Showing 1–50 of 68 results for author: Head, A

LitPivot: Developing Well-Situated Research Ideas Through Dynamic Contextualization and Critique within the Literature Landscape

Authors: Hita Kambhamettu, Bhavana Dalvi Mishra, Andrew Head, Jonathan Bragg, Aakanksha Naik, Joseph Chee Chang, Pao Siangliulue

Abstract: Developing a novel research idea is hard. It must be distinct enough from prior work to claim a contribution while also building on it. This requires iteratively reviewing literature and refining an idea based on what a researcher reads; yet when an idea changes, the literature that matters often changes with it. Most tools offer limited support for this interplay: literature tools help researcher… ▽ More Developing a novel research idea is hard. It must be distinct enough from prior work to claim a contribution while also building on it. This requires iteratively reviewing literature and refining an idea based on what a researcher reads; yet when an idea changes, the literature that matters often changes with it. Most tools offer limited support for this interplay: literature tools help researchers understand a fixed body of work, while ideation tools evaluate ideas against a static, pre-curated set of papers. We introduce literature-initiated pivots, a mechanism where engagement with literature prompts revision to a developing idea, and where that revision changes which literature is relevant. We operationalize this in LitPivot, where researchers concurrently draft and vet an idea. LitPivot dynamically retrieves clusters of papers relevant to a selected part of the idea and proposes literature-informed critiques for how to revise it. A lab study ($n{=}17$) shows researchers produced higher-rated ideas with stronger self-reported understanding of the literature space; an open-ended study ($n{=}5$) reveals how researchers use LitPivot to iteratively evolve their own ideas. △ Less

Submitted 13 April, 2026; v1 submitted 2 April, 2026; originally announced April 2026.

Explorable Theorems: Making Written Theorems Explorable by Grounding Them in Formal Representations

Authors: Hita Kambhamettu, Will Crichton, Sean Welleck, Harrison Goldstein, Andrew Head

Abstract: LLM-generated explanations can make technical content more accessible, but there is a ceiling on what they can support interactively. Because LLM outputs are static text, they cannot be executed or stepped through. We argue that grounding explanations in a formalized representation enables interactive affordances beyond what static text supports. We instantiate this idea for mathematical proof com… ▽ More LLM-generated explanations can make technical content more accessible, but there is a ceiling on what they can support interactively. Because LLM outputs are static text, they cannot be executed or stepped through. We argue that grounding explanations in a formalized representation enables interactive affordances beyond what static text supports. We instantiate this idea for mathematical proof comprehension with explorable theorems, a system that uses LLMs to translate a theorem and its written proof into Lean, a programming language for machine-checked proofs, and links the written proof with the Lean code. Readers can work through the proof at a step-level granularity, test custom examples or counterexamples, and trace the logical dependencies bridging each step. Each worked-out step is produced by executing the Lean proof on that example and extracting its intermediate state. A user study ($n = 16$) shows potential advantages of this approach: in a proof-reading task, participants who had access to the provided explorability features gave better, more correct, and more detailed answers to comprehension questions, demonstrating a stronger overall understanding of the underlying mathematics. △ Less

Submitted 10 April, 2026; v1 submitted 2 April, 2026; originally announced April 2026.

Connecting the Dots: Surfacing Structure in Documents through AI-Generated Cross-Modal Links

Authors: Alyssa Hwang, Hita Kambhamettu, Yue Yang, Ajay Patel, Joseph Chee Chang, Andrew Head

Abstract: Understanding information-dense documents like recipes and scientific papers requires readers to find, interpret, and connect details scattered across text, figures, tables, and other visual elements. These documents are often long and filled with specialized terminology, hindering the ability to locate relevant information or piece together related ideas. Existing tools offer limited support for… ▽ More Understanding information-dense documents like recipes and scientific papers requires readers to find, interpret, and connect details scattered across text, figures, tables, and other visual elements. These documents are often long and filled with specialized terminology, hindering the ability to locate relevant information or piece together related ideas. Existing tools offer limited support for synthesizing information across media types. As a result, understanding complex material remains cognitively demanding. This paper presents a framework for fine-grained integration of information in complex documents. We instantiate the framework in an augmented reading interface, which populates a scientific paper with clickable points on figures, interactive highlights in the body text, and a persistent reference panel for accessing consolidated details without manual scrolling. In a controlled between-subjects study, we find that participants who read the paper with our tool achieved significantly higher scores on a reading quiz without evidence of increased time to completion or cognitive load. Fine-grained integration provides a systematic way of revealing relationships within a document, supporting engagement with complex, information-dense materials. △ Less

Submitted 18 February, 2026; originally announced February 2026.

Comments: 40 pages, 16 figures

Toward the Origins of Binding Energy Shifts and Satellites Formation During Plasma-XPS Measurements

Authors: J. Trey Diulus, Ashley R. Head, Jorge Anibal Boscoboinik, Carles Corbella Roca, Alexander Tselev, Andrei Kolmakov

Abstract: In plasma X ray photoelectron spectroscopy emerges as a powerful platform for real time, in situ chemical analysis under conditions relevant to semiconductor processing and other plasma enabled technologies. This study investigates the origins of binding energy shifts and satellite peaks formation observed during plasma XPS measurements across conductive, dielectric, and gas phase systems. Using a… ▽ More In plasma X ray photoelectron spectroscopy emerges as a powerful platform for real time, in situ chemical analysis under conditions relevant to semiconductor processing and other plasma enabled technologies. This study investigates the origins of binding energy shifts and satellite peaks formation observed during plasma XPS measurements across conductive, dielectric, and gas phase systems. Using a standard laboratory based ambient pressure XPS apparatus coupled with an alternating current driven capacitively coupled plasma source, we show that metastable surface species, such as transient Au oxides, can be detected during plasma exposure, revealing chemical states hardly accessible using conventional ultrahigh vacuum XPS. In dielectric samples, we observe pressure- and plasma type dependent BE shifts up to 50 eV, attributed to X ray induced and plasma mediated surface charging. These shifts are mitigated at higher pressures plasmas or in electronegative plasmas, the latter due to enhanced charge compensation mechanisms involving slow negative ions. For gas phase species, AC plasma excitation leads to spectral broadening and the emergence of satellite peaks with a few eV energy separations, linked to oscillating local plasma potentials in the probing volume. These findings highlight the important and complex interplay of plasma parameters, surface charging, and local electric fields in shaping XPS spectra. Overall, plasma XPS emerges as a critical metrological tool for probing transient surface chemistry, with implications for semiconductor processing, material synthesis, and plasma diagnostics. △ Less

Submitted 18 December, 2025; originally announced December 2025.

Comments: 22 pages, 12 figures 1 table

MSC Class: na

Attribution Gradients: Incrementally Unfolding Citations for Critical Examination of Attributed AI Answers

Authors: Hita Kambhamettu, Alyssa Hwang, Philippe Laban, Andrew Head

Abstract: AI answer engines are a relatively new kind of information search tool: rather than returning a ranked list of documents, they generate an answer to a search question with inline citations to sources. But reading the cited sources is costly, and citation links themselves offer little guidance about what evidence they contain. We present attribution gradients, a technique to boost the informativene… ▽ More AI answer engines are a relatively new kind of information search tool: rather than returning a ranked list of documents, they generate an answer to a search question with inline citations to sources. But reading the cited sources is costly, and citation links themselves offer little guidance about what evidence they contain. We present attribution gradients, a technique to boost the informativeness of citations by consolidating scent and information prey in place. Its first feature is bringing evidence amounts, supporting/contradictory excerpts, links to source, contextual explanation into one place. Its second feature is the ability to unravel second-degree citations in place. In a lab study we demonstrate usage of the full gradient in a critical reading task and its support for deep engagement that increased the depth of what readers took away from the sources versus a standard citation and document QA design. △ Less

Submitted 2 April, 2026; v1 submitted 30 September, 2025; originally announced October 2025.

The Invisible Mentor: Inferring User Actions from Screen Recordings to Recommend Better Workflows

Authors: Litao Yan, Andrew Head, Ken Milne, Vu Le, Sumit Gulwani, Chris Parnin, Emerson Murphy-Hill

Abstract: Many users struggle to notice when a more efficient workflow exists in feature-rich tools like Excel. Existing AI assistants offer help only after users describe their goals or problems, which can be effortful and imprecise. We present InvisibleMentor, a system that turns screen recordings of task completion into vision-grounded reflections on tasks. It detects issues such as repetitive edits and… ▽ More Many users struggle to notice when a more efficient workflow exists in feature-rich tools like Excel. Existing AI assistants offer help only after users describe their goals or problems, which can be effortful and imprecise. We present InvisibleMentor, a system that turns screen recordings of task completion into vision-grounded reflections on tasks. It detects issues such as repetitive edits and recommends more efficient alternatives based on observed behavior. Unlike prior systems that rely on logs, APIs, or user prompts, InvisibleMentor operates directly on screen recordings. It uses a two-stage pipeline: a vision-language model reconstructs actions and context, and a language model generates structured, high-fidelity suggestions. In evaluation, InvisibleMentor accurately identified inefficient workflows, and participants found its suggestions more actionable, tailored, and more helpful for learning and improvement compared to a prompt-based spreadsheet assistant. △ Less

Submitted 30 September, 2025; originally announced September 2025.

