Scale-free static and dynamical correlations in melts of monodisperse and Flory-distributed homopolymers: A review of recent bond-fluctuation model studies

It has been assumed until very recently that all long-range correlations are screened in three-dimensional melts of linear homopolymers on distances beyond the correlation length $\xi$ characterizing the decay of the density fluctuations. Summarizing simulation results obtained by means of a variant of the bond-fluctuation model with finite monomer excluded volume interactions and topology violating local and global Monte Carlo moves, we show that due to an interplay of the chain connectivity and the incompressibility constraint, both static and dynamical correlations arise on distances $r \gg \xi$. These correlations are scale-free and, surprisingly, do not depend explicitly on the compressibility of the solution. Both monodisperse and (essentially) Flory-distributed equilibrium polymers are considered.Comment: 60 pages, 49 figure

Metabolomic analysis of male combat veterans with post traumatic stress disorder

10.1371/journal.pone.0213839PLoS ONE143e021383

Rational design of FRET-based sensor proteins

Real-time imaging of molecular events inside living cells is important for understanding the basis of physiological processes and diseases. Genetically encoded sensors that use fluorescence resonance energy transfer (FRET) between two fluorescent proteins are attractive in this respect because they do not require cell-invasive procedures, can be targeted to different locations in the cell and are easily adapted through mutagenesis and directed evolution approaches. Most FRET sensors developed so far show a relatively small difference in emission ratio upon activation, which severely limits their application in high throughput cell-based screening applications. In our work, we try to develop strategies that allow design of FRET-based sensors with intrinsically large ratiometric changes. This rational design approach requires a better understanding and quantitative description of the conformational changes in these fusion proteins. In this chapter, I first discuss some of the key factors and strategies that determine the ratiometric response of FRET sensors, followed by an overview of our recent work in this area. Important concepts that will be discussed are (1) the conformational behavior of flexible peptide linkers to quantitatively describe the dependence of energy transfer on linker length and (2) the control of intramolecular domain interactions using the concept of effective molecular concentration