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At least 73 records · Page 4

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

The design of protein–protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein–protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning–based methods to unlock the widespread application of designed protein–protein interfaces and self-assembling protein nanomaterials in biotechnology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modelling, simulation and sounding of cometary nuclei; Proceedings of the International Workshop, Cagliari, Italy, May 28-30, 1991

The present workshop on the modeling, simulation, and sounding of cometary nuclei discusses the Rosetta comet-nucleus sample return mission, the importance of comet models in the design of the Rosetta mission, the challenge of sample acquisition in a cometary environment, and a simulation of Rosetta on-comet operations. Attention is given to HST observations of the inner coma of Comet Levy 1990c, cometary coma particulate modeling for the Rosetta mission aphelion rendezvous, recent gas flux modeling and applications of cometary nuclei, and the 3D time-dependent modeling of comet nucleus surface layers. Topics addressed include models of cometary nuclei and future space mission, the composition of cometary materials, experiments with cometary analogs at the DLR, and crust formation in cometary analogs. Also considered are gaseous products from VUV photolysis of cometary solids, cosmic ray modification of organic cometary matter as simulated by cyclotron irradiation, and KOSI comet simulation experiments.

Source record↗

Contingency Operations during Failure of Inertial Attitude Acquisition Due to Star Tracker Blinding for Three-Axes-Stabilized Interplanetary Spacecraft

The three interplanetary ESA missions Mars-Express, Rosetta and Venus-Express (launched 2003, 2004 and 2005 resp.) are three-axes stabilized spacecraft (s/c) that estimate their inertial attitude (i.e. the attitude of the s/c w.r.t. the inertial frame) using measurements from a redundant set of star trackers (STR). Each s/c is equipped with four reaction wheels, a reaction control system based on thrusters and a redundant set of ring laser gyroscopes (gyros). The STR h/w layout of the three s/c is identical whereas there is a difference in the star pattern recognition algorithm of Rosetta which uses five neighbouring stars around a central star instead of star triads. The Rosetta algorithm has been implemented to cope with the presence of false stars which are expected to be seen during operations around the comet. The attitude acquisition capability from lost in space is different also in terms of AOCMS: The survival mode of Rosetta which is entered upon STR failure is presented. The AOCMS of Mars- and Venus-Express manages temporary STR outages during sky occultation by the planet not even by using redundancy. Though, a blinding of both STR during cruise lasting for the order of days confronts the ground operators with the limits of the AOCMS design. The operations and analyses that have been planned and partially been performed to compensate for the outage of the STR are demonstrated for Mars-Express. The caution measures taken before Venus orbit insertion of Venus-Express are detailed.

Keil, Joachim↗

De novo design of small beta barrel proteins

Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

59 BASIC BIOLOGICAL SCIENCES↗

Robust deep learning–based protein sequence design using ProteinMPNN

Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here, we describe a deep learning–based protein sequence design method, ProteinMPNN, that has outstanding performance in both in silico and experimental tests. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4% compared with 32.9% for Rosetta. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. We demonstrate the broad utility and high accuracy of ProteinMPNN using x-ray crystallography, cryo–electron microscopy, and functional studies by rescuing previously failed designs, which were made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target-binding proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing Cometary Electrons with Kappa Distributions

The Rosetta spacecraft has escorted comet 67P/Churyumov-Gerasimenko since 6 August 2014 and has offered an unprecedented opportunity to study plasma physics in the coma. We have used this opportunity to make the first characterization of cometary electrons with kappa distributions. Two three-dimensional kappa functions were fit to the observations, which we interpret as two populations of dense and warm (density 10 cubic centimeters, temperature 2 times 10 (sup 5) degrees Kelvin, invariant kappa index 10 to 1000), and rarefied and hot (density equals 0.005 cubic centimeters, temperature 5 times 10 (sup 5) degrees Kelvin, invariant kappa index equals 1 to 10) electrons. We fit the observations on 30 October 2014 when Rosetta was 20 kilometers from 67P, and 3 Astronomical Units from the Sun. We repeated the analysis on 15 August 2015 when Rosetta was 300 kilometers from the comet and 1.3 Astronomical Units from the Sun. Comparing the measurements on both days gives the first comparison of the cometary electron environment between a nearly inactive comet far from the Sun and an active comet near perihelion. We find that the warm population density increased by a factor of 3, while the temperature cooled by a factor of 2, and the invariant kappa index was unaffected. We find that the hot population density increased by a factor of 10, while the temperature and invariant kappa index were unchanged. We conclude that the hot population is likely the solar wind halo electrons in the coma. The warm population is likely of cometary origin, but its mechanism for production is not known.

