Towards the identification of the gold binding region within trypsin stabilized nanoclusters using microwave synthesis routes.

Elucidating the location of stabilized nanoclusters within their protein hosts is an existing challenge towards the optimized development of functional protein-nanoclusters. While nanoclusters of various metal compositions can be readily synthesized within a wide array of protein hosts and exhibit tailorable properties, the inability to identify the cluster stabilization region prevents controllable property manipulation of both metallic and protein components. Additionally, the ability to synthesize protein-nanoclusters in a consistent and high-throughput fashion is also highly desirable. In this effort, trypsin stabilized gold nanoclusters are synthesized through standard and microwave-enabled methodologies to determine the impact of processing parameters on the materials physical and functional properties. Density functional theory simulations are employed to localize high probability regions within the trypsin enzyme for Au25 cluster stabilization, which reveal that cluster location is likely within close proximity of the trypsin active region. Trypsin activity measurements support our findings from DFT, as trypsin enzymatic activity is eliminated following cluster growth and stabilization. Moreover, studies on the reactivity of Au NCs and synchrotron characterization measurements further reveal that clusters made by microwave-based techniques exhibit slight structural differences to those made via standard methodologies, indicating that microwave-based syntheses largely maintain the native structural attributes despite the faster synthetic conditions. Overall, this work illustrates the importance of understanding the connections between synthetic conditions, atomic-scale structure, and materials properties that can be potentially used to further tune the properties of metal cluster-protein materials for future applications.

Dissipative particle dynamics with reactions: Application to RDX decomposition.

We present a general, flexible framework for a constant-energy variant of the dissipative particle dynamics method that allows chemical reactions (DPD-RX). In our DPD-RX approach, reaction progress variables are assigned to each particle that monitor the time evolution of an extent-of-reaction associated with the prescribed reaction mechanisms and kinetics assumed to occur within the particle, where chemistry can be modeled using complex or reduced reaction mechanisms. We demonstrate our DPD-RX method by considering thermally initiated unimolecular decomposition of the energetic material, cyclotrimethylene trinitramine (RDX), into a molecular gas mixture. Studies are performed to demonstrate the effect of a spatially averaged particle internal temperature and a local reaction volume term in the chemical kinetics expressions, where both provide implicit mechanisms for capturing condensed phase reactivity. We also present an analysis of the expansion of the product gas mixture during decomposition. Finally, a discussion of other potential applications and extensions of the DPD-RX method is given.

Freestanding organogels by molecular velcro of unsaturated amphiphiles.

A simple amphiphile, N-cardanyltaurine amide (NCT) with different degrees of cis-unsaturation in its tail resulted in the formation of strong organogels. Interestingly, this is in contrast to the commonly accepted notion that introducing unsaturation in alkyl chains enhances fluidity in lipid assemblies. The physico-chemical and first-principles DFT calculations confirmed the pegging of 'kinked' unsaturated side chains, where the hydrophobic interlocking as in Velcro fasteners leads to a network of cylindrical micelles, resulting in self-standing organogels. Textural profile analysis and spectroscopic details substantiated the dynamic assembly to resemble a 3D network of gelators rather than being a cross-linked or polymerized matrix of monomers.

The microbiome of neotropical ticks parasitizing on passerine migratory birds.

Seasonal migration of passerine birds between temperate North America and tropical Central and South America is an ecological phenomenon. Migration of birds has been associated with the introduction of ectoparasites like ticks or tick-borne pathogens across the avian migration routes. In this study, the microbial diversity was determined in the ticks and bird DNA samples using 454 pyrosequencing of bacterial 16S rRNA gene. Tick DNA samples showed the dominance of genera Lactococcus, Francisella, Raoultella, Wolbachia and Rickettsia across all the ticks, but birds DNA did not share common microbial diversity with ticks. Furthermore, "Candidatus Rickettsia amblyommii" infection in the 91 ticks collected off the songbirds was also quantified by qPCR assay. Interestingly, "Candidatus R. amblyommii" was tested positive in 24 ticks (26% infection), and infection varied from as low as three copies to thousands of copies, but bird blood samples showed no amplification. Our results provide evidence that songbirds serve as transport carrier for immature ticks, and less likely to be a reservoir for "Candidatus R. amblyommii".

A coarse-grain force field for RDX: Density dependent and energy conserving.

We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.

Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model.

We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference. With this combination, only a handful of simulations are needed, whereby the absolute quantities of the chemical potentials are obtained, for use in other property calculations, such as the characterization of crystal polymorphs or the determination of the entropy. Using the LAMMPS molecular simulator, the Frenkel and Ladd and pseudo-supercritical path techniques are adapted to generate 3rd order fits of the solid and liquid chemical potentials. Results yield the thermodynamic melting point Tm = 488.75 K at 1.0 atm. We also validate these calculations and compare this melting point to one obtained from a typical superheated simulation technique.

Importation of exotic ticks and tick-borne spotted fever group rickettsiae into the United States by migrating songbirds.

Birds are capable of carrying ticks and, consequently, tick-transmitted microorganisms over long distances and across geographical barriers such as oceans and deserts. Ticks are hosts for several species of spotted fever group rickettsiae (SFGR), which can be transmitted to vertebrates during blood meals. In this study, the prevalence of this group of rickettsiae was examined in ticks infesting migratory songbirds by using polymerase chain reaction (PCR). During the 2009 and 2010 spring migration season, 2064 northward-migrating passerine songbirds were examined for ticks at Johnson Bayou, Louisiana. A total of 91 ticks was removed from 35 individual songbirds for tick species identification and spotted fever group rickettsia detection. Ticks were identified as Haemaphysalis juxtakochi (n=38, 42%), Amblyomma longirostre (n=22, 24%), Amblyomma nodosum (n=17, 19%), Amblyomma calcaratum (n=11, 12%), Amblyomma maculatum (n=2, 2%), and Haemaphysalis leporispalustris (n=1, 1%) by comparing their 12S rDNA gene sequence to homologous sequences in GenBank. Most of the identified ticks were exotic species originating outside of the United States. The phylogenetic analysis of the 71 ompA gene sequences of the rickettsial strains detected in the ticks revealed the occurrence of 6 distinct rickettsial genotypes. Two genotypes (corresponding to a total of 28 samples) were included in the Candidatus Rickettsia amblyommii clade (less than 1% divergence), 2 of them (corresponding to a total of 14 samples) clustered with Rickettsia sp. "Argentina" with less than 0.2% sequence divergence, and 2 of them (corresponding to a total of 27 samples), although closely related to the R. parkeri-R. africae lineage (2.50-3.41% divergence), exhibited sufficient genetic divergence from its members to possibly constitute a new rickettsial genotype. Overall, there does not seem to be a specific relationship between exotic tick species, the rickettsiae they harbor, or the reservoir competence of the corresponding bird species.

Lattice strain due to an atomic vacancy.

Volumetric strain can be divided into two parts: strain due to bond distance change and strain due to vacancy sources and sinks. In this paper, efforts are focused on studying the atomic lattice strain due to a vacancy in an FCC metal lattice with molecular dynamics simulation (MDS). The result has been compared with that from a continuum mechanics method. It is shown that using a continuum mechanics approach yields constitutive results similar to the ones obtained based purely on molecular dynamics considerations.