Vanadium pentoxide (V
2
O
5
) is a transition metallic oxide which is suitable for strain gauge application because of its good electrical properties and conductivity. Considering this, cerium oxide ...(CeO
2
)-doped vanadium oxide (V
2
O
5
) nanoparticles are synthesized with the varied concentrations of 5, 10, and 15 wt%, to study its characteristics for fabrication of thin film strain gauges. The structural, transmission spectral, morphological, compositional and the electrical properties of synthesized nanoparticles are characterized using XRD, FTIR, SEM, HRTEM, EDX and CLR meter respectively. The characterization results depict favorable changes within the nanoparticle samples on the addition of dopant. The transformation from amorphous to crystalline phase orthorhombic cubic structure is visible from the x-ray diffraction results. The morphological data depict improvement in the structural appearance of the samples without any cracks on its surface. The shift in transmission spectral peaks towards the lower wave number indicates the improved electronic transitioning due to high activation energy. The drastic improvement in its conductivity from 1 to 4.3 S/m, along with better temperature characteristics specially in case of 10-wt% CeO
2
:V
2
O
5
, depicts the improved sensitivity of the samples. The resulting gauge factor of 45.21 obtained through four-point bending arrangement highlights the better strain resistance behavior of synthesized nanoparticles.
Sodium montmorillonite (Na-MMT) is one of the most commonly found swelling clay minerals with diverse engineering and technological applications. The nanomechanical properties of this mineral have ...been extensively investigated computationally utilizing molecular dynamics (MD) simulations to portray the molecular-level changes at different environmental conditions. As the environmentally found Na-MMT clays are generally sized within hundreds of nanometers, all-atomistic (AA) MD simulations of clays within such size range are particularly challenging due to computational inefficiency. Informed from atomistic modeling, a coarse-grained (CG) modeling technique can be employed to overcome the spatiotemporal limitation. The current study presents a modeling strategy to develop a computationally efficient model of Na-MMT clay with a typical size over ≃100 nm by shrinking the atomistic platelet thickness and reducing the number of center-layer atoms. Using the “strain-energy conservation” approach, the force field parameters for the CG model are obtained and the developed CG model can well preserve in-plane tension, shear, and bending behaviors of atomistic counterparts. Remarkably, the CG tactoid model of Na-MMT, a hierarchical multilayer structure, can reproduce the interlayer shear and adhesion as well as d-spacing among the clay sheets as of atomistic one to a good approximation while gaining significantly improved computational speed. Our study demonstrates the efficacy of the CG modeling framework, paving the way for the bottom-up multiscale prediction of mechanical behaviors of clay and related minerals.
The objective of this study is to determine the ideal thickness and annealing temperature ranges for the derived 15 weight percent iron (Fe)-doped vanadium pentoxide (V
2
O
5
) nanoparticles by ...depositing them as thin films on a glass substrate using e-beam evaporation. The appropriateness of these films' structural, morphological, and electrical properties for the development of thin-film strain gauges is investigated. Through structural research, the nano-structured crystallite grain size of 0.1494 Å in an orthorhombic layered cubic structure was identified. The SEM images show the uniformly dispersed morphology of the deposited films. The greater adatom mobility seen as a result of surface diffusion kinetics and atomic shadowing is highlighted by the significant change in RMS surface roughness between 0.502 and 1.785 nm. Through examination of its electrical characteristics, it was discovered that when the film's thickness increased from 80 to 250 nm, the resistance decreased from 2.4 MΩ to 26.74 KΩ and ultimately to 24.38 KΩ. This decrease was further observed when the annealing temperature was raised to 500 °C. At the thickness range of 220 nm and the annealing temperature of 300 °C, the resistance also showed the lowest recorded dip of 11.75 KΩ. Therefore, it was concluded that these optimized process parameters of 220 nm and 300 °C would be appropriate for its utilization in the development of sensors, when addressing samples that contained 15 weight percent Fe: V
2
O
5
.
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•Only few ACE2 residues are strongly bound to Corona virus spike RBDs.•SARS-CoV-2 RBDs have strong attractive interactions with just two ACE2 residues.•Pull off force for SARS-CoV RBD ...from ACE2 is higher than that for SARS-CoV-2.•Attachment of ACE2 with both Corona viruses result in increased stiffness of ACE2.•Change in stiffness of ACE2 is six times higher for SARS-CoV-2 than SARS-CoV.
