Arbitrary Lagrangian-Eulerian finite-element method for computation of two-phase flows with soluble surfactants

A finite-element scheme based on a coupled arbitrary Lagrangian-Eulerian and Lagrangian approach is developed for the computation of interface flows with soluble surfactants. The numerical scheme is designed to solve the time-dependent Navier-Stokes equations and an evolution equation for the surfactant concentration in the bulk phase, and simultaneously, an evolution equation for the surfactant concentration on the interface. Second-order isoparametric finite elements on moving meshes and second-order isoparametric surface finite elements are used to solve these equations. The interface-resolved moving meshes allow the accurate incorporation of surface forces, Marangoni forces and jumps in the material parameters. The lower-dimensional finite-element meshes for solving the surface evolution equation are part of the interface-resolved moving meshes. The numerical scheme is validated for problems with known analytical solutions. A number of computations to study the influence of the surfactants in 3D-axisymmetric rising bubbles have been performed. The proposed scheme shows excellent conservation of fluid mass and of the total mass of the surfactant. (C) 2012 Elsevier Inc. All rights reserved.

Dimeric 1,3-Phenylene-bis(piperazinyl benzimidazole)s: Synthesis and Structure-Activity Investigations on their Binding with Human Telomeric G-Quadruplex DNA and Telomerase Inhibition Properties

Ligand-induced stabilization of G-quadruplex structures formed by the human telomeric DNA is an active area of research. The compounds which stabilize the G-quadruplexes often lead to telomerase inhibition. Herein we present the results of interaction of new monomeric and dimeric ligands having 1,3-phenylene-bis(piperazinyl benzimidazole) unit with G-quadruplex DNA (G4DNA) formed by human telomeric repeat d(G(3)T(2)A)(3)G(3)]. These ligands efficiently stabilize the preformed G4DNA in the presence of 100 mM monovalent alkali metal ions. Also, the G4DNA formed in the presence of low concentrations of ligands in 100 mM K+ adopts a highly stable parallel-stranded conformation. The G-quadruplexes formed in the presence of the dimeric compound are more stable than that induced by the corresponding monomeric counterpart. The dimeric ligands having oligo-oxyethylene spacers provide much higher stability to the preformed G4DNA and also exert significantly higher telomerase inhibition activity. Computational aspects have also been discussed.

Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface

Background: Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA) and phosphotransacetylase (Pta), key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism. Results: Here we report kinetic characterization of S. typhimurium AckA (StAckA) and structures of its unliganded (Form-I, 2.70 angstrom resolution) and citrate-bound (Form-II, 1.90 angstrom resolution) forms. The enzyme showed broad substrate specificity with k(cat)/K-m in the order of acetate > propionate > formate. Further, the K-m for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis) more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5'-triphosphates (GTP, UTP and CTP) and divalent cations (Mn2+ and Co2+), respectively. Form-I StAckA represents the first structural report of an unliganded AckA. StAckA protomer consists of two domains with characteristic beta beta beta alpha beta alpha beta alpha topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (MtAckA). Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II StAckA structure showed a drastic change in the conformation of residues 230-300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II StAckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I StAckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these enzymes. Conclusions: The biochemical and structural characterization of StAckA reported here provides insights into the biochemical specificity, overall fold, thermal stability, molecular basis of ligand binding and inter-domain motion in AckA family of enzymes. Dramatic conformational differences observed between unliganded and citrate-bound forms of StAckA led to identification of a putative ligand-binding pocket at the dimeric interface of StAckA with implications for enzymatic function.

Organogels from Dimeric Bile Acid Esters: In Situ Formation of Gold Nanoparticles

A new class of steroid dimers (bile acid derivatives) linked through ester functionalities were synthesized, which gelled various aromatic solvents. The organogels formed by the three dimeric ester molecules showed birefringent textures and fibrous nature by polarizing optical microscopy and scanning electron microscopy, respectively. A detailed rheological study was performed to estimate the mechanical strengths of two sets of organogels. In these systems, the storage modulus varied in the range of 0.8-3.5 X 10(4) at 1% w/v of the organogelators. The exponents of scaling of the storage modulus and yield stress of the two systems agreed well with those expected for viscoelastic soft colloidal gels with fibrillar flocs. The nanofibers in the organogel were utilized to engineer gold nanoparticles of different sizes and shapes and generate new gel-nanoparticle hybrid materials.

