Evolution of nanostructure and mechanical properties of silver nano-particle in the confined region between graphene sheets: An atomistic investigation

Solidification and organization of silver nano-particle in a confined region between graphene sheets, shows much importance for the various application in the field of biomedical, electrochemical, coating materials, catalyst, metal-matrix nanocomposite etc. To understand the processes involved, we have studied the atomistic behaviour of solidification, organizations and mechanical properties of silver nano-particle in the bulk and as well as in confined region by molecular dynamics simulations. In the bulk, silver nano-particle shows phase transition from liquid to crystalline phase at a temperature, T ≈ 1030 ± 25 K. However, in the confined region, silver nano-particle depicts the same phase transition at a relatively higher temperature. The tensile stress, initiation of cracks and subsequent detachment of silver during tensile deformation depends upon the temperature and interfacial interactions. The tuning of 12–6 Lennard Jones interaction potential energy parameter between graphene and silver (εAg-C) drastically influenced the phase transition of silver nano-particle in the confined region. At a high interaction potential energy (εAg-C), silver nano-particle shows good wettability over the graphene sheets and depicts the phase transition at a higher temperature compared to lower interaction potential energy

‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators

To characterize the behavior and robustness of cellular circuits with many unknown parameters is a major challenge for systems biology. Its difficulty rises exponentially with the number of circuit components. We here propose a novel analysis method to meet this challenge. Our method identifies the region of a high-dimensional parameter space where a circuit displays an experimentally observed behavior. It does so via a Monte Carlo approach guided by principal component analysis, in order to allow efficient sampling of this space. This ‘global’ analysis is then supplemented by a ‘local’ analysis, in which circuit robustness is determined for each of the thousands of parameter sets sampled in the global analysis. We apply this method to two prominent, recent models of the cyanobacterial circadian oscillator, an autocatalytic model, and a model centered on consecutive phosphorylation at two sites of the KaiC protein, a key circadian regulator. For these models, we find that the two-sites architecture is much more robust than the autocatalytic one, both globally and locally, based on five different quantifiers of robustness, including robustness to parameter perturbations and to molecular noise. Our ‘glocal’ combination of global and local analyses can also identify key causes of high or low robustness. In doing so, our approach helps to unravel the architectural origin of robust circuit behavior. Complementarily, identifying fragile aspects of system behavior can aid in designing perturbation experiments that may discriminate between competing mechanisms and different parameter sets

Circadian oscillator proteins across the kingdoms of life : Structural aspects 06 Biological Sciences 0601 Biochemistry and Cell Biology

Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms and control numerous biological processes in a range of organisms. These periodic rhythms are the result of a complex interplay of interactions among clock components. These components are specific to the organism but share molecular mechanisms that are similar across kingdoms. The elucidation of clock mechanisms in different kingdoms has recently started to attain the level of structural interpretation. A full understanding of these molecular processes requires detailed knowledge, not only of the biochemical and biophysical properties of clock proteins and their interactions, but also the three-dimensional structure of clockwork components. Posttranslational modifications (such as phosphorylation) and protein-protein interactions, have become a central focus of recent research, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. The three-dimensional structures for the cyanobacterial clock components are well understood, and progress is underway to comprehend the mechanistic details. However, structural recognition of the eukaryotic clock has just begun. This review serves as a primer as the clock communities move towards the exciting realm of structural biology

Force induced removal of an encapsulated semi-flexible polymer from single walled carbon nanotube

Encapsulation of a variety of atoms, molecules, polymers, bio-polymers into a Single Wall Carbon Nanotube (SWCNT) depict unexpected properties such as unique morphology, physical properties, high thermal stability etc. The encapsulation and pull-out processes are very important parts of synthesis and characterization of new materials at atomic length scale, which controls the overall desirable properties. Here, we investigate the encapsulation and the pullout process of a long-polymer chain into/from a SWCNT by molecular dynamics (MD). However, during externally applied force induced pull-out process of polymer chain from SWCNT depict a significant transition in an organization with the creation of additional surface area. We have observed that the amount of applied force highly influences the organization and creation of additional surface area of polymer chain during pull-out process

Reactivity-Controlled Aggregation of Graphene Nanoflakes in Aluminum Matrix: Atomistic Molecular Dynamics Simulation

