Network topology mapping of chemical compounds space.

We define bipartite and monopartite relational networks of chemical elements and compounds using two different datasets of inorganic chemical and material compounds, as well as study their topology. We discover that the connectivity between elements and compounds is distributed exponentially for materials, and with a fat tail for chemicals. Compounds networks show similar distribution of degrees, and feature a highly-connected club due to oxygen . Chemical compounds networks appear more modular than material ones, while the communities detected reveal different dominant elements specific to the topology. We successfully reproduce the connectivity of the empirical chemicals and materials networks by using a family of fitness models, where the fitness values are derived from the abundances of the elements in the aggregate compound data. Our results pave the way towards a relational network-based understanding of the inherent complexity of the vast chemical knowledge atlas, and our methodology can be applied to other systems with the ingredient-composite structure.

Hybrid Nanoparticle/DNAzyme Electrochemical Biosensor for the Detection of Divalent Heavy Metal Ions and Cr3.

A hybrid noble nanoparticle/DNAzyme electrochemical biosensor is proposed for the detection of Pb2+, Cd2+, and Cr3+. The sensor takes advantage of a well-studied material that is known for its selective interaction with heavy metal ions (i.e., DNAzymes), which is combined with metallic nanoparticles. The double-helix structure of DNAzymes is known to dissociate into smaller fragments in the presence of specific heavy metal ions; this results in a measurable change in device resistance due to the collapse of conductive inter-nanoparticle DNAzyme bridging. The paper discusses the effect of DNAzyme anchoring groups (i.e., thiol and amino functionalization groups) on device performance and reports on the successful detection of all three target ions in concentrations that are well below their maximum permitted levels in tap water. While the use of DNAzymes for the detection of lead in particular and, to some extent, cadmium has been studied extensively, this is one of the few reports on the successful detection of chromium (III) via a sensor incorporating DNAzymes. The sensor showed great potential for its future integration in autonomous and remote sensing systems due to its low power characteristics, simple and cost-effective fabrication, and easy automation and measurement.

Glassy, Gardner-like phenomenology in minimally polydisperse crystalline systems.

We report on a nonequilibrium phase of matter, the minimally disordered crystal phase, which we find exists between the maximally amorphous glasses and the ideal crystal. Even though these near crystals appear highly ordered, they display glassy and jamming features akin to those observed in amorphous solids. Structurally, they exhibit a power-law scaling in their probability distribution of weak forces and small interparticle gaps as well as a flat density of vibrational states. Dynamically, they display anomalous aging above a characteristic pressure. Quantitatively, this disordered crystal phase has much in common with the Gardner-like phase seen in maximally disordered solids. Near crystals should be amenable to experimental realizations in commercially available particulate systems and are to be indispensable in verifying the theory of amorphous materials.

Simple Law for Third-Body Friction.

A key difficulty to understanding friction is that many physical mechanisms contribute simultaneously. Here we investigate third-body frictional dynamics in a model experimental system that eliminates first-body interaction, wear, and fracture, and concentrates on the elastic interaction between sliding blocks and third bodies. We simultaneously visualize the particle motion and measure the global shear force. By systematically increasing the number of foreign particles, we find that the frictional dissipation depends only on the size ratio between surface asperities and the loose particles, irrespective of the particle's size or the surface's roughness. When the particles are comparable in size to the surface features, friction increases linearly with the number of particles. For particles smaller than the surface features, friction grows sublinearly with the number of particles. Our findings suggest that matching the size of surface features to the size of potential contaminants may be a good strategy for reliable lubrication.

Degree product rule tempers explosive percolation in the absence of global information.

We introduce a guided network growth model, which we call the degree product rule process, that uses solely local information when adding new edges. For small numbers of candidate edges our process gives rise to a second-order phase transition, but becomes first order in the limit of global choice. We provide the set of critical exponents required to characterize the nature of this percolation transition. Such a process permits interventions which can delay the onset of percolation while tempering the explosiveness caused by cluster product rule processes.

Label-free DNA biosensor based on resistance change of platinum nanoparticles assemblies.

A novel nanoparticle based biosensor for the fast and simple detection of DNA hybridization events is presented. The sensor utilizes hybridized DNA's charge transport properties, combining them with metallic nanoparticle networks that act as nano-gapped electrodes. The DNA hybridization events can be detected by a significant reduction in the sensor's resistance due to the conductive bridging offered by hybridized DNA. By modifying the nanoparticle surface coverage, which can be controlled experimentally being a function of deposition time, and the structural properties of the electrodes, an optimized biosensor for the in situ detection of DNA hybridization events is ultimately fabricated. The fabricated biosensor exhibits a wide response range, covering four orders of magnitude, a limit of detection of 1nM and can detect a single base pair mismatch between probe and complementary DNA.

Universal Quake Statistics: From Compressed Nanocrystals to Earthquakes.

Slowly-compressed single crystals, bulk metallic glasses (BMGs), rocks, granular materials, and the earth all deform via intermittent slips or "quakes". We find that although these systems span 12 decades in length scale, they all show the same scaling behavior for their slip size distributions and other statistical properties. Remarkably, the size distributions follow the same power law multiplied with the same exponential cutoff. The cutoff grows with applied force for materials spanning length scales from nanometers to kilometers. The tuneability of the cutoff with stress reflects "tuned critical" behavior, rather than self-organized criticality (SOC), which would imply stress-independence. A simple mean field model for avalanches of slipping weak spots explains the agreement across scales. It predicts the observed slip-size distributions and the observed stress-dependent cutoff function. The results enable extrapolations from one scale to another, and from one force to another, across different materials and structures, from nanocrystals to earthquakes.