Comments: 15 pages, 6 figures

ACM Class: H.5.2

Spatial variability of CH4 and C2H2 absorptions in Jupiter's auroral regions from Juno-UVS observations

Authors: J. Vinesse, B. Bonfond, B. Benmahi, A. Moirano, D. Grodent, T. K. Greathouse, V. Hue, G. Sicorello, L. A. Head, G. R. Gladstone, M. W. Davis

Abstract: Color ratios derived from molecular hydrogen emissions provide valuable diagnostics for the energy of precipitating electrons and the structure of the auroral atmosphere. We aim to characterize the horizontal and vertical variability of hydrocarbon absorption in Jupiter's auroral atmosphere using ultraviolet data from the Juno-UVS spectrograph and to investigate potential departures from the expec… ▽ More Color ratios derived from molecular hydrogen emissions provide valuable diagnostics for the energy of precipitating electrons and the structure of the auroral atmosphere. We aim to characterize the horizontal and vertical variability of hydrocarbon absorption in Jupiter's auroral atmosphere using ultraviolet data from the Juno-UVS spectrograph and to investigate potential departures from the expected structure. We constructed color ratio maps sensitive to CH$_4$ and C$_2$H$_2$ absorptions for perijoves (PJs) 6 and 10, two of Juno's close approaches to Jupiter, by integrating auroral H$_2$ emission over hydrocarbon-sensitive spectral intervals. For CH$_4$, we redefined the absorbed spectral band, replacing the traditionally used 125-130 nm interval with 135-140 nm, in order to mitigate higher-order calibration issues. In regions of intense auroral brightness, we developed a correction method to account for spectral distortion due to detector non-linearities at high fluxes. CH$_4$ and C$_2$H$_2$ absorptions generally follow the expected vertical distribution, with the CH$_4$ density extending to higher altitudes than C$_2$H$_2$. However, several localized regions show unexpected spatial distribution of the absorption. In PJ6, such anomalies are attributed to instrumental non-linearities. After correction, the CR distributions become consistent with standard hydrocarbon vertical distributions. In PJ10, however, some anomalous patterns persist despite correction. Spectral modeling indicates that these can be explained by modifying the relative abundances of CH$_4$ and C$_2$H$_2$, suggesting horizontal compositional variability and possible deviations in homopause altitude between species. These findings underscore the importance of accounting for local atmospheric composition when interpreting ultraviolet auroral spectra and retrieving electron energy distributions. △ Less

Submitted 19 August, 2025; originally announced August 2025.

Comments: 13 pages, 15 figures, to be published in Astronomy and Astrophysics

Journal ref: A&A 707, A330 (2026)

The Pedersen and Hall Conductances in the Jovian Polar Regions: New Maps based on a Broadband Electron Energy Distribution

Authors: G. Sicorello, D. Grodent, B. Bonfond, J. -C. Gérard, B. Benmahi, A. Salveter, A. Moirano, L. A. Head, J. Vinesse, T. Greathouse, G. R. Gladstone, M. Barthélémy

Abstract: The ionospheric Pedersen and Hall conductances play an important role in understanding the exchanges of angular momentum, energy and matter between the magnetosphere and the ionosphere/thermosphere at Jupiter, modifying the composition and temperature of the planet. In the high latitude regions, these conductances are enhanced by the auroral electron precipitation. The effect of a broadband precip… ▽ More The ionospheric Pedersen and Hall conductances play an important role in understanding the exchanges of angular momentum, energy and matter between the magnetosphere and the ionosphere/thermosphere at Jupiter, modifying the composition and temperature of the planet. In the high latitude regions, these conductances are enhanced by the auroral electron precipitation. The effect of a broadband precipitating electron energy distribution, similar to the observed electron distributions through particle measurements, on the conductance values is investigated. The new values are compared to the ones obtained from previous studies, notably when considering a mono-energetic distribution. The broadband precipitating electron energy distribution is modeled by a kappa distribution, which is used as an input in an electron transport model that computes the density vertical profiles of ionospheric ions. The vertical profiles of the Pedersen and Hall conductivities are then evaluated assuming that the conductivities are mostly governed by the densities of H3+ and CH5+. Finally, the Pedersen and Hall conductances are computed by integrating the corresponding conductivities over altitude. The Pedersen and Hall conductances are globally higher when considering a broadband electron energy distribution rather than a mono-energetic distribution. In addition, the use of the direct outputs of an electron transport model rather than the analytical expression presented in Hiraki and Tao (2008) as well as a change in the electron collision cross-sections also have significant impacts on the conductance values. Comparison between our results and the ones deduced from the corotation enforcement theory suggests that either a physical mechanism limits the field-aligned currents or the auroral electrons precipitating in the atmosphere are also accelerated by processes not associated with the field-aligned currents. △ Less

Submitted 14 July, 2025; originally announced July 2025.

Journal ref: A&A 703, A69 (2025)

Jupiter's ultraviolet auroral bridge: the influence of the solar wind on polar auroral morphology

Authors: L. A. Head, D. Grodent, B. Bonfond, A. Sulaiman, A. Moirano, G. Sicorello, S. Elliott, M. F. Vogt, C. K. Louis, N. Kruegler, J. Vinesse, T. K. Greathouse

Abstract: Jupiters ultraviolet aurora frequently shows a number of arcs between the dusk-side polar region and the main emission, which are denoted as bridges. This work presents a largely automated detection and statistical analysis of bridges over 248 Hubble-Space-Telescope observations, alongside a multi-instrument study of crossings of magnetic field lines connected to bridges by the Juno spacecraft dur… ▽ More Jupiters ultraviolet aurora frequently shows a number of arcs between the dusk-side polar region and the main emission, which are denoted as bridges. This work presents a largely automated detection and statistical analysis of bridges over 248 Hubble-Space-Telescope observations, alongside a multi-instrument study of crossings of magnetic field lines connected to bridges by the Juno spacecraft during its first 30 perijoves. Bridges are observed to arise on timescales of around 2 hours, can persist over a full Jupiter rotation, and are conjugate between hemispheres. The appearance of bridges is associated with compression of the magnetosphere, likely by the solar wind. Low-altitude bridge crossings are associated with upward-dominated, broadband electron distributions, consistent with Zone-II aurorae, as well as with plasma-wave emission observed by Juno-Waves, in agreement with existing theoretical models for the generation of polar-region aurorae. Main-emission crossings where no bridges are visible also show characteristics associated with bridges (more upward electron flux, plasma-wave emission), which is not the case for main-emission crossings with visible bridges, as though bridges remain present but spatially indistinguishable from the main emission in the former case. In all, compression of the magnetosphere may work to spatially separate the Zone-I and Zone-II regions of the main emission, in the form of Zone-II bridges. △ Less

Submitted 30 June, 2025; v1 submitted 25 March, 2025; originally announced April 2025.

Journal ref: A&A 700, A142 (2025)

Operando XPS in Reactive Plasmas: The Importance of The Wall Reactions

Authors: J. Trey Diulus, Ashley R. Head, Jorge Anibal Boscoboinik, Andrei Kolmakov

Abstract: Advancements in differential pumping and electron optics over the past few decades have enabled x-ray photoelectron spectroscopy (XPS) measurements at (near-)ambient pressures, bridging the pressure gap for characterizing realistic sample chemistries. Recently, we demonstrated the capabilities of an ambient pressure XPS (APXPS) setup for in-situ plasma environment measurements, allowing plasma-sur… ▽ More Advancements in differential pumping and electron optics over the past few decades have enabled x-ray photoelectron spectroscopy (XPS) measurements at (near-)ambient pressures, bridging the pressure gap for characterizing realistic sample chemistries. Recently, we demonstrated the capabilities of an ambient pressure XPS (APXPS) setup for in-situ plasma environment measurements, allowing plasma-surface interactions to be studied in operando rather than using the traditional before-and-after analysis approach. This new plasma-XPS technique facilitates the identification of reaction intermediates critical for understanding plasma-assisted surface processes relevant to semiconductor nanomanufacturing, such as physical vapor deposition, etching, atomic layer deposition, etc. In this report, we apply the plasma-XPS approach to monitor real-time surface chemical changes on a model Ag(111) single crystal exposed to oxidizing and reducing plasmas. We correlate surface-sensitive data with concurrent gas-phase XPS measurements and residual gas mass-spectra analysis of species generated during plasma exposure, highlighting the significant role of plasma-induced chamber wall reactions. Ultimately, we demonstrate that plasma-XPS provides comprehensive insights into both surface and gas-phase chemistry, establishing it as a versatile and dynamic characterization tool with broad applications in microelectronics research. △ Less

Submitted 26 February, 2025; originally announced February 2025.

Scaling Text-Rich Image Understanding via Code-Guided Synthetic Multimodal Data Generation

Authors: Yue Yang, Ajay Patel, Matt Deitke, Tanmay Gupta, Luca Weihs, Andrew Head, Mark Yatskar, Chris Callison-Burch, Ranjay Krishna, Aniruddha Kembhavi, Christopher Clark

Abstract: Reasoning about images with rich text, such as charts and documents, is a critical application of vision-language models (VLMs). However, VLMs often struggle in these domains due to the scarcity of diverse text-rich vision-language data. To address this challenge, we present CoSyn, a framework that leverages the coding capabilities of text-only large language models (LLMs) to automatically create… ▽ More Reasoning about images with rich text, such as charts and documents, is a critical application of vision-language models (VLMs). However, VLMs often struggle in these domains due to the scarcity of diverse text-rich vision-language data. To address this challenge, we present CoSyn, a framework that leverages the coding capabilities of text-only large language models (LLMs) to automatically create synthetic text-rich multimodal data. Given input text describing a target domain (e.g., "nutrition fact labels"), CoSyn prompts an LLM to generate code (Python, HTML, LaTeX, etc.) for rendering synthetic images. With the underlying code as textual representations of the synthetic images, CoSyn can generate high-quality instruction-tuning data, again relying on a text-only LLM. Using CoSyn, we constructed a dataset comprising 400K images and 2.7M rows of vision-language instruction-tuning data. Comprehensive experiments on seven benchmarks demonstrate that models trained on our synthetic data achieve state-of-the-art performance among competitive open-source models, including Llama 3.2, and surpass proprietary models such as GPT-4V and Gemini 1.5 Flash. Furthermore, CoSyn can produce synthetic pointing data, enabling VLMs to ground information within input images, showcasing its potential for developing multimodal agents capable of acting in real-world environments. △ Less

Submitted 21 May, 2025; v1 submitted 20 February, 2025; originally announced February 2025.

