Evolution Of Secondary Structures Research Articles

Evolution of unsteady secondary flow structures near the onset of stall in a tip-critical transonic axial flow compressor stage

The aerodynamic stability of an axial compressor stage depends on the rotor and stator. However, due to the specific design requirements, the evolving flow field and the resulting secondary flow structures are different in both components. This study investigates the evolution of dominant secondary flow structures occurring in the rotor and stator of a tip-critical transonic compressor stage at the near-stall condition using unsteady numerical analysis and validates performance characteristics with the experimental data. The investigation reveals that the presence of rotor tip shock creates a large difference in the pressure gradient across the pressure surface and the suction surface, intensifying tip leakage flow and shock-induced boundary layer separation. The higher incidence angle near the hub leading edge creates a local separation and reattachment zone. The radial pressure gradient causes the low momentum flow from this local separation zone to migrate radially upward. This migrated flow interacts with the tip leakage flow and separated blade boundary layer, eventually creating a colossal recirculation zone and subsequent rotor blockage of around 46%. The increasing streamwise adverse pressure gradient pushes the tip shock upstream, and at the onset of the stall, the flow directly separates from the rotor leading edge avoiding the shock formation. The stator flow field is dominated by the asymmetric hub corner separation induced by the streamwise adverse pressure gradient and the tip corner separation caused by the vortex structures convected downstream from the rotor tip region leading to stator blockage of around 48%. Along with the blade passing frequency, four other dominating frequencies (0.06×BPF, 0.12×BPF, 0.44×BPF, and 0.84×BPF) related to the aerodynamic instabilities are observed at the inception of stall.

Effect of additional periodic motion on gas-liquid two-phase secondary flow behavior in inclined pipes

Secondary flow significantly changes the flow structure and increases flow resistance. The pipeline motion further contributes to the evolution of secondary flow. This study aims to elucidate the characteristics of two-phase secondary flow in inclined pipelines under additional periodic motion conditions. Based on the CFD technique, three-dimensional oscillating two-phase flow fields were simulated using the VOF model and dynamic mesh method. The focus was on four common flow patterns observed in inclined pipes, namely stratified flow, slug flow, turbulence flow, and transitional flow. The impact mechanisms of swaying, heaving, and coupling motion on the structural evolution, velocity profile, and relative intensity of secondary flow were analyzed. The results indicate that additional periodic motion exhibits a significant dominant behavior on secondary flow when the amplitude exceeds 1.0D. Heave motion has a more pronounced effect on the secondary flow structure. Additional periodic motion induces periodic evolution of secondary flow structure in stratified flow, with the evolution period aligning with the period of the additional motion. Under additional periodic motion, there is no one-to-one correspondence between secondary flow velocity and axial velocity. Additional motion significantly suppresses the axial velocity of slug flow. Furthermore, additional periodic motion significantly increases the relative intensity of secondary flow, exceeding 10%. When the amplitude is less than 1.5D, additional motion suppresses the relative intensity of secondary flow in turbulence flow and transitional flow.

Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species.

Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 was high-throughput sequenced from 29 Corydalis species, and their GC contents were comparatively investigated in the context of ITS2's characteristic secondary structure and concerted evolution. Our results showed that the GC contents of ITS2 were 131% higher than those of their adjacent 5.8S regions, suggesting that ITS2 underwent GC-biased evolution. These GCs were distributed in a heterogeneous manner in the ITS2 secondary structure, with the paired regions being 130% larger than the unpaired regions, indicating that GC is chosen for thermodynamic stability. In addition, species with homogeneous ITS2 sequences were always GC-rich, supporting GC-biased gene conversion (gBGC), which occurred with ITS2's concerted evolution. The RNA substitution model inferred also showed a GC preference among base pair transformations, which again supports gBGC. Overall, structurally based GC investigation reveals that ITS2 evolves under structural stability and gBGC selection, significantly increasing its GC content.

