A Framework for Differential Calculus on Persistence Barcodes

Foundations of Computational Mathematics - We define notions of differentiability for maps from and to the space of persistence barcodes. Inspired by the theory of diffeological spaces, the...     

Dissipative dynamics within the electronic friction approach: the femtosecond laser desorption of H2/D2 from Ru(0001)

An electronic friction approach based on Langevin dynamics is used to describe the multidimensional (six-dimensional) dynamics of femtosecond laser induced desorption of H(2) and D(2) from a H(D)-covered Ru(0001) surface. The paper extends previous reduced-dimensional models, using a similar approach. In the present treatment forces and frictional coefficients are calculated from periodic density functional theory (DFT) and essentially parameter-free, while the action of femtosecond laser pulses on the metal surface is treated by using the two-temperature model. Our calculations shed light on the performance and validity of various adiabatic, non-adiabatic, and Arrhenius/Kramers type kinetic models to describe hot-electron mediated photoreactions at metal surfaces. The multidimensional frictional dynamics are able to reproduce and explain known experimental facts, such as strong isotope effects, scaling of properties with laser fluence, and non-equipartitioning of vibrational, rotational, and translational energies of desorbing species. Further, detailed predictions regarding translations are made, and the question for the controllability of photoreactions at surfaces with the help of vibrational preexcitation is addressed.     

Reduced charge transfer exciton recombination in organic semiconductor heterojunctions by molecular doping

We investigate the effect of molecular doping on the recombination of electrons and holes localized at conjugated-polymer-fullerene interfaces. We demonstrate that a low concentration of p-type dopant molecules (<4% weight) reduces the interfacial recombination via charge transfer excitons and results in a favored formation of separated carriers. This is observed by the ultrafast quenching of photoluminescence from charge transfer excitons and the increase in photoinduced polaron density by ~70%. The results are consistent with a reduced formation of emissive charge transfer excitons, induced by state filling of tail states.     

Equivalence of Linear Programming and Basis Pursuit

In this note, we show that linear programming and the prominent Basis Pursuit problem (i.e., minimizing the ℓ₁-norm of a vector x subject to an underdetermined linear equation system Ax = b) are theoretically equivalent, and briefly discuss possible ramifications regarding computational complexity and practical applicability. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Dipole switching in large molecules described by explicitly time-dependent configuration interaction

In this paper, we report laser-driven charge transfer simulations for Li-(Ph)(n)-CN (n=1,2,3) using the time-dependent configuration interaction single approach. These molecules serve as systematically extendable model systems, in order to investigate the selectivity, and thus controllability, of an ultrashort laser-induced electronic excitation as a function of the molecular size. For example, such control would be needed if a small electronic molecular switch is connected to a larger molecular device. We demonstrate that for larger molecules, the selectivity of the electronic transition is considerably reduced even for rather long pulses due to dynamic polarizations of the molecules. We also show that these dynamic polarizations might be substantially underestimated in few state models.     

Adsorption of sulfite oxidase on self-assembled monolayers from molecular dynamics simulations

Sulfite oxidase (SO) is an enzyme catalyzing the terminal step of the metabolism of sulfur-containing amino acids that is essential for almost all living organisms. The catalytic activity of SO in vertebrates strongly depends on the efficiency of the intramolecular electron transfer (IET) between the catalytic Moco domain and the cytochrome b5 (cyt b5) domain. The IET process is assumed to be mediated by large domain motions of the cyt b5 domains within the enzyme. Thus, the interaction of SO with charged surfaces may affect the mobility of the cyt b5 domain required for IET and consequently hinder SO activation. In this study, we present a molecular dynamics approach to investigating the ionic strength dependence of the initial surface adsorption of SO in two different conformations-the crystallographic structure and the model structure for an activated SO-onto mixed amino- and hydroxyl-terminated SAMs. The results show for both conformations at low ionic strengths a strong adsorption of the cyt b5 units onto the SAM, which inhibits the domain motion event required for IET. Under higher ion concentrations, however, the interaction with the surface is weakened by the negatively charged ions acting as a buffer and competing in adsorption with the cathodic cyt b5 domains. This competition prevents the immobilization of the cytochrome b5 units onto the surface, allowing the intramolecular domain motions favoring IET. Our predictions support the interpretation of recent experimental spectroelectrochemical studies on SO.