Comments: Published in ACL 2025, project page: https://yueyang1996.github.io/cosyn/

Predicting rigidity and connectivity percolation in disordered particulate networks using graph neural networks

Authors: D. A. Head

Abstract: Graph neural networks can accurately predict the chemical properties of many molecular systems, but their suitability for large, macromolecular assemblies such as gels is unknown. Here, graph neural networks were trained and optimised for two large-scale classification problems: the rigidity of a molecular network, and the connectivity percolation status which is non-trivial to determine for syste… ▽ More Graph neural networks can accurately predict the chemical properties of many molecular systems, but their suitability for large, macromolecular assemblies such as gels is unknown. Here, graph neural networks were trained and optimised for two large-scale classification problems: the rigidity of a molecular network, and the connectivity percolation status which is non-trivial to determine for systems with periodic boundaries. Models trained on lattice systems were found to achieve accuracies >95% for rigidity classification, with slightly lower scores for connectivity percolation due to the inherent class imbalance in the data. Dynamically generated off-lattice networks achieved consistently lower accuracies overall due to the correlated nature of the network geometry that was absent in the lattices. An open source tool is provided allowing usage of the highest-scoring trained models, and directions for future improved tools to surmount the challenges limiting accuracy in certain situations are discussed. △ Less

Submitted 28 March, 2025; v1 submitted 21 November, 2024; originally announced November 2024.

Comments: 8 pages, 5 figure files plus a supplementary material PDF. Revised as per reviewers' comments. To appear in Phys. Rev. E

Journal ref: Phys. Rev. E 111, 045411 (2025)

Molmo and PixMo: Open Weights and Open Data for State-of-the-Art Vision-Language Models

Authors: Matt Deitke, Christopher Clark, Sangho Lee, Rohun Tripathi, Yue Yang, Jae Sung Park, Mohammadreza Salehi, Niklas Muennighoff, Kyle Lo, Luca Soldaini, Jiasen Lu, Taira Anderson, Erin Bransom, Kiana Ehsani, Huong Ngo, YenSung Chen, Ajay Patel, Mark Yatskar, Chris Callison-Burch, Andrew Head, Rose Hendrix, Favyen Bastani, Eli VanderBilt, Nathan Lambert, Yvonne Chou , et al. (25 additional authors not shown)

Abstract: Today's most advanced vision-language models (VLMs) remain proprietary. The strongest open-weight models rely heavily on synthetic data from proprietary VLMs to achieve good performance, effectively distilling these closed VLMs into open ones. As a result, the community has been missing foundational knowledge about how to build performant VLMs from scratch. We present Molmo, a new family of VLMs t… ▽ More Today's most advanced vision-language models (VLMs) remain proprietary. The strongest open-weight models rely heavily on synthetic data from proprietary VLMs to achieve good performance, effectively distilling these closed VLMs into open ones. As a result, the community has been missing foundational knowledge about how to build performant VLMs from scratch. We present Molmo, a new family of VLMs that are state-of-the-art in their class of openness. Our key contribution is a collection of new datasets called PixMo, including a dataset of highly detailed image captions for pre-training, a free-form image Q&A dataset for fine-tuning, and an innovative 2D pointing dataset, all collected without the use of external VLMs. The success of our approach relies on careful modeling choices, a well-tuned training pipeline, and, most critically, the quality of our newly collected datasets. Our best-in-class 72B model not only outperforms others in the class of open weight and data models, but also outperforms larger proprietary models including Claude 3.5 Sonnet, and Gemini 1.5 Pro and Flash, second only to GPT-4o based on both academic benchmarks and on a large human evaluation. Our model weights, new datasets, and source code are available at https://molmo.allenai.org/blog. △ Less

Submitted 5 December, 2024; v1 submitted 25 September, 2024; originally announced September 2024.

Comments: Updated with ablations and more technical details

Traceable Text: Deepening Reading of AI-Generated Summaries with Phrase-Level Provenance Links

Authors: Hita Kambhamettu, Jamie Flores, Andrew Head

Abstract: As AI-generated summaries proliferate, how can we help people understand the veracity of those summaries? In this short paper, we design a simple interaction primitive, traceable text, to support critical examination of generated summaries and the source texts they were derived from. In a traceable text, passages of a generated summary link to passages of the source text that informed them. A trac… ▽ More As AI-generated summaries proliferate, how can we help people understand the veracity of those summaries? In this short paper, we design a simple interaction primitive, traceable text, to support critical examination of generated summaries and the source texts they were derived from. In a traceable text, passages of a generated summary link to passages of the source text that informed them. A traceable text can be generated with a straightforward prompt chaining approach, and optionally adjusted by human authors depending on application. In a usability study, we examined the impact of traceable texts on reading and understanding patient medical records. Traceable text helped readers answer questions about the content of the source text more quickly and markedly improved correctness of answers in cases where there were hallucinations in the summaries. When asked to read a text of personal importance with traceable text, readers employed traceable text as an understanding aid and as an index into the source note. △ Less

Submitted 19 September, 2024; originally announced September 2024.

Effect of magnetospheric conditions on the morphology of Jupiter's UV main auroral emission, as observed by Juno-UVS

Authors: L. A. Head, D. Grodent, B. Bonfond, A. Moirano, B. Benmahi, G. Sicorello, J-C Gérard, M. F. Vogt, V. Hue, T. Greathouse, G. R. Gladstone, Z. Yao

Abstract: Auroral emissions are a reflection of magnetospheric processes, and, at Jupiter, it is not entirely certain how the morphology of the UV main emission (ME) varies with magnetospheric compression or the strength of the central current sheet. This work leverages the observations from Juno-UVS to link ME variability with magnetospheric states. Novel arc-detection techniques are used to determine new… ▽ More Auroral emissions are a reflection of magnetospheric processes, and, at Jupiter, it is not entirely certain how the morphology of the UV main emission (ME) varies with magnetospheric compression or the strength of the central current sheet. This work leverages the observations from Juno-UVS to link ME variability with magnetospheric states. Novel arc-detection techniques are used to determine new reference ovals for the ME from perijoves 1 through 54, in both hemispheres, and analyse how the size and shape of the ME vary compared to this reference oval. The morphology and brightness of the ME vary in local time: the dawn-side ME is typically expanded and the dusk-side ME typically contracted compared to the reference oval, and the dusk-side ME being typically twice as bright as the dawn-side ME. Both the northern and southern ME, and the day-side and night-side ME, expand and contract from their reference ovals synchronously, which indicates that the variable size of the ME is caused by a process occurring throughout the jovian magnetosphere. The poleward latitudinal shift of the auroral footprint of Ganymede correlates with the poleward motion of the ME, whereas a similar relation is not present for the footprint of Io. Additionally, the expansion of the ME correlates well with an increase in magnetodisc current. These two results suggest that a changing current-sheet magnetic field is partially responsible for the variable size of the ME. Finally, magnetospheric compression is linked to a global ME contraction and brightening, though this brightening occurs predominantly in the day-side ME. This observation, and the observation that the dusk-side ME is typically brighter than the dawn-side ME, stands in contrast to the modelled and observed behaviour of field-aligned currents and thus weakens the theoretical link between field-aligned currents and the generation of the auroral ME. △ Less

Submitted 8 April, 2024; v1 submitted 5 April, 2024; originally announced April 2024.

Journal ref: A&A 688, A205 (2024)

Ivie: Lightweight Anchored Explanations of Just-Generated Code

Authors: Litao Yan, Alyssa Hwang, Zhiyuan Wu, Andrew Head

Abstract: Programming assistants have reshaped the experience of programming into one where programmers spend less time writing and more time critically examining code. In this paper, we explore how programming assistants can be extended to accelerate the inspection of generated code. We introduce an extension to the programming assistant called Ivie, or instantly visible in-situ explanations. When using Iv… ▽ More Programming assistants have reshaped the experience of programming into one where programmers spend less time writing and more time critically examining code. In this paper, we explore how programming assistants can be extended to accelerate the inspection of generated code. We introduce an extension to the programming assistant called Ivie, or instantly visible in-situ explanations. When using Ivie, a programmer's generated code is instantly accompanied by explanations positioned just adjacent to the code. Our design was optimized for extremely low-cost invocation and dismissal. Explanations are compact and informative. They describe meaningful expressions, from individual variables to entire blocks of code. We present an implementation of Ivie that forks VS Code, applying a modern LLM for timely segmentation and explanation of generated code. In a lab study, we compared Ivie to a contemporary baseline tool for code understanding. Ivie improved understanding of generated code, and was received by programmers as a highly useful, low distraction, desirable complement to the programming assistant. △ Less

Submitted 4 March, 2024; originally announced March 2024.

Comments: 15 pages, 10 figures, to be published in the CHI Conference on Human Factors in Computing Systems (CHI 24)

Operando Plasma-XPS for Process Monitoring: Hydrogenation of Copper Oxide Confined Under h-BN Case Study

Authors: J. Trey Diulus, Andrew E. Naclerio, Anibal Boscoboinik, Ashley R. Head, Evgheni Strelcov, Piran R. Kidambi, Andrei Kolmakov

Abstract: We demonstrate that ambient pressure x-ray photoelectron spectroscopy (APXPS) can be used for in situ studies of dynamic changes in surface chemistry in a plasma environment. Hexagonal boron nitride (h-BN) was used in this study as a model system since it exhibits a wide array of unique chemical, optical, and electrical properties that make it a prospective material for advanced electronics. To be… ▽ More We demonstrate that ambient pressure x-ray photoelectron spectroscopy (APXPS) can be used for in situ studies of dynamic changes in surface chemistry in a plasma environment. Hexagonal boron nitride (h-BN) was used in this study as a model system since it exhibits a wide array of unique chemical, optical, and electrical properties that make it a prospective material for advanced electronics. To better understand the stability and surface chemistry of h-BN during plasma-assisted processing, we used polycrystalline Cu foils with single-layer h-BN, grown via chemical vapor deposition (CVD), and tracked in real-time the plasma-induced reduction of the underlying Cu oxide using APXPS equipped with 22 kHz 75 W discharge plasma source operating at 13 Pa. Residual gas analysis (RGA) mass-spectra were concurrently collected during plasma-XPS to track reaction products formed during plasma exposure. A clear reduction of CuxO is seen, while an h-BN layer remains intact, suggesting H radical species can attack the exposed and h-BN-covered Cu oxide patches and partially reduce the underlying substrate. In addition to the demonstration and discussion of plasma-XPS capabilities, our results indicate the h-BN encapsulated metallic Cu interface might be repaired without significantly damaging the overlaying h-BN, which is of practical importance for the development of h-BN encapsulated devices and interfaces △ Less

Submitted 2 January, 2024; originally announced January 2024.