Broiles, T. W.↗

The CAESAR New Frontiers Comet Sample Return Mission

The Comet Astrobiology Exploration Sample Return (CAESAR) mission is one of two finalists selected by NASA for Phase A study in the New Frontiers program. CAESAR will acquire a minimum of 80 grams of material from the surface of comet 67P/Churuyumov-Gerasimenko and return it to Earth for laboratory analysis. CAESAR preserves much of the science of a cryogenic sample return by retaining volatiles in a dedicated reservoir securely separated from the solid sample. Comet 67P was selected based on its favorable orbital geometry and the risk reduction and scientific context provided by the ESA (European Space Agency)'s Rosetta mission. CAESAR's objectives are to understand the origins of the Solar System starting materials and how these components came together to form planets and give rise to life. We also seek to resolve the conflicting views of comet origins arising from the Stardust and Rosetta missions. While the greater than 1 micron solids returned by Stardust originated in the hot, inner solar nebula, measurements by Rosetta suggest 67P volatiles formed at cryogenic temperatures and remained unchanged for billions of years. This dichotomy provides the rationale for returning both solid and gaseous samples.

CAESAR New Frontiers↗

The Diversity of Refractory Organic Material in Comets

Organic matter exists in comets (most notably in 81P/Wild 2 [Stardust], 67P/Churyomov- Gerasimenko (67P/C-G) [Rosetta], chondritic porous IDPS, and UCAMMs) and in primitive carbonaceous chondrites that likely retain some chemistry that reflects an origin in the prenatal cold molecular cloud (Alexander+2017). Heavy isotopic enrichments, 15N/14N and possibly D/H, signify preserved molecular cloud organics. In the cold outer disk, if grains are lofted above the disk mid-plane then organics likely experience significant UV processing (Ciesla+2012). In remote sensing of comet comae, organics in the dust are considered refractory or semirefractory. Semi-refractory organics have limited comae lifetimes and produce distributed sources of molecules (H2CO and CO). Rosetta's close passes of 67P/C-G's nucleus (10-15 km) reveals a distributed source of glycine, methyl amine and ethylamine (Altwegg+2016). Cometary samples and primitive meteorites have two types of organic matter: (1) acid-insoluble organic matter (IOM), which is a macromolecular polymer with a mixture of aromatic and aliphatic moieties, and (2) labile, soluble organics, which includes the amino acids, such as glycine (Stardust, Elsila+2009). Meteoritic IOM is robust, withstanding experimental temperatures of 1200 K (Dobrica+2011, Cody+2008). Nanoglobules are a type of IOM; they have a distinct physical structure, but often share the same chemistry as the other IOM from the same meteorite. Moderate-sized PAHs (20 C-atoms) are detected in Stardust samples (Clemett+2010). Refractory organic IOM is ubiquitous yet has a great diversity of abundances between cometary samples. IOM is in primitive chondrites, 67P/C-G (Rosetta), 81P/Wild 2 (Stardust), 1P/Halley, 26P/Grigg-Skjellerup, UCAMMs, anhydrous IDPs, and in chondritic porous IDPs (CP IDPs) and larger cluster IDPs (e.g., Fray+2016, Fomenkova+94, Busemann+ 09, Dobrica+2011, Dobrica+2012). 81P's refractory organic matter is of two types (De Gregorio+2011): nanoglobules of highly aromatic refractory organic matter and polyaromatic carbonyl-containing organic matter, which is similar to IOM in primitive meteorites and IDPs. Fray+2017 estimate that 50% of carbon in 67P/C-G is in IOM. 67P/C-G's organics appear to lack the soluble organic matter, aliphatic carbon, amino acids, and PAHs (Fray+2016). Other notable aspects of the diversity in IOM in cometary samples are the ranges of atomic ratios of N/C, O/C, and H/C, and the range of isotopic enrichments of 15N/14N and D/H. Aqueous and thermal processing on asteroids changes the balance of soluble to insoluble organics, and may be important for diversifying the range of OM delivered to Earth.

