On the engulfment of antifreeze proteins by ice.

Antifreeze proteins (AFPs) are remarkable biomolecules that suppress ice formation at trace concentrations. To inhibit ice growth, AFPs must not only bind to ice crystals, but also resist engulfment by ice. The highest supercooling, [Formula: see text], for which AFPs are able to resist engulfment is widely believed to scale as the inverse of the separation, [Formula: see text], between bound AFPs, whereas its dependence on the molecular characteristics of the AFP remains poorly understood. By using specialized molecular simulations and interfacial thermodynamics, here, we show that in contrast with conventional wisdom, [Formula: see text] scales as [Formula: see text] and not as [Formula: see text]. We further show that [Formula: see text] is proportional to AFP size and that diverse naturally occurring AFPs are optimal at resisting engulfment by ice. By facilitating the development of AFP structure-function relationships, we hope that our findings will pave the way for the rational design of AFPs.

Paperfetcher: A tool to automate handsearching and citation searching for systematic reviews.

Systematic reviews are vital instruments for researchers to understand broad trends in a field and synthesize evidence on the effectiveness of interventions in addressing specific issues. The quality of a systematic review depends critically on having comprehensively surveyed all relevant literature on the review topic. In addition to database searching, handsearching is an important supplementary technique that helps increase the likelihood of identifying all relevant studies in a literature search. Traditional handsearching requires reviewers to manually browse through a curated list of field-specific journals and conference proceedings to find articles relevant to the review topic. This manual process is not only time-consuming, laborious, costly, and error-prone due to human fatigue, but it also lacks replicability due to its cumbersome manual nature. To address these issues, this paper presents a free and open-source Python package and an accompanying web-app, Paperfetcher, to automate the retrieval of article metadata for handsearching. With Paperfetcher's assistance, researchers can retrieve article metadata from designated journals within a specified time frame in just a few clicks. In addition to handsearching, it also incorporates a beta version of citation searching in both forward and backward directions. Paperfetcher has an easy-to-use interface, which allows researchers to download the metadata of retrieved studies as a list of DOIs or as an RIS file to facilitate seamless import into systematic review screening software. To the best of our knowledge, Paperfetcher is the first tool to automate handsearching with high usability and a multi-disciplinary focus.

Characterizing the Interplay between Polymer Solvation and Conformation.

Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.