Grounded Intuition of GPT-Vision's Abilities with Scientific Images

Authors: Alyssa Hwang, Andrew Head, Chris Callison-Burch

Abstract: GPT-Vision has impressed us on a range of vision-language tasks, but it comes with the familiar new challenge: we have little idea of its capabilities and limitations. In our study, we formalize a process that many have instinctively been trying already to develop "grounded intuition" of this new model. Inspired by the recent movement away from benchmarking in favor of example-driven qualitative e… ▽ More GPT-Vision has impressed us on a range of vision-language tasks, but it comes with the familiar new challenge: we have little idea of its capabilities and limitations. In our study, we formalize a process that many have instinctively been trying already to develop "grounded intuition" of this new model. Inspired by the recent movement away from benchmarking in favor of example-driven qualitative evaluation, we draw upon grounded theory and thematic analysis in social science and human-computer interaction to establish a rigorous framework for qualitative evaluation in natural language processing. We use our technique to examine alt text generation for scientific figures, finding that GPT-Vision is particularly sensitive to prompting, counterfactual text in images, and relative spatial relationships. Our method and analysis aim to help researchers ramp up their own grounded intuitions of new models while exposing how GPT-Vision can be applied to make information more accessible. △ Less

Submitted 3 November, 2023; originally announced November 2023.

Ultrathin Magnesium-based Coating as an Efficient Oxygen Barrier for Superconducting Circuit Materials

Authors: Chenyu Zhou, Junsik Mun, Juntao Yao, Aswin kumar Anbalagan, Mohammad D. Hossain, Russell A. McLellan, Ruoshui Li, Kim Kisslinger, Gengnan Li, Xiao Tong, Ashley R. Head, Conan Weiland, Steven L. Hulbert, Andrew L. Walter, Qiang Li, Yimei Zhu, Peter V. Sushko, Mingzhao Liu

Abstract: Scaling up superconducting quantum circuits based on transmon qubits necessitates substantial enhancements in qubit coherence time. Among the materials considered for transmon qubits, tantalum (Ta) has emerged as a promising candidate, surpassing conventional counterparts in terms of coherence time. However, the presence of an amorphous surface Ta oxide layer introduces dielectric loss, ultimately… ▽ More Scaling up superconducting quantum circuits based on transmon qubits necessitates substantial enhancements in qubit coherence time. Among the materials considered for transmon qubits, tantalum (Ta) has emerged as a promising candidate, surpassing conventional counterparts in terms of coherence time. However, the presence of an amorphous surface Ta oxide layer introduces dielectric loss, ultimately placing a limit on the coherence time. In this study, we present a novel approach for suppressing the formation of tantalum oxide using an ultrathin magnesium (Mg) capping layer deposited on top of tantalum. Synchrotron-based X-ray photoelectron spectroscopy (XPS) studies demonstrate that oxide is confined to an extremely thin region directly beneath the Mg/Ta interface. Additionally, we demonstrate that the superconducting properties of thin Ta films are improved following the Mg capping, exhibiting sharper and higher-temperature transitions to superconductive and magnetically ordered states. Based on the experimental data and computational modeling, we establish an atomic-scale mechanistic understanding of the role of the capping layer in protecting Ta from oxidation. This work provides valuable insights into the formation mechanism and functionality of surface tantalum oxide, as well as a new materials design principle with the potential to reduce dielectric loss in superconducting quantum materials. Ultimately, our findings pave the way for the realization of large-scale, high-performance quantum computing systems. △ Less

Submitted 25 September, 2023; v1 submitted 21 September, 2023; originally announced September 2023.

CALYPSO: LLMs as Dungeon Masters' Assistants

Authors: Andrew Zhu, Lara J. Martin, Andrew Head, Chris Callison-Burch

Abstract: The role of a Dungeon Master, or DM, in the game Dungeons & Dragons is to perform multiple tasks simultaneously. The DM must digest information about the game setting and monsters, synthesize scenes to present to other players, and respond to the players' interactions with the scene. Doing all of these tasks while maintaining consistency within the narrative and story world is no small feat of hum… ▽ More The role of a Dungeon Master, or DM, in the game Dungeons & Dragons is to perform multiple tasks simultaneously. The DM must digest information about the game setting and monsters, synthesize scenes to present to other players, and respond to the players' interactions with the scene. Doing all of these tasks while maintaining consistency within the narrative and story world is no small feat of human cognition, making the task tiring and unapproachable to new players. Large language models (LLMs) like GPT-3 and ChatGPT have shown remarkable abilities to generate coherent natural language text. In this paper, we conduct a formative evaluation with DMs to establish the use cases of LLMs in D&D and tabletop gaming generally. We introduce CALYPSO, a system of LLM-powered interfaces that support DMs with information and inspiration specific to their own scenario. CALYPSO distills game context into bite-sized prose and helps brainstorm ideas without distracting the DM from the game. When given access to CALYPSO, DMs reported that it generated high-fidelity text suitable for direct presentation to players, and low-fidelity ideas that the DM could develop further while maintaining their creative agency. We see CALYPSO as exemplifying a paradigm of AI-augmented tools that provide synchronous creative assistance within established game worlds, and tabletop gaming more broadly. △ Less

Submitted 14 August, 2023; originally announced August 2023.

Comments: 11 pages, 4 figures. AIIDE 2023

Journal ref: AAAI Conference on Artificial Intelligence and Interactive Digital Entertainment (AIIDE) 2023

Rewriting the Script: Adapting Text Instructions for Voice Interaction

Authors: Alyssa Hwang, Natasha Oza, Chris Callison-Burch, Andrew Head

Abstract: Voice assistants have sharply risen in popularity in recent years, but their use has been limited mostly to simple applications like music, hands-free search, or control of internet-of-things devices. What would it take for voice assistants to guide people through more complex tasks? In our work, we study the limitations of the dominant approach voice assistants take to complex task guidance: read… ▽ More Voice assistants have sharply risen in popularity in recent years, but their use has been limited mostly to simple applications like music, hands-free search, or control of internet-of-things devices. What would it take for voice assistants to guide people through more complex tasks? In our work, we study the limitations of the dominant approach voice assistants take to complex task guidance: reading aloud written instructions. Using recipes as an example, we observe twelve participants cook at home with a state-of-the-art voice assistant. We learn that the current approach leads to nine challenges, including obscuring the bigger picture, overwhelming users with too much information, and failing to communicate affordances. Instructions delivered by a voice assistant are especially difficult because they cannot be skimmed as easily as written instructions. Alexa in particular did not surface crucial details to the user or answer questions well. We draw on our observations to propose eight ways in which voice assistants can ``rewrite the script'' -- summarizing, signposting, splitting, elaborating, volunteering, reordering, redistributing, and visualizing -- to transform written sources into forms that are readily communicated through spoken conversation. We conclude with a vision of how modern advancements in natural language processing can be leveraged for intelligent agents to guide users effectively through complex tasks. △ Less

Submitted 16 June, 2023; originally announced June 2023.

Comments: To appear at Designing Interactive Systems 2023

Complex Mathematical Symbol Definition Structures: A Dataset and Model for Coordination Resolution in Definition Extraction

Authors: Anna Martin-Boyle, Andrew Head, Kyle Lo, Risham Sidhu, Marti A. Hearst, Dongyeop Kang

Abstract: Mathematical symbol definition extraction is important for improving scholarly reading interfaces and scholarly information extraction (IE). However, the task poses several challenges: math symbols are difficult to process as they are not composed of natural language morphemes; and scholarly papers often contain sentences that require resolving complex coordinate structures. We present SymDef, an… ▽ More Mathematical symbol definition extraction is important for improving scholarly reading interfaces and scholarly information extraction (IE). However, the task poses several challenges: math symbols are difficult to process as they are not composed of natural language morphemes; and scholarly papers often contain sentences that require resolving complex coordinate structures. We present SymDef, an English language dataset of 5,927 sentences from full-text scientific papers where each sentence is annotated with all mathematical symbols linked with their corresponding definitions. This dataset focuses specifically on complex coordination structures such as "respectively" constructions, which often contain overlapping definition spans. We also introduce a new definition extraction method that masks mathematical symbols, creates a copy of each sentence for each symbol, specifies a target symbol, and predicts its corresponding definition spans using slot filling. Our experiments show that our definition extraction model significantly outperforms RoBERTa and other strong IE baseline systems by 10.9 points with a macro F1 score of 84.82. With our dataset and model, we can detect complex definitions in scholarly documents to make scientific writing more readable. △ Less

Submitted 23 May, 2023; originally announced May 2023.

Comments: 9 pages, 4 figures

ACM Class: I.2.7

The Semantic Reader Project: Augmenting Scholarly Documents through AI-Powered Interactive Reading Interfaces

Authors: Kyle Lo, Joseph Chee Chang, Andrew Head, Jonathan Bragg, Amy X. Zhang, Cassidy Trier, Chloe Anastasiades, Tal August, Russell Authur, Danielle Bragg, Erin Bransom, Isabel Cachola, Stefan Candra, Yoganand Chandrasekhar, Yen-Sung Chen, Evie Yu-Yen Cheng, Yvonne Chou, Doug Downey, Rob Evans, Raymond Fok, Fangzhou Hu, Regan Huff, Dongyeop Kang, Tae Soo Kim, Rodney Kinney , et al. (30 additional authors not shown)

Abstract: Scholarly publications are key to the transfer of knowledge from scholars to others. However, research papers are information-dense, and as the volume of the scientific literature grows, the need for new technology to support the reading process grows. In contrast to the process of finding papers, which has been transformed by Internet technology, the experience of reading research papers has chan… ▽ More Scholarly publications are key to the transfer of knowledge from scholars to others. However, research papers are information-dense, and as the volume of the scientific literature grows, the need for new technology to support the reading process grows. In contrast to the process of finding papers, which has been transformed by Internet technology, the experience of reading research papers has changed little in decades. The PDF format for sharing research papers is widely used due to its portability, but it has significant downsides including: static content, poor accessibility for low-vision readers, and difficulty reading on mobile devices. This paper explores the question "Can recent advances in AI and HCI power intelligent, interactive, and accessible reading interfaces -- even for legacy PDFs?" We describe the Semantic Reader Project, a collaborative effort across multiple institutions to explore automatic creation of dynamic reading interfaces for research papers. Through this project, we've developed ten research prototype interfaces and conducted usability studies with more than 300 participants and real-world users showing improved reading experiences for scholars. We've also released a production reading interface for research papers that will incorporate the best features as they mature. We structure this paper around challenges scholars and the public face when reading research papers -- Discovery, Efficiency, Comprehension, Synthesis, and Accessibility -- and present an overview of our progress and remaining open challenges. △ Less

Submitted 23 April, 2023; v1 submitted 24 March, 2023; originally announced March 2023.

