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Protein-DNA Interaction Workflow (PDI Workflow), a pipeline that focuses on generating high-quality docking and molecular dynamics simulations for Protein-DNA complexes. This allows us to take DNA sequences with unknown tertiary structures, accurately predict their structure, dock them with the desired target protein, and then simulate their interactions using molecular dynamics simulations
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The space station will be deployed and assembled in low earth orbit with multiple Shuttle trips. Several construction phases will be required involving both ground and in-orbit operations. In this paper, the construction process of a four-panel space station and its control problems are discussed. The applicability of a direct model reference adaptive control technique with plant augmentation is investigated. Control during several key assembly operation periods has been simulated. These include Shuttle docking with initial-phase station, habitat module mating, and Shuttle docking with operational station. High rate of convergence and robust performance have been observed for all the simulated cases even with 40 percent model parameter errors and model truncations and more than 100 percent instant mass property variations. Controller with severe gain saturations is also discussed and results show only slight performance deterioration.
Amyloid fibrils are thought to grow by a two-step dock-lock mechanism. However, previous simulations of fibril formation (i) overlook the bi-molecular nature of the docking step and obtain rates with first-order units, or (ii) superimpose the docked and locked states when computing the potential of mean force for association and thereby muddle the docking and locking steps. Here, we developed a simple microkinetic model with separate locking and docking steps and with the appropriate concentration dependences for each step. We constructed a simple model comprised of chiral dumbbells that retains qualitative aspects of fibril formation. We used rare events methods to predict separate docking and locking rate constants for the model. The rate constants were embedded in the microkinetic model, with the microkinetic model embedded in a population balance model for “bottom-up” multiscale fibril growth rate predictions. These were compared to “top-down” results using simulation data with the same model and multiscale framework to obtain maximum likelihood estimates of the separate lock and dock rate constants. We used the same procedures to extract separate docking and locking rate constants from experimental fibril growth data. Our multiscale strategy, embedding rate theories, and kinetic models in conservation laws should help to extract docking and locking rate constants from experimental data or long molecular simulations with correct units and without compromising the molecular description.
Aerospace and space simulation including rendezvous and docking, lunar landing and operation of supersonic transports
A program of research, development, test, and evaluation is planned for the development of Spacecraft Handling Qualities guidelines. In this first experiment, the effects of Reaction Control System design characteristics and rotational control laws were evaluated during simulated proximity operations and docking. Also, the influence of piloting demands resulting from varying closure rates was assessed. The pilot-in-the-loop simulation results showed that significantly different spacecraft handling qualities result from the design of the Reaction Control System. In particular, cross-coupling between translational and rotational motions significantly affected handling qualities as reflected by Cooper-Harper pilot ratings and pilot workload, as reflected by Task-Load Index ratings. This influence is masked but only slightly by the rotational control system mode. While rotational control augmentation using Rate Command Attitude Hold can reduce the workload (principally, physical workload) created by cross-coupling, the handling qualities are not significantly improved. The attitude and rate deadbands of the RCAH introduced significant mental workload and control compensation to evaluate when deadband firings would occur, assess their impact on docking performance, and apply control inputs to mitigate that impact.
A study was conducted to investigate the space tug automatic docking control capabilities. The subjects considered are: (1) docking sensor requirements, (2) the influence of the docking mechanism, and (3) the implications and effects of a docking abort. A digital computer simulation, was developed which included the primary aspects of the docking maneuver.
For over fifty years, simulation has been a cornerstone technology for space missions. In many cases, one single simulator, developed by one team, is not enough to meet the simulation objectives. Astronaut crew training, docking, vehicle testing and complex mission planning all require several simulations to be connected and to interoperate, in order to achieve the goal of the simulation. To facilitate the development of interoperable simulations, an open standard, the SISO SpaceFOM was developed in collaboration between government, industry and academia. The standard was released in 2020. The initial release of SpaceFOM focuses on the core interoperability topics for space simulation: (i) specifying spatial data using several, well defined reference frames, (ii) managing time (including real-time, hard real-time, and as-fast-as-possible execution), (iii) composition of systems with subsystems such as space vehicles, and (iv) execution control, such as initializing, running, pausing, and terminating simulations. The initial release of SpaceFOM focuses on the core interoperability topics for space simulation: (i) specifying spatial data using several, well defined reference frames, (ii) managing time (including real-time, hard real-time, and as-fast-as-possible execution), (iii) composition of systems with subsystems such as space vehicles, and (iv) execution control, such as initializing, running, pausing, and terminating simulations. A number of requirements for the next version of SpaceFOM have been identified and proposed solutions are already under development. One key area is the object classes used for data exchange, where a richer set of classes have been proposed, based on practical use cases. For time management, the use of variable time resolutions and variable time steps is also proposed. For execution control, save and restore of simulations is considered as well as improved robustness, to handle failing components. A number of clarifications are also under consideration. This paper provides both a forward-looking view of the technical developments underway and a retrospective on the standard's evolution. The authors emphasize that prioritizing core challenges and delivering a practical first version were crucial steps. While not every idea was implemented in the initial release, the timely delivery of a functional standard enabled real-world applications, the growth of a user community, and the collection of valuable insights to shape future versions. The authors look forward to working with the next version of SpaceFOM together with the growing user community.
