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ToPolyAgent: AI agents for coarse-grained bead-spring topological polymer simulations

We introduce ToPolyAgent, a multi-agent AI framework for performing coarse-grained molecular dynamics (MD) simulations of topological polymers through natural language instructions. By integrating large language models (LLMs) with domain-specific computational tools, ToPolyAgent supports both interactive and autonomous simulation workflows across diverse polymer architectures, including linear, ring, brush, and star polymers, as well as dendrimers. The system consists of four LLM-powered agents: a Config Agent for generating initial polymer–solvent configurations, a Simulation Agent for executing LAMMPS-based MD simulations and conformational analyses, a Report Agent for compiling markdown reports, and a Workflow Agent for streamlined autonomous operations. Interactive mode incorporates user feedback loops for iterative refinements, while autonomous mode enables end-to-end task execution from detailed prompts. We demonstrate ToPolyAgent's versatility through case studies involving diverse polymer architectures under varying solvent conditions, thermostats, and simulation lengths. Furthermore, we highlight its potential as a research assistant by directing it to investigate the effect of interaction parameters on the linear polymer conformation, and the influence of grafting density on the persistence length of the brush polymer. By coupling natural language interfaces with rigorous simulation tools, ToPolyAgent lowers barriers to complex computational workflows and advances AI-driven materials discovery in polymer science. It lays the foundation for autonomous and extensible multi-agent scientific research ecosystems.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

CCD data acquisition systems at Lick and Keck Observatories

This paper will describe and compare two distinct but related CCD data acquisition systems (DAS) currently under development at Lick and Keck Observatories. Although these two systems have a number of major architectural differences, they share a considerable amount of common hardware and software. Both of these new systems build on a large body of proven software that is the foundation of the existing CCD DAS currently in use at Lick Observatory. Both will provide support for reading up to four on-chip amplifiers per CCD and/or reading out mosaics of CCD chips. In addition, they will provide the capability for interactive, real-time adjustment of CCD waveforms for engineering purposes. Each of these two systems is composed of three major subsystems: (1) an instrument computer and its software; (2) a data capture computer and its software; and (3) a CCD/dewar controller and its software. The instrument computer is a Unix workstation, and the functions it provides include user interfaces, the interactive real-time display of CCD images, and the recording of image and FITS header data to disk and/or tape. The data capture computer is responsible for the packaging and high-speed transfer of the CCD pixel data stream into a bulk RAM, and the subsequent transfer of this data to the instrument computer. The CCD/dewar controller generates the waveforms for clocking the CCD, digitizes the pixel data, and transmits it via high-speed link to the data capture computer. It is also responsible for monitoring and controlling the dewar temperature and cryogen levels. Given the number of different types of processors and high-speed data links employed in both systems, a major emphasis of this paper will be on the various forms of interprocessor communications utilized for data transfer and distributed process synchronization.

Kibrick, R. I.↗

The use of a multi-processor minicomputer for communication system simulation

An experimental facility is described which allows new computer communications techniques to be tested under conditions closely approximating those of real systems. A three-processor minicomputer configuration is used to achieve real-time operation at channel transmission rates of up to 50 Kbits per second. One processor runs a channel controller-concentrator program, a second is dedicated to simulation of the communication channel characteristics, and the third to the simulation of up to 1000 user terminals. The latter are divided into classes consisting of interactive time-sharing users of differing characteristics and file nodes, mixed in different proportions. Real user nodes are connected to the channel simulator processor, providing experience with actual operating characteristics under different channel loadings.

Binder, R.↗

The H-Metaphor as a Guideline for Vehicle Automation and Interaction

Good design is not free of form. It does not necessarily happen through a mere sampling of technologies packaged together, through pure analysis, or just by following procedures. Good design begins with inspiration and a vision, a mental image of the end product, which can sometimes be described with a design metaphor. A successful example from the 20th century is the desktop metaphor, which took a real desktop as an orientation for the manipulation of electronic documents on a computer. Initially defined by Xerox, then refined by Apple and others, it could be found on almost every computer by the turn of the 20th century. This paper sketches a specific metaphor for the emerging field of highly automated vehicles, their interactions with human users and with other vehicles. In the introduction, general questions on vehicle automation are raised and related to the physical control of conventional vehicles and to the automation of some late 20th century vehicles. After some words on design metaphors, the H-Metaphor is introduced. More details of the metaphor's source are described and their application to human-machine interaction, automation and management of intelligent vehicles sketched. Finally, risks and opportunities to apply the metaphor to technical applications are discussed.