Effect of surfactants on the instability of a two-layer film flow down an inclined plane

The effect of insoluble surfactants on the instability of a two-layer film flow down an inclined plane is investigated based on the Orr-Sommerfeld boundary value problem. The study, focusing on Stokes flow P. Gao and X.-Y. Lu, ``Effect of surfactants on the inertialess instability of a two-layer film flow,'' J. Fluid Mech. 591, 495-507 (2007)], is further extended by including the inertial effect. The surface mode is recognized along with the interface mode. The initial growth rate corresponding to the interface mode accelerates at sufficiently long-wave regime in the presence of surface surfactant. However, the maximum growth rate corresponding to both interface and surface modes decelerates in the presence of surface surfactant when the upper layer is more viscous than the lower layer. On the other hand, when the upper layer is less viscous than the lower layer, a new interfacial instability develops due to the inertial effect and becomes weaker in the presence of interfacial surfactant. In the limit of negligible surface and interfacial tensions, respectively, two successive peaks of temporal growth rate appear in the long-wave and short-wave regimes when the interface mode is analyzed. However, in the case of the surface mode, only the long-wave peak appears. (C) 2014 AIP Publishing LLC.

How does spacer length of imidazolium gemini surfactants control the fabrication of 2D-Langmuir films of silver-nanoparticles at the air-water interface?

A series of gemini surfactants based on cationic imidazolium ring as polar headgroup, abbreviated as lm-n-lm], 2Br(-) (n = 2, 5, 6 and 12), was synthesized. Their ability to stabilize silver nanoparticles in aqueous media was investigated. The resulting suspensions were characterized by UV-Vis spectroscopy and transmission electron microscopy (TEM). They exhibit specific morphologies by adopting different supramolecular assemblies in aqueous media depending on the internal packing arrangements and on the number of spacer methylene units -(CH2)(n)-]. Individual colloids were extracted from the aqueous to chloroform layer and spread at the air/water interface to allow the formation of well-defined Langmuir films. By analysis of the surface pressure-area isotherms, the details about the packing behavior and orientation of the imidazolium gemini surfactant capped silver nanoparticles were obtained. Morphological features of the dynamic process of monolayer compression at the air-water interface were elucidated using Brewster angle microscopy (BAM). These monolayers were further transferred on mica sheets by the Langmuir-Blodgett technique at their associated collapse pressure and the morphology of these monolayers was investigated by atomic force microscopy (AFM). The number of spacer methylene units -(CH2)(n)-] of the gemini surfactants exerted critical influence in modulating the characteristics of the resulting Langmuir films. (C) 2014 Elsevier Inc. All rights reserved.

Mycobacterium tuberculosis Cell Division Protein, FtsE, is an ATPase in Dimeric Form

FtsE is one of the earliest cell division proteins that assembles along with FtsX at the mid-cell site during cell division in Escherichia coli. Both these proteins are highly conserved across diverse bacterial genera and are predicted to constitute an ABC transporter type complex, in which FtsE is predicted to bind ATP and hydrolyse it, and FtsX is predicted to be an integral membrane protein. We had earlier reported that the MtFtsE of the human pathogen, Mycobacterium tuberculosis, binds ATP and interacts with MtFtsX on the cell membrane of M. tuberculosis and E. coli. In this study, we demonstrate that MtFtsE is an ATPase, the active form of which is a dimer, wherein the participating monomers are held together by non-covalent interactions, with the Cys84 of each monomer present at the dimer interface. Under oxidising environment, the dimer gets stabilised by the formation of Cys84-Cys84 disulphide bond. While the recombinant MtFtsE forms a dimer on the membrane of E. coli, the native MtFtsE seems to be in a different conformation in the M. tuberculosis membrane. Although disulphide bridges were not observed on the cytoplasmic side (reducing environment) of the membrane, the two participating monomers could be isolated as dimers held together by non-covalent interactions. Taken together, these findings show that MtFtsE is an ATPase in the non-covalent dimer form, with the Cys84 of each monomer present in the reduced form at the dimer interface, without participating in the dimerisation or the catalytic activity of the protein.

How does spacer length of imidazolium gemini surfactants control the fabrication of 2D-Langmuir films of silver-nanoparticles at the air-water interface?

