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We investigate the ensemble and time averaged mean squared displacements for particle diffusion in a simple model for disordered media by assuming that the local diffusivity is both fluctuating in time and has a deterministic average growth or decay in time. In this study we compare computer simulations of the stochastic Langevin equation for this random diffusion process with analytical results. We explore the regimes of normal Brownian motion as well as anomalous diffusion in the sub- and superdiffusive regimes. We also consider effects of the inertial term on the particle motion. The investigation of the resulting diffusion is performed for unconfined and confined motion.
We investigate the ensemble and time averaged mean squared displacements for particle diffusion in a simple model for disordered media by assuming that the local diffusivity is both fluctuating in time and has a deterministic average growth or decay in time. In this study we compare computer simulations of the stochastic Langevin equation for this random diffusion process with analytical results. We explore the regimes of normal Brownian motion as well as anomalous diffusion in the sub- and superdiffusive regimes. We also consider effects of the inertial term on the particle motion. The investigation of the resulting diffusion is performed for unconfined and confined motion.
What are the physical laws of the mutual interactions of objects bound to cell membranes, such as various membrane proteins or elongated virus particles? To rationalise this, we here investigate by extensive computer simulations mutual interactions of rod-like particles adsorbed on the surface of responsive elastic two-dimensional sheets. Specifically, we quantify sheet deformations as a response to adhesion of such filamentous particles. We demonstrate that tip-to-tip contacts of rods are favoured for relatively soft sheets, while side-by-side contacts are preferred for stiffer elastic substrates. These attractive orientation-dependent substrate-mediated interactions between the rod-like particles on responsive sheets can drive their aggregation and self-assembly. The optimal orientation of the membrane-bound rods is established via responding to the elastic energy profiles created around the particles. We unveil the phase diagramme of attractive–repulsive rod–rod interactions in the plane of their separation and mutual orientation. Applications of our results to other systems featuring membrane-associated particles are also discussed.
What are the physical laws of the mutual interactions of objects bound to cell membranes, such as various membrane proteins or elongated virus particles? To rationalise this, we here investigate by extensive computer simulations mutual interactions of rod-like particles adsorbed on the surface of responsive elastic two-dimensional sheets. Specifically, we quantify sheet deformations as a response to adhesion of such filamentous particles. We demonstrate that tip-to-tip contacts of rods are favoured for relatively soft sheets, while side-by-side contacts are preferred for stiffer elastic substrates. These attractive orientation-dependent substrate-mediated interactions between the rod-like particles on responsive sheets can drive their aggregation and self-assembly. The optimal orientation of the membrane-bound rods is established via responding to the elastic energy profiles created around the particles. We unveil the phase diagramme of attractive–repulsive rod–rod interactions in the plane of their separation and mutual orientation. Applications of our results to other systems featuring membrane-associated particles are also discussed.
Changes in extratropical storm track activity and their implications for extreme weather events
(2016)
In this thesis, the two prototype catalysts Fe(CO)₅ and Cr(CO)₆ are investigated with time-resolved photoelectron spectroscopy at a high harmonic setup. In both of these metal carbonyls, a UV photon can induce the dissociation of one or more ligands of the complex. The mechanism of the dissociation has been debated over the last decades. The electronic dynamics of the first dissociation occur on the femtosecond timescale.
For the experiment, an existing high harmonic setup was moved to a new location, was extended, and characterized. The modified setup can induce dynamics in gas phase samples with photon energies of 1.55eV, 3.10eV, and 4.65eV. The valence electronic structure of the samples can be probed with photon energies between 20eV and 40eV. The temporal resolution is 111fs to 262fs, depending on the combination of the two photon energies.
