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Akash Pallath

Publications and source records attributed to Akash Pallath.

2 recordsLinked to original sources

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, $\Delta T^{*}$, for which AFPs are able to resist engulfment is widely believed to scale as the inverse of the separation, $L$, 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, $\Delta T^{*}$ scales as $L^{-2}$ and not as $L^{-1}$. We further show that $\Delta T^{*}$ 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 novel AFPs.

physics.bio-ph

Paperfetcher: A tool to automate handsearch for systematic reviews

Handsearch is an important technique that contributes to thorough literature search in systematic reviews. Traditional handsearch requires reviewers to systematically browse through each issue of a curated list of field-specific journals and conference proceedings to find articles relevant to their review. This manual process is not only time-consuming, laborious, costly, and error-prone, but it also lacks replicability and cross-checking mechanisms. In an attempt to solve these problems, this paper presents a free and open-source Python package and an accompanying web-app, Paperfetcher, to automate handsearch for systematic reviews. With Paperfetcher's assistance, researchers can retrieve articles from designated journals within a specified time frame with just a few clicks. In addition to handsearch, this tool also incorporates snowballing in both directions. Paperfetcher allows researchers to download retrieved studies as a list of DOIs or as an RIS database to facilitate seamless import into citation management and systematic review screening software. To our knowledge, Paperfetcher is the first tool that automates handsearch with high usability and a multi-disciplinary focus.

cs.IR