Search

Helices are the quintessential geometric motif of microscale self-assembly, from $\alpha$-helices in proteins to double helices in DNA. Assembly of the helical geometry of biopolymers is a foundational step in a hierarchy of structure that eventually leads to biological activity. Simulating self-assembly in a simplified and controlled setting allows us to probe the relevance of the solvent as a component of the system of collaborative processes governing biomaterials. Using a simulation technique based on the morphometric approach to solvation, we performed computer experiments which fold a short open flexible tube, modelling a biopolymer in an aqueous environment, according to the interaction of the tube with the solvent alone. Different fluid environments may favour quite different solute geometry: We find an array of helical geometries that self-assemble depending on the solvent conditions, including overhand knot shapes and symmetric double helices where the strand folds back on itself. Interestingly these shapes-in all their variety-are energetically favoured over the $\alpha$-helix. In differentiating the role of solvation in self-assembly our study helps illuminate the energetic background scenery in which all soluble biomolecules live, indeed our results demonstrate that the solvent is capable of quite fundamental rearrangements even up to tying a simple overhand knot.

We consider the problem of building non-invertible quantum symmetries (as characterized by actions of unitary fusion categories) on noncommutative tori. We introduce a general method to construct actions of fusion categories on inductive limit C*-algberas using finite dimenionsal data, and then apply it to obtain AT-actions of arbitrary Haagerup-Izumi categories on noncommutative 2-tori, of the even part of the $E_{8}$ subfactor on a noncommutative 3-torus, and of $\text{PSU}(2)_{15}$ on a noncommutative 4-torus.

Diagrams enable the use of various algebraic and geometric tools for analysing and classifying knots. In this paper we introduce a new diagrammatic representation of triply periodic entangled structures (TP tangles), which are embeddings of simple curves in $\mathbb{R}^3$ that are invariant under translations along three non-coplanar axes. As such, these entanglements can be seen as preimages of links embedded in the 3-torus $\mathbb{T}^3 = \mathbb{S}^1 \times \mathbb{S}^1 \times \mathbb{S}^1$ in its universal cover $\mathbb{R}^3$, where two non-isotopic links in $\mathbb{T}^3$ may possess the same TP tangle preimage. We consider the equivalence of TP tangles in $\mathbb{R}^3$ through the use of diagrams representing links in $\mathbb{T}^3$. These diagrams require additional moves beyond the classical Reidemeister moves, which we define and show that they preserve ambient isotopies of links in $\mathbb{T}^3$. The final definition of a tridiagram of a link in $\mathbb{T}^3$ allows us to then consider additional notions of equivalence relating non-isotopic links in $\mathbb{T}^3$ that possess the same TP tangle preimage., Comment: Corrections

We present fast simulation methods for the self-assembly of complex shapes in two dimensions. The shapes are modeled via a general boundary curve and interact via a standard volume term promoting overlap and an interpenetration penalty. To efficiently realize the Gibbs measure on the space of possible configurations we employ the hybrid Monte Carlo algorithm together with a careful use of signed distance functions for energy evaluation. Motivated by the self-assembly of identical coat proteins of the tobacco mosaic virus which assemble into a helical shell, we design a particular nonconvex 2D model shape and demonstrate its robust self-assembly into a unique final state. Our numerical experiments reveal two essential prerequisites for this self-assembly process: blocking and matching (i.e., local repulsion and attraction) of different parts of the boundary; and nonconvexity and handedness of the shape.