The electronically excited intermediates of the two complexes, as well as of the reaction product Fe(CO)₄, could be observed with photoelectron spectroscopy in the gas phase for the first time. However, photoelectron spectroscopy gives access only to the final ionic states. Corresponding calculations to simulate these spectra are still in development. The peak energies and their evolution in time with respect to the initiation pump pulse have been determined, these peaks have been assigned based on literature data. The spectra of the two complexes show clear differences. The dynamics have been interpreted with the assumption that the motion of peaks in the spectra relates to the movement of the wave packet in the multidimensional energy landscape. The results largely confirm existing models for the reaction pathways. In both metal carbonyls, this pathway involves a direct excitation of the wave packet to a metal-to-ligand charge transfer state and the subsequent crossing to a dissociative ligand field state. The coupling of the electronic dynamics to the nuclear dynamics could explain the slower dissociation in Fe(CO)₅ as compared to Cr(CO)₆.
The cell interior is a highly packed environment in which biological macromolecules evolve and function. This crowded media has effects in many biological processes such as protein-protein binding, gene regulation, and protein folding. Thus, biochemical reactions that take place in such crowded conditions differ from diluted test tube conditions, and a considerable effort has been invested in order to understand such differences.
In this work, we combine different computationally tools to disentangle the effects of molecular crowding on biochemical processes. First, we propose a lattice model to study the implications of molecular crowding on enzymatic reactions. We provide a detailed picture of how crowding affects binding and unbinding events and how the separate effects of crowding on binding equilibrium act together. Then, we implement a lattice model to study the effects of molecular crowding on facilitated diffusion. We find that obstacles on the DNA impair facilitated diffusion. However, the extent of this effect depends on how dynamic obstacles are on the DNA. For the scenario in which crowders are only present in the bulk solution, we find that at some conditions presence of crowding agents can enhance specific-DNA binding. Finally, we make use of structure-based techniques to look at the impact of the presence of crowders on the folding a protein. We find that polymeric crowders have stronger effects on protein stability than spherical crowders. The strength of this effect increases as the polymeric crowders become longer. The methods we propose here are general and can also be applied to more complicated systems.
Recombination of free charge is a key process limiting the performance of solar cells. For low mobility materials, such as organic semiconductors, the kinetics of non-geminate recombination (NGR) is strongly linked to the motion of charges. As these materials possess significant disorder, thermalization of photogenerated carriers in the inhomogeneously broadened density of state distribution is an unavoidable process. Despite its general importance, knowledge about the kinetics of NGR in complete organic solar cells is rather limited. We employ time delayed collection field (TDCF) experiments to study the recombination of photogenerated charge in the high-performance polymer:fullerene blend PCDTBT:PCBM. NGR in the bulk of this amorphous blend is shown to be highly dispersive, with a continuous reduction of the recombination coefficient throughout the entire time scale, until all charge carriers have either been extracted or recombined. Rapid, contact-mediated recombination is identified as an additional loss channel, which, if not properly taken into account, would erroneously suggest a pronounced field dependence of charge generation. These findings are in stark contrast to the results of TDCF experiments on photovoltaic devices made from ordered blends, such as P3HT:PCBM, where non-dispersive recombination was proven to dominate the charge carrier dynamics under application relevant conditions.
Recombination of free charge is a key process limiting the performance of solar cells. For low mobility materials, such as organic semiconductors, the kinetics of non-geminate recombination (NGR) is strongly linked to the motion of charges. As these materials possess significant disorder, thermalization of photogenerated carriers in the inhomogeneously broadened density of state distribution is an unavoidable process. Despite its general importance, knowledge about the kinetics of NGR in complete organic solar cells is rather limited. We employ time delayed collection field (TDCF) experiments to study the recombination of photogenerated charge in the high-performance polymer:fullerene blend PCDTBT:PCBM. NGR in the bulk of this amorphous blend is shown to be highly dispersive, with a continuous reduction of the recombination coefficient throughout the entire time scale, until all charge carriers have either been extracted or recombined. Rapid, contact-mediated recombination is identified as an additional loss channel, which, if not properly taken into account, would erroneously suggest a pronounced field dependence of charge generation. These findings are in stark contrast to the results of TDCF experiments on photovoltaic devices made from ordered blends, such as P3HT:PCBM, where non-dispersive recombination was proven to dominate the charge carrier dynamics under application relevant conditions.