MHD flow of submerged jets behind the inlet disturbance

AbstractIn a broad variety of configurations in technology and industrial applications, the properties of liquid metal flows subjected to strong magnetic fields, are largely governed by the dynamics of coherent structures, known to settle several basic types, such as thin shear layers, forming near the walls or within the fluid domain, vortices extended along the field, or planar and round jets. In some cases, these structures are created by the design, like a submerged jet formed by a sudden expansion from the nozzle into a blanket channel, or jets formed behind some flow obstruction. In the other cases this may be due to instability and evolution of secondary structures, for example, descending and ascending jets appearing as a result of convective instability in blanket channels. In this study, we undertake an attempt to affect liquid metal flow via inlet disturbance formed by a simple rod placed along the magnetic induction lines. The disturbance can generate flat jets behind the rod and, furthermore, a sustainable flow of anisotropic vortical perturbations further downstream the flow. We seek to analyze the most important mechanisms of the flow dynamics and effects of magnetic field on the integral system properties of enhancing mixing, mass and heat transport for such flow. The most optimal regimes of vortex generation are found to be governed by the magnetic interaction parameter (Stuart number). The exact ratio of the optimal Stuart number is found to be in a range between 20 and 40, based on the channel double width as a characteristic size. The observed vortices attain quasi‐2D shape and exist at a length of dozens of duct calibers, being the strongest at higher flow rates. The obtained flow regimes and their turbulent properties are also found to resemble significant similarity to the results on quasi‐2D turbulence found in prior studies of channel and duct flows under spanwise magnetic field.

Probing the biotoxicity of starch nanoparticles in vivo and their mechanism to desensitize β-lactoglobulin

Starch nanoparticles (SNPs) were synthesized and characterized in vivo for their subacute biotoxicity. Animal experiments revealed that SNPs would not induce changes in inflammatory cytokines and gut microbiota, avoiding damage to mice's organs. Moreover, SNPs were rapidly excreted from the body after 6 h without any accumulation, demonstrating their biosafety. Based on these findings, SNPs were used for β-lactoglobulin (βLg) desensitization by formation of a protein corona. The thermodynamics and time evolution of βLg's secondary structure were investigated to address the desensitization mechanism. The results showed ∼1600 βLg molecules onto a single SNP coupled with significant changes in secondary structure formed a stable SNPs-βLg corona with binding affinity (Ka) of 8.4 ± 0.5 × 10 5 M −1 . Functionally, the decrease of β-sheet destroyed the conformation of immunoglobulin E (IgE) epitopes and inhibited IgE combining capacity, achieving SNPs' desensitization to βLg. Additionally, it takes ∼2 h to complete changes in βLg's surface hydrophobicity and immunoglobulin E (IgE) combining capacity after incubation with SNPs, consistent with the time evolution of structure changes, indicating protein corona is response for the desensitization. SNPs-βLg corona changed βLg structure, inhibiting the combing with IgE. • Starch nanoparticles (SNPs) were characterized the subacute biotoxicity in vivo and showed biosafety to the mice. • It takes about 2 h to complete secondary structure changes, forming a stable SNPs-βLg corona with about1000 βLg molecules adsorbed. • The time evolution of surface hydrophobicity and IgE combining capacity is corresponding to the changes of secondary structure induce by protein corona.

Using Maxwell’s Theory to model and quantify the fracture evolution of cyclothymic deposition phosphate rock

