arXiv subjects

Philip Nelson

Publications and source records attributed to Philip Nelson.

At least 19 recordsLinked to original sources

arXiv2026

Making Videos Accessible for Blind and Low Vision Users Using a Multimodal Agent Video Player

Video content remains largely inaccessible to blind and low-vision (BLV) users. To address this, we introduce a prototype that leverages a multimodal agent - powered by a novel conversational architecture using a multimodal large language model (MLLM) - to provide BLV users with an interactive, accessible video experience. This Multimodal Agent Video Player (MAVP) demonstrates that an interactive accessibility mode can be added to a video through multilayered prompt orchestration. We describe a user-centered design process involving 18 sessions with BLV users that showed that BLV users do not just want accessibility features, but desire independence and personal agency over the viewing experience. We conducted a qualitative study with an additional 8 BLV participants; in this, we saw that the MAVP's conversational dialogue offers BLV users a sense of personal agency, fostering collaboration and trust. Even in the case of hallucinations, it is meta-conversational dialogues about AI's limitations that can repair trust.

cs.HC↗

arXiv2025

"Does the cafe entrance look accessible? Where is the door?" Towards Geospatial AI Agents for Visual Inquiries

Interactive digital maps have revolutionized how people travel and learn about the world; however, they rely on pre-existing structured data in GIS databases (e.g., road networks, POI indices), limiting their ability to address geo-visual questions related to what the world looks like. We introduce our vision for Geo-Visual Agents--multimodal AI agents capable of understanding and responding to nuanced visual-spatial inquiries about the world by analyzing large-scale repositories of geospatial images, including streetscapes (e.g., Google Street View), place-based photos (e.g., TripAdvisor, Yelp), and aerial imagery (e.g., satellite photos) combined with traditional GIS data sources. We define our vision, describe sensing and interaction approaches, provide three exemplars, and enumerate key challenges and opportunities for future work.

cs.HC↗

arXiv2020

Scientific Discovery by Generating Counterfactuals using Image Translation

Model explanation techniques play a critical role in understanding the source of a model's performance and making its decisions transparent. Here we investigate if explanation techniques can also be used as a mechanism for scientific discovery. We make three contributions: first, we propose a framework to convert predictions from explanation techniques to a mechanism of discovery. Second, we show how generative models in combination with black-box predictors can be used to generate hypotheses (without human priors) that can be critically examined. Third, with these techniques we study classification models for retinal images predicting Diabetic Macular Edema (DME), where recent work showed that a CNN trained on these images is likely learning novel features in the image. We demonstrate that the proposed framework is able to explain the underlying scientific mechanism, thus bridging the gap between the model's performance and human understanding.

cs.CV↗

arXiv2002

The bend stiffness of S-DNA

We formulate and solve a two-state model for the elasticity of nicked, double-stranded DNA that borrows features from both the Worm Like Chain and the Bragg--Zimm model. Our model is computationally simple, and gives an excellent fit to recent experimental data through the entire overstretching transition. The fit gives the first value for the bending stiffness of the overstretched state as about 10 nm*kbt, a value quite different from either B-form or single-stranded DNA.

physics.bio-ph↗

arXiv2002

Theory of High-Force DNA Stretching and Overstretching

Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA. We demonstrate that this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the Discrete Persistent Chain, or ``DPC'') that borrows features from both the FJC and the Wormlike Chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple, and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first values for the elastic constants of the stretched state. In particular we find the effective bend stiffness for DNA in this state to be about 10 nm*kbt, a value quite different from either B-form or single-stranded DNA

physics.bio-ph↗

arXiv2000

Charge-Reversal Instability in Mixed Bilayer Vesicles

Bilayer vesicles form readily from mixtures of charged and neutral surfactants. When such a mixed vesicle binds an oppositely-charged object, its membrane partially demixes: the adhesion zone recruits more charged surfactants from the rest of the membrane. Given an unlimited supply of adhering objects one might expect the vesicle to remain attractive until it was completely covered. Contrary to this expectation, we show that a vesicle can instead exhibit {\it adhesion saturation,} partitioning spontaneously into an attractive zone with definite area fraction, and a repulsive zone. The latter zone rejects additional incoming objects because counterions on the interior of the vesicle migrate there, effectively reversing the membrane's charge. The effect is strongest at high surface charge densities, low ionic strength, and with thin, impermeable membranes. Adhesion saturation in such a situation has recently been observed experimentally [H. Aranda-Espinoza {\it et al.}, {\sl Science} {\bf285} 394--397 (1999)].

cond-mat.soft↗

arXiv1999

Transport of Torsional Stress in DNA

It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional stress requires the DNA to be anchored, forming a limited topological domain, since otherwise it would spin almost freely about its axis. Previous estimates of the rotational drag have, however, neglected the role of small natural bends in the helix backbone. We show how these bends can increase the drag several thousandfold relative to prior estimates, allowing significant torsional stress even in linear, unanchored DNA. The model helps explain several puzzling experimental results on structural transitions induced by transcription of DNA.

cond-mat.soft↗

arXiv1999

Electrostatic Repulsion of Positively Charged Vesicles and Negatively Charged Objects

A positively charged, mixed bilayer vesicle in the presence of negatively charged surfaces (for example, colloidal particles) can spontaneously partition into an adhesion zone of definite area, and another zone that repels additional negative objects. Although the membrane itself has nonnegative charge in the repulsive zone, negative counterions on the interior of the vesicle spontaneously aggregate there, and present a net negative charge to the exterior. Beyond the fundamental result that oppositely charged objects can repel, our mechanism helps explain recent experiments on surfactant vesicles.

