Computational modeling of nanorod growth

The structure rearrangement of polyelectrolyte shell on the surface of a charged spherical nanoparticle is investigated by methods of statistical theory of macromolecules and molecular dynamics. A mathematical model of conformational changes of adsorbed polyelectrolyte on the surface of a spherical nanoparticle is presented, and radial dependences of the concentration of macrochain links depending on the sign and magnitude of the nanoparticle charge are obtained. Molecular dynamic modeling of polypeptides with different degrees of polyelectrolyte on the surface of a charged spherical gold nanoparticle was performed. When the absolute value of the opposite sign charge on the spherical nanoparticle increased with respect to the charge of the macrochain, the polyelectrolyte shell at the surface of the nanoparticle was dense, while a loose layer of neutral macrochain links was formed at the periphery. On the uniformly charged surface of the spherical nanoparticle, the polyelectrolyte shell gradually swelled with increase in the absolute value of the nanoparticle charge and desorbed the earlier the higher the degree of polyelectrolyticity of the macrochain was.

A facile solution process for the preparation of anisotropic silica nanoparticles (ASNPs) is presented. ASNPs are prepared via controlled self-assembly of spherical silica seeds (22 nm) in alcohol-water mixed media, followed by their in situ fixation and overgrowth with tetraethoxysilane (TEOS). Ethanol and L-arginine (Arg) are used to modify the dielectric constant and ionic strength of the reaction media, by which seed assembly is controlled through the adjustment of electrostatic interaction. Ethanol and Arg also serve as a cosolvent and a catalyst for hydrolysis and condensation of TEOS, respectively, which enables us to produce ASNPs in a simple one-pot process. In addition to ASNPs with wormlike structures, different kinds of NPs (bimodal spherical NPs, monodisperse spherical NPs, and spherical aggregates) have also been obtained by changing the concentrations of ethanol and Arg. The length, thickness, or both of ASNPs are controlled systematically by varying the concentrations of Arg, seed NPs, and TEOS. Other alcoholic cosolvents, such as methanol, 1-propanol, 2-propanol, and t-butanol, are also effective to give ASNPs when the dielectric constant of the alcohol-water mixed media is properly adjusted, showing the versatility of the present method.

A facile synthesis of broad plasmon wavelength tunable silver nanoparticles in citrate aqueous solutions by laser ablation and light irradiation

Rett Syndrome is a rare genetic disorder exclusively seen in girls. Approximately 95% of RTT cases is caused by mutations in the MeCP2 gene which codes for Methyl-CpG-binding protein 2 (MeCP2). In this review, first, a brief introductory review of Rett Syndrome, MeCP2 protein structure and function, mutation types and frequencies, and phenotype–genotype relationships were provided. After that, the current knowledge on the wild-type and mutant MeCP2 protein structure and dynamics as well as its binding to DNA is reviewed. The review particularly focuses on computational (such as molecular dynamics) and experimental (such as electrophoretic mobility shift assays) studies on the MeCP2 binding to different types of DNA as well as the computational and experimental (such as circular dichroism) studies on the stability changes upon mutations. In the end, a brief opinion on future outlook for further computational studies is provided.

Effects of copper nanoparticles on elastic and thermal properties of conductive polymer nanocomposites

Mechanisms of bulk and surface diffusion in metallic glasses determined from molecular dynamics simulations

In this study, we address the computational modeling of biological soft tissue growth, focusing on the development of epithelial tissues. The formulation of the corresponding constitutive growth law using non-linear continuum mechanics and its implementation within a total-Lagrangian-type finite element method are described. In describing the growth law, we use multiplicative decomposition of the deformation gradient into a growth part and an elastic part. We propose two surface growth deformation gradients; isotropic surface growth and anisotropic surface growth with relative shrinkage in the principal direction of maximum stress at the initial state. We first apply our laws to a hollow thick-walled hemiellipsoid that idealizes a structure generally observed in the early development of epithelial tissues. Our simulation shows the following: (i) under isotropic surface growth, the hemiellipsoid becomes sphere-like, i.e., the ratio between the longest and shortest axial length tends to 1; (ii) in contrast, under anisotropic surface growth, the tissue elongates and flattens, i.e., the ratio between the longest and shortest axial length is enhanced. These results motivate us to apply the latter growth law to the realistic example of a vertebrate limb bud, which shows similar elongation and flattening during development. As expected, our numerical simulation succeeded in reproducing the essential aspects of morphological change in the limb bud, providing a new hypothesis for the vertebrate limb development.