CiteSee: Augmenting Citations in Scientific Papers with Persistent and Personalized Historical Context

Authors: Joseph Chee Chang, Amy X. Zhang, Jonathan Bragg, Andrew Head, Kyle Lo, Doug Downey, Daniel S. Weld

Abstract: When reading a scholarly article, inline citations help researchers contextualize the current article and discover relevant prior work. However, it can be challenging to prioritize and make sense of the hundreds of citations encountered during literature reviews. This paper introduces CiteSee, a paper reading tool that leverages a user's publishing, reading, and saving activities to provide person… ▽ More When reading a scholarly article, inline citations help researchers contextualize the current article and discover relevant prior work. However, it can be challenging to prioritize and make sense of the hundreds of citations encountered during literature reviews. This paper introduces CiteSee, a paper reading tool that leverages a user's publishing, reading, and saving activities to provide personalized visual augmentations and context around citations. First, CiteSee connects the current paper to familiar contexts by surfacing known citations a user had cited or opened. Second, CiteSee helps users prioritize their exploration by highlighting relevant but unknown citations based on saving and reading history. We conducted a lab study that suggests CiteSee is significantly more effective for paper discovery than three baselines. A field deployment study shows CiteSee helps participants keep track of their explorations and leads to better situational awareness and increased paper discovery via inline citation when conducting real-world literature reviews. △ Less

Submitted 14 February, 2023; originally announced February 2023.

Chemical profiles of the oxides on tantalum in state of the art superconducting circuits

Authors: Russell A. McLellan, Aveek Dutta, Chenyu Zhou, Yichen Jia, Conan Weiland, Xin Gui, Alexander P. M. Place, Kevin D. Crowley, Xuan Hoang Le, Trisha Madhavan, Youqi Gang, Lukas Baker, Ashley R. Head, Iradwikanari Waluyo, Ruoshui Li, Kim Kisslinger, Adrian Hunt, Ignace Jarrige, Stephen A. Lyon, Andi M. Barbour, Robert J. Cava, Andrew A. Houck, Steven L. Hulbert, Mingzhao Liu, Andrew L. Walter , et al. (1 additional authors not shown)

Abstract: Over the past decades, superconducting qubits have emerged as one of the leading hardware platforms for realizing a quantum processor. Consequently, researchers have made significant effort to understand the loss channels that limit the coherence times of superconducting qubits. A major source of loss has been attributed to two level systems that are present at the material interfaces. We recently… ▽ More Over the past decades, superconducting qubits have emerged as one of the leading hardware platforms for realizing a quantum processor. Consequently, researchers have made significant effort to understand the loss channels that limit the coherence times of superconducting qubits. A major source of loss has been attributed to two level systems that are present at the material interfaces. We recently showed that replacing the metal in the capacitor of a transmon with tantalum yields record relaxation and coherence times for superconducting qubits, motivating a detailed study of the tantalum surface. In this work, we study the chemical profile of the surface of tantalum films grown on c-plane sapphire using variable energy X-ray photoelectron spectroscopy (VEXPS). We identify the different oxidation states of tantalum that are present in the native oxide resulting from exposure to air, and we measure their distribution through the depth of the film. Furthermore, we show how the volume and depth distribution of these tantalum oxidation states can be altered by various chemical treatments. By correlating these measurements with detailed measurements of quantum devices, we can improve our understanding of the microscopic device losses. △ Less

Submitted 20 January, 2023; v1 submitted 11 January, 2023; originally announced January 2023.

Scim: Intelligent Skimming Support for Scientific Papers

Authors: Raymond Fok, Hita Kambhamettu, Luca Soldaini, Jonathan Bragg, Kyle Lo, Andrew Head, Marti A. Hearst, Daniel S. Weld

Abstract: Researchers need to keep up with immense literatures, though it is time-consuming and difficult to do so. In this paper, we investigate the role that intelligent interfaces can play in helping researchers skim papers, that is, rapidly reviewing a paper to attain a cursory understanding of its contents. After conducting formative interviews and a design probe, we suggest that skimming aids should a… ▽ More Researchers need to keep up with immense literatures, though it is time-consuming and difficult to do so. In this paper, we investigate the role that intelligent interfaces can play in helping researchers skim papers, that is, rapidly reviewing a paper to attain a cursory understanding of its contents. After conducting formative interviews and a design probe, we suggest that skimming aids should aim to thread the needle of highlighting content that is simultaneously diverse, evenly-distributed, and important. We introduce Scim, a novel intelligent skimming interface that reifies this aim, designed to support the skimming process by highlighting salient paper contents to direct a skimmer's focus. Key to the design is that the highlights are faceted by content type, evenly-distributed across a paper, with a density configurable by readers at both the global and local level. We evaluate Scim with an in-lab usability study and deployment study, revealing how skimming aids can support readers throughout the skimming experience and yielding design considerations and tensions for the design of future intelligent skimming tools. △ Less

Submitted 25 September, 2023; v1 submitted 9 May, 2022; originally announced May 2022.

Comments: Updated to reflect version published in proceedings of IUI 2023

From Who You Know to What You Read: Augmenting Scientific Recommendations with Implicit Social Networks

Authors: Hyeonsu B. Kang, Rafal Kocielnik, Andrew Head, Jiangjiang Yang, Matt Latzke, Aniket Kittur, Daniel S. Weld, Doug Downey, Jonathan Bragg

Abstract: The ever-increasing pace of scientific publication necessitates methods for quickly identifying relevant papers. While neural recommenders trained on user interests can help, they still result in long, monotonous lists of suggested papers. To improve the discovery experience we introduce multiple new methods for \em augmenting recommendations with textual relevance messages that highlight knowledg… ▽ More The ever-increasing pace of scientific publication necessitates methods for quickly identifying relevant papers. While neural recommenders trained on user interests can help, they still result in long, monotonous lists of suggested papers. To improve the discovery experience we introduce multiple new methods for \em augmenting recommendations with textual relevance messages that highlight knowledge-graph connections between recommended papers and a user's publication and interaction history. We explore associations mediated by author entities and those using citations alone. In a large-scale, real-world study, we show how our approach significantly increases engagement -- and future engagement when mediated by authors -- without introducing bias towards highly-cited authors. To expand message coverage for users with less publication or interaction history, we develop a novel method that highlights connections with proxy authors of interest to users and evaluate it in a controlled lab study. Finally, we synthesize design implications for future graph-based messages. △ Less

Submitted 21 April, 2022; originally announced April 2022.

Comments: to be published in ACM SIGCHI 2022

Paper Plain: Making Medical Research Papers Approachable to Healthcare Consumers with Natural Language Processing

Authors: Tal August, Lucy Lu Wang, Jonathan Bragg, Marti A. Hearst, Andrew Head, Kyle Lo

Abstract: When seeking information not covered in patient-friendly documents, like medical pamphlets, healthcare consumers may turn to the research literature. Reading medical papers, however, can be a challenging experience. To improve access to medical papers, we introduce a novel interactive interface-Paper Plain-with four features powered by natural language processing: definitions of unfamiliar terms,… ▽ More When seeking information not covered in patient-friendly documents, like medical pamphlets, healthcare consumers may turn to the research literature. Reading medical papers, however, can be a challenging experience. To improve access to medical papers, we introduce a novel interactive interface-Paper Plain-with four features powered by natural language processing: definitions of unfamiliar terms, in-situ plain language section summaries, a collection of key questions that guide readers to answering passages, and plain language summaries of the answering passages. We evaluate Paper Plain, finding that participants who use Paper Plain have an easier time reading and understanding research papers without a loss in paper comprehension compared to those who use a typical PDF reader. Altogether, the study results suggest that guiding readers to relevant passages and providing plain language summaries, or "gists," alongside the original paper content can make reading medical papers easier and give readers more confidence to approach these papers. △ Less

Submitted 28 February, 2022; originally announced March 2022.

Comments: 39 pages, 10 figures

ACM Class: H.5.2

Fine-Grained Lineage for Safer Notebook Interactions

Authors: Stephen Macke, Hongpu Gong, Doris Jung-Lin Lee, Andrew Head, Doris Xin, Aditya Parameswaran

Abstract: Computational notebooks have emerged as the platform of choice for data science and analytical workflows, enabling rapid iteration and exploration. By keeping intermediate program state in memory and segmenting units of execution into so-called "cells", notebooks allow users to execute their workflows interactively and enjoy particularly tight feedback. However, as cells are added, removed, reorde… ▽ More Computational notebooks have emerged as the platform of choice for data science and analytical workflows, enabling rapid iteration and exploration. By keeping intermediate program state in memory and segmenting units of execution into so-called "cells", notebooks allow users to execute their workflows interactively and enjoy particularly tight feedback. However, as cells are added, removed, reordered, and rerun, this hidden intermediate state accumulates in a way that is not necessarily correlated with the notebook's visible code, making execution behavior difficult to reason about, and leading to errors and lack of reproducibility. We present NBSafety, a custom Jupyter kernel that uses runtime tracing and static analysis to automatically manage lineage associated with cell execution and global notebook state. NBSafety detects and prevents errors that users make during unaided notebook interactions, all while preserving the flexibility of existing notebook semantics. We evaluate NBSafety's ability to prevent erroneous interactions by replaying and analyzing 666 real notebook sessions. Of these, NBSafety identified 117 sessions with potential safety errors, and in the remaining 549 sessions, the cells that NBSafety identified as resolving safety issues were more than $7\times$ more likely to be selected by users for re-execution compared to a random baseline, even though the users were not using NBSafety and were therefore not influenced by its suggestions. △ Less

Submitted 19 June, 2021; v1 submitted 13 December, 2020; originally announced December 2020.

