Engineering topics

Kaplan, David L.

Publications and source records attributed to Kaplan, David L..

13 records

DOE OSTI2024

ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model

Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here, we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as the target to enable the discovery of protein materials with superior mechanical properties.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

The NANOGrav 15 yr Data Set: Search for Signals from New Physics

The 15 yr pulsar timing data set collected by the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) shows positive evidence for the presence of a low-frequency gravitational-wave (GW) background. In this paper, we investigate potential cosmological interpretations of this signal, specifically cosmic inflation, scalar-induced GWs, first-order phase transitions, cosmic strings, and domain walls. We find that, with the exception of stable cosmic strings of field theory origin, all these models can reproduce the observed signal. When compared to the standard interpretation in terms of inspiraling supermassive black hole binaries (SMBHBs), many cosmological models seem to provide a better fit resulting in Bayes factors in the range from 10 to 100. However, these results strongly depend on modeling assumptions about the cosmic SMBHB population and, at this stage, should not be regarded as evidence for new physics. Furthermore, we identify excluded parameter regions where the predicted GW signal from cosmological sources significantly exceeds the NANOGrav signal. These parameter constraints are independent of the origin of the NANOGrav signal and illustrate how pulsar timing data provide a new way to constrain the parameter space of these models. Finally, we search for deterministic signals produced by models of ultralight dark matter (ULDM) and dark matter substructures in the Milky Way. We find no evidence for either of these signals and thus report updated constraints on these models. In the case of ULDM, these constraints outperform torsion balance and atomic clock constraints for ULDM coupled to electrons, muons, or gluons.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

A matched-filter approach to radio variability and transients: searching for orphan afterglows in the VAST Pilot Survey

Radio transient searches using traditional variability metrics struggle to recover sources whose evolution time-scale is significantly longer than the survey cadence. Motivated by the recent observations of slowly evolving radio afterglows at gigahertz frequency, we present the results of a search for radio variables and transients using an alternative matched-filter approach. We designed our matched-filter to recover sources with radio light curves that have a high-significance fit to power-law and smoothly broken power-law functions; light curves following these functions are characteristic of synchrotron transients, including ‘orphan’ gamma-ray burst afterglows, which were the primary targets of our search. Applying this matched-filter approach to data from Variables and Slow Transients Pilot Survey conducted using the Australian SKA Pathfinder, we produced five candidates in our search. Subsequent Australia Telescope Compact Array observations and analysis revealed that: one is likely a synchrotron transient; one is likely a flaring active galactic nucleus, exhibiting a flat-to-steep spectral transition over 4 months; one is associated with a starburst galaxy, with the radio emission originating from either star formation or an underlying slowly evolving transient; and the remaining two are likely extrinsic variables caused by interstellar scintillation. The synchrotron transient, VAST J175036.1–181454, has a multifrequency light curve, peak spectral luminosity, and volumetric rate that is consistent with both an off-axis afterglow and an off-axis tidal disruption event; interpreted as an off-axis afterglow would imply an average inverse beaming factor $\langle f^{-1}_{\text{b}} \rangle = 860^{+1980}_{-710}$, or equivalently, an average jet opening angle of $\langle \theta _{\textrm {j}} \rangle = 3^{+4}_{-1}\,$ deg.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A Search for Extragalactic Fast Blue Optical Transients in ZTF and the Rate of AT2018cow-like Transients

We present a search for extragalactic fast blue optical transients (FBOTs) during Phase I of the Zwicky Transient Facility (ZTF). We identify 38 candidates with durations above half-maximum light 1 day < t 1/2 < 12 days, of which 28 have blue ( g – r ≲ –0.2 mag) colors at peak light. Of the 38 transients (28 FBOTs), 19 (13) can be spectroscopically classified as core-collapse supernovae (SNe): 11 (8) H- or He-rich (Type II/IIb/Ib) SNe, 6 (4) interacting (Type IIn/Ibn) SNe, and 2 (1) H&He-poor (Type Ic/Ic-BL) SNe. Two FBOTs (published previously) had predominantly featureless spectra and luminous radio emission: AT2018lug (The Koala) and AT2020xnd (The Camel). Seven (five) did not have a definitive classification: AT 2020bdh showed tentative broad H α in emission, and AT 2020bot showed unidentified broad features and was 10 kpc offset from the center of an early-type galaxy. Ten (eight) have no spectroscopic observations or redshift measurements. We present multiwavelength (radio, millimeter, and/or X-ray) observations for five FBOTs (three Type Ibn, one Type IIn/Ibn, one Type IIb). Additionally, we search radio-survey (VLA and ASKAP) data to set limits on the presence of radio emission for 24 of the transients. All X-ray and radio observations resulted in nondetections; we rule out AT2018cow-like X-ray and radio behavior for five FBOTs and more luminous emission (such as that seen in the Camel) for four additional FBOTs. We conclude that exotic transients similar to AT2018cow, the Koala, and the Camel represent a rare subset of FBOTs and use ZTF’s SN classification experiments to measure the rate to be at most 0.1% of the local core-collapse SN rate.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Generative design of de novo proteins based on secondary-structure constraints using an attention-based diffusion model