Flemisch, Frank O.↗

Telemetry Monitoring and Display Using LabVIEW

The Measurement Technology Center of the Instrumentation Section configures automated data acquisition systems to meet the diverse needs of JPL's experimental research community. These systems are based on personal computers or workstations (Apple, IBM/Compatible, Hewlett-Packard, and Sun Microsystems) and often include integrated data analysis, visualization and experiment control functions in addition to data acquisition capabilities. These integrated systems may include sensors, signal conditioning, data acquisition interface cards, software, and a user interface. Graphical programming is used to simplify configuration of such systems. Employment of a graphical programming language is the most important factor in enabling the implementation of data acquisition, analysis, display and visualization systems at low cost. Other important factors are the use of commercial software packages and off-the-shelf data acquisition hardware where possible. Understanding the experimenter's needs is also critical. An interactive approach to user interface construction and training of operators is also important. One application was created as a result of a competative effort between a graphical programming language team and a text-based C language programming team to verify the advantages of using a graphical programming language approach. With approximately eight weeks of funding over a period of three months, the text-based programming team accomplished about 10% of the basic requirements, while the Macintosh/LabVIEW team accomplished about 150%, having gone beyond the original requirements to simulate a telemetry stream and provide utility programs. This application verified that using graphical programming can significantly reduce software development time. As a result of this initial effort, additional follow-on work was awarded to the graphical programming team.

graphical user interface LabVIEW graphical program↗

Miniature Exercise Device-2 (MED-2): Preliminary ISS Evaluation Results for a Compact Motorized Resistive and Aerobic Rowing Exercise Device

Future human missions beyond Low Earth Orbit (LEO) will require onboard equipment to provide exercise capabilities for the crew to counter the adverse physiological effects of long-duration microgravity. To accomplish this within the physical constraints of a space vehicle or transit module, a single miniature device that provides both resistive and aerobic exercise modalities is required. To meet this need, Johnson Space Center’s (JSC) Software, Robotics, and Simulation Division (ER) developed the Miniature Exercise Device-2 (MED-2). MED-2 integrates a torque-controlled servomotor and a series-elastic actuator to provide highly-controllable load profiles and a large magnitude output performance in a very small package. This innovative technology is derived from years of JSC/ER design, development and operational experience with cutting-edge robotics, motor controllers, software and actuator/sensor miniaturization, including Robonaut 2 and MED-1. MED-2 was presented at the 2016 ISS R&D Conference. This is an update now that the last of six crewmembers will have completed planned MED-2 sessions on the International Space Station (ISS) in May 2018.Current state-of-the-art ISS exercise equipment consists of two treadmills, a resistive exercise device and two cycle ergometers with a total mass of several thousand pounds and a total volume of several cubic yards. This equipment has proven vital to mitigate the musculoskeletal and cardiovascular degradation effects of microgravity. However, due to the large operational volume and mass of these ISS devices, tailoring them for smaller vehicles, such as Orion, is not possible. In addition, each of the current ISS devices targets a single specific modality. Compared to the existing spaceflight (and even terrestrial) exercise equipment, MED-2 is a new archetype altogether. The combined features of compact size, multi-modality and high-performance is attributable to its innovative series elastic actuator and motor controller. Following its arrival on ISS in 2016, MED-2 was evaluated in two parts. The first and shorter evaluation was an engineering functional checkout of the hardware. As this was a novel exercise device previously never used on ISS, the initial checkout assessed the operation of the hardware and ensured the motion and dynamic range of the crew did not present any collision or other hazards. The second portion of the study collected the heart rates, kinematics and utilized operational volumes of six astronauts to determine the quality of both the resistive and aerobic exercise modalities as delivered by MED-2. Investigators from JSC Biomedical Research and Environmental Science Division (SK) and Glenn Research Center are currently evaluating the data and preparing preliminary results. For the resistive exercise modality, MED-2 demonstrated a range of constant resistive loads from 10-150 lbf. With a displacement range of 84 inches, the MED-2 accommodates users from 5th percentile Japanese female through 95th percentile American male for all of its certified exercises. The displacement measurement accuracy has also been verified within 2.5 percent full range. The crew was able to successfully perform all prescribed resistive exercises, except Goblet Squats which were not feasible with a constant load profile. For the aerobic exercise modality, MED-2 simulated a rowing motion with prescribed and user-selected resistance levels. It has demonstrated rates up to 60 strokes per minute on the ground. MED-2 loads and displacements performance are the same as those cited for the resistive modality. Although each of the crew was able to perform the prescribed aerobic rowing sets, there was considerable variability in the rowing motion among different crewmembers. Also, as expected, the crew was unable to get the full benefits of a typical terrestrial rowing stroke because the current configuration does not allow the user to reach past their feet. These observations have already informed the requirements for other microgravity rowing devices currently in development. One of the unique features of the MED-2 device is the intuitive touch-screen control system. This One Portal graphical user interface (GUI) was developed based on JSC/ER’s heritage knowledge and experience of developing and sustaining the current ISS exercise equipment. Through this interface, the crew easily performed prepared prescriptions as well as had the ability to adjust exercise modality, load and other exercise details such as number of repetitions and number of sets. This touch-screen and GUI fulfilled the MED-2 project goal to simplify the interaction between the user and the device. Furthermore, the extent to which MED-2 utilizes a touchscreen and GUI to control exercise equipment is unmatched among the existing ISS exercise devices. As a motorized device, MED-2 technology can provide a customizable force profile that can be varied as a function of strap displacement, strap velocity or a combination of these and other variables. During 2017, JSC/ER developed and flight-certified a resistive exercise algorithm that mimics the 1-G inertial effects of free-weights and enables adjustable eccentric-to-concentric loading ratios. Subsequent development will explore varying the load profiles and incorporating additional exercises beyond the current list of certified movements.

