Machine learning for predictive condensed-phase simulation

We show how machine learning techniques based on Bayesian inference can be used to reach new levels of realism in the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using accurate, correlated quantum chemistry, and predict energies and forces in molecular aggregates ranging from clusters to solid and liquid phases. The widely used electronic-structure methods based on density-functional theory (DFT) give poor accuracy for molecular materials like water, and we show how our techniques can be used to generate systematically improvable corrections to DFT. The resulting corrected DFT scheme gives remarkably accurate predictions for the relative energies of small water clusters and of different ice structures, and greatly improves the description of the structure and dynamics of liquid water.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation.

Engineering hierarchical nanostructures by elastocapillary self-assembly

Surfaces coated with nanoscale filaments such as silicon nanowires and carbon nanotubes are potentially compelling for high-performance battery and capacitor electrodes, photovoltaics, electrical interconnects, substrates for engineered cell growth, dry adhesives, and other smart materials. However, many of these applications require a wet environment or involve wet processing during their synthesis. The capillary forces introduced by these wet environments can lead to undesirable aggregation of nanoscale filaments, but control of capillary forces can enable manipulation of the filaments into discrete aggregates and novel hierarchical structures. Recent studies suggest that the elastocapillary self-assembly of nanofilaments can be a versatile and scalable means to build complex and robust surface architectures. To enable a wider understanding and use of elastocapillary self-assembly as a fabrication technology, we give an overview of the underlying fundamentals and classify typical implementations and surface designs for nanowires, nanotubes, and nanopillars made from a wide variety of materials. Finally, we discuss exemplary applications and future opportunities to realize new engineered surfaces by the elastocapillary self-assembly of nanofilaments. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bending of nanoscale filament assemblies by elastocapillary densification

We report a mechanism by which nanoscale filaments self-assemble into asymmetric aggregates by elastocapillary action. Specifically, capillary rise of liquid into an asymmetric pattern of vertically aligned filaments causes the filaments to deflect laterally during elastocapillary densification. We quantitatively show that the lateral deflection can be controlled precisely by the pattern shape and the coupling strength among the filaments. We exploit this mechanism to fabricate asymmetric micropillars and multidirectional bridges of densely packed carbon nanotubes. Analogous behavior occurs as biological filaments interact with liquids, and these findings enable scalable fabrication of anisotropic filament assemblies for manipulating surface interactions between solids and liquids. © 2010 The American Physical Society.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.

Thermal annealing effect on the nanomechanical properties and structure of P3HT:PCBM thin films

Nanostructured polymer-fullerene thin films are among the most prominent materials for application in high efficient polymer solar cells. Specifically, poly(3-hexylthiophene) (P3HT) and fullerene derivatives (PCBM) blends are used as the donor/acceptor materials forming a bulk heterojunction. Although P3HT:PCBM properties have been extensively studied, less light has been set on its nanomechanical properties, which affect the device service life. In this work Atomic Force Acoustic Microscopy (AFAM), Atomic Force Spectroscopy and Nanoindentation were used to study the effect of the fullerene presence and the annealing on the P3HT:PCBM nanomechanical behavior. The P3HT:PCBM thin films were prepared by spin coating on glass substrates and then annealed at 100 °C and 145 °C for 30 min. Large phase separation was identified by optical and Atomic Force Microscopy (AFM) for the annealed samples. Needle-like PCBM crystals were formed and an increase of the polymer crystallinity degree with the increase of the annealing temperature was confirmed by X-ray diffraction. AFAM characterization revealed the presence of aggregates close to stiff PCBM crystals, possibly consisting of amorphous P3HT material. AFM force-distance curves showed a continuous change in stiffness in the vicinity of the PCBM crystals, due to the PCBM depletion near its crystals, and the AFM indentation provided qualitative results about the changes in P3HT nanomechanical response after annealing. © 2011 Elsevier B.V. All rights reserved.

Graphene nanoribbon blends with P3HT for organic electronics.

In organic field-effect transistors (OFETs) the electrical characteristics of polymeric semiconducting materials suffer from the presence of structural/morphological defects and grain boundaries as well as amorphous domains within the film, hindering an efficient transport of charges. To improve the percolation of charges we blend a regioregular poly(3-hexylthiophene) (P3HT) with newly designed N = 18 armchair graphene nanoribbons (GNRs). The latter, prepared by a bottom-up solution synthesis, are expected to form solid aggregates which cannot be easily interfaced with metallic electrodes, limiting charge injection at metal-semiconductor interfaces, and are characterized by a finite size, thus by grain boundaries, which negatively affect the charge transport within the film. Both P3HT and GNRs are soluble/dispersible in organic solvents, enabling the use of a single step co-deposition process. The resulting OFETs show a three-fold increase in the charge carrier mobilities in blend films, when compared to pure P3HT devices. This behavior can be ascribed to GNRs, and aggregates thereof, facilitating the transport of the charges within the conduction channel by connecting the domains of the semiconductor film. The electronic characteristics of the devices such as the Ion/Ioff ratio are not affected by the addition of GNRs at different loads. Studies of the electrical characteristics under illumination for potential use of our blend films as organic phototransistors (OPTs) reveal a tunable photoresponse. Therefore, our strategy offers a new method towards the enhancement of the performance of OFETs, and holds potential for technological applications in (opto)electronics.