The evolution and stability of fracturing in the cyclothymic deposition of phosphate rocks are strongly affected by the viscoelasticity and structural form of the rock-forming minerals. Presently, there is no standardized method that has been widely accepted to accurately quantify the elastic-plastic deformation and fracturing of such striped structural rock nor reflect the role of the different lithogenous minerals in phosphate rocks when subjected to viscoelastic strain loading. In this study, integrated mathematical equations were formulated for modelling the mechanical and fracture behaviour of cyclothymic deposition in structured phosphate rocks. These constitutive equations were developed based on Maxwell’s Theory after the elastic modulus and damping coefficient of the rock-forming mineral from the mechanical testing were substituted into the derived-equations. In these new models, the apatite stripes and dolomite stripes were incorporated into the transverse isotropic model through the analysis of structural characteristics of the phosphate rock. Through experimental validation, the response curves of the creep and stress relaxation tests were found to be consistent with the deformation curves generated by modelling using the mathematical equations. Overall, the formulated model along with the corresponding equations was found to exhibit good applicability properties to describe phosphate’s mechanical and fracture behaviour under low horizontal compressive stresses. In the study, the creep mechanism in phosphate rocks were satisfactorily analysed from the angles of microscopic morphology, cracks evolution, and inter-crystalline strength. The hard brittle apatite was found to be surrounded and separated by high creep variant dolomite. Furthermore, the analysis showed that dolomite crystals possessing high creep properties dominated the distribution and evolution of secondary structures in the phosphate rock, under the condition of long-term low-stress loading.

Characterization of the complete mitochondrial genome of Dendroctonus valens and elimination of nuclear mitochondrial pseudogene interference

AbstractNuclear mitochondrial pseudogenes (numts) are short, nonfunctional DNA sequences resulting from mitochondrial gene transfer to the nuclear genome; these sequences seriously affect the accuracy of mitochondrial gene for population genetic and phylogenetic analyses. The nuclear genome of Dendroctonus valens (Coleoptera: Curculionidae: Scolytidae), a major forest quarantine pest that seriously threatens the ecological security of pine forests, contains a large number of numts, and these interfere with analyses of genetic variation based on the mitochondrial cox1 gene. To eliminate interference by numts, we sequenced, assembled and analysed the complete mitochondrial genome of D. valens. The mitogenome is a circular molecule of 16,547 bp and shows typical gene content and arrangement. We identified its codon preference, tRNA secondary structure and nucleotide evolution rate. Furthermore, we designed primers for long fragment amplification to eliminate numts in the mitochondrial cox1 gene. Finally, amplified products were sequenced with universal primers, and cox1 gene sequences (464 bp) without numts were successfully obtained. The Heilihe Nature Reserve (harbouring Pinus tabulaeformis) in Inner Mongolia, is in the early stage of D. valens northward invasion, with a high population genetic diversity. We hypothesized that the high genetic diversity was related to human activities around the reserve and the reproductive characteristics in the early stage of D. valens invasion. The newly developed method resolves the issue of numt interference and lays a foundation for the analyses of genetic diversity in D. valens populations in the region as well as its invasion routes.

An electro-peroxone oxidation-Fe(III) coagulation sequential conditioning process for the enhanced waste activated sludge dewatering: Bound water release and organics multivariate change

As a by-product of wastewater treatment, waste activated sludge (WAS) has complex composition, strong hydrophilic extracellular polymeric substance (EPS), which make it difficult to dewater. In this study, an electro-peroxone oxidation-Fe(III) coagulation (E-peroxone-Fe(III)) sequential conditioning approach was developed to improve WAS dewaterability. At E-peroxone oxidation stage, hydrogen peroxide was generated through 2-electron path on a carbon polytetrafluoroethylene cathode, and reacted with the sparged O3 to produce hydroxyl radicals. At the subsequent coagulation stage, Fe(III) was dosed to coagulate the small WAS fragments and release water from WAS. Along E-peroxone-Fe(III) subsequent conditioning process, the physicochemical properties of WAS, main components, functional groups and evolution of protein secondary structure, and typical amino acids in EPS, as well as the type and semi-quantitative of elements in WAS, were investigated. The results indicated that under the optimal conditions, the reductions of specific resistance to filterability (SRF) and capillary suction time (CST) for WAS equalled 78.18% and 71.06%, respectively, and its bound water content decreased from 8.87 g/g TSS to 7.67 g/g TSS. After E-peroxone oxidation, part of protein and polysaccharide migrated outside from TB-EPS to slime, the ratio of α-helix/(β-sheet + random coil) declined, even some of organic-N disintegrated to inorganic-N. At Fe(III) coagulation stage, re-coagulation of the dispersed WAS fragments and easy extraction from inner EPS for protein and polysaccharide occurred. Furthermore, the protein secondary structure of β-sheet increased by 13.48%, the contents of hydrophobic and hydrophilic amino acids also increased. In addition, a strong negative correlation between the hydrophobic amino acid content of Met in slime and CST or SRF (R2CST = −0.999, p < 0.05 or R2SRF = −0.948, p < 0.05) occurred, while a strong positive correlation between the hydrophilic amino acid content of Cys in TB-EPS and CST or SRF (R2CST = 0.992, p < 0.05 or R2SRF = 0.921, p < 0.05) occurred, which could be related to the WAS dewaterability.