The SARS-CoV-2 coronavirus (COVID-19) that is causing the massive global pandemic exhibits similar human cell invasion mechanism as the coronavirus SARS-CoV, which had significantly lower fatalities. The cell membrane protein Angiotensin-converting enzyme 2 (ACE2) is the initiation point for both the coronavirus infections in humans. Here, we model the molecular interactions and mechanical properties of ACE2 with both SARS-CoV and COVID-19 spike protein receptor-binding domains (RBD). We report that the COVID-19 spike RBD interacts with ACE2 more strongly and at only two protein residues, as compared to multi-residue interaction of the SARS-CoV. Although both coronaviruses stiffen the ACE2, the impact of COVID-19 is six times larger, which points towards differences in the severity of the reported respiratory distress. The recognition of specific residues of ACE2 attachments to coronaviruses is important as the residues suggest potential sites of intervention to inhibit attachment and subsequent entry of the COVID-19 into human host cells
The synthesized 10 wt% cerium oxide-doped vanadium pentoxide nano-particles are deposited in the form of thin films on a glass substrate by e-beam evaporation to study their best appropriate ...thickness and annealing temperature ranges. The structural, morphological, and electrical characteristics of these films are examined for their suitability toward the development of thin film strain gauges. The nano-structured crystallite grain size of 0.1537 Å in an orthorhombic layered cubic structure was recognized through its structural analysis. Uniformly distributed morphology of the deposited films is visible through the SEM images. The small variation in RMS surface roughness between 1.346 and 1.354 nm highlights the stabilized film formation on the surface of the substrate. It was noticed through its electrical properties that, with the increase in thickness of the film from 80 to 250 nm, the resistance was found to decrease from 2.5 MΩ to 27.52 KΩ and up to 25.83 KΩ with the subsequent raise in annealing temperature till 500 °C. There was also an observed lowest dip in resistance of 12.13 KΩ, at the annealing temperature of 300 °C and the thickness range of 220 nm.
Actin molecules are essential structural components of the cellular cytoskeleton. Here, we report a comprehensive analysis of F-actin’s deformation behavior and highlight underlying mechanisms using ...steered molecular dynamics simulations (SMD). The investigation of F-actin was done under tension, compression, bending, and torsion. We report that the dissociation pattern of conformational locks at intrastrand and interstrand G-actin interfaces regulates the deformation response of F-actin. The conformational locks at the G-actin interfaces are portrayed by a spheroidal joint, interlocking serrated plates’ analogy. Further, the SMD simulation approach was utilized to evaluate Young’s modulus, flexural rigidity, persistent length, and torsional rigidity of F-actin, and the values obtained were found to be consistent with available experimental data. The evaluation of the mechanical properties of actin and the insight into the fundamental mechanisms contributing to its resilience described here are necessary for developing accurate models of eukaryotic cells and for assessing cellular viability and mobility.
COVID-19 has become a global pandemic caused by the SARS-CoV-2 coronavirus. SARS-CoV-2 shares many similarities with SARS coronavirus (SARS-CoV). A viral replication complex containing non-structural ...proteins (nsps) is the toolbox for RNA replication and transcription of both coronaviruses. In both cases, the RNA-dependent RNA polymerase (RdRp) domain of the coronaviral replication complex dictates the primary polymerase activity by cooperating with cofactors. The higher transmissibility and mortality due to SARS-CoV-2 are related to its higher RNA replication activity compared to SARS-CoV. The discrepancy between the RNA replication efficiency of SARS-CoV and SARS-CoV-2 can be understood by exploring interactions within their viral replication complexes. Our modeling of molecular interactions within the viral replication complexes of SARS-CoV and SARS-CoV-2 using molecular dynamics simulations suggests that in contrast to SARS-CoVnsp12, SARS-CoV2nsp12 prefers helices as the dominant interacting secondary motifs. The relative differences in nonbonded interactions between nsps could suggest viral RNA replication ability in coronaviruses.
Abstract
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from a range of model organisms. It summarizes ...complex composition, topology and function along with links to a large range of domain-specific resources (i.e. wwPDB, EMDB and Reactome). Since the last update in 2019, we have produced a first draft complexome for Escherichia coli, maintained and updated that of Saccharomyces cerevisiae, added over 40 coronavirus complexes and increased the human complexome to over 1100 complexes that include approximately 200 complexes that act as targets for viral proteins or are part of the immune system. The display of protein features in ComplexViewer has been improved and the participant table is now colour-coordinated with the nodes in ComplexViewer. Community collaboration has expanded, for example by contributing to an analysis of putative transcription cofactors and providing data accessible to semantic web tools through Wikidata which is now populated with manually curated Complex Portal content through a new bot. Our data license is now CC0 to encourage data reuse. Users are encouraged to get in touch, provide us with feedback and send curation requests through the ‘Support’ link.
Green River oil shale, a sedimentary rock, and an agglomerate of organic kerogen and minerals is the largest reserve of shale oil in the world. The production of shale oil requires the extraction of ...kerogen from the rock. Our prior experiments have shown that the kerogen in the shale lies in pores of tens of nanometers and is influenced by molecular interactions with the minerals. Calcite (CaCO3) is one of the predominant minerals present in Green River oil shale, and thus finding its interaction with kerogen is important. Molecular dynamics simulation is utilized in the present study to investigate the interactions between calcite mineral and the Green River kerogen, which is type I kerogen. The CHARMm force field parameters of calcite are derived from available parameters that are based on a rigid ion model. The expanded model of calcite is merged on top of the 12-unit kerogen model to study their interactions at NTP (Normal Temperature and Pressure) conditions. All the hydrocarbon fragments of kerogen in the proximity of calcite interact with the mineral with the exception of fragment 3. Fragments having olefinic hydrocarbons are attracted to the calcite mineral. These nonbonded interactions are primarily electrostatic. An energy table is developed to reveal the interfragment energy changes inside the kerogen macromolecule, in both the absence and presence of calcite. The presence of calcite mineral brings changes in the interfragment energies within the kerogen. The larger hydrocarbon fragments and independent ammonium ions are seen to have significant interactions among themselves. These findings provide an insight into the role of calcite–kerogen interactions on calcite–kerogen binding and the interfragment energies within the kerogen, which can help identify technologies to isolate kerogen from the Green River oil shale.
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