cond-mat.soft↗

arXiv1998

Entropic Elasticity of Twist-Storing Polymers

We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to an applied torque through the relation Lk = Tw + Wr. We explore this coupling and find agreement between the predictions of our model and recent experimental results on single lambda-DNA molecules. This analysis affords an experimental determination of the microscopic twist stiffness (averaged over a helix repeat). Quantitative agreement between theory and experiment is obtained using C=109 nm. The theory further predicts a thermal reduction of the effective twist rigidity induced by bend fluctuations. Finally, we find a small reflection of molecular chirality in the experimental data and interpret it in terms of a twist-stretch coupling of the DNA duplex.

cond-mat.soft↗

arXiv1997

Sequence Effects on DNA Entropic Elasticity

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.

cond-mat.soft↗

arXiv1997

Hard Spheres in Vesicles: Curvature-Induced Forces and Particle-Induced Curvature

We explore the interplay of membrane curvature and nonspecific binding due to excluded-volume effects among colloidal particles inside lipid bilayer vesicles. We trapped submicron spheres of two different sizes inside a pear-shaped, multilamellar vesicle and found the larger spheres to be pinned to the vesicle's surface and pushed in the direction of increasing curvature. A simple model predicts that hard spheres can induce shape changes in flexible vesicles. The results demonstrate an important relationship between the shape of a vesicle or pore and the arrangement of particles within it.

cond-mat.soft↗

arXiv1997

Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness

DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional directed walk'. Motivated by a recent experiment on single lambda-DNA molecules [Strick et al., Science 271 (1996) 1835], we formulate the torsional directed walk problem and solve it analytically in the appropriate force regime. Our technique affords a direct physical determination of the microscopic twist stiffness C and twist-stretch coupling D relevant for DNA functionality. The theory quantitatively fits existing experimental data for relative extension as a function of overtwist over a wide range of applied force; fitting to the experimental data yields the numerical values C=120nm and D=50nm. Future experiments will refine these values. We also predict that the phenomenon of reduction of effective twist stiffness by bend fluctuations should be testable in future single-molecule experiments, and we give its analytic form.

cond-mat.soft↗

arXiv1997

New Measurements of DNA Twist Elasticity

The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this new material parameter. We extract its value from a recent experiment. We also present a very simple microscopic theory predicting a value comparable to the one observed. Finally we sketch the effect of constrained twist on entropic elasticity of DNA arising from the connection between Link, Twist, and Writhe.

cond-mat.soft↗

arXiv1997

Elasticity Theory of a Twisted Stack of Plates

We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a macroscopic elasticity theory of DNA to four. We derive an effective twist-stretch energy in terms of the macroscopic stretch epsilon along and relative excess twist sigma about the DNA molecular axis. In addition to the bulk stretch and twist moduli found previously, we obtain a twist-stretch modulus with the following remarkable properties: 1) it vanishes when the radius of the helical curve following the geometric center of each plate is zero, 2) it vanishes with the elastic constant K_{23} that couples compression normal to the plates to a shear strain, if the plates are perpendicular to the molecular axis, and 3) it is nonzero if the plates are tilted relative to the molecular axis. This implies that a laminated helical structure carved out of an isotropic elastic medium will not twist in response to a stretching force, but an isotropic material will twist if it is bent into the shape of a helix.

cond-mat.soft↗

arXiv1997

Dynamically-Stabilized Pores in Bilayer Membranes

Zhelev and Needham have recently created large, quasi-stable pores in artificial lipid bilayer vesicles [Biochim. Biophys. Acta 1147 (1993) 89]. Initially created by electroporation, the pores remain open for up to several seconds before quickly snapping shut. This result is surprising in light of the large line tension for holes in bilayer membranes and the rapid time scale for closure of large pores. We show how pores can be dynamically stabilized via a new feedback mechanism. We also explain quantitatively the observed sudden pore closure as a tangent bifurcation. Finally we show how Zhelev and Needham's experiment can be used to measure accurately the pore line tension, an important material parameter. For their SOPC/CHOL mixture we obtain a line tension of 2.6 10^{-6} erg/cm.

cond-mat.soft↗

arXiv1996

Twist-Stretch Elasticity of DNA

The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this important material parameter. We extract its value from a recent experiment of Strick, et al. and find rough agreement with an independent experimental estimate recently given by Marko. We also present a very simple microscopic theory predicting a value comparable to the one observed.

cond-mat.soft↗

arXiv1996

Direct Determination of DNA Twist-Stretch Coupling

The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this important material parameter. We extract its value from a recent experiment of Strick et al. [Science 271 (1996) 1835] and find rough agreement with an independent experimental estimate recently given by Marko. We also present a very simple microscopic theory predicting a value comparable to the one observed.

cond-mat.soft↗

arXiv1996

Straightening of Thermal Fluctuations in Semi-Flexible Polymers by Applied Tension

We investigate the propagation of a suddenly applied tension along a thermally excited semi-flexible polymer using analytical approximations, scaling arguments and numerical simulation. This problem is inherently non-linear. We find sub-diffusive propagation with a dynamical exponent of 1/4. By generalizing the internal elasticity, we show that tense strings exhibit qualitatively different tension profiles and propagation with an exponent of 1/2.

cond-mat.soft↗