Decoding the Host-Parasite Protein Interactions Involved in Cerebral Malaria Through Glares of Molecular Dynamics Simulations.

Malaria causes millions of deaths every year. The malaria parasite spends a substantial part of its life cycle inside human erythrocytes. Inside erythrocytes, it synthesizes and displays various proteins onto the erythrocyte surface, such as Plasmodium falciparum erythrocytic membrane protein-1 (PfEMP1). This protein contains cysteine-rich interdomain region (CIDR) domains which have many subtypes based on sequence diversity and can cross-talk with host molecules. The CIDRα1.4 subtype can attach host endothelial protein C receptor (EPCR). This interaction facilitates infected erythrocyte adherence to brain endothelium and subsequent development of cerebral malaria. Through molecular dynamics simulations in conjunction with the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, we explored the mechanism of interaction in the CIDRα1-EPCR complex. We examined the structural behavior of two CIDRα1 molecules (encoded by HB3-isolate var03-gene and IT4-isolate var07-gene) with EPCR unbound and bound (complex) forms. HB3var03CIDRα1 in apo and complexed with EPCR was comparatively more stable than IT4var07CIDRα1. Both of the complexes adopted two distinct conformational energy states. The hydrophobic residues played a crucial role in the binding of both complexes. For HB3var03CIDRα1-EPCR, the dominant energetic components were total polar interactions, while in IT4var07CIDRα1-EPCR, the primary interaction was van der Waals and nonpolar solvation energy. The study also revealed details such as correlated conformational motions and secondary structure evolution. Further, it elucidated various hotspot residues involved in protein-protein recognition. Overall, our study provides additional information on the structural behavior of CIDR molecules in unbound and receptor-bound states, which will help to design potent inhibitors.

Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective Variable.

Recently, we have shown that the residue folding degree, a network-based measure of folded content in proteins, is able to capture backbone conformational transitions related to the formation of secondary structures in molecular dynamics (MD) simulations. In this work, we focus primarily on developing a collective variable (CV) for MD based on this residue-bound parameter to be able to trace the evolution of secondary structure in segments of the protein. We show that this CV can do just that and that the related energy profiles (potentials of mean force, PMF) and transition barriers are comparable to those found by others for particular events in the folding process of the model mini protein Trp-cage. Hence, we conclude that the relative segment folding degree (the newly proposed CV) is a computationally viable option to gain insight into the formation of secondary structures in protein dynamics. We also show that this CV can be directly used as a measure of the amount of -helical content in a selected segment.

Siderite/PMS conditioning-pressurized vertical electro-osmotic dewatering process for activated sludge volume reduction: Evolution of protein secondary structure and typical amino acid in EPS