Document-Level Definition Detection in Scholarly Documents: Existing Models, Error Analyses, and Future Directions

Authors: Dongyeop Kang, Andrew Head, Risham Sidhu, Kyle Lo, Daniel S. Weld, Marti A. Hearst

Abstract: The task of definition detection is important for scholarly papers, because papers often make use of technical terminology that may be unfamiliar to readers. Despite prior work on definition detection, current approaches are far from being accurate enough to use in real-world applications. In this paper, we first perform in-depth error analysis of the current best performing definition detection s… ▽ More The task of definition detection is important for scholarly papers, because papers often make use of technical terminology that may be unfamiliar to readers. Despite prior work on definition detection, current approaches are far from being accurate enough to use in real-world applications. In this paper, we first perform in-depth error analysis of the current best performing definition detection system and discover major causes of errors. Based on this analysis, we develop a new definition detection system, HEDDEx, that utilizes syntactic features, transformer encoders, and heuristic filters, and evaluate it on a standard sentence-level benchmark. Because current benchmarks evaluate randomly sampled sentences, we propose an alternative evaluation that assesses every sentence within a document. This allows for evaluating recall in addition to precision. HEDDEx outperforms the leading system on both the sentence-level and the document-level tasks, by 12.7 F1 points and 14.4 F1 points, respectively. We note that performance on the high-recall document-level task is much lower than in the standard evaluation approach, due to the necessity of incorporation of document structure as features. We discuss remaining challenges in document-level definition detection, ideas for improvements, and potential issues for the development of reading aid applications. △ Less

Submitted 10 October, 2020; originally announced October 2020.

Comments: Workshop on Scholarly Document Processing (SDP), EMNLP 2020

Augmenting Scientific Papers with Just-in-Time, Position-Sensitive Definitions of Terms and Symbols

Authors: Andrew Head, Kyle Lo, Dongyeop Kang, Raymond Fok, Sam Skjonsberg, Daniel S. Weld, Marti A. Hearst

Abstract: Despite the central importance of research papers to scientific progress, they can be difficult to read. Comprehension is often stymied when the information needed to understand a passage resides somewhere else: in another section, or in another paper. In this work, we envision how interfaces can bring definitions of technical terms and symbols to readers when and where they need them most. We int… ▽ More Despite the central importance of research papers to scientific progress, they can be difficult to read. Comprehension is often stymied when the information needed to understand a passage resides somewhere else: in another section, or in another paper. In this work, we envision how interfaces can bring definitions of technical terms and symbols to readers when and where they need them most. We introduce ScholarPhi, an augmented reading interface with four novel features: (1) tooltips that surface position-sensitive definitions from elsewhere in a paper, (2) a filter over the paper that "declutters" it to reveal how the term or symbol is used across the paper, (3) automatic equation diagrams that expose multiple definitions in parallel, and (4) an automatically generated glossary of important terms and symbols. A usability study showed that the tool helps researchers of all experience levels read papers. Furthermore, researchers were eager to have ScholarPhi's definitions available to support their everyday reading. △ Less

Submitted 27 April, 2021; v1 submitted 29 September, 2020; originally announced September 2020.

Comments: 18 pages, 17 figures, 2 tables. To appear at the 2021 ACM CHI Conference on Human Factors in Computing Systems. For associated video, see https://youtu.be/yYcQf-Yq8B0. v2 changes: expanded discussion of design process and implementation; improved figure design. v3 changes: fixed typo in cell of Table 2; updated HEDDEx and Schwarz-Hearst accuracy in Section 5.3

ACM Class: H.5.2

TraceDiff: Debugging Unexpected Code Behavior Using Trace Divergences

Authors: Ryo Suzuki, Gustavo Soares, Andrew Head, Elena Glassman, Ruan Reis, Melina Mongiovi, Loris D'Antoni, Bjoern Hartmann

Abstract: Recent advances in program synthesis offer means to automatically debug student submissions and generate personalized feedback in massive programming classrooms. When automatically generating feedback for programming assignments, a key challenge is designing pedagogically useful hints that are as effective as the manual feedback given by teachers. Through an analysis of teachers' hint-giving pract… ▽ More Recent advances in program synthesis offer means to automatically debug student submissions and generate personalized feedback in massive programming classrooms. When automatically generating feedback for programming assignments, a key challenge is designing pedagogically useful hints that are as effective as the manual feedback given by teachers. Through an analysis of teachers' hint-giving practices in 132 online Q&A posts, we establish three design guidelines that an effective feedback design should follow. Based on these guidelines, we develop a feedback system that leverages both program synthesis and visualization techniques. Our system compares the dynamic code execution of both incorrect and fixed code and highlights how the error leads to a difference in behavior and where the incorrect code trace diverges from the expected solution. Results from our study suggest that our system enables students to detect and fix bugs that are not caught by students using another existing visual debugging tool. △ Less

Submitted 12 August, 2017; originally announced August 2017.

Comments: VL/HCC 2017

ACM Class: H.5.2

In silico modeling of the rheological properties of covalently crosslinked collagen triple helices

Authors: David A. Head, Giuseppe Tronci, Stephen J. Russell, David J. Wood

Abstract: Biomimetic hydrogels based on natural polymers are a promising class of biomaterial, mimicking the natural extra-cellular matrix of biological tissues and providing cues for cell attachment, proliferation and differentiation. With a view to providing an upstream method to guide subsequent experimental design, the aim of this study was to introduce a mathematical model that described the rheologica… ▽ More Biomimetic hydrogels based on natural polymers are a promising class of biomaterial, mimicking the natural extra-cellular matrix of biological tissues and providing cues for cell attachment, proliferation and differentiation. With a view to providing an upstream method to guide subsequent experimental design, the aim of this study was to introduce a mathematical model that described the rheological properties of a hydrogel system based on covalently crosslinked collagen triple helices. In light of their organization, such gels exhibit limited collagen bundling that cannot be described by existing fibril network models. The model presented here treats collagen triple helices as discrete semi-flexible polymers, permits full access to metrics for network microstructure, and should provide a comprehensive understanding of the parameter space associated with the development of such multi-functional materials. Triple helical hydrogel networks were experimentally obtained via reaction of type I collagen with both aromatic and aliphatic diacids. The complex modulus G* was found from rheological testing in linear shear and quantitatively compared to model predictions. In silico data from the computational model successfully described the experimental trends in hydrogel storage modulus with either (i) the concentration of collagen triple helices during crosslinking reaction or (ii) the type of crosslinking segment introduced in resulting hydrogel networks. This approach may pave the way to a step change in the rational design of biomimetic triple helical collagen systems with controlled multi-functionality. △ Less

Submitted 23 October, 2016; originally announced October 2016.

Comments: 9 figures, 1 scheme, 1 table, ACS Biomaterials Science and Engineering 2016

Importance of non-affine viscoelastic response in disordered fibre networks

Authors: L. G. Rizzi, S. Auer, D. A. Head

Abstract: Disordered fibre networks are ubiquitous in nature and have a wide range of industrial applications as novel biomaterials. Predicting their viscoelastic response is straightforward for affine deformations that are uniform over all length scales, but when affinity fails, as has been observed experimentally, modelling becomes challenging. Here we introduce a numerical methodology to predict the stea… ▽ More Disordered fibre networks are ubiquitous in nature and have a wide range of industrial applications as novel biomaterials. Predicting their viscoelastic response is straightforward for affine deformations that are uniform over all length scales, but when affinity fails, as has been observed experimentally, modelling becomes challenging. Here we introduce a numerical methodology to predict the steady-state viscoelastic spectra and degree of affinity for disordered fibre networks driven at arbitrary frequencies. Applying this method to a peptide gel model reveals a monotonic increase of the shear modulus as the soft, non-affine normal modes are successively suppressed as the driving frequency increases. In addition to being dominated by fibril bending, these low frequency network modes are also shown to be delocalised. The presented methodology provides insights into the importance of non-affinity in the viscoelastic response of peptide gels, and is easily extendible to all types of fibre networks. △ Less

Submitted 21 December, 2015; originally announced December 2015.

Comments: 5 pages, 4 figures

Journal ref: Soft Matter, 2016,12, 4332-4338

Universality in the morphology and mechanics of coarsening amyloid fibril networks

Authors: Leandro G. Rizzi, David A. Head, Stefan Auer

Abstract: Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in nanotechnology, but their applicability often depends on their mechanical properties for which we currently have no predictive capability. Here we use a peptide model… ▽ More Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in nanotechnology, but their applicability often depends on their mechanical properties for which we currently have no predictive capability. Here we use a peptide model to simulate the formation of amyloid fibril networks, and couple these to elastic network theory to determine their mechanical properties. The simulations reveal that the time-dependence of morphological quantities characterizing the network length scales can be collapsed onto master curves by using a time scaling function that depends on the interaction parameter between the peptides. The same scaling function is used to unveil a universal, non-monotonic dependence of the shear modulus with time. The obtained insight into the structure-function relationship between the peptide building blocks, network morphology and network mechanical properties can aid experimentalists to design amyloid fibril networks with tailored mechanical properties. △ Less

Submitted 24 September, 2014; originally announced September 2014.

Comments: Article (6 pages, 4 figures) + Supplementary Information (6 pages, 6 figures)

Journal ref: Phys. Rev. Lett. 114 (2015) 078102

Non-equilibrium structure and dynamics in a microscopic model of thin film active gels

Authors: D. A. Head, W. J. Briels, G. Gompper

Abstract: In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to quantify the relationship between individual motors plus filaments to organisation and dynamics on molecular and supra-molecular length scales. Here we present resul… ▽ More In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to quantify the relationship between individual motors plus filaments to organisation and dynamics on molecular and supra-molecular length scales. Here we present results of extensive numerical simulations of active gels where the motors and filaments are confined between two infinite parallel plates. Thermal fluctuations and excluded-volume interactions between filaments are included. A systematic variation of rates for motor motion, attachment and detachment, including a differential detachment rate from filament ends, reveals a range of non-equilibrium behaviour. Strong motor binding produces structured filament aggregates that we refer to as asters, bundles or layers, whose stability depends on motor speed and differential end-detachment. The gross features of the dependence of the observed structures on the motor rate and the filament concentration can be captured by a simple one-filament model. Loosely bound aggregates exhibit super-diffusive mass transport, where filament translocation scales with lag time with non-unique exponents that depend on motor kinetics. An empirical data collapse of filament speed as a function of motor speed and end-detachment is found, suggesting a dimensional reduction of the relevant parameter space. We conclude by discussing the perspectives of microscopic modelling in the field of active gels. △ Less

Submitted 26 February, 2014; v1 submitted 9 October, 2013; originally announced October 2013.