Acute lymphoblastic leukemia (ALL) is a heterogeneous hematologic malignancy involving the abnormal proliferation of immature lymphocytes, accounting for most pediatric cancer cases. ALL management in children has seen great improvement in the last decades thanks to better understanding of the disease leading to improved treatment strategies evidenced through clinical trials. Commonly a first course of chemotherapy (induction phase) is administered, followed by treatment with a combination of anti-leukemia drugs. A measure of the efficacy early in the course of therapy is minimal residual disease (MRD). MRD quantifies residual tumor cells and indicates the effectiveness of the treatment over the course of therapy. MRD positivity is defined for values of MRD greater than 0.01%, yielding left-censored observations. We propose a Bayesian model to study the relationship between patient features and MRD observed at two time points during the induction phase. Specifically, we model the observed MRD values via an auto-regressive model, accounting for left-censoring of the data and for the fact that some patients are already in remission after the induction phase. Patient characteristics are included in the model via linear regression terms. In particular, patient-specific drug sensitivity based on ex-vivo assays of patient samples is exploited to identify groups of subjects with similar profiles. We include this information as a covariate in the model for MRD. We adopt horseshoe priors for the regression coefficients to perform variable selection to identify important covariates. We fit the proposed approach to data from three prospective pediatric ALL clinical trials carried out at the St. Jude Children's Research Hospital. Our results highlight that drug sensitivity profiles and leukemic subtypes play an important role in the response to induction therapy as measured by serial MRD measures.

Magnetic fields play an important role in plasma dynamics, yet it is a quantity difficult to measure accurately with physical probes, whose presence disturbs the very field they measure. The Faraday rotation of a polarized beam of light provides a mechanism to measure the magnetic field without disturbing the dynamics, and has been used with great success in astrophysics and high energy density plasma science, where physical probes cannot be used. However, the rotation is typically small, which degrades the accuracy of the measurement. Paradoxically, the main source of error is the probe beam itself. Since polarization cannot be measured directly, detectors rely on a polarizer to measure a small change in beam intensity instead. In this work, we show how suppress the beam intensity that is not part of the Faraday rotation signal by taking forming an optical derivative. Since the rotation measurement is now strictly proportional to the beam intensity, the system allows to amplify the rotation measurement simply by increasing the laser power.

Motivated by the Freed-Hopkins-Teleman theorem we study graded equivariant higher twists of $K$-theory for the groups $G = SU(n)$ induced by exponential functors. We compute the rationalisation of these groups for all $n$ and all non-trivial functors $F$ using the Mayer-Vietoris spectral sequence. Similar to the classical case only the $K$-theory in degree $\dim(G)$ is non-trivial and the non-vanishing group is a quotient of a localisation of the representation ring $R(G) \otimes \mathbb{Q}$ by a higher fusion ideal $J_{F,\mathbb{Q}}$. We give generators for this ideal and prove that these can be obtained as derivatives of a potential., Comment: 33 pages, one figure, minor mistake fixed in Section 3.1.1, setting has been adjusted to exponential functors that are symmetric monoidal and take values in graded vector spaces

Superhydrophobic materials are often inspired by nature, whereas metamaterials are engineered to have properties not usually found in naturally occurring materials. In both cases, the key that unlocks their unique properties is structure. Here, we show that a negative Poisson's ratio (auxetic) mechanical metamaterial is capable of transforming into a unique type of superhydrophobic material. When stretched its surface has the counterintuitive property that it also expands in the orthogonal lateral direction. We model the change in the solid surface fraction as strain is applied and show it decreases as the space between solid elements of the auxetic lattice expands. This results in a unique dependence of the superhydrophobicity on strain. We construct experimental models illustrating the relationship between different states of strain and superhydrophobicity as the lattice structure transitions from an auxetic to a conventional (positive Poisson's ratio) one. The principles we have discovered offer a new approach to designing superhydrophobic materials for self-cleaning surfaces, droplet transportation, droplet encapsulation and oil-water separation., Comment: 10 pages, 4 figures, 13 page supplementary information

We present the first results from the JWST ASPIRE program (A SPectroscopic survey of biased halos In the Reionization Era). This program represents an imaging and spectroscopic survey of 25 reionization-era quasars and their environments by utilizing the unprecedented capabilities of NIRCam Wide Field Slitless Spectroscopy (WFSS) mode. ASPIRE will deliver the largest ($\sim280~{\rm arcmin}^2$) galaxy redshift survey at 3-4 $\mu$m among JWST Cycle-1 programs and provide extensive legacy values for studying the formation of the earliest supermassive black holes (SMBHs), the assembly of galaxies, early metal enrichment, and cosmic reionization. In this first ASPIRE paper, we report the discovery of a filamentary structure traced by the luminous quasar J0305-3150 and ten [OIII] emitters at $z=6.6$. This structure has a 3D galaxy overdensity of $\delta_{\rm gal}=12.6$ over 637 cMpc$^3$, one of the most overdense structures known in the early universe, and could eventually evolve into a massive galaxy cluster. Together with existing VLT/MUSE and ALMA observations of this field, our JWST observations reveal that J0305-3150 traces a complex environment where both UV-bright and dusty galaxies are present, and indicate that the early evolution of galaxies around the quasar is not simultaneous. In addition, we discovered 31 [OIII] emitters in this field at other redshifts, $5.3