Wooden, Diane↗

Better together: Elements of successful scientific software development in a distributed collaborative community

Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities

97 MATHEMATICS AND COMPUTING↗

K in an Urban World: New Contexts for Hydraulic Conductivity

Abstract Hydraulic conductivity ( K ) is a key hydrologic parameter widely recognized to be difficult to estimate and constrain, with little consistent assessment in disturbed, urbanized soils. To estimate K , it is either measured, or simulated by pedotransfer functions, which relate K to easily measured soil properties. We measured K in urbanized soils by double‐ring infiltrometer ( K dring ), near‐saturated tension infiltrometry ( K minidisk ), and constant head borehole permeametry ( K borehole ), along with other soil properties across the major soil orders in 12 United States cities. We compared measured K with that predicted from the pedotransfer function, ROSETTA. We found that regardless of soil texture, K dring was consistently larger than K minidisk ; with the latter having slightly less sample variance. K borehole was dependent upon specific subsurface conditions, and contrary to common expectations, did not always decrease with depth. Based on either soil textural class, or percent textural separates (sand, silt clay), ROSETTA did not accurately predict measured K for surface nor subsurface soils. We go on to discuss how K varies in urban landscapes, the role of measurement methods and artifacts in the perception of this metric, and implications for hydrologic modeling. Overall, we aim to inspire consistency and coherence when addressing K ‐related challenges in sustainable urban water management.

Shuster, W. D.↗

MIRO Calibration Switch Mechanism

The Jet Propulsion Laboratory has designed, analyzed, built, and tested a calibration switch mechanism for the MIRO instrument on the ROSETTA spacecraft. MIRO is the Microwave Instrument for the Rosetta Orbiter; this instrument hopes to investigate the origin of the solar system by studying the origin of comets. Specifically, the instrument will be the first to use submillimeter and millimeter wave heterodyne receivers to remotely examine the P-54 Wirtanen comet. In order to calibrate the instrument, it needs to view a hot and cold target. The purpose of the mechanism is to divert the instrument's field of view from the hot target, to the cold target, and then back into space. This cycle is to be repeated every 30 minutes for the duration of the 1.5 year mission. The paper describes the development of the mechanism, as well as analysis and testing techniques.

Suchman, Jason↗

Planetary Exploration in ESA

A viewgraph presentation on planetary exploration in the European Space Agency is shown. The topics include: 1) History of the Solar System Material; 2) ROSETTA: The Comet Mission; 3) A New Name For The Lander: PHILAE; 4) The Rosetta Mission; 5) Lander: Design Characteristics; 6) SMART-1 Mission; 7) MARS Express VENUS Express; 8) Planetary Exploration in ESA The Future.

Schwehm, Gerhard H.↗

Operational Experience with Autonomous Star Trackers on ESA Interplanetary Spacecraft

Mars Express (MEX), Rosetta and Venus Express (VEX) are ESA interplanetary spacecrafts (S/C) launched in June 2003, March 2004 and November 2005, respectively. Mars Express was injected into Mars orbit end of 2003 with routine operations starting in spring 2004. Rosetta is since launch on its way to rendezvous comet Churyumov-Gerasimenko in 2014. It has completed several test and commissioning activities and is performing several planetary swingbys (Earth in spring 2005, Mars in spring 2007, Earth in autumn 2007 and again two years later). Venus Express has also started routine operations since the completion of the Venus orbit insertion maneuver sequence beginning of May 2006. All three S/C are three axes stabilized with a similar attitude and orbit control system (AOCS). The attitude is estimated on board using star and rate sensors and controlled using four reaction wheels. A bipropellant reaction control system with 10N thrusters serves for wheel off loadings and attitude control in safe mode. Mars Express and Venus Express have an additional 400N engine for the planetary orbit insertion. Nominal Earth communication is accomplished through a high gain antenna. All three S/C are equipped with a redundant set of autonomous star trackers (STR) which are based on almost the same hardware. The STR software is especially adapted for the respective mission. This paper addresses several topics related to the experience gained with the STR operations on board the three S/C so far.

Lauer, Mathias↗

Effects on Spacecraft Radiometric Data at Superior Solar Conjunction

During 2006, three ESA interplanetary spacecraft, Rosetta, Mars Express (MEX) and Venus Express (VEX), passed through superior solar conjunction. For all three spacecraft, the noise in the post-fit range-rate residuals from the orbit determination was analysed. At small Sun-Earth-Probe (SEP) angles the level was almost two orders of magnitude higher than normal. The main objective was to characterize the Doppler (rangerate) noise as a function of SEP angle. At least then the range-rate data can be appropriately weighted within the orbit determination so that the solution uncertainties are realistic. For VEX, some intervals of particularly noisy Doppler data could be correlated with unusual solar activity. For Rosetta, the biases in the range data residuals were analysed with the aim of improving the model used for calibrating the signal delay due to the solar plasma. The model, which originally had fixed coefficients, was adjusted to achieve better fits to the data. Even the relatively small Doppler biases were well represented. Using the improved model, the electron density at 20 solar radii was compared with earlier results obtained by radio science studies using Voyager 2 and Ulysses radiometric data. There is some evidence for a dependency of the density on the phase within the 11 years solar cycle.

