Is there a case for "moderate" inflation?

Inflation (Finance)

Resolution exchange simulation

We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models. Such ``resolution exchange'' can be applied to molecular systems or spin systems. The second extension is to ``pseudo-exchange'' simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduces the need for overlap between levels. Pseudo exchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.Comment: revised manuscript: 4.2 pages, 3 figure

Simple estimation of absolute free energies for biomolecules

One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is irrelevant, however, if the absolute free energy of each state can be computed. We present a method for calculating the absolute free energy that employs a simple construction of an exactly computable reference system which possesses high overlap with the state of interest. The approach requires only a physical ensemble of conformations generated via simulation, and an auxiliary calculation of approximately equal central-processing-unit (CPU) cost. Moreover, the calculations can converge to the correct free energy value even when the physical ensemble is incomplete or improperly distributed. As a "proof of principle," we use the approach to correctly predict free energies for test systems where the absolute values can be calculated exactly, and also to predict the conformational equilibrium for leucine dipeptide in implicit solvent.Comment: To appear in J. Chem. Phys., 10 pages, 6 figure

Deep, effortless concentration: re-examining the flow concept and exploring relations with inattention, absorption, and personality

This is a post-peer-review, pre-copyedit version of an article published in Psychological Research. The final authenticated version is available online at: https://doi.org/10.1007/s00426-018-1031-6Conceptualizing the construct of flow in terms of ‘deep and effortless concentration’, we developed two measurement scales designed to index individual differences in flow during ‘internal’ tasks, such as thinking (deep effortless concentration: internal—DECI) and during ‘external’ tasks, such as while playing a sport (deep effortless concentration: external—DECE). These scales were highly correlated, indicating that individuals prone to experiencing flow in external contexts are also prone to experience flow in internal contexts. Nonetheless, a measurement model construing internal and external flow as related, but separate, constructs was found to fit the data significantly better than a model where they were construed as a single construct. We then explored associations between flow and various forms of everyday inattention. In addition, we explored the relation between flow and the Tellegen Absorption Scale (TAS), an index of absorption, as well as the Big Five personality traits. Amongst other things, we found that flow was negatively related to inattention, indicating that people who experience flow more frequently may experience relatively less inattention in everyday contexts.NSERC Discovery Grant, RGPIN-2014-0645

New insights into the tonoplast architecture of plant vacuoles and vacuolar dynamics during osmotic stress

BACKGROUND: The vegetative plant vacuole occupies >90% of the volume in mature plant cells. Vacuoles play fundamental roles in adjusting cellular homeostasis and allowing cell growth. The composition of the vacuole and the regulation of its volume depend on the coordinated activities of the transporters and channels localized in the membrane (named tonoplast) surrounding the vacuole. While the tonoplast protein complexes are well studied, the tonoplast itself is less well described. To extend our knowledge of how the vacuole folds inside the plant cell, we present three-dimensional reconstructions of vacuoles from tobacco suspension cells expressing the tonoplast aquaporin fusion gene BobTIP26-1::gfp. RESULTS: 3-D reconstruction of the cell vacuole made possible an accurate analysis of large spanning folds of the vacuolar membrane under both normal and stressed conditions, and suggested interactions between surrounding plastids. Dynamic, high resolution 3-D pictures of the vacuole in tobacco suspension cells monitored under different growth conditions provide additional details about vacuolar architecture. The GFP-decorated vacuole is a single continuous compartment transected by tubular-like transvacuolar strands and large membrane surfaces. Cell culture under osmotic stress led to a complex vacuolar network with an increased tonoplast surface area. In-depth 3-D realistic inspections showed that the unity of the vacuole is maintained during acclimation to osmotic stress. Vacuolar unity exhibited during stress adaptation, coupled with the intimate associations of vacuoles with other organelles, suggests a physiological role for the vacuole in metabolism, and communication between the vacuole and organelles, respectively, in plant cells. Desiccation stress ensuing from PEG treatment generates "double" membrane structures closely linked to the tonoplast within the vacuole. These membrane structures may serve as membrane reservoirs for membrane reversion when cells are reintroduced to normal growth conditions. CONCLUSION: 3-D processing of a GFP-labeled tonoplast provides compelling visual constructions of the plant cell vacuole and elaborates on the nature of tonoplast folding and architecture. Furthermore, these methods allow real-time determination of membrane rearrangements during stresses