In this study, the siderite/PMS conditioning-pressurized vertical electro-osmotic dewatering (PEOD) process was used to reduce the volume of activated sludge (AS). The changes in water content, cell, extracellular polymeric substances (EPS) distribution, protein secondary structures and typical amino acids in EPS fractions of AS along siderite/PMS conditioning-PEOD process were investigated. Results showed that the final water content (WC) of dewatered AS was 58.02% under the RSM optimized conditioning conditions of 0.05 g/g TSS siderite dosage, 0.23 g/g TSS PMS dosage, 600 kPa mechanical pressure and 20 V voltage. At conditioning and PEOD stages, the bound water content(BWC) of AS decreased by 25.23% and 91.76%, respectively. The HO• and SO4−· generated from siderite activating PMS could lead to the disruption of cells. The ratio of Ala-to Lys (Ala/Lys) showed strong negative correlations with BWC or WC in slime (RBWC2=−0.803, p<0.01; RWC2=−0.771, p<0.01) and TB-EPS (RBWC2=−0.693, p<0.01; RWC2=−0.705, p<0.01), and could be considered as an indicator of AS dewaterability. Compared with raw AS, conditioning led to the occurrence of the denser protein structure in TB-EPS and the looser one in slime. The contact number between Ala-and water decreased in TB-EPS and increased in slime, which indicated that the migration of water adhered in TB-EPS to outer layer. At the DG, MC and EC process, while the looser protein structure in TB-EPS and the denser one in slime occurred, as well as higher contact number between Ala-and water in TB-EPS than that in slime, which indicated that more water flowed outsider of slime than TB-EPS. This implied that the variations of the compactness of protein secondary structures and the contact number between Ala-and water in EPS layers correlated with AS dewaterability.

Investigation by Synchrotron Radiation Circular Dichroism of the Secondary Structure Evolution of Pepsin under Oxidative Environment.

Food processing affects the structure and chemical state of proteins. In particular, protein oxidation occurs and may impair protein properties. These chemical reactions initiated during processing can develop during digestion. Indeed, the physicochemical conditions of the stomach (oxygen pressure, low pH) favor oxidation. In that respect, digestive proteases may be affected as well. Yet, very little is known about the link between endogenous oxidation of digestive enzymes, their potential denaturation, and, therefore, food protein digestibility. Thus, the objective of this study is to understand how oxidative chemical processes will impact the pepsin secondary structure and its hydrolytic activity. The folding and unfolding kinetics of pepsin under oxidative conditions was determined using Synchrotron Radiation Circular Dichroism. SRCD gave us the possibility to monitor the rapid kinetics of protein folding and unfolding in real-time, giving highly resolved spectral data. The proteolytic activity of control and oxidized pepsin was investigated by MALDI-TOF mass spectrometry on a meat protein model, the creatine kinase. MALDI-TOF MS allowed a rapid evaluation of the proteolytic activity through peptide fingerprint. This study opens up new perspectives by shifting the digestion paradigm taking into account the gastric digestive enzyme and its substrate.

Development of pore structure characteristics of a weathered crust elution-deposited rare earth ore during leaching with different valence cations

To explore the evolution of characteristics of pore structure of a weathered crust elution-deposited rare earth orebody during the leaching process with different valence cations, leaching solutions with NH4+, Mg2+, Al3+ as cations were prepared to carry out simulated column leaching experiments. Nuclear magnetic resonance (NMR), scanning electron microscope (SEM) and energy dispersive spectrometry (EDS) were used to measure the microscopic characteristics of samples, then the and mechanisms of pore structure evolution of samples during leaching with different valence cations were analyzed. The results showed that: in the main reaction stage, ion displacement reaction in three different leaching solutions resulted in the top-down migration of solid fine particles; then the continuous evolution of secondary pore structure occurred, and then the drainage characteristics of leaching solution were affected. The evolution of pore structure of rare earth orebody induced by leaching solution with different valence cations was generally similar: the pore structure of the orebody firstly evolved from large pores to small pores; whereas at the end of ion exchange, the pore structure evolved from small pores to larger pores. However, there were significant differences in the pore proportion of different sizes. The number of large pores and extra-large pores in the samples of the ammonium sulfate leaching group was the largest, followed by the magnesium sulfate leaching group, and the least were found in the aluminum sulfate leaching group. The mechanism study showed that this difference was caused by the dynamic transformation (deposition and release) of fine particles of rare earth ore on the pore surface, which was affected by the change of ionic strength, the valence cation and the pH value of leaching solution caused by ion substitution.