Exercise↗

Interactive design and analysis of future large spacecraft concepts

Recent developments in interactive computer-aided design and analysis of future large spacecraft concepts are presented. The primary emphases are on automatic spacecraft modeling for lattice (truss-like) structures and simplified multidiscipline design and analysis modules. Capabilities and performance of the twenty some applications modules, the executive and data management software, and graphics display features are reviewed. Data generated for an earth-orbiting large diameter (750 meter) antenna satellite are used to illustrate current capabilities. A single user at an interactive terminal can create, design, analyze, and conduct parametric studies of earth-orbiting spacecraft with relative ease. The approach is particularly useful in the conceptual design phase of advanced space missions when a multiplicity of concepts must be evaluated in a cost-effective and timely manner

Garrett, L. B.↗

SE-FIT

The mathematical theory of capillary surfaces has developed steadily over the centuries, but it was not until the last few decades that new technologies have put a more urgent demand on a substantially more qualitative and quantitative understanding of phenomena relating to capillarity in general. So far, the new theory development successfully predicts the behavior of capillary surfaces for special cases. However, an efficient quantitative mathematical prediction of capillary phenomena related to the shape and stability of geometrically complex equilibrium capillary surfaces remains a significant challenge. As one of many numerical tools, the open-source Surface Evolver (SE) algorithm has played an important role over the last two decades. The current effort was undertaken to provide a front-end to enhance the accessibility of SE for the purposes of design and analysis. Like SE, the new code is open-source and will remain under development for the foreseeable future. The ultimate goal of the current Surface Evolver Fluid Interface Tool (SEFIT) development is to build a fully integrated front-end with a set of graphical user interface (GUI) elements. Such a front-end enables the access to functionalities that are developed along with the GUIs to deal with pre-processing, convergence computation operation, and post-processing. In other words, SE-FIT is not just a GUI front-end, but an integrated environment that can perform sophisticated computational tasks, e.g. importing industry standard file formats and employing parameter sweep functions, which are both lacking in SE, and require minimal interaction by the user. These functions are created using a mixture of Visual Basic and the SE script language. These form the foundation for a high-performance front-end that substantially simplifies use without sacrificing the proven capabilities of SE. The real power of SE-FIT lies in its automated pre-processing, pre-defined geometries, convergence computation operation, computational diagnostic tools, and crash-handling capabilities to sustain extensive computations. SE-FIT performance is enabled by its so-called file-layer mechanism. During the early stages of SE-FIT development, it became necessary to modify the original SE code to enable capabilities required for an enhanced and synchronized communication. To this end, a file-layer was created that serves as a command buffer to ensure a continuous and sequential execution of commands sent from the front-end to SE. It also establishes a proper means for handling crashes. The file layer logs input commands and SE output; it also supports user interruption requests, back and forward operation (i.e. undo and redo), and others. It especially enables the batch mode computation of a series of equilibrium surfaces and the searching of critical parameter values in studying the stability of capillary surfaces. In this way, the modified SE significantly extends the capabilities of the original SE.