A simple and rapid wet-chemical technique for the deposition of silver triangles on conventional glass substrates, which alleviates the need for lithography, has been developed. The technique is based on the seed-mediated cetyltrimethylammonium-bromide-directed growth of silver triangles on glass surfaces, where smaller spherical silver seeds that were attached to the surface were subsequently converted and grown into silver triangles in the presence of a cationic surfactant and silver ions. The size of the silver triangles was controlled by sequential immersion of silver seed-coated glass substrates into a growth solution and by the duration time of immersion. Atomic force microscopy studies revealed that the size of the silver triangles ranged between 100 and 500 nm. Interestingly, these new surfaces are a significant improvement over traditional silver island films for applications in metal-enhanced fluorescence. A routine 16-fold enhancement in emission intensity was typically observed, for protein-immobilized indocyanine green, with a relatively very low loading density of silver triangles on the glass surface.

Introduction: Computational simulation study was carried out on bioactive compounds of Ganoderma lucidum (G. lucidum). Methods: Molecular docking and molecular dynamics (MD) simulations were performed. The input files for protein and ligands were retrieved from Protein Data Bank (PDB) and PubChem database. Human maltase-glucoamylase (PDB ID: 3L4Y) is the protein (α-glucosidase enzyme). The ligands are thirteen compounds derived from G. lucidum together with acarbose and miglitol as controls. Results: Docking result showed the lowest binding energy is from Ganomycin B (-7.8 kcal/mol) compared to acarbose and miglitol (-5.0 kcal/mol and -4.4 kcal/mol) respectively. MD simulation showed interaction of 3L4Y-Ganomycin B achieved stable interaction and conformation as follows: root mean square deviation (RMSD) is ± 2.7 Å, average distance of ±1.8 Å and constant hydrogen bonds around 1 - 3. Conclusion: Ganomycin B was found to have good binding affinity, embarking its potential as a potent α-glucosidase inhibitor.

Effects of ammonium salts and anionic amphiphiles on the photochemical formation of gold nanorods

Polymerized ionic liquids (PolyILs) are a novel class of functional polymers that combine the unique physicochemical properties of molecular ionic liquids with the outstanding mechanical characteristics of polymers. This special mix of features might help to circumvent the key limitations of low molecular weight ionic liquids, namely, leakage and poor mechanical properties while utilizing their outstanding characteristics such as low vapor pressures, wide liquidus ranges, high thermal stability, high ionic conductivity, and wide electrochemical windows. PolyILs have shown remarkable advantages when employed in electrochemical devices such as dye-sensitized solar cells, lithium batteries, actuators, field-effect transistors, light emitting electrochemical cells, and electrochromic devices, among others. Despite their promising prospects as ideal polymer electrolytes, the role of molecular structure, morphology, and polymer dynamics on charge transport in PolyILs remains poorly understood. According to classical theories, the self-diffusion and ion transport in electrolytes are controlled by structural relaxation. These approaches predict similar temperature dependence for the dc conductivity and structural dynamics. Although this prediction has been shown to hold reasonably well for low molecular weight aprotic ionic liquids, it fails for PolyILs. In addition, the impact of morphology on charge transport is not considered within the framework of these theories. This talk will focus on new insights obtained from experimental studies employing broadband dielectric spectroscopy, temperature-modulated differential scanning calorimetry, rheology, and scattering techniques to elucidate the impact of morphology on charge transport and structural dynamics in systematic series of polymerized ammonium- and imidazolium- based ionic liquids. Detailed analyses reveal strong decoupling of these processes in the PolyILs, implying the limitation of the classical theories in describing charge transport and molecular dynamics in these materials, in contrast to low molecular weight systems. In addition, the strong correlation observed between ionic conductivity from dielectric experiments and morphologies from scattering and computational studies will be discussed.