Studies of rest-frame optical emission in quasars at $z>6$ have historically been limited by the wavelengths accessible by ground-based telescopes. The James Webb Space Telescope (JWST) now offers the opportunity to probe this emission deep into the reionization epoch. We report the observations of eight quasars at $z>6.5$ using the JWST/NIRCam Wide Field Slitless Spectroscopy, as a part of the ''A SPectroscopic survey of biased halos In the Reionization Era (ASPIRE)" program. Our JWST spectra cover the quasars' emission between rest frame $\sim$ 4100 and 5100 \r{A}. The profiles of these quasars' broad H$\beta$ emission lines span a FWHM from 3000 to 6000 $\rm{km~s^{-1}}$. The H$\beta$-based virial black hole (BH) masses, ranging from 0.6 to 2.1 billion solar masses, are generally consistent with their MgII-based BH masses. The new measurements based on the more reliable H$\beta$ tracer thus confirm the existence of billion solar-mass BHs in the reionization epoch. In the observed [OIII] $\lambda\lambda$4960,5008 doublets of these luminous quasars, broad components are more common than narrow core components ($\le~1200~\rm{km~s^{-1}}$), and only one quasar shows stronger narrow components than broad. Two quasars exhibit significantly broad and blueshifted [OIII] emission, thought to trace galactic-scale outflows, with median velocities of $-610~\rm{km~s^{-1}}$ and $-1430~\rm{km~s^{-1}}$ relative to the [CII] $158\,\mu$m line. All eight quasars show strong optical FeII emission, and follow the Eigenvector 1 relations defined by low-redshift quasars. The entire ASPIRE program will eventually cover 25 quasars and provide a statistical sample for the studies of the BHs and quasar spectral properties., Comment: 13 pages, 4 figures, accepted for publication in ApJL

Framework materials and their deformations provide a compelling relation between materials science and algebraic geometry. Physical distance constraints within the material transform into polynomial constraints, making algebraic geometry and associated numerical strategies feasible for finding equilibrium configurations and deformation pathways. In this paper, we build the necessary geometric formulations and numerical strategies to explore the mechanics of two examples of 3-periodic tensegrity frameworks through non-linear optimization, eventually showing that the structures are auxetic by multiple definitions., Comment: 20 pages, 10 figures

This paper surveys the long-standing connections and impact between Vaughan Jones's theory of subfactors and various topics in mathematical physics, namely statistical mechanics,quantum field theory,quantum information and two-dimensional conformal field theory., Comment: 22 pages, 1 figure. To appear in an issue of the Bulletin of the AMS, dedicated to the mathematical legacy of Vaughan Jones

The orientation between a star's spin axis and a planet's orbital plane provides valuable information about the system's formation and dynamical history. For non-transiting planets at wide separations, true stellar obliquities are challenging to measure, but lower limits on spin-orbit orientations can be determined from the difference between the inclination of the star's rotational axis and the companion's orbital plane ($\Delta i$). We present results of a uniform analysis of rotation periods, stellar inclinations, and obliquities of cool stars (SpT $\gtrsim$ F5) hosting directly imaged planets and brown dwarf companions. As part of this effort, we have acquired new $v \sin i_*$ values for 22 host stars with the high-resolution Tull spectrograph at the Harlan J. Smith telescope. Altogether our sample contains 62 host stars with rotation periods, most of which are newly measured using light curves from the Transiting Exoplanet Survey Satellite. Among these, 53 stars have inclinations determined from projected rotational and equatorial velocities, and 21 stars predominantly hosting brown dwarfs have constraints on $\Delta i$. Eleven of these (52$^{+10}_{-11}$% of the sample) are likely misaligned, while the remaining ten host stars are consistent with spin-orbit alignment. As an ensemble, the minimum obliquity distribution between 10-250 AU is more consistent with a mixture of isotropic and aligned systems than either extreme scenario alone--pointing to direct cloud collapse, formation within disks bearing primordial alignments and misalignments, or architectures processed by dynamical evolution. This contrasts with stars hosting directly imaged planets, which show a preference for low obliquities. These results reinforce an emerging distinction between the orbits of long-period brown dwarfs and giant planets in terms of their stellar obliquities and orbital eccentricities., Comment: AJ, accepted