Aluminum graphene nanoflakes composite depicts many useful properties such as excellent mechanical strength, lightweight, high electrical, thermal properties, etc. Aggregation and dispersion of graphene nanoflakes in aluminum matrix highly influence the above -mentioned properties. In this paper, aggregation of graphene nanoflakes in aluminum matrix has been studied using molecular dynamics simulation. During simulations, adaptive intermolecular reactive empirical bond order (AIREBO) and embedded atom method force field were used for graphene nanoflakes and aluminum, respectively. AIREBO potential is capable of reproducing sp2 sp2 (covalent) bond formation or breaking between the reactive edge of graphene nanoflakes. The reactive edges of graphene nanoflakes form covalent bond with the neighboring graphene that produces a unique interconnected network in aluminum matrix. However, reactivity of graphene edge exclusively depends on the interfacial interaction between graphene and aluminum. Further, interfacial interactions significantly influence the crystallization temperature of aluminum. The adaptive common neighbor analysis, radial distribution function, mean square displacement, solvent -accessible surface area, and potential energy evolution have been used to characterize the properties of aluminum graphene nanoflakes composite. The results of this study may provide a comprehensive understanding of the interfacial properties of graphene aluminum nanocomposites, which help to improve the performance of nanocomposites materials

Effect of Multiaxial Tensile Deformation on the Mechanical Properties of Semiflexible Polymeric Samples

Molecular dynamics simulation is used to investigate the mechanical properties of the semiflexible polymer during multiaxial tensile deformations. The multiaxial tensile deformations can be imposed in totally or partially constrained modes. These types of deformations may be observed during the sudden deformation of polymeric material in the areas of aerospace, automobile, defense applications, etc. It is found that the constrained multiaxial deformation leads to the formation of nanovoids into the polymer sample. The high Young's modulus and yield strength for the totally constrained modes of tensile deformation are due to the energy required to create voids. The variation in von Misses stress, void volume, and bond order parameter with strain indicates the occurrence of brittle fracture during totally constrained tensile deformations. The partially constrained tensile deformations lead to the improvement in bond order parameter and lesser creation of nanovoids within the system. The system shows the characteristic strain hardening before failures

Properties of Adsorbed Bovine Serum Albumin and Fibrinogen on Self-Assembled Monolayers

International audienceWe have studied kinetics of adsorption and properties of adsorbed bovine serum albumin (BSA) and fibrinogen (Fb) on a hydrophobic octyl surface, a hydrophilic amine surface, and a mixture of octyl and amine self-assembled monolayer (SAM) and newly synthesized hybrid SAM by using quartz crystal microbalance (QCM). In addition, we have proposed a combined kinetic and mass transfer constrained protein adsorption model. The model is fitted to a change in resonance frequency, Delta F-n/n versus time data obtained from QCM to get the kinetic rate constants, mass transfer coefficient, and spreading of adsorbed proteins. Initial rate of adsorption increases with a decrease in surface energy of the substrate. The equilibrium adsorbed amount of BSA on the hybrid surface is less than that on the mixed surface and lies in between that on octyl and amine surfaces and that of Fb is the least on hybrid surface. The analysis of variation of the dissipation factor, Delta D, with Delta F-n/n indicates that BSA is more flexible than Fb and the adsorbed layer of both proteins is softest on the hybrid surface. The relaxation times of adsorbed proteins are the slowest on the octyl surface, while those on the hybrid surface are the fastest. The analysis of secondary structures of proteins using ATR-FTIR suggests secondary structures of the proteins change during adsorption. The content of alpha-helix of the proteins increases due to adsorption on the amine surface, while that decreases on all other surfaces. The total content of a-helix and beta-sheet strongly depends on the adsorbed mass of the proteins and is weakly dependent related to elasticity and viscosity of the adsorbed proteins, respectively

Single-Walled Carbon Nanotube Engendered Pseudo-1D Morphologies of Silver Nanowire

Silver nanowires show enhancement in desired properties, due to high surface area and high aspect ratio, which increases the possibility in design and development of many advanced optoelectronic devices. The organization of silver atoms and the morphology of cylindrical nanowire highly influence the desired properties at various physical conditions during applications. Therefore, the synthesis of nanowires with desired atomic organization becomes essential. In the present study, a pseudo-1D morphology of silver nanowires, encapsulated into a Single Wall Carbon Nanotubes (SWCNTs), has been investigated by employing Molecular Dynamics (MD) simulation. At high temperature (T = 1500 K), molten silver encapsulated into a SWCNT attaining a low energy state followed by restricted thermal motion or vibration. With an increase in SWCNT diameter, various unique pseudo-1D morphologies of encapsulated silver atoms were observed during cooling from 1500 to 10 K. Silver atoms, encapsulated into a SWCNT having a diameter of 10.85 Å, mainly reveal 5-fold symmetrical icosahedral (ico) having pseudo-1D morphology. With a further increase in diameter (d = 40.68 Å) of SWCNT, a decagonal pattern consisting of face centered cubic (fcc), hexagonal closed packed (hcp) and body centered cubic (bcc) was evolved due to nonhomogenous packing of silver atoms into SWCNT. Simulation results indicate that the diameter of SWCNT is the one of the major factors controlling the pseudo-1D morphology of silver nanowire. The present theoretical investigations provide a guideline and enhance the current understanding related to solid state physical phenomena of metal nanowires synthesis