Hybrid Elements for Modelling Squeeze Film Effects Coupled with Structural Interactions in Vibratory MEMS Devices

We present a hybrid finite element based methodology to solve the coupled fluid structure problem of squeeze film effects in vibratory MEMS devices, such as gyroscopes, RF switches, and 2D resonators. The aforementioned devices often have a thin plate like structure vibrating normally to a fixed substrate, and are generally not perfectly vacuum packed. This results in a thin air film being trapped between the vibrating plate and the fixed substrate which behaves like a squeeze film offering both stiffness and damping. For accurate modelling of such devices the squeeze film effects must be incorporated. Extensive literature is available on squeeze film modelling, however only a few studies address the coupled fluid elasticity problem. The majority of the studies that account for the plate elasticity coupled with the fluid equation, either use approximate mode shapes for the plate or use iterative solution strategies. In an earlier work we presented a single step coupled methodology using only one type of displacement based element to solve the coupled problem. The displacement based finite element models suffer from locking issues when it comes to modelling very thin structures with the lateral dimensions much larger than the plate thickness as is typical in MEMS devices with squeeze film effects. In this work we present another coupled formulation where we have used hybrid elements to model the structural domain. The numerical results show a huge improvement in convergence and accuracy with coarse hybrid mesh as compared to displacement based formulations. We further compare our numerical results with experimental data from literature and find them to be in good accordance.

The peptide NCbz-Val-Tyr-OMe and aromatic pi-pi interactions

The peptide N-benzyloxycarbonyl-L-valyl-L-tyrosine methyl ester or NCbz-Val-Tyr-OMe (where NCbz is N-benzyloxycarbonyl and OMe indicates the methyl ester), C23H28N2O6, has an extended backbone conformation. The aromatic rings of the Tyr residue and the NCbz group are involved in various attractive intra- and intermolecular aromatic - interactions which stabilize the conformation and packing in the crystal structure, in addition to NH...O and OH...O hydrogen bonds. The aromatic - interactions include parallel-displaced, perpendicular T-shaped, perpendicular L-shaped and inclined orientations.

Role of synergistic pi-pi stacking and X-H center dot center dot center dot Cl (X = C, N, O) H-bonding interactions in gelation and gel phase crystallization

The self-assembly of p-pyridyl-ended oligo-p-phenylenevinylenes (OPVs) in ethanol leads to the formation of either hollow or solid microrods. The corresponding protonated OPVs with n-butyl chains induce transparent gelation and also gel phase crystallization owing to various synergistic noncovalent interactions. The chloride ion-selective gelation, AIEE and stimuli responsiveness of the gel are also observed.

The Self-Association of Graphane Is Driven by London Dispersion and Enhanced Orbital Interactions

We investigated the nature of the cohesive energy between graphane sheets via multiple CH center dot center dot center dot HC interactions, using density functional theory (DFT) including dispersion correction (Grimmes D3 approach) computations of n]graphane sigma dimers (n = 6-73). For comparison, we also evaluated the binding between graphene sheets that display prototypical pi/pi interactions. The results were analyzed using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory. BLW interprets the intermolecular interactions in terms of frozen interaction energy (Delta E-F) composed of electrostatic and Pauli repulsion interactions, polarization (Delta E-pol), charge-transfer interaction (Delta E-CT), and dispersion effects (Delta E-disp). The BLW analysis reveals that the cohesive energy between graphane sheets is dominated by two stabilizing effects, namely intermolecular London dispersion and two-way charge transfer energy due to the sigma CH -> sigma*(HC) interactions. The shift of the electron density around the nonpolar covalent C-H bonds involved in the intermolecular interaction decreases the C-H bond lengths uniformly by 0.001 angstrom. The Delta E-CT term, which accounts for similar to 15% of the total binding energy, results in the accumulation of electron density in the interface area between two layers. This accumulated electron density thus acts as an electronic glue for the graphane layers and constitutes an important driving force in the self-association and stability of graphane under ambient conditions. Similarly, the double faced adhesive tape style of charge transfer interactions was also observed among graphene sheets in which it accounts for similar to 18% of the total binding energy. The binding energy between graphane sheets is additive and can be expressed as a sum of CH center dot center dot center dot HC interactions, or as a function of the number of C-H bonds.