Secondary structural analysis of non-mulberry silk fibroin nanoparticles synthesized by using microwave and acetone method

The 3D structure analysis for Muga silk protein was predicted through homology modeling and Ramachandran plot with the determination of quality index for Stereo/packing and 3D quality index. Silk Nanoparticles were synthesized using conventional desolvation and microwave-assisted radiolysis method from Muga silk fibroin. The secondary structure evolution due to two different synthesis methods was investigated using FTIR and Circular Dichroism (CD) spectroscopy. The microwave synthesized nanoparticles showed enhanced β-sheet content than desolvation synthesized nanoparticles. The conformational changes of Muga silk fibroin protein to nanoparticle followed an ordered transition from random coil to α-helix then from α-helix to β-turn and from β-turn to β-sheets where α-helix and β-turn are the intermediate forms before getting stabilized to the metastable β-sheets structure. The thermodynamics involved in secondary structure evolution was studied from CD analysis and activation energy involved in the formation of the secondary structure was determined. Communicated by Ramaswamy H. Sarma

Probing gold nanoparticles for the desensitization to β-lactoglobulin from binding mechanism, structure and IgE binding changes

Because of the adsorption of proteins, gold nanoparticles (AuNPs) create potential biological risks in biomedicine, leading to the formation of the protein corona. This adsorption is mainly due to the formation of gold–sulfur (AuS) covalent bonds between the AuNPs and the -SH groups, causing bioactivity denaturation and biological problems; however, it could also lead to some biological benefits. We explored AuNPs as a potential material for desensitization to allergens, such as β-lactoglobulin (βLG). To address the desensitization of AuNPs, we investigated the binding mechanism and the specific relationship of the time evolution of AuS bond, secondary structure, and allergy changes. The formation of AuS bond takes approximately 9 h, consistent with the complete changes time in secondary structure and immunoglobulin E (IgE) combining capacity of the βLG, decreasing allergic reactions. These results indicate that AuNPs have the potential to minimize allergic reactions in the future.

Probing the Stepwise Unfolding of Bovine Serum Albumin Using 2D Correlation Raman Spectroscopic Analysis.

Protein denaturation involves a change in the protein structure with the loss of activity, which proceeds via various intermediates. The possible intermediate structures account largely for understanding the process of unfolding. Hence, considerable attention is required to characterize partially unfolded protein states and to gain more insight into the information about the sequence and steps involved in protein folding mechanisms. In this report, a stepwise unfolding of bovine serum albumin (BSA) with guanidine hydrochloride (GuHCl) has been investigated using Raman spectroscopy in the amide I and III regions. Two-dimensional (2D) correlation analysis has been applied to reveal information on the sequential order and the dynamic properties of interaction during the unfolding process. Raman spectral signatures in the amide I region revealed that there is no significant change in secondary structures up to 2 M concentration of GuHCl. However, 2D correlation analysis further supports the observation by inferring the strengthening of secondary structure at the expense of tertiary structure. At a higher concentration of GuHCl (2-4 M), there is an accumulation of random and β-sheet structures that is mediated by small connecting segments of helices. It further accelerates the unfolding of helices and a complete collapse of structure. These analyses establish the ability of Raman spectroscopy to estimate the ensemble of secondary structures present in proteins. The results reveal the mechanistic details of unfolding, characterizing structure of intermediates even at high concentrations, and understanding the evolution of various secondary structures with respect to each other during unfolding. Such observations can be helpful in understanding the factors affecting the shape and size of proteins during folding/unfolding.

Antibacterial Effect of Silver Nanomaterials on Staphylococcal Protein A by Molecular Dynamics Simulation.

