For the first time, the present research examines the free vibration responses, Natural Frequencies (NFs), of Graphene Oxide Powder (GOP) nanocomposite cylindrical shells surrounded by three types of elastic foundations considering different Boundary Conditions (BCs). To support this, the effects of various BCs are examined on the NFs related to the GOP Nanocomposite Cylindrical Shells (GOPNCS). In addition, elastic foundations are characterized by three factors: Winkler, Pasternak, and Kerr. Addedly, First-order Shear Deformation Theory (FSDT) and Donnell's shell theory are combined to discover the fundamental formulations related to the GOPNCS structures. Then, the equations of motion related to the GOPNCS are formulated employing Hamilton's principle. In subsequent, the equations associated with the previous step are discretized by implementing the Generalized Differential Quadrature Method (GDQM), counted as the mesh reduction method. Afterward, the standard eigenvalue determination is employed to determine the NFs associated with the GOPNCS. Ultimately, multiple benchmarks are answered to authenticate the scheme recommended for determining the NFs of the GOPNCS. Further, numerous original problems are arranged and highlight the effects of changes in material and geometrical features, various BCs, and three types of elastic foundations on the NFs related to the GOPNCS. 

Natural frequency investigation of graphene oxide powder nanocomposite cylindrical shells surrounded by Winkler/Pasternak/Kerr elastic foundations with a focus on various boundary conditions

This work aims to evaluate dynamic stability of micro-shell panels enriched by nanocomposites based on an analytical approach. In order to capture the effects of size on the mechanical behaviour of the micro-shell panels, the modified couple stress theory is employed which uses the material length scale parameter. The fundamental equations incorporating kinematic, constitutive, equilibrium and compatibility equations, are developed based on the first-order shear deformation theory (FSDT) which supports analysis of thin and moderately thick micro-shells. The extended fundamental differential equations are solved by the Galerkin method which results a closed-form solution for evaluating the dynamic stability of the proposed micro-shell panels. Then, some comparative studies are conducted to validate accuracy of the proposed method. Finally, by performing an extended parametric study, effects of the material length scale parameter on the dynamic stability of the proposed micro-shell panels are investigated. 

Size-dependent dynamic stability of nanocomposite enriched micro-shell panels in thermal environment using the modified couple stress theory

The plasma membrane (PM) of cells is a dynamic structure whose morphology and composition is in constant flux. PM morphologic changes are particularly relevant for the assembly and disassembly of signaling platforms involving surface-bound signaling proteins, as well as for many other mechanochemical processes that occur at the PM surface. Surface-bound membrane proteins (SBMP) require efficient association with the PM for their function, which is often achieved by the coordinated interactions of intrinsically disordered regions (IDRs) and globular domains with membrane lipids. This review focuses on the role of IDR-containing SBMPs in remodeling the composition and curvature of the PM. The ability of IDR-bearing SBMPs to remodel the Gaussian and mean curvature energies of the PM is intimately linked to their ability to sort subsets of phospholipids into nanoclusters. We therefore discuss how IDRs of many SBMPs encode lipid-binding specificity or facilitate cluster formation, both of which increase their membrane remodeling capacity, and how SBMP oligomers alter membrane shape by monolayer surface area expansion and molecular crowding. 

Remodeling of the Plasma Membrane by Surface-Bound Protein Monomers and Oligomers: The Critical Role of Intrinsically Disordered Regions

Research on vibrational characteristics of nanocomposite double-variable-edge plates immersed in liquid under the effect of explosive loads