Morley, Trevor↗

Estimation of Cometary Rotation Parameters Based on Camera Images

The purpose of the Rosetta mission is the in situ analysis of a cometary nucleus using both remote sensing equipment and scientific instruments delivered to the comet surface by a lander and transmitting measurement data to the comet-orbiting probe. Following a tour of planets including one Mars swing-by and three Earth swing-bys, the Rosetta probe is scheduled to rendezvous with comet 67P/Churyumov-Gerasimenko in May 2014. The mission poses various flight dynamics challenges, both in terms of parameter estimation and maneuver planning. Along with spacecraft parameters, the comet's position, velocity, attitude, angular velocity, inertia tensor and gravitatonal field need to be estimated. The measurements on which the estimation process is based are ground-based measurements (range and Doppler) yielding information on the heliocentric spacecraft state and images taken by an on-board camera yielding informaton on the comet state relative to the spacecraft. The image-based navigation depends on te identification of cometary landmarks (whose body coordinates also need to be estimated in the process). The paper will describe the estimation process involved, focusing on the phase when, after orbit insertion, the task arises to estimate the cometary rotational motion from camera images on which individual landmarks begin to become identifiable.

Spindler, Karlheinz↗

MIRO calibration switch mechanism

The Jet Propulsion Laboratory has design, analyzed, built, and tested a calibration switch mechanism for the MIRO instrument on the ROSETTA spacecraft. MIRO is the Microwave Instrument for the Rosetta Orbiter; this instrument hopes to investigate the origin of the solar system by studying the origin of comets. Specifically, the instrument will be the first to use submillimeter and millimeter wave heterodyne receivers to remotely examine the P-54 Wirtanen comet. In order to calibrate the instrument, it needs to view a hot and cold target. The purpose of the mechanism is to divert the instrument’s field of view from the hot target, to the cold target, and then back into space. This cycle is to be repeated every 30 minutes for the duration of the 1.5 year mission. The paper hopes to explain the development of the mechanism, as well as analysis and testing techniques.

Kubo, Holly↗

Optical Navigation for Autonomous Approach of Small Unknown Bodies

State of the practice in navigation around small celestial bodies heavily relies on ground sup- port and human skill, in particular, for perception-based operations such as optical navigation and mapping. This leads to longer duration and more complex mission operations and sub- sequently higher cost. Furthermore, it imposes limitations for certain missions such as fast fly-bys or multi-agent operations. In this work, we present an autonomous navigation strat- egy suitable for approaching small unexplored bodies. During the approach, we estimate the body’s physical properties as well as the spacecraft’s relative trajectory and associated un- certainties. The autonomous navigation strategy, which is solely based on optical measure- ments, begins as soon as the body becomes resolved in the navigation camera and terminates at the start of proximity operations, when the spacecraft makes its first trajectory correction to stay in the vicinity of the body. Our strategy uses multiple image-processing algorithms: light-curve analysis for estimating the target body’s rotation rate, Shape-from-Silhouette for reconstructing the 3D shape and estimating its rotation pole, and feature tracking tailored to Small-Body images for estimating relative navigation parameters. We used the Mission Analysis, Operations, and Navigation Toolkit Environment (MONTE) developed by the Jet Propulsion Laboratory to evaluate the feasibility of this multi-phase navigation strategy using simulated images of an approach trajectory. We used the Rosetta mission data to generate photorealistic images to characterise the performance of this approach. This work is based on the assumptions that the spacecraft attitude is known, the body is a principal-axis rotator, a-priori estimates of ephemerides and scale are available, and the body is observed from a zero sun phase only during initial approach. Preliminary results show orbit determination performance that is on par with the human navigation from the Rosetta mission; albeit with a 1% bias in spacecraft-target radial distance estimate. The bias error is likely due to the robustness and accuracy of the visual tracking under dynamic lighting conditions and per- spective changes, which decrease accuracy.

Villa, Jacopo↗

Origin of Molecular Oxygen in Comets: Current Knowledge and Perspectives

The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) instrument onboard the Rosetta spacecraft has measured molecular oxygen (O 2 ) in the coma of comet 67P/Churyumov-Gerasimenko (67P/C-G) in surprisingly high abundances. These measurements mark the first unequivocal detection of O 2 in a cometary environment. The large relative abundance of O 2 in 67P/C-G despite its high reactivity and low interstellar abundance poses a puzzle for its origin in comet 67P/C-G, and potentially other comets. Since its detection, there have been a number of hypotheses put forward to explain the production and origin of O 2 in the comet. These hypotheses cover a wide range of possibilities from various in situ production mechanisms to protosolar nebula and primordial origins. Here, we review the O2 formation mechanisms from the literature, and provide a comprehensive summary of the current state of knowledge of the sources and origin of cometary O 2 .

Molecular oxygen↗