Chen, Yongkang↗

Bindee

Bindee is a clang tool that outputs a simple pybind11 template given a C++ file for efficient generation of C++-Python bindings. Bindee is intended to be a helper tool for minimizing initial user effort and safeguarding against common runtime errors. Bindee relies on two open-source software to produce bindings. Clang's LibTooling enables bindee to traverse a C++ file's AST to pick out bindable variables and functions, or "bindees." PyBind11 is templated, header-only library for generating C++-Python bindings for variables and functions. Operating purely in C++, bindee does not require learning any new API for accomplishing its task. Additionally, picking the correct pybind11 API for a given bindable element is handled without interaction from the user. Any user input is denoted by '@TEXT@' string substitution. Bindee is capable of generating modular bindings for public class methods, public class variables, enumerations, and free functions and variables. Bindings for templates are also supported. For those familiar with pybind11, bindee does not handle trampolines, C++ extensions through lambdas, or custom type casters.

Kimkno, JasonS.↗

RAPID and HTML5's potential

Just as important as the engineering that goes into building a robot is the method of interaction, or how human users will use the machine. As part of the Human-System Interactions group (Conductor) at JPL, I explored using a web interface to interact with ATHLETE, a prototype lunar rover. I investigated the usefulness of HTML 5 and Javascript as a telemetry viewer as well as the feasibility of having a rover communicate with a web server. To test my ideas I built a mobile-compatible website and designed primarily for an Android tablet. The website took input from ATHLETE engineers, and upon its completion I conducted a user test to assess its effectiveness.

All-Terrain Hex-Limbed Extra-Terrestrial Explorer ↗

Browser-Based Application for Telemetry Monitoring of Robotic Assets

AEGSE Virtuoso Charting is an application that enables animated, real-time charting of telemetry streams of data from a rover. These automatically scaled charts are completely interactive, and allow users to choose the variables that they want to monitor. The charts can process data from streams with many variables. This application allows for the simultaneous viewing of up to four individually configured charts on a small touch-screen laptop. The charting application has been tested and found to be extremely robust during long operations. It was left running overnight, with incoming telemetry at 100 Hz, and it did not experience any signs of lost functionality or memory leaks. This robustness is critical for an application that will be used to support vital tests for the Mars Science Laboratory rover. The charting component also provides an interactive interface that allows the engineers to decide how many charts they want on their screen, and which attributes should be plotted on each chart. The application is optimized to make the charts on display take up as much of the available space as possible to maximize the use of the screen real estate. Engineers are also able to plot multiple attributes on the same chart, which enables them to observe the correlation between various attributes.

Breed, Kelly S.↗

Remote Sensing Time Series Product Tool

The TSPT (Time Series Product Tool) software was custom-designed for NASA to rapidly create and display single-band and band-combination time series, such as NDVI (Normalized Difference Vegetation Index) images, for wide-area crop surveillance and for other time-critical applications. The TSPT, developed in MATLAB, allows users to create and display various MODIS (Moderate Resolution Imaging Spectroradiometer) or simulated VIIRS (Visible/Infrared Imager Radiometer Suite) products as single images, as time series plots at a selected location, or as temporally processed image videos. Manually creating these types of products is extremely labor intensive; however, the TSPT development tool makes the process simplified and efficient. MODIS is ideal for monitoring large crop areas because of its wide swath (2330 km), its relatively small ground sample distance (250 m), and its high temporal revisit time (twice daily). Furthermore, because MODIS imagery is acquired daily, rapid changes in vegetative health can potentially be detected. The new TSPT technology provides users with the ability to temporally process high-revisit-rate satellite imagery, such as that acquired from MODIS and from its successor, the VIIRS. The TSPT features the important capability of fusing data from both MODIS instruments onboard the Terra and Aqua satellites, which drastically improves cloud statistics. With the TSPT, MODIS metadata is used to find and optionally remove bad and suspect data. Noise removal and temporal processing techniques allow users to create low-noise time series plots and image videos and to select settings and thresholds that tailor particular output products. The TSPT GUI (graphical user interface) provides an interactive environment for crafting what-if scenarios by enabling a user to repeat product generation using different settings and thresholds. The TSPT Application Programming Interface provides more fine-tuned control of product generation, allowing experienced programmers to bypass the GUI and to create more user-specific output products, such as comparison time plots or images. This type of time series analysis tool for remotely sensed imagery could be the basis of a large-area vegetation surveillance system. The TSPT has been used to generate NDVI time series over growing seasons in California and Argentina and for hurricane events, such as Hurricane Katrina.