We present an extension of the Monte Carlo based mesoscopic membrane model, where the membrane is represented as a dynamically triangulated surface and the proteins are modeled as anisotropic inclusions formulated as in-plane nematic field variables adhering to the deformable elastic sheet. The local orientation of the nematic field lies in the local tangent plane of the membrane and is free to rotate in this plane. Protein-membrane interactions are modeled as anisotropic spontaneous curvatures of the membrane and protein-protein interactions are modeled by the splay and bend terms of Frank’s free energy for nematic liquid crystals. In the extended model, we have augmented the Hamiltonian to study membrane deformation due to a mixture of multiple types of curvature generating proteins. This feature opens the door for understanding how multiple kinds of curvature-generating proteins may be working in a coordinated manner to induce desired membrane morphologies. For example, among other things, we study membrane deformations and tubulation due to a mixture of positive and negative curvature proteins as mimics of various proteins from BAR domain family working together for curvature formation and stabilization. We also study the effect of membrane anisotropy, which manifests as membrane localization and differential binding affinity of a given curvature protein, leading to insights into the tightly regulated cargo sorting and transport processes. Our simulation results show different morphologies of deformed vesicles that depend on the curvatures and densities of the participating proteins as well as on the protein-protein and membrane-proteins interactions. PACS numbers:

https://www.biorxiv.org/content/biorxiv/early/2021/10/02/2021.10.02.462266.full.pdf

Membrane remodeling due to mixture of multiple curvature proteins: Insights from mesoscopic continuum modeling

Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein's ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure-function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins. 

/pdf/insights-into-membrane-curvature-sensing-and-membrane-34o90hg4.pdf

Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions

On the stability of thin-walled circular cylindrical shells under static and periodic radial loading

Curvature induced sorting of lipid membrane bound proteins has been widely studied through experiments that induce curvature variation in a giant unilamellar lipid-bilayer vesicle with adsorbed proteins by pulling thin cylindrical tethers. In the theoretical space, this has been supplemented with models that capture curvature dependent interaction between membrane and idealized protein particles, through free energy contributions. Many membrane proteins such as the BAR domain proteins are known to have extremely anisotropic shapes and soft interacting potentials, whereas the idealizations of protein particles explored in models have only assumed them as hard disk-like particles with curvature anisotropy. Here, we present a model of sorting of the proteins while including the effects of softness in their interaction potentials, shape anisotropy in the protein structure, and curvature anisotropy in the interactions with the membrane. This is based on a clean separation of free energy contributions from non-ideal fluid behavior of soft anisotropic particles and curvature interactions between proteins and membranes. We probe the behavior of the sorting function under limiting conditions and show that it converges to the previously derived models. In addition to this, we present a comparison of the variation in sorting ratio due to the observed variation in the shape parameter values in known membrane proteins. Finally, using published experimental data for membrane proteins, we perform fitting and derive model parameters. We observe that shape anisotropy adversely affects the sorting of proteins to a high curvature region, whereas curvature anisotropy and softer interaction between proteins favor sorting.

Sorting of proteins with shape and curvature anisotropy on a lipid bilayer tube.

Indentation of geometrically exact beams

The study was aimed to compare different RNA isolation methods from sperm and testicular tissue. A suitable sperm purification technique is required as sperm RNA yield is strongly correlated with the number of sperms. Goat (Capra hircus) semen was purified by swim-up method. Motile sperm were selected for the process of RNA isolation. Four different RNA isolation methods namely cold Trizol, Gunidinium thiocyanate method and SDS lysis method and silica column based spin column method were used to isolate total RNA from sperm and testicular tissue. The hot Trizol method yielded good amount of RNA with less contamination of DNA and proteins. The modification of heating the sample in Trizol and an additional chloroform phase separation step increased the yield of total RNA. The modified method yielded highest amount of RNA for both tissue and sperm samples which was 139.5 ng/μL and 38.6 ng/μL respectively. The RNA integrity was high as was defined by a sharp 28S and 18S rRNA band in the agarose gel. The A260/A280 ratio was 2.1 and 1.923 for tissue and sperm samples which signifies purity of RNA. The mRNA was also reverse transcribed and GAPDH amplified. A modified Trizol method was developed which resulted in increased yield (38.60 ng/μL) and purity (A260/A280: 1.923).

Sovan Das

Papers

Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions

On the stability of thin-walled circular cylindrical shells under static and periodic radial loading

Sorting of proteins with shape and curvature anisotropy on a lipid bilayer tube.

Indentation of geometrically exact beams

Evaluation of Spermatozoal Rna Extraction Methods