A series of gemini surfactants based on cationic imidazolium ring as polar headgroup, abbreviated as Im-n-Im], 2Br(-) (n = 2, 5,6 and 12), was synthesized. Their ability to stabilize silver nanoparticles in aqueous media was investigated. The resulting suspensions were characterized by UV-Vis spectroscopy and transmission electron microscopy (TEM). They exhibit specific morphologies by adopting different supramolecular assemblies in aqueous media depending on the internal packing arrangements and on the number of spacer methylene units -(CH2)(n)-]. Individual colloids were extracted from the aqueous to chloroform layer and spread at the air/water interface to allow the formation of well-defined Langmuir films. By analysis of the surface pressure-area isotherms, the details about the packing behavior and orientation of the imidazolium gemini surfactant capped silver nanoparticles were obtained. Morphological features of the dynamic process of monolayer compression at the air-water interface were elucidated using Brewster angle microscopy (BAM). These monolayers were further transferred on mica sheets by the Langmuir-Blodgett technique at their associated collapse pressure and the morphology of these monolayers was investigated by atomic force microscopy (AFM). The number of spacer methylene units (CH2)(n)-] of the gemini surfactants exerted critical influence in modulating the characteristics of the resulting Langmuir films. (C) 2014 Elsevier Inc. All rights reserved.

Nanorod to quantum dot conversion in ZnO dispersions with co-surfactants

A chemically-induced nanorod to quantum dot transition is reported in ZnO. This transition is achieved using co-surfactants in a marginally polar solvent in chimie douce (soft chemical) conditions. This is different from the physical instability driven transitions reported so far in metal nanowires and polymers. We propose a suitable mechanism for the observed phenomenon.

Efficacious redox-responsive gene delivery in serum by ferrocenylated monomeric and dimeric cationic cholesterols

Herein, we present the design and synthesis of new redox-active monomeric and dimeric (gemini) cationic lipids based on ferrocenylated cholesterol derivatives for gene delivery. The cationic cholesterols are shown to be transfection efficient after being formulated with the neutral helper lipid DOPE in the presence of serum (FBS). The redox activity of the resulting co-liposomes and their lipoplexes could be regulated using the alkanyl ferrocene moiety attached to the ammonium head groups of the cationic cholesterols. Atomic force microscopy (AFM), dynamic light scattering (DLS) and zeta potential measurements were performed to characterize the co-liposomal aggregates and their complexes with pDNA. The transfection efficiency of lipoplexes could be tuned by changing the oxidation state of the ferrocene moiety. The gene transfection capability was assayed in terms of green fluorescence protein (GFP) expression using pEGFP-C3 plasmid DNA in three cell lines of different origins, namely Caco-2, HEK293T and HeLa, in the presence of serum. The vesicles possessing ferrocene in the reduced state induced an efficient transfection, even better than a commercial reagent Lipofectamine 2000 (Lipo 2000) as evidenced by flow cytometry and fluorescence microscopy. All the co-liposomes containing the oxidized ferrocene displayed diminished levels of gene expression. Gene transfection events from the oxidized co-liposomes were further potentiated by introducing ascorbic acid (AA) as a reducing agent during lipoplex incubation with cells, leading to the resumption of transfection activity. Assessment of transfection capability of both reduced and oxidized co-liposomes was also undertaken following cellular internalization of labelled pDNA using confocal microscopy and flow cytometry. Overall, we demonstrate here controlled gene transfection activities using redox-driven, transfection efficient cationic monomeric and dimeric cholesterol lipids. Such systems could be used in gene delivery applications where transfection needs to be performed spatially or temporally.

New dimeric carbazole-benzimidazole mixed ligands for the stabilization of human telomeric G-quadruplex DNA and as telomerase inhibitors. A remarkable influence of the spacer

for selectively targeting cancer cells. Herein, we report the design and evolution of a new kind of carbazole-based benzimidazole dimers for their efficient telomerase inhibition activity. Spectroscopic titrations reveal the ligands high affinity toward the G4 DNA with significantly higher selectivity over duplex-DNA. The electrophoretic mobility shift assay shows that the ligands efficiently promote the formation of 04 DNA even at a lower concentration of the stabilizing K+ ions. The TRAP-LIG assay demonstrates the ligand's potential telomerase inhibition activity and also establishes that the activity proceeds via G4 DNA stabilization. An efficient nuclear internalization of the ligands in several common cancer cells (HeLa, HT1080, and A549) also enabled differentiation between normal HFF cells in co-cultures of cancer and normal ones. The ligands induce significant apoptotic response and antiproliferative activity toward cancer cells selectively when compared to the normal cells.