Predos, Don↗

A 'user friendly' geographic information system in a color interactive digital image processing system environment

NASA's Eastern Regional Remote Sensing Applications Center (ERRSAC) has recognized the need to accommodate spatial analysis techniques in its remote sensing technology transfer program. A computerized Geographic Information System to incorporate remotely sensed data, specifically Landsat, with other relevant data was considered a realistic approach to address a given resource problem. Questions arose concerning the selection of a suitable available software system to demonstrate, train, and undertake demonstration projects with ERRSAC's user community. The very specific requirements for such a system are discussed. The solution found involved the addition of geographic information processing functions to the Interactive Digital Image Manipulation System (IDIMS). Details regarding the functions of the new integrated system are examined along with the characteristics of the software.

Campbell, W. J.↗

The NAS Computational Aerosciences Archive

In order to further the state-of-the-art in computational aerosciences (CAS) technology, researchers must be able to gather and understand existing work in the field. One aspect of this information gathering is studying published work available in scientific journals and conference proceedings. However, current scientific publications are very limited in the type and amount of information that they can disseminate. Information is typically restricted to text, a few images, and a bibliography list. Additional information that might be useful to the researcher, such as additional visual results, referenced papers, and datasets, are not available. New forms of electronic publication, such as the World Wide Web (WWW), limit publication size only by available disk space and data transmission bandwidth, both of which are improving rapidly. The Numerical Aerodynamic Simulation (NAS) Systems Division at NASA Ames Research Center is in the process of creating an archive of CAS information on the WWW. This archive will be based on the large amount of information produced by researchers associated with the NAS facility. The archive will contain technical summaries and reports of research performed on NAS supercomputers, visual results (images, animations, visualization system scripts), datasets, and any other supporting meta-information. This information will be available via the WWW through the NAS homepage, located at http://www.nas.nasa.gov/, fully indexed for searching. The main components of the archive are technical summaries and reports, visual results, and datasets. Technical summaries are gathered every year by researchers who have been allotted resources on NAS supercomputers. These summaries, together with supporting visual results and references, are browsable by interested researchers. Referenced papers made available by researchers can be accessed through hypertext links. Technical reports are in-depth accounts of tools and applications research projects performed by NAS staff members and collaborators. Visual results, which may be available in the form of images, animations, and/or visualization scripts, are generated by researchers with respect to a certain research project, depicting dataset features that were determined important by the investigating researcher. For example, script files for visualization systems (e.g. FAST, PLOT3D, AVS) are provided to create visualizations on the user's local workstation to elucidate the key points of the numerical study. Users can then interact with the data starting where the investigator left off. Datasets are intended to give researchers an opportunity to understand previous work, 'mine' solutions for new information (for example, have you ever read a paper thinking "I wonder what the helicity density looks like?"), compare new techniques with older results, collaborate with remote colleagues, and perform validation. Supporting meta-information associated with the research projects is also important to provide additional context for research projects. This may include information such as the software used in the simulation (e.g. grid generators, flow solvers, visualization). In addition to serving the CAS research community, the information archive will also be helpful to students, visualization system developers and researchers, and management. Students (of any age) can use the data to study fluid dynamics, compare results from different flow solvers, learn about meshing techniques, etc., leading to better informed individuals. For these users it is particularly important that visualization be integrated into dataset archives. Visualization researchers can use dataset archives to test algorithms and techniques, leading to better visualization systems, Management can use the data to figure what is really going on behind the viewgraphs. All users will benefit from fast, easy, and convenient access to CFD datasets. The CAS information archive hopes to serve as a useful resource to those interested in computational sciences. At present, only information that may be distributed internationally is made available via the archive. Studies are underway to determine security requirements and solutions to make additional information available. By providing access to the archive via the WWW, the process of information gathering can be more productive and fruitful due to ease of access and ability to manage many different types of information. As the archive grows, additional resources from outside NAS will be added, providing a dynamic source of research results.