We report two generative deep-learning models that predict amino acid sequences and 3D protein structures on the basis of secondary-structure design objectives via either the overall content or the per-residue structure. Both models are robust regarding imperfect inputs and offer de novo design capacity because they can discover new protein sequences not yet discovered from natural mechanisms or systems. The residue-level secondary-structure design model generally yields higher accuracy and more diverse sequences. These findings suggest unexplored opportunities for protein designs and functional outcomes within the vast amino acid sequences beyond known proteins. Our models, based on an attention-based diffusion model and trained on a dataset extracted from experimentally known 3D protein structures, offer numerous downstream applications in the conditional generative design of various biological or engineering systems. Future work could include additional conditioning and an exploration of other functional properties of the generated proteins for various properties beyond structural objectives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Snowmass2021 Cosmic Frontier White Paper: Observational Facilities to Study Dark Matter

We present an overview of future observational facilities that will significantly enhance our understanding of the fundamental nature of dark matter. These facilities span a range of observational techniques including optical/near-infrared imaging and spectroscopy, measurements of the cosmic microwave background, pulsar timing, 21-cm observations of neutral hydrogen at high redshift, and the measurement of gravitational waves. Such facilities are a critical component of a multi-pronged experimental program to uncover the nature of dark matter, while often providing complementary measurements of dark energy, neutrino physics, and inflation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Searching for Gravitational Waves from Cosmological Phase Transitions with the NANOGrav 12.5-Year Dataset

We search for a first-order phase transition gravitational wave signal in 45 pulsars from the NANOGrav 12.5-year dataset. We find that the data can be modeled in terms of a strong first order phase transition taking place at temperatures below the electroweak scale. However, we do not observe any strong preference for a phase-transition interpretation of the signal over the standard astrophysical interpretation in terms of supermassive black hole mergers; but we expect to gain additional discriminating power with future datasets, improving the signal to noise ratio and extending the sensitivity window to lower frequencies. An interesting open question is how well gravitational wave observatories could separate such signals.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Waterproof stretchable optoelectronics

Described herein are flexible and stretchable LED arrays and methods utilizing flexible and stretchable LED arrays. Assembly of flexible LED arrays alongside flexible plasmonic crystals is useful for construction of fluid monitors, permitting sensitive detection of fluid refractive index and composition. Co-integration of flexible LED arrays with flexible photodetector arrays is useful for construction of flexible proximity sensors. Application of stretchable LED arrays onto flexible threads as light emitting sutures provides novel means for performing radiation therapy on wounds.

Rogers, John A.↗

NASA NTRS2019

2900 Square Degree Search for the Optical Counterpart of Short Gamma-Ray Burst GRB 180523B with the Zwicky Transient Facility

There is significant interest in the models for production of short gamma-ray bursts (GRBs). Until now, the number of known short GRBs with multi-wavelength afterglows has been small. While the Fermi GRB Monitor detects many GRBs relative to the Neil Gehrels Swift Observatory, the large localization regions makes the search for counterparts difficult. With the Zwicky Transient Facility (ZTF - part of Palomar Observatory) recently achieving first light, it is now fruitful to use its combination of depth (m (sub AB) approximating 20.6), field of view (approximately 47 square degrees), and survey cadence (every approximately 3 days) to perform Target of Opportunity observations. We demonstrate this capability on GRB 180523B, which was recently announced by the Fermi GRB Monitor as a short GRB. ZTF imaged 2900 square degrees of the localization region, resulting in the coverage of 61.6 percent of the enclosed probability over two nights to a depth of m (sub AB) approximating 20.5. We characterized 14 previously unidentified transients, and none were found to be consistent with a short GRB counterpart. This search with the ZTF shows it is an efficient camera for searching for coarsely localized short GRB and gravitational-wave counterparts, allowing for a sensitive search with minimal interruption to its nominal cadence.

Coughlin, Michael W.↗

NASA NTRS2018

The NANOGrav 11-year Data Set: High-Precision Timing of 45 Millisecond Pulsars

We present high-precision timing data over time spans of up to 11 years for 45 millisecond pulsars observed as part of the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) project, aimed at detecting and characterizing low-frequency gravitational waves. The pulsars were observed with the Arecibo Observatory and/or the Green Bank Telescope at frequencies ranging from 327 MHz to 2.3 GHz. Most pulsars were observed with approximately monthly cadence, and six high-timing-precision pulsars were observed weekly. All were observed at widely separated frequencies at each observing epoch in order to fit for time-variable dispersion delays. We describe our methods for data processing, time-of-arrival (TOA) calculation, and the implementation of a new, automated method for removing outlier TOAs. We fit a timing model for each pulsar that includes spin, astrometric, and (for binary pulsars) orbital parameters; time-variable dispersion delays; and parameters that quantify pulse-profile evolution with frequency. The timing solutions provide three new parallax measurements, two new Shapiro delay measurements, and two new measurements of significant orbital-period variations. We fit models that characterize sources of noise for each pulsar. We find that 11 pulsars show significant red noise, with generally smaller spectral indices than typically measured for non-recycled pulsars, possibly suggesting a different origin. A companion paper uses these data to constrain the strength of the gravitational-wave background

