Marianne Bauer

Interpolation schemes for peptide rearrangements

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.

Optical recombination of biexcitons in semiconductors

We calculate the photoluminescence spectrum and lifetime of a biexciton in a semiconductor using Fermis golden rule. Our biexciton wavefunction is obtained using a Quantum Monte Carlo calculation. We consider a recombination process where one of the excitons within the biexciton annihilates. For hole masses greater than or equal to the electron mass, we find that the surviving exciton is most likely to populate the ground state. We also investigate how the confinement of excitons in a quantum dot would modify the lifetime in the limit of a large quantum dot where confinement principally affects the centre of mass wavefunction. The lifetimes we obtain are in reasonable agreement with experimental values. Our calculation can be used as a benchmark for comparison with approximate methods.

Dipolar gases in coupled one-dimensional lattices.

We consider dipolar bosons in two tubes of one-dimensional lattices, where the dipoles are aligned to be maximally repulsive and the particle filling fraction is the same in each tube. In the classical limit of zero intersite hopping, the particles arrange themselves into an ordered crystal for any rational filling fraction, forming a complete devils staircase like in the single tube case. Turning on hopping within each tube then gives rise to a competition between the crystalline Mott phases and a liquid of defects or solitons. However, for the two-tube case, we find that solitons from different tubes can bind into pairs for certain topologies of the filling fraction. This provides an intriguing example of pairing that is purely driven by correlations close to a Mott insulator.

Exploiting ecology in drug pulse sequences in favour of population reduction

A deterministic population dynamics model involving birth and death for a two-species system, comprising a wild-type and more resistant species competing via logistic growth, is subjected to two distinct stress environments designed to mimic those that would typically be induced by temporal variation in the concentration of a drug (antibiotic or chemotherapeutic) as it permeates through the population and is progressively degraded. Different treatment regimes, involving single or periodical doses, are evaluated in terms of the minimal population size (a measure of the extinction probability), and the population composition (a measure of the selection pressure for resistance or tolerance during the treatment). We show that there exist timescales over which the low-stress regime is as effective as the high-stress regime, due to the competition between the two species. For multiple periodic treatments, competition can ensure that the minimal population size is attained during the first pulse when the high-stress regime is short, which implies that a single short pulse can be more effective than a more protracted regime. Our results suggest that when the duration of the high-stress environment is restricted, a treatment with one or multiple shorter pulses can produce better outcomes than a single long treatment. If ecological competition is to be exploited for treatments, it is crucial to determine these timescales, and estimate for the minimal population threshold that suffices for extinction. These parameters can be quantified by experiment.

On the role of multiple scales in metapopulations of public good producers

Multiple scales in metapopulations can give rise to paradoxical behavior: in a conceptual model for a public goods game, the species associated with a fitness cost due to the public good production can be stabilized in the well-mixed limit due to the mere existence of these scales. The scales in this model involve a length scale corresponding to separate patches, coupled by mobility, and separate time scales for reproduction and interaction with a local environment. Contrary to the well-mixed high mobility limit, we find that for low mobilities, the interaction rate progressively stabilizes this species due to stochastic effects, and that the formation of spatial patterns is not crucial for this stabilization.

Delayed adaptation in stochastic metapopulation models

How does delayed fitnesses adaptation after local habitat changes affect survival of species metapopulation? We study this question in a two-species model system, where the species composition of a local patch determines the reference fitness of all its individuals. When individuals move, this local species composition changes. As the local environment on the patch might, adapt, slowly to this change, we assume that individuals in turn adapt their fitness with a stochastic delay. We show that the combination of delay and spatial substructure can yield significantly different phase diagrams for the survival of these species with respect to models with immediate response. We investigate this exemplarily for the case where the two species interact via an exoproduct: thus, our population consists of a slow-growing producer species and a fast-growing dominant species. We provide a conceptual understanding of the role of delay by presenting analytic result,s in tlie well-mixed and low-mobility limit,. By studying intermediate mobilities numerically, we ensure that our results are robust,, and may be relevant to different ecological situations as well as microbial metapopulation experiments.