Statistics of dislocation slip avalanches in nanosized single crystals show tuned critical behavior predicted by a simple mean field model.

We show that slowly sheared metallic nanocrystals deform via discrete strain bursts (slips), whose size distributions follow power laws with stress-dependent cutoffs. We show for the first time that plasticity reflects tuned criticality, by collapsing the stress-dependent slip-size distributions onto a predicted scaling function. Both power-law exponents and scaling function agree with mean-field theory predictions. Our study of 7 materials and 2 crystal structures, at various deformation rates, stresses, and crystal sizes down to 75 nm, attests to the universal characteristics of plasticity.

Dislocations jam at any density.

Crystalline materials deform in an intermittent way via dislocation-slip avalanches. Below a critical stress, the dislocations are jammed within their glide plane due to long-range elastic interactions and the material exhibits plastic response, while above this critical stress the dislocations are mobile (the unjammed phase) and the material flows. We use dislocation dynamics and scaling arguments in two dimensions to show that the critical stress grows with the square root of the dislocation density. Consequently, dislocations jam at any density, in contrast with granular materials, which only jam below a critical density.

Plasticity and dislocation dynamics in a phase field crystal model.

The critical dynamics of dislocation avalanches in plastic flow is examined using a phase field crystal model. In the model, dislocations are naturally created, without any ad hoc creation rules, by applying a shearing force to the perfectly periodic ground state. These dislocations diffuse, interact and annihilate with one another, forming avalanche events. By data collapsing the event energy probability density function for different shearing rates, a connection to interface depinning dynamics is confirmed. The relevant critical exponents agree with mean field theory predictions.

Labeless AC impedimetric antibody-based sensors with pgml(-1) sensitivities for point-of-care biomedical applications.

This paper describes the development and characterisation of labeless immunosensors for (a) the cardiac drug digoxin and (b) bovine serum albumin (BSA). Commercial screen-printed carbon electrodes were used as the basis for the sensors. Two methods were used to immobilise antibodies at the electrode surface. Aniline was electropolymerised onto these electrodes to form a thin planar film of conductive polyaniline; the polyaniline film was then utilised as a substrate to immobilise biotinylated anti-digoxin using a classical avidin-biotin affinity approach. As an alternative approach, poly(1,2-diaminobenzene) was electrodeposited onto the carbon electrodes and this modified surface was then sonochemically ablated to form an array of micropores. A second electropolymerisation step was then used to co-deposit conductive polyaniline along with antibodies for BSA within these pores to produce a microarray of polyaniline protrusions with diameters of several mum, containing entrapped anti-BSA. The resulting antibody grafted electrodes were interrogated using an AC impedance protocol before and following exposure to digoxin or BSA solutions, along with control samples containing a non-specific IgG antibody. The impedance characteristics of both types of electrode were changed by increasing concentrations of antigen up to a saturation level. Calibration curves were obtained by subtraction of the non-specific response from the specific response, thereby eliminating the effects of non-specific adsorption of antigen. Both the use of microelectrode arrays and affinity binding protocols showed large enhancements in sensitivity over planar electrodes containing entrapped antibodies and gave similar sensitivities to our other published work using affinity-based planar electrodes. Detection limits were in the order of 0.1ngml(-1) for digoxin and 1.5ngml(-1) for BSA.

Label-less immunosensor assay for myelin basic protein based upon an ac impedance protocol.

This paper describes the development and characterization of a label-less immunosensor for myelin basic protein (MBP) and its interrogation using an ac impedance protocol. Commercial screen-printed carbon electrodes were used as the basis for the sensor. Polyaniline was electrodeposited onto the sensors, and this modified surface then utilized to immobilize a biotinylated antibody for MBP using a classical avidin-biotin approach. Electrodes containing the antibodies were exposed to solutions of MBP and interrogated using an ac impedance protocol. The real component of the impedance of the electrodes was found to increase with increasing concentration of antigen. Control samples containing a nonspecific IgG antibody were also studied, and calibration curves were obtained by subtraction of the responses for specific and nonspecific antibody-based sensors, thereby accounting for and eliminating the effects of nonspecific adsorption of MBP. A logarithmic relationship between the concentration of MBP in buffer solutions and the impedimetric response was observed.

Detection of fluoroquinolone antibiotics in milk via a labeless immunoassay based upon an alternating current impedance protocol.

This paper describes the construction of a labeless immunosensor for the antibiotic ciprofloxacin in milk and its interrogation using an ac impedance protocol. Commercial screen-printed carbon electrodes were used as the basis for the sensor. Polyaniline was electrodeposited onto the sensors and then utilized to immobilize a biotinylated antibody for ciprofloxacin using classical avidin-biotin interactions. Antibody loaded electrodes were exposed to solutions of antigen in milk and interrogated using an ac impedance protocol. The faradaic component of the impedance of the electrodes was found to increase with increasing concentration of antigen. Control samples containing a nonspecific IgG antibody were also studied but were found to display large nonspecific responses, probably due to the antibody binding some of the large number of components found in milk. Control sensors could, however, be fabricated using antibodies specific for species not found in milk. Calibration curves could be obtained by subtraction of the responses for specific and control antibody-based sensors, thereby eliminating the effects of nonspecific adsorption of antigen. Sensors exposed to ciprofloxacin in milk gave increases in impedance whereas ciprofloxacin in phosphate buffer led to decreases, indicating the possibility of developing sensors which can both detect and differentiate between free and chelated antigen.