Comments: 11 pages, 13 figures. Extended parameter range and clarification. To appear in Phys. Rev. E

Journal ref: Phys. Rev. E 89, 032705 (2014)

Local mechanical response in semiflexible polymer networks subjected to an axisymmetric prestress

Authors: D. A. Head, D. Mizuno

Abstract: Analytical and numerical calculations are presented for the mechanical response of fiber networks in a state of axisymmetric prestress, in the limit where geometric non-linearities such as fiber rotation are negligible. This allows us to focus on the anisotropy deriving purely from the non-linear force-extension curves of individual fibers. The number of independent elastic coefficients for isotro… ▽ More Analytical and numerical calculations are presented for the mechanical response of fiber networks in a state of axisymmetric prestress, in the limit where geometric non-linearities such as fiber rotation are negligible. This allows us to focus on the anisotropy deriving purely from the non-linear force-extension curves of individual fibers. The number of independent elastic coefficients for isotropic, axisymmetric and fully anisotropic networks are enumerated, before deriving expressions for the response to a locally applied force that can be tested against e.g. microrheology experiments. Localised forces can generate anisotropy away from the point of application, so numerical integration of non-linear continuum equations is employed to determine the stress field, and induced mechanical anisotropy, at points located directly behind and in front of a force monopole. Results are presented for the wormlike chain model in normalised forms, allowing them to be easily mapped to a range of systems. Finally, the relevance of these findings to naturally occurring systems and directions for future investigation are discussed. △ Less

Submitted 21 August, 2013; v1 submitted 13 February, 2013; originally announced February 2013.

Comments: 11 pages; 10 figures. To appear in Phys. Rev. E

Journal ref: Phys. Rev. E 88, 022717 (2013)

Linear surface roughness growth and flow smoothening in a three-dimensional biofilm model

Authors: D. A. Head

Abstract: The sessile microbial communities known as biofilms exhibit varying architectures as environmental factors are varied, which for immersed biofilms includes the shear rate of the surrounding flow. Here we modify an established agent-based biofilm model to include affine flow, and employ it to analyse the growth of surface roughness of single-species, three-dimensional biofilms. We find linear growt… ▽ More The sessile microbial communities known as biofilms exhibit varying architectures as environmental factors are varied, which for immersed biofilms includes the shear rate of the surrounding flow. Here we modify an established agent-based biofilm model to include affine flow, and employ it to analyse the growth of surface roughness of single-species, three-dimensional biofilms. We find linear growth laws for surface geometry in both horizontal and vertical directions, and measure the thickness of the active surface layer, which is shown to anti-correlate with roughness. Flow is shown to monotonically reduce surface roughness without affecting the thickness of the active layer. We argue that the rapid roughening is due to non-local surface interactions mediated by the nutrient field, which are curtailed when advection competes with diffusion. We further argue the need for simplified models to elucidate the underlying mechanisms coupling flow to growth. △ Less

Submitted 21 August, 2013; v1 submitted 30 October, 2012; originally announced October 2012.

Comments: 11 pages, 11 figures. To appear in Phys. Rev. E

Journal ref: Phys. Rev. E 88, 032702 (2013)

Spindles and active vortices in a model of confined filament-motor mixtures

Authors: David A. Head, W. J. Briels, Gerhard Gompper

Abstract: Robust self-organization of subcellular structures is a key principle governing the dynamics and evolution of cellular life. In fission yeast cells undergoing division, the mitotic spindle spontaneously emerges from the interaction of microtubules, motor proteins and the confining cell walls, and asters and vortices have been observed to self-assemble in quasi-two dimensional microtubule-kinesin a… ▽ More Robust self-organization of subcellular structures is a key principle governing the dynamics and evolution of cellular life. In fission yeast cells undergoing division, the mitotic spindle spontaneously emerges from the interaction of microtubules, motor proteins and the confining cell walls, and asters and vortices have been observed to self-assemble in quasi-two dimensional microtubule-kinesin assays. Their is no clear microscopic picture of the role of the active motors driving this pattern formation, and the relevance of continuum modeling to filament-scale structures remains uncertain. Here we present results of numerical simulations of a discrete filament-motor protein model confined to a pressurised cylindrical box. Stable spindles, nematic configurations, asters and high-density semi-asters spontaneously emerge, the latter pair having also been observed in cytosol confined within emulsion droplets. State diagrams are presented delineating each stationary state as the pressure, motor speed and motor density are varied. We further highlight a parameter regime where vortices form exhibiting collective rotation of all filaments, but have a finite life-time before contracting to a semi-aster. Quantifying the distribution of life-times suggests this contraction is a Poisson process. Equivalent systems with fixed volume exhibit persistent vortices with stochastic switching in the direction of rotation, with switching times obeying similar statistics to contraction times in pressurised systems. Furthermore, we show that increasing the detachment rate of motors from filament plus-ends can both destroy vortices and turn some asters into vortices. Based on our findings we argue the need for a deeper understanding of the microscopic activities underpinning macroscopic self-organization in active gels and urge further experiments to help bridge these lengths. △ Less

Submitted 22 July, 2011; originally announced July 2011.

Comments: 10 pages, 12 figures

Journal ref: BMC Biophysics 4, 18 (2011)

Microscopic basis for pattern formation and anomalous transport in two-dimensional active gels

Authors: David A. Head, Gerhard Gompper, W. J. Briels

Abstract: Active gels are a class of biologically-relevant material containing embedded agents that spontaneously generate forces acting on a sparse filament network. In vitro experiments of protein filaments and molecular motors have revealed a range of non- equilibrium pattern formation resulting from motor motion along filament tracks, and there are a number of hydrodynamic models purporting to describe… ▽ More Active gels are a class of biologically-relevant material containing embedded agents that spontaneously generate forces acting on a sparse filament network. In vitro experiments of protein filaments and molecular motors have revealed a range of non- equilibrium pattern formation resulting from motor motion along filament tracks, and there are a number of hydrodynamic models purporting to describe such systems. Here we present results of extensive simulations designed to elucidate the microscopic basis underpinning macroscopic flow in active gels. Our numerical scheme includes thermal fluctuations in filament positions, excluded volume interactions, and filament elasticity in the form of bending and stretching modes. Motors are represented individually as bipolar springs governed by rate-based rules for attachment, detachment and unidirectional motion of motor heads along the filament contour. We systematically vary motor density and speed, and uncover parameter regions corresponding to unusual statics and dynamics which overlap but do not coincide. The anomalous statics arise at high motor densities and take the form of end-bound localized filament bundles for rapid motors, and extended clusters exhibiting enhanced small-wavenumber density fluctuations and power-law cluster-size distributions for slow, processive motors. Anomalous dynamics arise for slow, processive motors over a range of motor densities, and are most evident as superdiffusive mass transport, which we argue is the consequence of a form of effective self-propulsion resulting from the polar coupling between motors and filaments. △ Less

Submitted 19 November, 2010; v1 submitted 10 September, 2010; originally announced September 2010.

Comments: 14 pages, 17 figures. Minor clarifications and updated/additional references. To appear in Soft Matter

Journal ref: Soft Matter 7, 3116 (2011)

Large-scale structure from superdiffusion in a driven dissipative system

Authors: David A. Head, Hajime Tanaka

Abstract: A system far from equilibrium is characterized by unconventional many-body dynamical effects, which can lead to anomalous density fluctuations and mass transport. Interestingly, these structural and dynamic features often emerge simultaneously in driven dissipative systems. Here we seek an origin of their co-existence by numerical simulations of a two-dimensional driven granular gas. We reveal a c… ▽ More A system far from equilibrium is characterized by unconventional many-body dynamical effects, which can lead to anomalous density fluctuations and mass transport. Interestingly, these structural and dynamic features often emerge simultaneously in driven dissipative systems. Here we seek an origin of their co-existence by numerical simulations of a two-dimensional driven granular gas. We reveal a causal link between superdiffusive transport and giant density fluctuations. The kinetic dissipation upon particle collisions depends on the relative velocity of colliding particles, and is responsible for the self-generated large-scale persistent directional motion of particles that underlies the link between structure and transport. This scenario is supported by a simple scaling argument. △ Less

Submitted 8 March, 2010; originally announced March 2010.

Comments: 4 pages, 4 figures + 1 table.

Non-local fluctuation correlations in active gels

Authors: D. A. Head, D. Mizuno

Abstract: Many active materials and biological systems are driven far from equilibrium by embedded agents that spontaneously generate forces and distort the surrounding material. Probing and characterizing these athermal fluctuations is essential for understanding the properties and behaviors of such systems. Here we present a mathematical procedure to estimate the local action of force-generating agents fr… ▽ More Many active materials and biological systems are driven far from equilibrium by embedded agents that spontaneously generate forces and distort the surrounding material. Probing and characterizing these athermal fluctuations is essential for understanding the properties and behaviors of such systems. Here we present a mathematical procedure to estimate the local action of force-generating agents from the observed fluctuating displacement fields. The active agents are modeled as oriented force dipoles or isotropic compression foci, and the matrix on which they act is assumed to be either a compressible elastic continuum or a coupled network-solvent system. Correlations at a single point and between points separated by an arbitrary distance are obtained, giving a total of three independent fluctuation modes that can be tested with microrheology experiments. Since oriented dipoles and isotropic compression foci give different contributions to these fluctuation modes, ratiometric analysis allows us characterize the force generators. We also predict and experimentally find a high-frequency ballistic regime, arising from individual force generating events in the form of the slow build-up of stress followed by rapid but finite decay. Finally, we provide a quantitative statistical model to estimate the mean filament tension from these athermal fluctuations, which leads to stiffening of active networks. △ Less

Submitted 18 March, 2010; v1 submitted 18 February, 2010; originally announced February 2010.

Comments: 12 pages, 7 figures; some clarifications and ammended figure notation.

