Peptide Folding in Cellular Environments: A Monte Carlo and Markov Modeling Approach

Steric interactions with surrounding macromolecules tend to favor the compact native state of a globular protein over its unfolded state. However, in experiments conducted in cells and concentrated protein solutions, both stabilization and destabilization of proteins have been observed, compared to dilute-solution conditions. Therefore, in order to understand the effects of surrounding macromolecules on protein properties such as stability, there is a need for computational modeling beyond the level of hard-sphere crowders. Here, we discuss some recent exploratory studies of peptide folding in the presence of explicit protein crowders, carried out by us using an all-atom Monte Carlo-based approach along with an implicit solvent force field. For interpreting the simulation data, time-lagged independent component analysis and Markov state modeling are used

The Battle for a Sustainable Food Supply

Since the time that Homo sapiens took up farming, a battle has been waged against pests and diseases which can cause significant losses in crop yield and threaten a sustainable food supply. Initially, early control techniques included religious practices or folk magic, hand removal of weeds and insects, and “chemical” techniques such as smokes, easily available minerals, oils and plant extracts known to have pesticidal activity. But it was not until the early twentieth century that real progress was made when a large number of compounds became available for testing as pesticides due to the upsurge in organic chemistry. The period after the 1940s saw the introduction of important families of chemicals, such as the phenoxy acid herbicides, the organochlorine insecticides and the dithiocarbamate fungicides. The introduction of new pesticides led to significant yield increases, but concern arose over their possible negative effects on human health and the environment. In time, resistance started to occur, making these pesticides less effective. This led agrochemical companies putting in place research looking for new modes of action and giving less toxic and more environmentally friendly products. These research programmes gave rise to new pesticide families, such as the sulfonylurea herbicides, the strobilurin fungicides and the neonicotinoid insecticide classes

Integrating Archaeological Theory and Predictive Modeling: a Live Report from the Scene

Archaeological predictive modeling has been used successfully for over20 years as a decision-making tool in cultural resources management. Itsappreciation in academic circles however has been mixed because of its perceivedtheoretical poverty. In this paper, we discuss the issue of integrating currentarchaeological theoretical approaches and predictive modeling. We suggest amethodology for doing so based on cognitive archaeology, middle range theory,and paleoeconomic modeling. We also discuss the problems associated with testingpredictive models