Topic: Synthesis and in-depth characterization of mono- and bimetallic nanoparticles. Due to their high surface to volume ratio and differing properties to the bulk material, nanoparticles play a major role in modern science. Especially silver nanomaterials and the antibacterial and antifungal silver ions are particular interesting in medical applications to replace, for example, antibiotics. In the scope of this work, different monometallic and bimetallic nanoparticles based on silver were synthesized and characterized. In subsequently dissolution experiments those particles where monitored for several days to quantify the amount of released silver ions. This was done because former research showed a possible sacrificial anode effect in bimetallic silver based systems. The effect might lead to a higher ion release which would be preferred in possible applications. Furthermore, in situ powder diffraction at a synchrotron source was performed to investigate the influence on precursor concentration and temperature on the growth of silver nanoparticles synthesized in a microwave. The outcome of the experiments showed huge influence on polydispersity as well as particle size. The last part of this work investigated the possible synthesis of spherical iridium nanoparticles using different routes. As a result, highly porous spherical nanoparticles which consist of a mixture of iridium and iridium dioxide were discovered. These particles showed promising properties for possible catalytic applications, which were partially proven by accomplished linear sweep voltammetry experiments.

Our work investigates the interaction of synthesized graphene with the SARS-CoV-2 virus using molecular docking and molecular dynamics (MD) simulation method. The layer dependent inhibitory effect of graphene nanosheets on spike receptor-binding domain of 6LZG, complexed with host receptor i.e. angiotensin-converting enzyme 2 (ACE2) of SARS-CoV-2 was investigated through computational study. Graphene sample was synthesized using mechanical exfoliation with shear stress and its mechanism of inhibition towards the SARS-CoV-2 virus was explored by molecular docking and molecular dynamics (MD) simulation method. The thermodynamics study for the free binding energy of graphene towards the SARS-CoV-2 virus was analyzed. The binding energy of graphene towards the virus increased with an increasing number of layers. It shows the highest affinity of −17.5 Kcal/mol in molecular docking while ΔGbinding is in the order of −28.01 ± 0.04 5 Kcal/mol for the seven-layers structure. The increase in carbon layers is associated with an increasing number of edge sp3 –type carbon, providing greater curvature, further increase the surface reactivity responsible for high binding efficiency. The MD simulation data reveals the high inhibition efficiency of the synthesized graphene towards SARS-CoV-2 virus which would help to design future in-vitro studies. The graphene system could find potential applications in personal protective equipment and diagnostic kits. Communicated by Ramaswamy H. Sarma

In this study, the thermal denaturation mechanism and secondary structures of two types of human insulin nanoparticles produced by a process of solution-enhanced dispersion by supercritical fluids using dimethyl sulfoxide (DMSO) and ethanol (EtOH) solutions of insulin are investigated using spectroscopic approaches and molecular dynamics calculations. First, the temperature-dependent IR spectra of spherical and rod-shaped insulin nanoparticles prepared from DMSO and EtOH solution, respectively, are analyzed using principal component analysis (PCA) and 2D correlation spectroscopy to obtain a deeper understanding of the molecular structures and thermal behavior of the two insulin particle shapes. All-atom molecular dynamics (AAMD) calculations are performed to investigate the influence of the solvent molecules on the production of the insulin nanoparticles and to elucidate the geometric differences between the two types of nanoparticles. The results of the PCA, the 2D correlation spectroscopic analysis, and the AAMD calculations clearly reveal that the thermal denaturation mechanisms and the degrees of hydrogen bonding in the spherical and rod-shaped insulin nanoparticles are different. The polarity of the solvent might not alter the structure or function of the insulin produced, but the solvent polarity does influence the synthesis of different shapes of insulin nanoparticles.

We study the influence of spherical, triangular, and rod-like nanoparticles on the mechanical properties of a polymer nanocomposite (PNC), via coarse-grained molecular dynamics simulations. We focus on how the nanoparticle size, loading, mass, and shape influence the PNC's elastic modulus, stress at failure and resistance against cavity formation and growth, under external stress. We find that in the regime of strong polymer-nanoparticle interactions, the formation of a polymer network via temporary polymer-nanoparticle crosslinks has a predominant role on the PNC reinforcement. Spherical nanoparticles, whose size is comparable to that of the polymer monomers, are more effective at toughening the PNC than larger spherical particles. When comparing particles of spherical, triangular, and rod-like geometries, the rod-like nanoparticles emerge as the best PNC toughening agents.