Different ferrite-martensite dual-phase (DP) steel microstructures were subjected to controlled electrochemical hydrogen charging followed by tensile deformation. An increase in hydrogen content enhanced strengthening and dynamic recovery, but lowered non-uniform elongation. Hydrogen embrittlement originated from the severity of microscopic post-necking strain localizations in the ferrite phase, and preferential/accelerated damage initiation at the ferrite-martensite boundaries. Atomistic diffusion-based hydrogen concentrations, at different microstructural features, were captured by multi-scale molecular dynamics (MD) and kinetic Monte Carlo (KMC) simulations. The hydrogen content, in particular, reduced with an increase in martensite tetragonality. This, in turn, enhanced the phase boundary hydrogen concentrations leading to interface decohesion.

Plastic deformation is associated with developments in both dislocation density and residual strain. This study used multi-scale diffraction-based, X-ray as well as electron diffraction, measurements to quantify and relate them. Though both increased with progressive tensile deformation, an inverse orientation dependent relationship clearly emerged. In particular, higher elastically strained regions were accommodated by dislocation walls of lower residual strain. These experimental observations provided a combined perspective of elastic-plastic strain gradients in experimental plasticity. This study was then extended towards anelasticity, or internal friction, as induced by plastic deformation and elastic-plastic strains. Plastic deformation is known to enhance internal friction loss factor, tanδ, which then leads to the so-called dislocation enhanced Snoek (DES) peak. However, the atomistic origin of DES, role of elastic versus plastic strain, has never been established. Experimental nano dynamic mechanical analysis (nano-dma) measurements were used to bring out the plasticity induced DES of near-(001) grains. Experimental DES, however, scaled with both dislocation density and residual strain. This ambiguity necessitated use of numerical simulations to decouple respective contributions. Firstly, continuum finite element simulations indicated a stronger impact of residual stress, than the total stress, on the experimental DES. Further, atomistic modeling simulated (i) single-crystal nano-dma response and (ii) corresponding developments in residual stress as well as dislocation density. In particular, the DES emerged as an attribute of the non-uniform residual strain field(s) associated with dislocation(s). The corresponding change(s) in the anisotropies of local activation energy landscape, for interstitial diffusion of carbon, determined the enhanced Snoek response. Our experiments plus numerical modeling, thus brought out, and for the first time, a unique atomistic perspective towards anelasticity induced by plastic deformation.

Selecting suitable glucose-binding proteins (GBPs) is vital for biosensor development for medical diagnostics and quality control in the food industry. Biosensors offer advantages such as high specificity, selectivity, fast response time, continuous measurement, and cost-effectiveness. The current work utilized a combination of molecular docking, molecular dynamics (MD) simulations, and free energy calculations to develop a high-throughput bioinformatics pipeline to select GBP candidates from an extensive protein database (37,325 proteins). Using molecular docking, GBPs with good binding affinity to glucose (1,447 candidates) were virtually screened from the Protein Data Bank. MD simulations ascertained the binding dynamics of a few selected candidates. Further, steered MD (Brownian dynamics fluctuation-dissipation-theorem) was used to estimate binding free energies of the ligand-protein complex. Correlations between ligand-binding parameters obtained from longer MD simulations and binding parameters interpreted from significantly faster docking simulations were investigated. The correlation plots suggested that a combination of threshold values of the following three docking parameters: docking binding energy, binding cavity depth, and the number of hydrogen bonds between the ligand and binding site residues can be used to predict candidate GBPs reliably. Thus, a high-throughput and accurate protein selection process based on relatively faster docking simulations was proposed to screen GBPs for glucose biosensing.### Competing Interest StatementThe authors have declared no competing interest.

