On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase

Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas phase simulations. Introducing a charged Lys+ at the C terminal stabilizes the helix and leads to a higher transition temperature. On the other hand, adding the Lys+ at the N terminal inhibits helix formation. Instead, a more globular structure was found. These results are in agreement with recent experiments on alanine based polypeptides in gas phase. They indicate that present force fields describe accurately the intramolecular interactions in proteins

Making a Bee-Line for Food with Octopamine

How do you find the newest, trendiest restaurants with the best food in your neighborhood (that is, of course, during non-pandemic times when restaurants are all open)? Well, one way that you may notice the new hip spot is to follow the crowds. If you wander by a spot filled with folks enjoying mouth-wateringly delicious food, you will likely be drawn to visit that restaurant yourself. But, how does your brain process these signals about food resources and quality? Tianfei Peng and two of his colleagues from the University of Mainz in Germany dug into this question by looking at the inner-workings of a slightly simpler brain – that of the stingless bee – to uncover the brain's role in social animal foraging.The trio suspected that the compound octopamine could play a role in how both individuals and social groups find food and perceive its value. Octopamine is a major player in the brain function of invertebrate animals, including many insects, equivalent to the fight-or-flight hormone noradrenaline in vertebrates, including human

Flies Walk the Line for Serotonin

In the grand scheme of the animal kingdom, insects are often overlooked for their impressive locomotor skills. They can walk forwards, backwards and even upside down, traversing challenging environments with relative ease. But how do insects achieve this coordination? Clare Howard (Columbia University) and colleagues teach us that the insect nervous system employs a multifaceted signalling network to optimize their speed, gait and reaction timing to gracefully navigate through life.Using the vinegar fly (Drosophila melanogaster), Howard and colleagues surveyed the fly nervous system to establish the sequence of signals involved in locomotion

Serotonin: Octopus Love Potion?

When you think about human social behaviour, what animals do you immediately think of as most similar to us? Apes, dolphins, wolves? Sure, these animals display incredibly complex social interactions, just like us. But Eric Edsinger from the Marine Biological Laboratory, USA, and Gül Dölen from Johns Hopkins University, USA, teach us in their latest study that we aren't actually all that different from our more distant cousin: the octopus. While octopuses typically hang out by themselves and fight when they come across each other, they let bygones be bygones during the mating season. Until now, we had no idea why octopuses suddenly set aside their aggressive tendencies during this ‘special’ time. Using a unique combination of molecular and behavioural studies, Edsinger and Dölen delved into the brain of the octopus to uncover the neurological mechanisms that regulate their social behaviour.<br/

Birds Ruffled by Big-City Lights

The blazing lights of Times Square in New York City may be impressive for tourists, yet this blindingly bright attraction can cause problems for urban wildlife. Artificial light at night, typical of cities and suburban areas around the globe, can cause problems for the animals that we share space with, although the impact on local wildlife is often disregarded. Given the current global COVID-19 pandemic, understanding how stressors, such as artificial nocturnal light, alter infectious disease transmission is now even more pressing. So, Daniel Becker and colleagues from Indiana University in the USA delved into this question, looking at how persistent artificial light at night alters immunity and infection risk in wild animal communities

The relation of phase noise and luminance contrast to overt attention in complex visual stimuli

Models of attention are typically based on difference maps in low-level features but neglect higher order stimulus structure. To what extent does higher order statistics affect human attention in natural stimuli? We recorded eye movements while observers viewed unmodified and modified images of natural scenes. Modifications included contrast modulations (resulting in changes to first- and second-order statistics), as well as the addition of noise to the Fourier phase (resulting in changes to higher order statistics). We have the following findings: (1) Subjects' interpretation of a stimulus as a “natural” depiction of an outdoor scene depends on higher order statistics in a highly nonlinear, categorical fashion. (2) Confirming previous findings, contrast is elevated at fixated locations for a variety of stimulus categories. In addition, we find that the size of this elevation depends on higher order statistics and reduces with increasing phase noise. (3) Global modulations of contrast bias eye position toward high contrasts, consistent with a linear effect of contrast on fixation probability. This bias is independent of phase noise. (4) Small patches of locally decreased contrast repel eye position less than large patches of the same aggregate area, irrespective of phase noise. Our findings provide evidence that deviations from surrounding statistics, rather than contrast per se, underlie the well-established relation of contrast to fixation

Coarse-graining the Dynamics of a Driven Interface in the Presence of Mobile Impurities: Effective Description via Diffusion Maps

Developing effective descriptions of the microscopic dynamics of many physical phenomena can both dramatically enhance their computational exploration and lead to a more fundamental understanding of the underlying physics. Previously, an effective description of a driven interface in the presence of mobile impurities, based on an Ising variant model and a single empirical coarse variable, was partially successful; yet it underlined the necessity of selecting additional coarse variables in certain parameter regimes. In this paper we use a data mining approach to help identify the coarse variables required. We discuss the implementation of this diffusion map approach, the selection of a similarity measure between system snapshots required in the approach, and the correspondence between empirically selected and automatically detected coarse variables. We conclude by illustrating the use of the diffusion map variables in assisting the atomistic simulations, and we discuss the translation of information between fine and coarse descriptions using lifting and restriction operators.Comment: 28 pages, 10 figure

Optimizing Replica Exchange Moves For Molecular Dynamics

In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.Comment: 4 pages, 3 figures; revised version (1 figure added), PRE in pres