Miceli, Kristina D.↗

Software for Viewing Landsat Mosaic Images

A Windows-based computer program has been written to enable novice users (especially educators and students) to view images of large areas of the Earth (e.g., the continental United States) generated from image data acquired in the Landsat observations performed circa the year 1990. The large-area images are constructed as mosaics from the original Landsat images, which were acquired in several wavelength bands and each of which spans an area (in effect, one tile of a mosaic) of .5 in latitude by .6 in longitude. Whereas the original Landsat data are registered on a universal transverse Mercator (UTM) grid, the program converts the UTM coordinates of a mouse pointer in the image to latitude and longitude, which are continuously updated and displayed as the pointer is moved. The mosaic image currently on display can be exported as a Windows bitmap file. Other images (e.g., of state boundaries or interstate highways) can be overlaid on Landsat mosaics. The program interacts with the user via standard toolbar, keyboard, and mouse user interfaces. The program is supplied on a compact disk along with tutorial and educational information.

Watts, Zack↗

Software for Viewing Landsat Mosaic Images

A Windows-based computer program has been written to enable novice users (especially educators and students) to view images of large areas of the Earth (e.g., the continental United States) generated from image data acquired in the Landsat observations performed circa the year 1990. The large-area images are constructed as mosaics from the original Landsat images, which were acquired in several wavelength bands and each of which spans an area (in effect, one tile of a mosaic) of approx. 5 in latitude by approx. 6 deg in longitude. Whereas the original Landsat data are registered on a universal transverse Mercator (UTM) grid, the program converts the UTM coordinates of a mouse pointer in the image to latitude and longitude, which are continuously updated and displayed as the pointer is moved. The mosaic image currently on display can be exported as a Windows bit-map file. Other images (e.g., of state boundaries or interstate highways) can be overlaid on Landsat mosaics. The program interacts with the user via standard toolbar, keyboard, and mouse user interfaces. The program is supplied on a compact disk along with tutorial and educational information.

Source record↗

Software for Viewing Landsat Mosaic Images

A Windows-based computer program has been written to enable novice users (especially educators and students) to view images of large areas of the Earth (e.g., the continental United States) generated from image data acquired in the Landsat observations performed circa the year 1990. The large-area images are constructed as mosaics from the original Landsat images, which were acquired in several wavelength bands and each of which spans an area (in effect, one tile of a mosaic) of 5 in latitude by approximately equal to 6 degrees in longitude. Whereas the original Landsat data are registered on a universal transverse Mercator (UTM) grid, the program converts the UTM coordinates of a mouse pointer in the image to latitude and longitude, which are continuously updated and displayed as the pointer is moved. The mosaic image currently on display can be exported as a Windows bit-map file. Other images (e.g., of state boundaries or interstate highways) can be overlaid on Landsat mosaics. The program interacts with the user via standard toolbar, keyboard, and mouse user interfaces. The program is supplied on a compact disk along with tutorial and educational information.

Watts, Jack↗

STRUTEX: A prototype knowledge-based system for initially configuring a structure to support point loads in two dimensions

Only recently have engineers begun making use of Artificial Intelligence (AI) tools in the area of conceptual design. To continue filling this void in the design process, a prototype knowledge-based system, called STRUTEX has been developed to initially configure a structure to support point loads in two dimensions. This prototype was developed for testing the application of AI tools to conceptual design as opposed to being a testbed for new methods for improving structural analysis and optimization. This system combines numerical and symbolic processing by the computer with interactive problem solving aided by the vision of the user. How the system is constructed to interact with the user is described. Of special interest is the information flow between the knowledge base and the data base under control of the algorithmic main program. Examples of computed and refined structures are presented during the explanation of the system.

Robers, James L.↗