Membrane-peptide interactions are key to the formation of helical intermediates in the early stages of amyloidogenesis. Aqueous solutions of 2,2,2-trifluoroethanol (TFE) provide a membrane-mimetic environment capable of promoting and stabilizing local peptide interactions. Uperin 3.5 (U3.5), a 17-residue and amidated antimicrobial peptide, is unstructured in water but self-assembles into fibrils in the presence of salt. Secondary structure transitions linked to U3.5 self-assembly were investigated in TFE/water mixtures, in both the absence and presence of salt, to assess the role of membrane-peptide interactions on peptide self-assembly and amyloid formation. A 5-to-7-fold increase in fibril yield of U3.5 was observed at low TFE concentrations (10% TFE/water v/v) compared with physiological buffer but only in the presence of salt. No aggregation was observed in salt-free TFE/water mixtures. Circular dichroism spectra showed that partial helical structures, initially stabilized by TFE, transitioned to β-sheet-rich aggregates in a saline buffer. Molecular dynamics simulations confirmed that TFE and salt act synergistically to enhance peptide-peptide interactions, resulting in β-sheet-rich U3.5 oligomers at low TFE concentrations. Specifically, TFE stabilized amphipathic, helical intermediates, leading to increased peptide-peptide attraction through hydrophobic interactions. The presence of salt further enhanced the peptide-peptide interactions by screening positively charged residues. Thus, the study revealed the role of a membrane mimic in stabilizing helical intermediates on the pathway to amyloid formation in the antimicrobial U3.5 peptide.

Dispersing and stabilising proteins in ionic liquids (ILs) provides significant opportunities for green solvent-based biocatalysis, especially in industrial processes at elevated temperatures. While unmodified proteins undergo denaturation, their polymer-conjugated counterparts have been stabilised in neat ILs. However, the nature of interactions and the generality of protein-bioconjugate stabilisation in neat ILs require further understanding. Using a combination of different physio-chemical experimental tools and molecular dynamics (MD) simulations, here we investigate the dispersion and driving force for the stabilisation of bioconjugates in neat ILs. Solvent-free bioconjugates of different proteins, viz. myoglobin, α-chymotrypsin, and regenerated silk fibroin having predominant α-helical, β-sheet, and random coiled secondary structures, respectively, were prepared by electrostatic coupling with polyethylene-glycol (PEG)-based polymer-surfactant (PS). Protic IL (PIL, N-methyl-2-pyrolidonium trifluoromethane sulfonate; [NMP][OTF]) and aprotic ionic liquid (AIL, 1-methyl-3-(4-sulfobutyl)-1H-imidazol-3-ium trifluoromethane sulfonate; [MEZ][OTF]) were synthesized to study the bioconjugate dispersion. Interestingly, time-dependent polarised optical microscopy combined with transmittance measurements showed complete dispersion of all bioconjugates only in AIL. MD simulations of the PS-cCT bioconjugate were carried out in the same ILs as the experiments. The surface electrostatic potential of PS-cCT reversed from positive in PIL to negative in AIL due to overcharging by the AIL anion and lower mobility of the AIL cation. Strong screening of electrostatic potentials between two PS-cCT complexes in PIL resulted in reduced dispersion stability. Lower diffusivity of long alkyl chain [MEZ] cations of AIL leads to a depletion zone of IL ions between the two PS-cCT complexes (separation <70 Å), thus resulting in a significant negative potential between the complexes. Hence, protein bioconjugates in AIL were stabilised by a combination of surface overcharging and steric exclusion of [MEZ] cations from the space between the approaching bioconjugate complexes.