Arzoumanian, Zaven↗

NASA NTRS2006

A Search for the X-ray Counterpart of the Unidentified Gamma-ray Source 3EG J2020+4017 (2CG078+2)

We report observations with the Chandra X-ray Observatory of a field in the gamma-Cygni supernova remnant (SNR78.2+2.1) centered on the cataloged location of the unidentified, bright gamma-ray source 3EG J2020+4017. In this search for an X-ray counterpart to the gamma-ray source, we detected 30 X-ray sources. Of these, we found 17 strong-candidate counterparts in optical (visible through near-infrared) cataloged and an additional 3 through our optical observations. Based upon colors and (for several objects) optical spectra, nearly all the optically identified objects appear to be reddened main-sequence stars: None of the X-ray sources with an optical counterpart is a plausible X-ray counterpart to 3EG J2020+4017-if that gamma-ray source is a spin-powered pulsar. Many of the 10 X-ray sources lacking optical counterparts are likely (extragalactic) active galactic nuclei, based upon the sky density of such sources. Although one of the 10 optically unidentified X-ray sources could be the gamma-ray source, there is no auxiliary evidence supporting such an identification

Weisskopf, Martin↗

NASA NTRS2005

Ex Vivo Growth of Bioengineered Ligaments and Other Tissues

A method of growing bioengineered tissues for use in surgical replacement of damaged anterior cruciate ligaments has been invented. An anterior cruciate ligament is one of two ligaments (the other being the posterior cruciate ligament) that cross in the middle of a knee joint and act to prevent the bones in the knee from sliding forward and backward relative to each other. Anterior cruciate ligaments are frequently torn in sports injuries and traffic accidents, resulting in pain and severe limitations on mobility. By making it possible to grow replacement anterior cruciate ligaments that structurally and functionally resemble natural ones more closely than do totally synthetic replacements, the method could create new opportunities for full or nearly full restoration of functionality in injured knees. The method is also adaptable to the growth of bioengineered replacements for other ligaments (e.g., other knee ligaments as well as those in the hands, wrists, and elbows) and to the production of tissues other than ligaments, including cartilage, bones, muscles, and blood vessels. The method is based on the finding that the histomorphological properties of a bioengineered tissue grown in vitro from pluripotent cells within a matrix are affected by the direct application of mechanical force to the matrix during growth generation. This finding provides important new insights into the relationships among mechanical stress, biochemical and cell-immobilization methods, and cell differentiation, and is applicable to the production of the variety of tissues mentioned above. Moreover, this finding can be generalized to nonmechanical (e.g., chemical and electromagnetic) stimuli that are experienced in vivo by tissues of interest and, hence, the method can be modified to incorporate such stimuli in the ex vivo growth of replacements for the various tissues mentioned above. In this method, a three-dimensional matrix made of a suitable material is seeded with pluripotent stem cells. The patient s bone-marrow stromal cells are preferably used as the pluripotent cells in this method. Suitable matrix materials are materials to which cells can adhere for example, collagen type I. The seeded matrix is attached to anchors at opposite ends and then the cells in the matrix are cultured under conditions appropriate for the growth and regeneration of cells. Suitable anchor materials are materials to which the matrix can attach; examples include demineralized bone and Goinopra coral that has been treated to convert its calcium carbonate to calcium phosphate.

Altman, Gregory↗

NASA NTRS2003

Nanolayered Features of Collagen-like Peptides

We have been investigating collagen-like model oligopeptides as molecular bases for complex ordered biomimetic materials. The collagen-like molecules incorporate aspects of native collagen sequence and secondary structure. Designed modifications to native primary and secondary structure have been incorporated to control the nanostructure and microstructure of the collagen-like materials produced. We find that the collagen-like molecules form a number of lyotropic rod liquid crystalline phases, which because of their strong temperature dependence in the liquid state can also be viewed as solvent intercalated thermotropic liquid crystals. The liquid crystalline phases formed by the molecules can be captured in the solid state by drying off solvent, resulting in solid nanopatterned (chemically and physically) thermally stable (to greater than 100 C) materials. Designed sequences which stabilize smectic phases have allowed a variety of nanoscale multilayered biopolymeric materials to be developed. Preliminary investigations suggest that chemical patterns running perpendicular to the smectic layer plane can be functionalized and used to localize a variety of organic, inorganic, and organometallic moieties in very simple multilayered nanocomposites. The phase behavior of collagen-like oligopeptide materials is described, emphasizing the correlation between mesophase, molecular orientation, and chemical patterning at the microscale and nanoscale. In many cases, the textures observed for smectic and hexatic phase collagens are remarkably similar to the complex (and not fully understood) helicoids observed in biological collagen-based tissues. Comparisons between biological morphologies and collagen model liquid crystalline (and solidified materials) textures may help us understand the molecular features which impart order and function to the extracellular matrix and to collagen-based mineralized tissues. Initial studies have utilized synthetic collagen-like peptides while future work will also focus on similar sequences generated via genetic engineering methods.

Valluzzi, Regina↗