Cocrystals of Hydrochlorothiazide: Solubility and Diffusion/Permeability Enhancements through Drug-Coformer Interactions

Hydrochlorothiazide (HCT) is a diuretic and a BCS class IV drug with low solubility and low permeability, exhibiting poor oral absorption. The present study attempts to improve the physicochemical properties of the drug using a crystal engineering approach with cocrystals. Such multicomponent crystals of HCT with nicotinic acid (NIC), nicotinamide (NCT), 4-aminobenzoic acid (PABA), succinamide (SAM), and resorcinol (RES) were prepared using liquid-assisted grinding, and their solubilities in pH 7.4 buffer were evaluated. Diffusion and membrane permeability were studied using a Franz diffusion cell. Except for the SAM and NIC cocrystals, all other binary systems exhibited improved solubility. All of the cocrystals showed improved diffusion/membrane permeability compared to that of HCT with the exception of the SAM cocrystal. When the solubility was high, as in the case of PABA, NCT, and RES cocrystals, the flux/permeability dropped slightly. This is in agreement with the expected interplay between solubility and permeability. Improved solubility/permeability is attributed to new drug-coformer interactions. Cocrystals of SAM, however, showed poor solubility and flux This cocrystal contains a primary sulfonamide dimer synthon similar to that of HCT polymorphs, which may be a reason for its unusual behavior. Hirshfeld surface analysis was carried out in all cases to determine whether a correlation exists between cocrystal permeability and drug-coformer interactions.

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Current trends in modeling hostpathogen interactions

The rapid emergence of infectious diseases calls for immediate attention to determine practical solutions for intervention strategies. To this end, it becomes necessary to obtain a holistic view of the complex hostpathogen interactome. Advances in omics and related technology have resulted in massive generation of data for the interacting systems at unprecedented levels of detail. Systems-level studies with the aid of mathematical tools contribute to a deeper understanding of biological systems, where intuitive reasoning alone does not suffice. In this review, we discuss different aspects of hostpathogen interactions (HPIs) and the available data resources and tools used to study them. We discuss in detail models of HPIs at various levels of abstraction, along with their applications and limitations. We also enlist a few case studies, which incorporate different modeling approaches, providing significant insights into disease. (c) 2013 Wiley Periodicals, Inc.

The X-C---Y (X = O/F, Y = O, S, F, Cl, Br, N, P,) Carbon bond and hydrophobic interactions

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C···Y interaction, which could be called 'carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the 'hydrophobic interactions'.

An ultrastable conjugate of silver nanoparticles and protein formed through weak interactions

In recent years, silver nanoparticles (AgNPs) have attracted significant attention owing to their unique physicochemical, optical, conductive and antimicrobial properties. One of the properties of AgNPs which is crucial for all applications is their stability. In the present study we unravel a mechanism through which silver nanoparticles are rendered ultrastable in an aqueous solution in complex with the protein ubiquitin (Ubq). This involves a dynamic and reversible association and dissociation of ubiquitin from the surface of AgNP. The exchange occurs at a rate much greater than 25 s(-1) implying a residence time of <40 ms for the protein. The AgNP-Ubq complex remains stable for months due to steric stabilization over a wide pH range compared to unconjugated AgNPs. NMR studies reveal that the protein molecules bind reversibly to AgNP with an approximate dissociation constant of 55 mu M and undergo fast exchange. At pH > 4 the positively charged surface of the protein comes in contact with the citrate capped AgNP surface. Further, NMR relaxation-based experiments suggest that in addition to the dynamic exchange, a conformational rearrangement of the protein takes place upon binding to AgNP. The ultrastability of the AgNP-Ubq complex was found to be useful for its anti-microbial activity, which allowed the recycling of this complex multiple times without the loss of stability. Altogether, the study provides new insights into the mechanism of protein-silver nanoparticle interactions and opens up new avenues for its application in a wide range of systems.

Modelling the influence of land-use changes on biophysical and biochemical interactions at regional and global scales

Land-use changes since the start of the industrial era account for nearly one-third of the cumulative anthropogenic CO2 emissions. In addition to the greenhouse effect of CO2 emissions, changes in land use also affect climate via changes in surface physical properties such as albedo, evapotranspiration and roughness length. Recent modelling studies suggest that these biophysical components may be comparable with biochemical effects. In regard to climate change, the effects of these two distinct processes may counterbalance one another both regionally and, possibly, globally. In this article, through hypothetical large-scale deforestation simulations using a global climate model, we contrast the implications of afforestation on ameliorating or enhancing anthropogenic contributions from previously converted (agricultural) land surfaces. Based on our review of past studies on this subject, we conclude that the sum of both biophysical and biochemical effects should be assessed when large-scale afforestation is used for countering global warming, and the net effect on global mean temperature change depends on the location of deforestation/afforestation. Further, although biochemical effects trigger global climate change, biophysical effects often cause strong local and regional climate change. The implication of the biophysical effects for adaptation and mitigation of climate change in agriculture and agroforestry sectors is discussed. center dot Land-use changes affect global and regional climates through both biochemical and biophysical process. center dot Climate effect from biophysical process depends on the location of land-use change. center dot Climate mitigation strategies such as afforestation/reforestation should consider the net effect of biochemical and biophysical processes for effective mitigation. center dot Climate-smart agriculture could use bio-geoengineering techniques that consider plant biophysical characteristics such as reflectivity and water use efficiency.

Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein

The survival protein SurE from Salmonella typhimurium (StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of beta-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167 degrees. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11 degrees between the B chains upon superposition of the A chains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.

Suspensions of polymer-grafted nanoparticles with added polymers-Structure and effective pair-interactions

We present the results of combined experimental and theoretical (molecular dynamics simulations and integral equation theory) studies of the structure and effective interactions of suspensions of polymer grafted nanoparticles (PGNPs) in the presence of linear polymers. Due to the absence of systematic experimental and theoretical studies of PGNPs, it is widely believed that the structure and effective interactions in such binary mixtures would be very similar to those of an analogous soft colloidal material-star polymers. In our study, polystyrene-grafted gold nanoparticles with functionality f = 70 were mixed with linear polystyrene (PS) of two different molecular weights for obtaining two PGNP: PS size ratios, xi = 0.14 and 2.76 (where, xi = M-g/M-m, M-g and M-m being the molecular weights of grafting and matrix polymers, respectively). The experimental structure factor of PGNPs could be modeled with an effective potential (Model-X), which has been found to be widely applicable for star polymers. Similarly, the structure factor of the blends with xi = 0.14 could be modeled reasonably well, while the structure of blends with xi = 2.76 could not be captured, especially for high density of added polymers. A model (Model-Y) for effective interactions between PGNPs in a melt of matrix polymers also failed to provide good agreement with the experimental data for samples with xi = 2.76 and high density of added polymers. We tentatively attribute this anomaly in modeling the structure factor of blends with xi = 2.76 to the questionable assumption of Model-X in describing the added polymers as star polymers with functionality 2, which gets manifested in both polymer-polymer and polymer-PGNP interactions especially at higher fractions of added polymers. The failure of Model-Y may be due to the neglect of possible many-body interactions among PGNPs mediated by matrix polymers when the fraction of added polymers is high. These observations point to the need for a new framework to understand not only the structural behavior of PGNPs but also possibly their dynamics and thermo-mechanical properties as well. (C) 2015 AIP Publishing LLC.

Graphene scavenges free radicals to synergistically enhance structural properties in a gamma-irradiated polyethylene composite through enhanced interfacial interactions

A unique strategy for scavenging free radicals in situ on exposure to gamma irradiation in polyethylene (PE) nanocomposites is presented. Blends of ultra-high molecular weight PE and linear low-density PE (PEB) and their nanocomposites with graphene (GPEB) were prepared by melt mixing to develop materials for biomedical implants. The effect of gamma irradiation on the microstructure and mechanical properties was systematically investigated. The neat blend and the nanocomposite were subjected to gamma-ray irradiation in order to improve the interfacial adhesion between PE and graphene sheets. Structural and thermal characterization revealed that irradiation induced crosslinking and increased the crystallinity of the polymer blend. The presence of graphene further enhanced the crystallinity via crosslinks between the polymer matrix and the filler on irradiation. Graphene was found to scavenge free radicals as confirmed by electron paramagnetic resonance spectroscopy. Irradiation of graphene-containing polymer composites resulted in the largest increase in modulus and hardness compared to either irradiation or addition of graphene to PEB alone. This study provides new insight into the role of graphene in polymer matrices during irradiation and suggests that irradiated graphene-polymer composites could emerge as promising materials for use as articulating surfaces in biomedical implants.

Anomalous Viscosity Reduction and Hydrodynamic Interactions of Polymeric Nanocolloids in Polymers

One of the central dogmas of fluid physics is the no-slip boundary condition, whose validity has come under scrutiny, especially in the fields of micro and nanofluidics. Although various studies show the violation of the no-slip condition its effect on flow of colloidal particles in viscous media has been rarely explored. Here we report unusually large reduction of effective viscosity experienced by polymeric nano colloids moving through a highly viscous and confined polymer, well above its glass transition temperature. The extent of reduction in effective interface viscosity increases with decreasing temperature and polymer film thickness. Concomitant with the reduction in effective viscosity we also observe apparent divergence of the wave vector dependent hydrodynamic interaction function of these colloids with an anomalous power law exponent of similar to 2 at the lowest temperatures and film thickness studied. Such strong hydrodynamic interactions are not expected for polymeric colloidal motion in polymer melts. We suggest hydrodynamics, especially slip present at the colloid-polymer interface which determines the observed reduction in interface viscosity and presence of strong hydrodynamic interactions.