The role of hydrophobicity of phenylalanine-glycine nucleoporins (FG-Nups) in determining the transport of receptor-bound cargo across the nuclear pore complex (NPC) is investigated using Langevin dynamics simulations. A coarse-grained, minimal model of the NPC, comprising a cylindrical pore and hydrophobic-hydrophilic random copolymers for FG-Nups was employed. Karyopherin-bound receptor-cargo complexes (Kaps) were modeled as rigid, coarse-grained spheres without (inert) and with (patchy) FG-binding hydrophobic domains. With a sequence-agnostic description of FG-Nups and the absence of any anisotropies associated with either NPC or cargo, the model described tracer transport only as a function of FG-Nup hydrophobicity, f. The simulations showed the emergence of two important features of cargo transport, namely, NPC selectivity and specificity. NPC selectivity to patchy tracers emerged due to hydrophobic Kap-FG interactions and despite the sequence-agnostic description of FG-Nups. Furthermore, NPC selectivity was observed only in a specific range of FG-hydrophobic fraction, 0.05 ≤ f ≤ 0.20, resulting in specificity of NPC transport with respect to f. Significantly, this range corresponded to the number fraction of FG-repeats observed in both S. cerevisiae and H. sapiens NPCs. This established the central role of the FG-hydrophobic fraction in determining NPC transport, and provided a biophysical basis for conservation of the FG-Nup hydrophobic fraction across evolutionarily distant NPCs. Specificity in NPC transport emerged from the formation of a hydrogel-like network inside the pore with a characteristic mesh size dependent on f. This network rejected cargo for f > 0.2 based on size exclusion, which resulted in enhanced translocation probability for 0.05 ≤ f ≤ 0.20. Extended brush configurations outside the pore resulted in entropic repulsion and exclusion of inert cargo in this range. Thus, our minimal NPC model exhibited a hybrid cargo translocation mechanism, with aspects of both virtual gate and selective-phase models, in this range of FG-hydrophobic fraction.

Mutations in TDP-43 are known to cause Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). TDP-43 binds to and regulates splicing of several RNA including Zmynd11 . Zmynd11 is a transcriptional repressor and a potential E3 ubiquitin ligase family member, known for its role in neuron and muscle differentiation. Mutations in Zmynd11 have been associated with autism with significant developmental motor delays, intellectual disability, and ataxia. Here, we show that Zmynd11 is aberrantly spliced in the brain and spinal cord of transgenic mice overexpressing a mutant human TDP-43 (A315T), and that these changes occur before the onset of motor symptoms.

Helical intermediates appear to be crucial in amyloid formation of several amyloidogenic peptides, including Aβ, that are implicated in different neurodegenerative diseases. Intermediate species have been reported to be more toxic than mature amyloid fibrils. Hence, the focus of the current work is to understand both structural and mechanistic role of intermediates in the early stages of amyloid self-assembly in amyloidogenic peptides. Molecular dynamics (MD) simulations and the adaptive biasing force (ABF) method were utilized to investigate structural changes that lead to amyloid formation in amphibian peptide uperin-3.5 (U3.5), an antimicrobial and amyloidogenic peptide. Microsecond time-scale MD simulations revealed that peptide aggregation, intoβ-sheet dominated aggregates, is centred on two important factors; evolution ofα-helical intermediates and the critical role of local peptide concentration inside these aggregates. Electrostatic attraction between the oppositely charged aspartate (D) and arginine (R) residues located near the N-terminus induced hydrogen bonding resulting in formation of precursor 310-helices close to the N-terminus. The 310-helices transitioned intoα-helices, thereby imparting partial helical conformations to the peptides. In the initial stages of aggregation, U3.5 peptides with amphipathic, partial helices aggregated to form small clusters of helical intermediates directed via hydrophobic interactions. These helices imparted stability to the helical intermediates, which promoted growth of clusters by further addition of peptides. This led to an increase in the local peptide concentration which enabled stronger peptide-peptide interactions and triggered aβ-sheet transition in these aggregates. Thus, the study emphasized that stabilisation of peptide helical content may be crucial to the evolution ofβ-sheet-rich amyloid structures.