Effect of substrates and surfactants over the evolution of crystallographic texture of nanostructured ZnO thin films deposited through microwave irradiation

In spite of intense research on ZnO over the past decade, the detailed investigation about the crystallographic texture of as obtained ZnO thin films/coatings, and its deviation with growth surface is scarce. We report a systematic study about the orientation distribution of nanostructured ZnO thin films fabricated by microwave irradiation with the variation of substrates and surfactants. The nanostructured films comprising of ZnO nanorods are grown on semiconductor substrates such as Si(100), Ge(100)], conducting substrates (ITO-coated glass, Cr coated Si), and polymer coated Si (PMMA/Si) to examine the respective development of crystallographic texture. The ZnO deposited on semiconductor substrates yieldsmixed texture, whereas c-axis oriented ZnO nanostructured films are obtained by conducting substrate, and PMMA coated Si substrates. Among all the surfactants, nanostructured film produced by using the lower molecular weight of polymeric surfactants (polyvinylpyrrolidone) shows a stronger (0002) texture, and that can be tuned to (10 - 10) by increasing the molecular weight of the surfactant. The strongest basal pole is achieved for the ZnO deposited on PMMA coated Si as substrate, and cetyl-trimethyl ammonium bromide as cationic surfactant. The texture analysis is carried out by X-ray pole figure analysis using the Schultz reflection method. (C) 2015 Elsevier B.V. All rights reserved.

Role of spacer length in interaction between novel gemini imidazolium surfactants and Rhizopus oryzae lipase

An insight into the effects of new ionic liquid-type gemini imidazolium cationic surfactants on the structure and function of the lipases is of prime importance for their potential application. Changes in the activity, stability and structure of Rhizopus ouzae lipase in the presence of novel gemini surfactants, C-16-3-C(16)im]Br-2 and C-16-12-C(16)im]Br-2 were probed in the present study. Surfactant with shorter spacer length, C-16-3-C(i6)im]Br-2 was found to be better in improving the hydrolytic activity and thermal stability of the lipase. For both the surfactants, activation was concentration dependent. CD spectroscopy results showed a decrease in a-helix and an increase in beta-sheet content in the presence of these surfactants. A higher structural change observed in presence of C-16-12-C(16)im]Br-2 correlated with lower enzyme activity. Isothermal titration calorimetric studies showed the binding to be spontaneous in nature based on sequential two site binding model. The forces involved in binding were found to differ for the two surfactants proving that the spacer length is an important factor which governs the interaction. These surfactants could be used as promising components both in enzyme modification and media engineering for attaining the desired goals in biocatalytic reactions. (C) 2015 Elsevier B.V. All rights reserved.

Polysiloxane surfactants for the dispersion of carbon nanotubes in nonpolar organic solvents.

We develop two new amphiphilic molecules that are shown to act as efficient surfactants for carbon nanotubes in nonpolar organic solvents. The active conjugated groups, which are highly attracted to the graphene nanotube surface, are based on pyrene and porphyrin. We show that relatively short (C18) carbon tails are insufficient to provide stabilization. As our ultimate aim is to disperse and stabilize nanotubes in siloxane matrix (polymer and cross-linked elastomer), both surfactant molecules were made with long siloxane tails to facilitate solubility and steric stabilization. We show that the pyrene-siloxane surfactant is very effective in dispersing multiwall nanotubes, while the porphyrin-siloxane makes single-wall nanotubes soluble, both in petroleum ether and in siloxane matrix.

Structural Characterizations of the Dimeric Anti-HIV Antibody 2G12 and the HIV-2 Envelope Glycoprotein

More than thirty years after the discovery that Human Immunodeficiency Virus (HIV) was the causative agent of Acquired Immunodeficiency Syndrome (AIDS), the disease remains pandemic as long as no effective universal vaccine is found. Over 34 million individuals in the world are infected with the virus, and the vast majority of them have no access to the antiretroviral therapies that have largely reduced HIV to a chronic disease in the developed world. The first chapter of this thesis introduces the history of the virus. The key to the infectious mechanism of the virus lies in its envelope glycoprotein (Env), a trimeric spike on the viral surface that utilizes host T cell receptors for entry. Though HIV-1 Env is immunogenic, most infected patients do not mount an effective neutralizing antibody response against it. Broadly-neutralizing anti-Env antibodies (bNAbs) present in the serum of a minority of infected individuals are usually sufficient to prevent the progression to full blown AIDS. Thus, the molecular details of these bNAbs as well as the antibody-antigen interface are of prime interest for structural studies, as insight gained would contribute to the design of a more effective immunogen and potential vaccine candidate. The second chapter of this thesis describes the low-resolution crystal structure of one such antibody, 2G12 dimer, which targets a high mannose epitope on the surface of Env. Patients infected with HIV-2, a related virus with ~35% sequence identity in the Env region, can generally mount a robust antibody response sufficient for viral control for reasons still unknown. The final two chapters of this thesis focus on the first reported structural studies of HIV-2 Env, the molecular details of which may inform HIV-1 therapy and immunogen design.