This paper shows analytically and numerically that a vortex plate coupled to a neutral density filter can deliver a true optical derivative when placed at the focal plane of a $2f$ lens pair. This technique turns spatial variations in intensity into an intensity, which square root is the spatial derivative of the initial intensity variation. More surprisingly, it also turns any spatial variations in phase into an intensity, which square root is the spatial derivative of the initial phase variation. Since the optical derivative drops the DC component of the signal, it is possible to measure the full electron plasma turbulence spectrum optically, without using any interferometer.

In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinement. We hypothesized that the topological connectivity of protein structures is invariant, and they are distinctive for the purpose of protein identification from distorted data presented in volume densities. Three-dimensional densities of a protein or a complex from simulated tomographic volumes were transformed into mathematical graphs as observables. We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. A similarity score between the graphs from the simulated volumes and the graphs transformed from the physical protein structures in point data was calculated by comparing their network theory order parameters including node degrees, betweenness centrality, and graph densities. By capturing the essential topological features defining the heterogeneous morphologies of a network, we were able to accurately identify proteins and homo-multimeric complexes from ten topologically distinctive samples without realistic noise added. Our approach empowers future developments of tomogram processing by providing pattern mining with interpretability, to enable the classification of single-domain protein native topologies as well as distinct single-domain proteins from multimeric complexes within noisy volumes., Comment: submitted for peer review

A coasting hadron beam with an elliptical transverse profile, uniform charge density, and small transverse four-dimensional (4D) emittance could improve accelerator performance in several contexts. A phase space painting method to generate such a distribution is being tested in the Spallation Neutron Source (SNS) accumulator ring. A critical component of these efforts is to measure the 4D emittance of the beam during accumulation. The 4D emittance can be reconstructed from measured beam profiles in two ways: in the multi-optics method, the optics between a reconstruction and measurement location are varied; in the fixed-optics method, multiple measurement locations are used without modifying the optics. The fixed-optics method is faster but can lead to large uncertainty in the reconstructed 4D emittance. In this paper, we implement a variant of the multi-optics method using the four available wire-scanners near the SNS target. We also modify the wire-scanner region to reduce the uncertainty of the fixed-optics method. We then demonstrate the usefulness of the fixed-optics method by reconstructing the 4D emittance evolution during accumulation in the SNS ring.

We develop an equivariant Dixmier-Douady theory for locally trivial bundles of $C^*$-algebras with fibre $D \otimes \mathbb{K}$ equipped with a fibrewise $\mathbb{T}$-action, where $\mathbb{T}$ denotes the circle group and $D = \operatorname{End}\left(V\right)^{\otimes \infty}$ for a $\mathbb{T}$-representation $V$. In particular, we show that the group of $\mathbb{T}$-equivariant $*$-automorphisms $\operatorname{Aut}_{\mathbb{T}}(D \otimes \mathbb{K})$ is an infinite loop space giving rise to a cohomology theory $E^*_{D,\mathbb{T}}(X)$. Isomorphism classes of equivariant bundles then form a group with respect to the fibrewise tensor product that is isomorphic to $E^1_{D,\mathbb{T}}(X) \cong [X, B\operatorname{Aut}_{\mathbb{T}}(D \otimes \mathbb{K})]$. We compute this group for tori and compare the case $D = \mathbb{C}$ to the equivariant Brauer group for trivial actions on the base space., Comment: 37 pages, published version (except for a typo in the description of the order structure on page 19 and the proof of Lemma 3.5, which was fixed after publication, and did not change the main result)