Applications of cast irons, from mundane to more challenging, are decided by the morphology of free graphite in the metallic matrix. The morphology changes from flake to spheroidal, as controlled by magnesium (Mg) addition during metal castings. Though this technology dates back several decades, the exact mechanism remains debatable. This study used a combination of industrial casting trials, analytical microscopy, and molecular dynamics (MD) simulations to address this question. It was experimentally established that the shape change was accompanied by a change in the growth direction, from prism to basal in the graphite, and atomic segregation of Mg at the interface. MD simulations indicated a combination of migration of oxygen (O) atoms and Mg-O interactions, respectively in the prism and basal oriented graphite, resulted in cross-over in interfacial free energy with Mg concentration. The anisotropic growth by high energy interface, controlled by interface chemistry, thus defined the mechanistic origin for the graphite morphology in cast iron.

Secondary structure changes are an inherent part of antimicrobial (AMP) and amyloidogenic peptide activity, especially in close proximity to membranes, and impact the peptides' function and dysfunction roles. The formation, and stability of α-helical components are regarded as essential 'intermediates' for both these functions. To illuminate the conformational transitions leading to amyloid formation we use short cationic AMPs, from an Australian toadlet, Uperoleia mjobergii, (Uperin 3 family, U3) and assess the impact on secondary structural elements in the presence of a membrane mimetic surfactant, sodium dodecyl sulfate (SDS). Specifically, Uperin 3.x, where x=4, 5, 6 wild-type peptides and position seven variants for each, R7A or K7A, were investigated using a combination of experimental and simulation approaches. In water, U3 peptides remain largely unstructured as random coils, with the addition of salts initiating structural transitions leading to assembly towards amyloid. Solution NMR data show that an unstructured U3.5 wt peptide transitions in the presence of SDS to a well-defined α-helical structure that spans nearly the entire sequence. Circular dichroism (CD) and ThT fluorescence studies show that all six U3 peptides aggregate in solution, albeit with vastly varying rates, and a dynamic equilibrium between soluble aggregates rich in either α-helices or β-sheets may exist in solution. However, the addition of SDS leads to a rapid disaggregation for all peptides and stabilisation of predominantly α-helical content in all the U3 peptides. Molecular dynamics (MD) simulations show that the adsorption of U3.5 wt/R7A peptides onto the SDS micelle is driven by Coulombic attraction between peptide cationic residues and the negatively charged sulfate head-groups on SDS. Simulating the interactions of various kinds of β-sheet dimers (of both U3.5 wt and its variant U3.5 R7A) with SDS micelles confirmed β-sheet content decreases in the dimers after their attachment to the SDS micelle. Adsorbed peptides interact favourably with the hydrophobic core of the micelle, promoting intramolecular hydrogen bonds leading to stabilisation of the α-helical structure in peptides, and resulting in a corresponding decrease in intermolecular hydrogen bonds responsible for β-sheets.

Internal friction is often sensitive to microstructural features. However, there is a clear absence of rational approach for decoupling internal friction spectra for diverse microstructural inputs. In this study, a robust multi-scale atomistic computational framework, combining atomistic kinetic Monte Carlo and molecular dynamics simulations, has been proposed. Predictions from our simulations were then compared with careful experiments on engineered microstructures in bcc steel. Specifically, theoretical contributions from interstitial solute type and concentration, crystallographic orientation, and residual stress (RS), were compared to actual experimental results. The atomistic computational framework successfully demonstrated that the overall internal friction response was composed, almost entirely, of Snoek relaxations from interstitial atoms. Ideal single-crystal simulations correctly predicted peak dissipation temperatures and Snoek peak height, $${\text{tan}}{\delta }_{\text{max}}$$ , when compared with available single-crystal experimental data. The simulations also captured the correct experimental trends with residual stress and crystallographic orientation in polycrystalline bcc steel. In particular, both RS and crystallographic orientation affected internal friction response by altering diffusion barriers for interstitial migration. Our study, thus, established that an integrated computational framework, supported with careful experiments, can be extremely effective in decoupling various microstructural inputs to complex experimental internal friction spectrum.