Critical scaling and aging in cooling systems near the jamming transition

Authors: D. A. Head

Abstract: We conduct athermal simulations of freely-cooling, viscous soft spheres around the jamming transition density φ_{J}, and find evidence for a growing length ξ(t) that governs relaxation to mechanical equilibrium. ξ(t) is manifest in both the velocity correlation function, and the spatial correlations in a scalar measure of local force balance which we define. Data for different densities φcan be… ▽ More We conduct athermal simulations of freely-cooling, viscous soft spheres around the jamming transition density φ_{J}, and find evidence for a growing length ξ(t) that governs relaxation to mechanical equilibrium. ξ(t) is manifest in both the velocity correlation function, and the spatial correlations in a scalar measure of local force balance which we define. Data for different densities φcan be collapsed onto two master curves by scaling ξ(t) and t by powers of |φ-φ_{J}|, indicative of critical scaling. Furthermore, particle transport for φ>φ_{J} exhibits aging and superdiffusion similar to a range of soft matter experiments, suggesting a common origin. Finally, we explain how ξ(t) at late times maps onto known behavior away from φ_{J}. △ Less

Submitted 1 April, 2009; originally announced April 2009.

Comments: 5 pages, 5 figures

Journal ref: Phys. Rev. Lett. 102, 138001 (2009)

Well defined transition to gel-like aggregates of attractive athermal particles

Authors: D. A. Head

Abstract: In an attempt to extend the range of model jamming transitions, we simulate systems of athermal particles which attract when slightly overlapping. Following from recent work on purely repulsive systems, dynamics are neglected and relaxation performed via a potential energy minimisation algorithm. Our central finding is of a transition to a low-density tensile solid which is sharp in the limit of… ▽ More In an attempt to extend the range of model jamming transitions, we simulate systems of athermal particles which attract when slightly overlapping. Following from recent work on purely repulsive systems, dynamics are neglected and relaxation performed via a potential energy minimisation algorithm. Our central finding is of a transition to a low-density tensile solid which is sharp in the limit of infinite system size. The critical density depends on the range of the attractive regime in the pair-potential. Furthermore, solidity is shown to be related to the coordination number of the packing according to the approximate constraint-counting scheme known as Maxwell counting, although more corrections need to be considered than with the repulsive-only case, as explained. We finish by discussing how the numerical difficulties encountered in this work could be overcome in future studies. △ Less

Submitted 20 February, 2007; v1 submitted 3 January, 2007; originally announced January 2007.

Comments: 5 pages, 5 figs, Maxwell counting argument clarified and limits of simulation method explained. To appear in Euro. Phys. J. E

Volume-controlled buckling of thin elastic shells: Application to crusts formed on evaporating partially-wetted droplets

Authors: D. A. Head

Abstract: Motivated by the buckling of glassy crusts formed on evaporating droplets of polymer and colloid solutions, we numerically model the deformation and buckling of spherical elastic caps controlled by varying the volume between the shell and the substrate. This volume constraint mimics the incompressibility of the unevaporated solvent. Discontinuous buckling is found to occur for sufficiently thin… ▽ More Motivated by the buckling of glassy crusts formed on evaporating droplets of polymer and colloid solutions, we numerically model the deformation and buckling of spherical elastic caps controlled by varying the volume between the shell and the substrate. This volume constraint mimics the incompressibility of the unevaporated solvent. Discontinuous buckling is found to occur for sufficiently thin and/or large contact angle shells, and robustly takes the form of a single circular region near the boundary that `snaps' to an inverted shape, in contrast to externally pressurised shells. Scaling theory for shallow shells is shown to well approximate the critical buckling volume, the subsequent enlargement of the inverted region and the contact line force. △ Less

Submitted 27 July, 2006; originally announced July 2006.

Comments: 7 pages in J. Phys. Cond. Mat. spec; 4 figs (2 low-quality to reach LANL's over-restrictive size limits; ask for high-detailed versions if required)

Modeling the elastic deformation of polymer crusts formed by sessile droplet evaporation

Authors: D. A. Head

Abstract: Evaporating droplets of polymer or colloid solution may produce a glassy crust at the liquid-vapour interface, which subsequently deforms as an elastic shell. For sessile droplets, the known radial outward flow of solvent is expected to generate crusts that are thicker near the pinned contact line than the apex. Here we investigate, by non-linear quasi-static simulation and scaling analysis, the… ▽ More Evaporating droplets of polymer or colloid solution may produce a glassy crust at the liquid-vapour interface, which subsequently deforms as an elastic shell. For sessile droplets, the known radial outward flow of solvent is expected to generate crusts that are thicker near the pinned contact line than the apex. Here we investigate, by non-linear quasi-static simulation and scaling analysis, the deformation mode and stability properties of elastic caps with a non-uniform thickness profile. By suitably scaling the mean thickness and the contact angle between crust and substrate, we find data collapse onto a master curve for both buckling pressure and deformation mode, thus allowing us to predict when the deformed shape is a dimple, mexican hat, and so on. This master curve is parameterised by a dimensionless measure of the non-uniformity of the shell. We also speculate on how overlapping timescales for gelation and deformation may alter our findings. △ Less

Submitted 9 July, 2006; v1 submitted 2 December, 2005; originally announced December 2005.

Comments: 8 pages, 7 figs. Some extra clarification of a few points, and minor corrections. To appear in Phys. Rev. E

The mechanical response of semiflexible networks to localized perturbations

Authors: D. A. Head, A. J. Levine, F. C. MacKintosh

Abstract: Previous research on semiflexible polymers including cytoskeletal networks in cells has suggested the existence of distinct regimes of elastic response, in which the strain field is either uniform (affine) or non-uniform (non-affine) under external stress. Associated with these regimes, it has been further suggested that a new fundamental length scale emerges, which characterizes the scale for t… ▽ More Previous research on semiflexible polymers including cytoskeletal networks in cells has suggested the existence of distinct regimes of elastic response, in which the strain field is either uniform (affine) or non-uniform (non-affine) under external stress. Associated with these regimes, it has been further suggested that a new fundamental length scale emerges, which characterizes the scale for the crossover from non-affine to affine deformations. Here, we extend these studies by probing the response to localized forces and force dipoles. We show that the previously identified nonaffinity length [D.A. Head et al. PRE 68, 061907 (2003).] controls the mesoscopic response to point forces and the crossover to continuum elastic behavior at large distances. △ Less

Submitted 20 September, 2005; v1 submitted 27 May, 2005; originally announced May 2005.

Comments: 16 pages, 18 figures; substantial changes to text and figures to clarify the crossover to continuum elasticity and the role of finite-size effects

A mean field description of jamming in non-cohesive frictionless particulate systems

Authors: D. A. Head

Abstract: A theory for kinetic arrest in isotropic systems of repulsive, radially-interacting particles is presented that predicts exponents for the scaling of various macroscopic quantities near the rigidity transition that are in agreement with simulations, including the non-trivial shear exponent. Both statics and dynamics are treated in a simplified, one-particle level description, and coupled via the… ▽ More A theory for kinetic arrest in isotropic systems of repulsive, radially-interacting particles is presented that predicts exponents for the scaling of various macroscopic quantities near the rigidity transition that are in agreement with simulations, including the non-trivial shear exponent. Both statics and dynamics are treated in a simplified, one-particle level description, and coupled via the assumption that kinetic arrest occurs on the boundary between mechanically stable and unstable regions of the static parameter diagram. This suggests the arrested states observed in simulations are at (or near) an elastic buckling transition. Some additional numerical evidence to confirm the scaling of microscopic quantities is also provided. △ Less

Submitted 19 June, 2005; v1 submitted 17 April, 2005; originally announced April 2005.

Comments: 9 pages, 3 figs; additional clarification of different elastic moduli exponents, plus typo fix. To appear in PRE

First order rigidity transition and multiple stability regimes for random networks with internal stresses

Authors: D. A. Head

Abstract: By applying effective medium-style calculations to random spring networks, we demonstrate that internal stresses fundamentally alter the nature of the rigidity transition in disordered materials, changing it from continuous to first-order and increasing the mean coordination number z at which rigidity first occurs. Furthermore, we predict the existence of a novel stability regime at low z when t… ▽ More By applying effective medium-style calculations to random spring networks, we demonstrate that internal stresses fundamentally alter the nature of the rigidity transition in disordered materials, changing it from continuous to first-order and increasing the mean coordination number z at which rigidity first occurs. Furthermore, we predict the existence of a novel stability regime at low z when the distribution of stresses is asymmetric. Means of verifying these predictions are suggested. △ Less

Submitted 18 March, 2005; originally announced March 2005.

Comments: 9 pages in JPhysA-spec, 2 figs

Journal ref: J. Phys. A 37, 10771 (2004)

Distinct regimes of elastic response and deformation modes of cross-linked cytoskeletal and semiflexible polymer networks

Authors: D. A. Head, A. J. Levine, F. C. MacKintosh

Abstract: Semiflexible polymers such as filamentous actin play a vital role in the mechanical behavior of cells, yet the basic properties of cross-linked F-actin networks remain poorly understood. To address this issue, we have performed numerical studies of the linear response of homogeneous and isotropic two-dimensional networks subject to an applied strain at zero temperature. The elastic moduli are fo… ▽ More Semiflexible polymers such as filamentous actin play a vital role in the mechanical behavior of cells, yet the basic properties of cross-linked F-actin networks remain poorly understood. To address this issue, we have performed numerical studies of the linear response of homogeneous and isotropic two-dimensional networks subject to an applied strain at zero temperature. The elastic moduli are found to vanish for network densities at a rigidity percolation threshold. For higher densities, two regimes are observed: one in which the deformation is predominantly affine and the filaments stretch and compress; and a second in which bending modes dominate. We identify a dimensionless scalar quantity, being a combination of the material length scales, that specifies to which regime a given network belongs. A scaling argument is presented that approximately agrees with this crossover variable. By a direct geometric measure, we also confirm that the degree of affinity under strain correlates with the distinct elastic regimes. We discuss the implications of our findings and suggest possible directions for future investigations. △ Less

Submitted 7 October, 2003; v1 submitted 14 August, 2003; originally announced August 2003.

Comments: New discussion on possible consequences of orienting and/or rigid crosslinks; some other minor corrections. To appear in Phys. Rev. E