNA-dependent RNA polymerase (RdRp) receptor is an attractive target for treating human norovirus (HNV). A computer-aided approach like e-pharmacophore, molecular docking, and single point energy calculations were performed on the compounds retrieved from the Development Therapeutics Program (DTP) AIDS Antiviral Screen Database to identify the antiviral agent that could target the HNV RdRp receptor. Induced-fit docking (IFD) results showed that compounds ZINC1617939, ZINC1642549, ZINC6425208, ZINC5887658 and ZINC32068149 bind with the residues in the active site-B of HNV RdRp receptor via hydrogen bonds, salt bridge, and electrostatic interactions. During the molecular dynamic simulations, compounds ZINC6425208, ZINC5887658 and ZINC32068149 displayed an unbalanced backbone conformation with HNV RdRp protein, while ZINC1617939 and ZINC1642549 maintained stability with the protein backbone when interacting with the residues. Hence, the two new concluding compounds discovered by the computational approach can be used as a chemotype to design promising antiviral agents aimed at HNV RdRp.


2022 ◽  
Author(s):  
Said Mikki

A new computational approach to quantum antennas based on first principle open stochastic quantum dynamics.<div><br></div><div>We develop a general computational approach for the analysis and design of quantum antenna systems comprised of coupled quantum dot arrays interacting with external fields and producing quantum radiation. The method is based on using the GKSL master equation to model quantum dissipation and decoherence. The density operator of a coupled two-level quantum dot (qbit) array, excited by classical external signals with variable amplitude and phase, is evolved in time using a quantum Liouville-like equation (the master equation). We illustrate the method in a numerical example where it is shown that manipulating the phase excitations of individual quantum dots may significantly enhance the directive radiation properties of the quantum dot antenna system<br></div>


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