Non-fullerene acceptors have recently ignited extensive interest in organic solar cells (OSCs) because of their higher power conversion efficiency (PCE) than their fullerene counterparts. Though the effect of solvent additive 1, 8-diiodooctane (DIO) has been studied extensively for fullerene-based acceptor OSCs, not much is known for non-fullerene acceptors OSCs. In our work, bulk-heterojunction (BHJ) OSCs were fabricated by blending fullerene (PC71BM) and non-fullerene (ITIC and IEICO-4F) acceptors with low bandgap polymer donor (PTB7-Th). Further, the effects of non-fullerene acceptors on the nanomorphology, performance, and photostability of the devices were investigated. In the absence of DIO, devices with IEICO-4F acceptor showed higher PCE than PTB7-Th: ITIC and PTB7-Th: PC71BM BHJ-OSCs due to their absorption in near infrared along with high J (sc). The addition of DIO increased PCE in PTB7-Th: PC71BM BHJ-OSCs due to improved miscibility of fullerene molecules, higher donor/acceptor interface area, and improved phase separation. However, DIO adversely affected the overall device performance in PTB7-Th: IEICO-4F and PTB7-Th: ITIC BHJ-OSCs. Furthermore, devices processed with DIO were less photostable and exhibited faster degradation due to the photoacid effect of the DIO additive.

The compatibility of the third component mixing into binary blends primarily decides the device performance in ternary organic solar cells (t-OSCs). We added a wide-bandgap PCDTBT polymer as a third component into PTB7-Th: PC71BM binary blend, which improves photoconversion efficiency (PCE) with efficient energy transfer, enhanced light absorption, and better morphology of the ternary blends. The enhanced PCE is attributed to the absorption improvement and non-radiative Fo & BULL;rster resonance energy transfer (FRET) between PTB7-Th/PCDTBT polymers and the formation of a more fine bi-continuous interpenetrating network with a large donor/acceptor interfacial area with improved phase separation in the ternary system. Simultaneously, the addition of PCDTBT into PTB7-Th: PC71BM binary blend promotes the energetic disorder at the donor/acceptor interface in t-OSCs. This energetic disorder is studied in terms of Urbach energy and electroluminescence quantum efficiency. It was observed that the addition of PCDTBT into PTB7-Th: PC71BM affects the Urbach energy of PTB7-Th: PC71BM, which changes in bulk from 42 to 40.50 meV, and 42.70-50 meV for donor/acceptor interface. Interestingly, the energetic disorder at the donor/acceptor interface increases while the disorder in bulk decreases after the addition of PCDTBT polymer. Our results indicate that incorporating a wide-bandgap polymer as a third component is an appropriate way to design high-performance devices.

Melt-mixing was employed to prepare multiwall carbon nanotubes (MWCNTs) based polypropylene (PP) composites, wherein MWCNTs vary in "agglomerate" size and also in terms of "agglomerate" structure. Morphological analysis revealed MWCNTs-D type exhibits bigger "agglomerate" size with compact "agglomerate" structure with respect to MWCNTs-N type, that show smaller "agglomerate" size with porous "agglomerate" structure in the corresponding PP/MWCNTs composites. Melt-rheological analysis showed a rheological percolation threshold of 2 to 3 wt% in PP/MWCNTs-N composites, whereas PP/MWCNTs-D composites exhibited a rheological percolation of 3 to 4 wt% of MWCNTs. AC electrical conductivity measurements exhibited an electrical percolation threshold of 0.5 to 1 wt% of MWCNTs-N, whereas MWCNTs-D type depicts an electrical percolation threshold of 2 to 3 wt% of MWCNTs in the respective composites. Further, an unique dispersant; Li salt of 6-aminohexanoic acid (Li-AHA) was utilized to "deagglomerate" MWCNTs. Moreover, PP-g-MA was also utilized in combination with Li-AHA encapsulated MWCNTs in the corresponding composites. An extensive morphological, rheological, and electrical conductivity measurements suggested the influence of Li-AHA encapsulated MWCNTs and PP-g-MA on the transformation of MWCNTs "agglomerate" into "individualized" and smaller MWCNTs "agglomerate" in PP/MWCNTs composites.

