Carla Goldman

ON THE CONTRIBUTION OF ELECTRON TRANSFER REACTIONS TO THE QUENCHING OF TRYPTOPHAN FLUORESCENCE

We present a theoretical calculation of rates for excited state electron transfer (ET) reactions in zwitterionic tryptophan for each of its six rotameric conformers. Within the Born–Oppenheimer approximation, we calculate the electronic part of the rate, using the renormalized perturbation expansion (RPE) method. The vibrational part is extracted from experimental data, assuming that at neutral pH, the observed fluorescence decay profile is composed of two exponentials corresponding to two competing populations in the sample; one in which fluorescence is accompanied by ET and other that is not. Complementary data, namely, ionization potentials and charge distributions are obtained using a combination of classical molecular mechanics simulation to determine the geometry of the six rotamers, and semiempirical (INDO/S) molecular orbital calculation. Our results indicate that conformers perpχ2g− and antiχ2g− give the main contribution to ET in the time scale of fluorescence.

The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes

We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of an asymmetric simple exclusion process (ASEP). The model is formulated to account for (i) excluded-volume interactions, (ii) the observed asymmetry of the stochastic movement of individual motors and (iii) interactions between motors and cargo. Items (i) and (ii) form the basis of ASEP models and have already been considered to study the behavior of motor density profile [A. Parmeggiani, T. Franosch, E. Frey, Phase Coexistence in driven one-dimensional transport, Phys. Rev. Lett. 90 (2003) 086601-1–086601-4]. Item (iii) is new. It is introduced here as an attempt to describe explicitly the dependence of cargo movement on the dynamics of motors in this context. The steady-state solutions of the model indicate that the system undergoes a phase transition of condensation type as the motor density varies. We study the consequences of this transition to the behavior of the average cargo velocity.

The efficiency of photolyase and indole complexes to repair DNA containing dimers of pyrimidine: A theoretical analysis of the electron transfer reactions

We analyze the effects of competing reactions to the efficiency of enzymatic splitting of pyrimidine dimers formed in DNA by the incidence of ultraviolet radiation. This is accomplished with the aid of a formula that expresses the efficiency of the repair in terms of parameters that regulate the reaction rates for primary and for back long-range electron transfers taking place in the process. Comparison of experimental data with estimations on account of this formula supports early conjectures in the literature that attribute the relative high performance of the enzymatic complexes of photolyase to its ability to suppress the back reaction.

Modified surface fluctuations by impurity binding in amphiphilic dispersions

We have shown that the thermodynamics of a 2D multicomponent ideal gas model describes well the thermal behavior of light-scattering (LS) data in lipid dispersions of dimyristoyl phosphatidylglycerol (DMPG) [C. Goldman, K. A. Riske, and M. T. Lamy-Freund, Phys. Rev. E 60, 7349 (1999)]. The components (species) of the gas are distinguished by size and by their ability to display shape fluctuations. Here, the model is extended to include the presence of thermalized impurities bound to the fluctuating species. We show that with this modification the model accounts also for additional LS data from DMPG under variation of ionic strength.

On the analysis of large-scale genomic structures.

We apply methods from statistical physics (histograms, correlation functions, fractal dimensions, and singularity spectra) to characterize large-scale structure of the distribution of nucleotides along genomic sequences. We discuss the role of the extension of noncoding segments (“junk DNA”) for the genomic organization, and the connection between the coding segment distribution and the high-eukaryotic chromatin condensation. The following sequences taken from GenBank were analyzed: complete genome of Xanthomonas campestri, complete genome of yeast, chromosome V of Caenorhabditis elegans, and human chromosome XVII around gene BRCA1. The results are compared with the random and periodic sequences and those generated by simple and generalized fractal Cantor sets.

A phenomenological analysis of eco-evolutionary coupling under dilution

Evolutionary dynamics experienced by mixed microbial populations of cooperators and cheaters has been examined in experiments in the literature using a protocol of periodic dilution to investigate the properties of resilience and adaptability to environmental changes. Data depicted on an appropriate phase diagram indicate, among other features, a stable equilibrium point at which cooperators and cheaters coexist (Sanchez and Gore, 2013). We present here a phenomenological analysis of these data focusing on an eco-evolutionary-game perspective. To that end, we work on an extension of the model proposed in Tao and Cressman (2007). Its original version takes into account changes of the total population density while the individuals experience a pairwise Prisoners Dilemma game. The extension devised here contains a dilution parameter to conform with the experimental procedure, in addition to a term accounting for Allee effects. In contrast to other descriptions proposed in similar contexts, however, the model here does not account for assortative encounters, group or kin selection. Nonetheless, it describes surprisingly well both qualitatively and quantitatively the features of the observed phase diagram. We discuss these results in terms of the behavior of an effective payoff matrix defined accordingly.