Nanotechnologies have changed this world in various aspects including the oral medicine. It has been demonstrated that silver (Ag) nanomaterials can exhibit strong inhibition and killing effect on oral bacteria. Furthermore, the Ag nanomaterials have superb antimicrobial activity and nonacute toxic effects on human cells. Previously, the impact of Ag on oral bacteria was demonstrated by experiments. In this work, we applied molecular dynamics (MD) simulations to investigate the influence of Ag nanomaterials on oral bacteria. Firstly, by comparing change of molecular structure of staphylococcal protein A (SPA) with and without Ag, we found that Ag nanomaterials have strong effect on evolution of protein secondary structure of SPA. Secondly, it was observed that Ag has negligible effect on Solvent Accessible Surface Area (SASA) of SPA indicating that the Ag only changed its microstructure. Finally, it was found that the average amount of hydrogen bond in SPA was reduced in the presence of Ag which was origin of antimicrobial activity of Ag. It is believed that the growing interest in dental medicine with nanomaterials would lead molecular dynamics simulations to be an effective method for studying inhibition and killing pathological process of nanomaterials on oral bacteria.

Structural Characterization of Individual α-Synuclein Oligomers Formed at Different Stages of Protein Aggregation by Atomic Force Microscopy-Infrared Spectroscopy.

Aberrant α-synuclein aggregation is strongly associated with the onset and development of Parkinson's disease (PD). Therefore, characterizing the structure of toxic intermediate oligomers plays an essential role in better understanding their neurotoxicity. Using atomic force microscopy-infrared spectroscopy (AFM-IR), we were able to reveal the structure of α-synuclein oligomers present at different stages of protein aggregation and establish a relationship between morphology and structure on the single oligomer level. We were also able to probe the secondary structure evolution of individual oligomers. Moreover, the IR spectra of individual oligomers suggest structural rearrangement that is necessary for oligomers with an antiparallel β-sheet to propagate into fibrils that have a parallel-β-sheet secondary structure. Detailed investigation of structural organization of α-synuclein oligomers reported in this study is critically important to understand the toxicity of these protein species. We also anticipate that this work will help developing approaches for oligomer detection and consequently presymptomatic diagnostic of PD.

Numerical studies on convective mass transfer augmentation in high-speed flows with lateral sweep vortex generator and dimple cavity

A numerical study on convective mass transfer enhancement by a lateral sweep vortex generator (LSVG)-dimple combination is presented. Surface features that can generate secondary flow structures are widely used for overcoming the difficulties in the transport process encountered in high-speed flows. Unsteady, three dimensional, turbulent fluid flow and mass transfer has been simulated using an Advection Upstream Splitting Method (AUSM) based finite volume solver. An improvised Temperature-Dependent Mass Efflux (TDME) condition is invoked to simulate mass evolution from a liquefying boundary as a function of adjoining fluid temperature. The computational procedure has been validated using experimental data of heat transfer coefficients obtained for a similar vortex generator. Extensive numerical simulations have been performed for various geometry and flow conditions to analyze the nature of the evolution of secondary flow structures and their role in promotion of mass advection. Q-Criterion estimates have been used for identifying regions of intense vortex fluid motion and its role in the promotion of mass transfer. The present vortex generator dimple combination can enhance mass transfer for a wider expanse of the domain. Correlations for the estimation of spatiotemporal convective mass transfer effects have also been derived from unsteady numerical computations.

Self-assembly dynamics and antimicrobial activity of all l- and d-amino acid enantiomers of a designer peptide.

Recent studies have shown that antimicrobial peptides (AMPs) can self-assemble into supramolecular structures, but this has been overlooked as causative of their antimicrobial activity. Also, the higher antimicrobial potency of d-enantiomers compared to l-enantiomers of AMPs cannot always be attributed to their different resistance to protease degradation. Here, we tested all l- and d-amino acid versions of GL13K, an AMP derived from a human protein, to study structural links between the AMP secondary structure, supramolecular self-assembly dynamics, and antimicrobial activity. pH dependence and the evolution of secondary structures were related to a self-assembly process with differences among these AMPs. The two GL13K enantiomers formed analogous self-assembled twisted nanoribbon structures, but d-GL13K initiated self-assembly faster and had notably higher antimicrobial potency than l-GL13K. A non-antimicrobial scrambled amino acid version of l-GL13K assembled at a much higher pH to form distinctively different self-assembled structures than l-GL13K. Our results support a functional relationship between the AMP self-assembly and their antimicrobial activity.