Molecular dynamics simulations were used to quantify chiral transitions in an isolated isotactic polypropylene (iPP) chain on a nucleating agent substrate during the early stages of ordering. The effects of temperature, dihedral rigidity, and epitaxy of a single iPP chain placed on α-iPP, β-iPP, and TPDT surfaces were investigated. Using the adaptive biasing force (ABF) method, potentials of mean force (PMF) were computed for iPP segments to explain the selective stabilization of helical segments on various epitaxies. Whereas, chiral selection of helices from the extended-coil conformations was found to be more efficient, the selection of helices from coiled segments was poor. For α-iPP and β-iPP substrates, the stability of the extended-coils and formation of helices from extended-coils were positively correlated with each other. In contrast, a negatively correlation was found for the TPDT substrate, showing that a helix existed as a competitive conformation with the extended-coils when selective stabilization was absent. These observations support the validity of multi-stage nucleation routes during polymer crystallization, Further, they show that selective stabilization of helices by an epitaxy plays a vital role in the dynamics of multi-stage nucleation.

AbstractPolypropylene (PP) and multi‐walled carbon nanotubes (MWCNTs) composites were prepared by melt‐mixing with two types of MWCNTs of varying agglomerate size. Agglomerate dominated dispersion was observed in the PP matrix, wherein N‐MWCNTs exhibit a finer dispersion as compared to D‐MWCNTs. Further, MWCNTs were encapsulated by Li‐salt of 6‐amino caproic acid in various proportions along with PP‐g‐maleic anhydride in order to achieve finer MWCNTs dispersion. Thermogravimetric analysis exhibited an increase in onset of degradation temperature and higher residual weight (%) at 500 °C of PP with increased MWCNTs concentration, which suggests the formation of a thicker “interphase.” Glass transition temperature of the PP phase was increased monotonically as a function of unmodified MWCNTs concentration, which suggests a strong interfacial interaction between PP and MWCNTs. An extensive analysis was carried out with modified MWCNTs based PP composites. Moreover, MWCNTs act as a strong hetero‐nucleating agent manifesting in smaller spherulite size of PP, wherein bulk crystallization temperature is increased to ~130 °C of the PP phase at 5 wt% MWCNTs content. The influence of unmodified and modified MWCNTs on the interaction between the PP chains and MWCNTs in the amorphous phase as well as in the crystalline domains are analyzed in PP/MWCNTs composites.

In this work, controlled bidirectional deformation of suspended nanostructures by site-specific ion irradiation is presented. Multiscale modeling of the bidirectional deformation of nanostructures by site-specific ion irradiation is presented, incorporating molecular dynamics (MD) simulations together with finite element analysis, to substantiate the bending mechanism. Strain engineering of the free-standing nanostructure is employed for controlled deformation through site-specific kiloelectronvolt ion irradiation experimentally using a focused ion beam. We report the detailed bending mechanism of suspended silicon (Si) nanostructures through ion-induced irradiations. MD simulations are presented to understand the ion-solid interactions, defects formation in the silicon nanowire. The atomic-scale simulations reveal that the ion irradiation-induced bidirectional bending occurs through the development of localized tensile-compressive stresses in the lattice due to defect formation associated with atomic displacements. With an increasing ion dose, the evolution of localized tensile to compressive stress is observed, developing the alternate bending directions calculated through finite element analysis. The findings of multiscale modeling are in excellent agreement with the bidirectional nature of bending observed through the experiments. The developed in situ approach for bidirectional controlled manipulation of nanostructures in this work can be used for nanofabrication of numerous novel three-dimensional configurations and can provide a route toward functional nanostructures and devices.

