Kinetic lattice grand canonical Monte Carlo simulation for ion current calculations in a model ion channel system

An algorithm in which kinetic lattice grand canonical Monte Carlo simulations are combined with mean field theory (KLGCMC/MF) is presented to calculate ion currents in a model ion channel system. In this simulation, the relevant region of the system is treated by KLGCMC simulations, while the rest of the system is described by modified Poisson-Boltzmann mean field theory. Calculation of reaction field due to induced charges on the channel/water and membrane/water boundaries is carried out using a basis-set expansion method [Im and Roux, J. Chem. Phys. 115, 4850 (2001)]. Calculation of ion currents, electrostatic potentials, and ion concentrations, as obtained from the KLGCMC/MF simulations, shows good agreement with Poisson-Nernst-Planck (PNP) theory predictions when the channel and membrane have the same dielectric constant as water. If the channel and membrane have a lower dielectric constant than water, however, there is a considerable difference between the KLGCMC/MF and PNP predictions. This difference is attributed to the reaction field, which is missing in PNP theory. It is demonstrated that the reaction field as well as fixed charges in the channel play key roles in selective ion transport. Limitations and further development of the current KLGCMC/MF approach are also discussed.     

Inelastic insights for molecular tunneling pathways: bypassing the terminal groups

As an example of the use of inelastic transport to deduce structure in molecular transport junctions, we compute the orientation dependence of the Inelastic Electron Tunneling (IET) spectrum of the 1-pentane monothiolate. We find that upon increasing the tilting angle of the molecule with respect to the normal to the electrode the spectrum changes as the intensity of some vibrations is enhanced. These differences occur because for higher tilting angles the tunneling path that bypasses the terminal group grows in importance. IETS can therefore be used to establish the molecular orientation in junctions terminating with alkyl chains and to investigate experimentally the relative importance of the available tunneling paths.     

Effect of chamber pressure on spreading and splashing of liquid drops upon impact on a dry smooth stationary surface

Liquid drop impacts on a smooth surface were studied at elevated chamber pressures to characterize the effect of gas pressure on drop spreading and splashing. Five common liquids were tested at impact speeds between 1.0 and 3.5 m/s and pressure up to 12 bars. Based on experiments at atmospheric pressure, a modification to the “free spreading” model (Scheller and Bousfield in AIChE Paper 41(6):1357–1367, 1995) has been proposed that improves the prediction accuracy of maximum spread factors from an error of 15–5%. At high chamber pressures, drop spreading and maximum spread factor were found to be independent of pressure. The splash ratio (Xu et al. in Phys Rev Lett 94:184505, 2005) showed a non-constant behavior, and a power-law model was demonstrated to predict the increase in splash ratio with decreasing impact speed in the low impact speed regime. Also, drop shape was found to affect splash promotion or suppression for an asymmetry greater than 7–8% of the equivalent drop diameter. The observations of the current work could be especially useful for the study of formation of deposits and wall combustion in engine cylinders.     

DNA-based optomechanical molecular motor

An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol(-1) of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.     

Organic Photovoltaics: Elucidating the Ultra‐Fast Exciton Dissociation Mechanism in Disordered Materials

Organic photovoltaics (OPVs) offer the opportunity for cheap, lightweight and mass‐producible devices. However, an incomplete understanding of the charge generation process, in particular the timescale of dynamics and role of exciton diffusion, has slowed further progress in the field. We report a new Kinetic Monte Carlo model for the exciton dissociation mechanism in OPVs that addresses the origin of ultra‐fast (<1 ps) dissociation by incorporating exciton delocalization. The model reproduces experimental results, such as the diminished rapid dissociation with increasing domain size, and also lends insight into the interplay between mixed domains, domain geometry, and exciton delocalization. Additionally, the model addresses the recent dispute on the origin of ultra‐fast exciton dissociation by comparing the effects of exciton delocalization and impure domains on the photo‐dynamics.This model provides insight into exciton dynamics that can advance our understanding of OPV structure–function relationships.     

Challenges in distinguishing superexchange and hopping mechanisms of intramolecular charge transfer through fluorene oligomers

The temperature dependence of intramolecular charge separation in a series of donor-bridge-acceptor molecules having phenothiazine (PTZ) donors, 2,7-oligofluorene FL(n) (n = 1-4) bridges, and perylene-3,4:9,10-bis(dicarboximide) (PDI) acceptors was studied. Photoexcitation of PDI to its lowest excited singlet state results in oxidation of PTZ via the FL(n) bridge. In toluene, the temperature dependence of the charge separation rate constants for PTZ-FL(n)-PDI, (n = 1-4) is relatively weak and is successfully described by the semiclassical Marcus equation. The activation energies for charge separation suggest that bridge charge carrier injection is not the rate limiting step. The difficulty of using temperature and length dependence to differentiate hopping and superexchange is discussed, with difficulties in the latter topic explored via an extension of a kinetic model proposed by Bixon and Jortner.     

Nanoscale clustering of carbohydrate thiols in mixed self-assembled monolayers on gold

Self-assembled monolayers (SAMs) bearing pendant carbohydrate functionality are frequently employed to tailor glycan-specific bioactivity onto gold substrates. The resulting glycoSAMs are valuable for interrogating glycan-mediated biological interactions via surface analytical techniques, microarrays, and label-free biosensors. GlycoSAM composition can be readily modified during assembly by using mixed solutions containing thiolated species, including carbohydrates, oligo(ethylene glycol) (OEG), and other inert moieties. This intrinsic tunability of the self-assembled system is frequently used to optimize bioavailability and antibiofouling properties of the resulting SAM. However, until now, our nanoscale understanding of the behavior of these mixed glycoSAMs has lacked detail. In this study, we examined the time-dependent clustering of mixed sugar + OEG glycoSAMs on ultraflat gold substrates. Composition and surface morphologic changes in the monolayers were analyzed by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), respectively. We provide evidence that the observed clustering is consistent with a phase separation process in which surface-bound glycans self-associate to form dense glycoclusters within the monolayer. These observations have significant implications for the construction of mixed glycoSAMs for use in biosensing and glycomics applications.     

Geometry dependent features of optically induced forces between silver nanoparticles

A recently devised, discrete-dipole approximation (DDA) based method for computing optical forces is used to explore geometry dependent aspects of the light induced interactions between pairs of silver nanoparticles, including the influence of particle shape, relative positioning of the particles, and incident field orientation. The interactions are observed to have a large degree of generic character, independent of the details of the particle shape. The size of the optical forces is also compared to estimates for the van der Waals forces, and the results are used to assess the potential importance of radiation forces on recent experiments demonstrating photoinduced self-assembly of triangular silver nanoprisms.     

Singlet fission for dye-sensitized solar cells: can a suitable sensitizer be found?

We discuss possible improvements in the efficiency of dye-sensitized photovoltaic cells using dyes capable of singlet fission into two triplets, thus producing two electron-hole pairs from a single photon. It is pointed out that, in addition to derivatives of large alternant hydrocarbons, those of biradicals are also likely candidates for a favorable ordering of excited-state energy levels, E(T2), E(S1) > 2E(T1). A large number of potentially favorable structures has been examined by the semiempirical Pariser-Parr-Pople method and some also by the time-dependent density functional theory method. Several likely candidates have been identified for experimental examination.