This investigation was aimed to enhance the dispersibility of multi-walled carbon nanotubes (MWCNT) using sodium polystyrene sulfonate (Na-PSS) polyelectrolyte. Subsequently, electrically conducting, multi-layer thin films are prepared utilizing layer by layer assembly method with poly(vinyl alcohol) as a host matrix. The highest extent of MWCNT dispersion was observed in MWCNT:Na-PSS ratio of 1:9 (wt/wt), which was estimated from UV-Vis spectroscopic analysis. Zeta potential measurements of Na-PSS modified MWCNT dispersion showed large negative potentials ranging from -52 to -64 mV in the most stable pH range of 4 to 10, suggesting the colloidal stability is due to the long-range repulsive nature of electrostatic interactions from negatively charged sulfonate groups. Complementary molecular dynamics simulations showed that adsorption of Na-PSS imparts a large negative potential to the carbon nanotube surface, which increases with an increase in Na-PSS concentration. The multi-layer thin film of (1:9) MWCNT:Na-PSS exhibited a DC electrical conductivity of 2.96 x 10(2) S/m.

Phase selective nucleation of single chain isotactic polypropylene (iPP) into specific crystalline polymorphs is enabled by heterogeneous nucleating agents. Molecular dynamics simulations were used to investigate the ordering of isolated iPP chains over ideal (α-iPP and β-iPP) and commercial (triphenodithiazine, TPDT) heterogeneous nucleating surfaces during the early stages of nucleation. The ordering of an iPP chain during nucleation is analyzed by following the evolution of helix conformations, chiral order parameter, chain orientation and radius of gyration. The results show that α-iPP and β-iPP have a greater tendency to select chirality. However, TPDT is the most efficient in orienting the chain because of bulky phenyl groups on its surface. Based on helix evolution and segment orientation, early-stage ordering of iPP on crystalline surfaces is proposed to proceed by two different routes; (i) CTEH (coil-to-extended helix) where helix formation and segment orientation occur simultaneously, and (ii) CTEC (coil-to-extended coil) where segment orientation occurs without helix formation, thus indicating multistage nucleation through an intermediate mesomorphic phase. Whereas, CTEC is the predominant ordering route on TPDT, both CTEC and CTEH occur simultaneously on α-iPP and β-iPP, emphasizing the important role of epitaxy in early-stage ordering during crystallization.

Antimicrobial peptides of the uperin 3.x family, obtained from the skin secretions of Uperoleia mjobergii, have an inherent ability to form amyloid with possible functional roles and can serve as model peptides to understand mechanistic aspects of amyloidogenesis. The substitution of a positively charged amino acid with a nonpolar alanine residue increased aggregation, fibril content, and propensity for β-sheet formation for the uperin 3.5 R7A variant when compared with the uperin 3.5 wild-type peptides. We use molecular dynamics (MD) simulations and circular dichroism (CD) measurements on three uperin 3.x peptides and their corresponding seventh position alanine variants to understand the effect of substitution of a positively charged amino acid with a nonpolar alanine residue on the process of β-aggregation. Both CD experiments and simulations show that the uperin 3.x wild-type peptides demonstrated lower β-sheet content and propensity than with the corresponding alanine variants. Significantly, simulations of helix-to-coil transitions in individual peptides show an inverse relationship between the helical stability of peptides and their propensity to form structures rich in β-sheets as observed in CD experiments. A simulation scheme based on a conformational search of helix-to-coil transition trajectories to select peptide conformers was used to assemble propagating peptide oligomers. Whereas octamers consisting of lower helical stability peptide conformers evolve into compact aggregates with a large β-sheet component, octamers composed of high helical stability conformers disintegrate and show the least amounts of β-sheet components. The highlight of the current work is that MD simulations are able to predict the correct order of β-sheet propensity among the six peptides derived from the CD experiments and indicate the importance of helical intermediates in the amyloidogenesis pathway for uperin 3.x peptides.