For over fifty years, simulation has been a cornerstone technology for space missions. In many cases, one single simulator, developed by one team, is not enough to meet the simulation objectives. Astronaut crew training, docking, vehicle testing and complex mission planning all require several simulations to be connected and to interoperate, in order to achieve the goal of the simulation. To facilitate the development of interoperable simulations, an open standard, the SISO SpaceFOM was developed in collaboration between government, industry and academia. The standard was released in 2020. The initial release of SpaceFOM focuses on the core interoperability topics for space simulation: (i) specifying spatial data using several, well defined reference frames, (ii) managing time (including real-time, hard real-time, and as-fast-as-possible execution), (iii) composition of systems with subsystems such as space vehicles, and (iv) execution control, such as initializing, running, pausing, and terminating simulations. A number of requirements for the next version of SpaceFOM have been identified and proposed solutions are already under development. One key area is the object classes used for data exchange, where a richer set of classes have been proposed, based on practical use cases. For time management, the use of variable time resolutions and variable time steps is also proposed. For execution control, save and restore of simulations is considered as well as improved robustness, to handle failing components. A number of clarifications are also under consideration. This paper provides both a forward-looking view of the technical developments underway and a retrospective on the standard's evolution. The authors emphasize that prioritizing core challenges and delivering a practical first version were crucial steps. While not every idea was implemented in the initial release, the timely delivery of a functional standard enabled real-world applications, the growth of a user community, and the collection of valuable insights to shape future versions. The authors look forward to working with the next version of SpaceFOM together with the growing user community.
Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic–inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. Here, to understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31–calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ∼2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31–calcite interactions. While this work provides the first experimental confirmation that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31–calcite interface has advanced our fundamental understanding of the atomic interactions at the organic–inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.
Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.
As part of the RICIS project, the reinforcement learning techniques developed at Ames Research Center are being applied to proximity and docking operations using the Shuttle and Solar Maximum Mission (SMM) satellite simulation. In utilizing these fuzzy learning techniques, we use the Approximate Reasoning based Intelligent Control (ARIC) architecture, and so we use these two terms interchangeably to imply the same. This activity is carried out in the Software Technology Laboratory utilizing the Orbital Operations Simulator (OOS) and programming/testing support from other contractor personnel. This report is the final deliverable D4 in our milestones and project activity. It provides the test results for the special testcase of approach/docking scenario for the shuttle and SMM satellite. Based on our experience and analysis with the attitude and translational controllers, we have modified the basic configuration of the reinforcement learning algorithm in ARIC. The shuttle translational controller and its implementation in ARIC is described in our deliverable D3. In order to simulate the final approach and docking operations, we have set-up this special testcase as described in section 2. The ARIC performance results for these operations are discussed in section 3 and conclusions are provided in section 4 along with the summary for the project.
The Orbital Maneuvering Vehicle (OMV) is a teleoperated vehicle designed to dock with a target vehicle in space to peform certain tasks. This vehicle is not yet in production, but a simulator of the OMV is located at Marshall Space Flight Center (MSFC). The MSFC facility provides a realistic simulation of the OMV. Various docking maneuvers can be studied in some detail. A special robot has been constructed that provides a moving target for the simulator to dock with. This facility is valuable for conducting studies on the OMV; it also is excellent for personnel training.
Mathematical model and computerized simulation of flexible space vehicle response to docking impact
The establishment of those in-orbit operations like 'Rendez-Vous/Docking' and 'Manipulator Berthing' with the assistance of robotics or autonomous control technology, is essential for the near future space programs. In order to study the control methods, develop the flight models, and verify how the system works, we need a tool or a testbed which enables us to simulate mechanically the micro-gravity environment. There have been many attempts to develop the micro-gravity testbeds, but once the simulation goes into the docking and berthing operation that involves mechanical contacts among multi bodies, the requirement becomes critical. A group at the Tokyo Institute of Technology has proposed a method that can simulate the 3D micro-gravity producing a smooth response to the impact phenomena with relatively simple apparatus. Recently the group carried out basic experiments successfully using a prototype hardware model of the testbed. This paper will present our idea of the 3D micro-gravity simulator and report the results of our initial experiments.
The crew of the STS-114 Discovery Mission is seen in various aspects of training for space flight. The crew activities include: 1) STS-114 Return to Flight Crew Photo Session; 2) Tile Repair Training on Precision Air Bearing Floor; 3) SAFER Tile Inspection Training in Virtual Reality Laboratory; 4) Guidance and Navigation Simulator Tile Survey Training; 5) Crew Inspects Orbital Boom and Sensor System (OBSS); 6) Bailout Training-Crew Compartment; 7) Emergency Egress Training-Crew Compartment Trainer (CCT); 8) Water Survival Training-Neutral Buoyancy Lab (NBL); 9) Ascent Training-Shuttle Motion Simulator; 10) External Tank Photo Training-Full Fuselage Trainer; 11) Rendezvous and Docking Training-Shuttle Engineering Simulator (SES) Dome; 12) Shuttle Robot Arm Training-SES Dome; 13) EVA Training Virtual Reality Lab; 14) EVA Training Neutral Buoyancy Lab; 15) EVA-2 Training-NBL; 16) EVA Tool Training-Partial Gravity Simulator; 17) Cure in Place Ablator Applicator (CIPAA) Training Glove Vacuum Chamber; 16) Crew Visit to Merritt Island Launch Area (MILA); 17) Crew Inspection-Space Shuttle Discovery; and 18) Crew Inspection-External Tank and Orbital Boom and Sensor System (OBSS). The crew are then seen answering questions from the media at the Space Shuttle Landing Facility.
Low-leakage seals are an enabling technology for future lunar surface systems, and they must be kept clean to ensure that crews have sufficient breathable air for extended lunar surface missions. Previous testing on representative state-of-the-art seals showed that while seals can tolerate some level of lunar simulant dust contamination, dust can degrade seal performance to a point at which seal leak rates exceed maximum allowable values. The ability to clean simulant from seals had not been thoroughly studied, and the effectiveness and potential complications of using different cleaning methods for lunar seals were not well understood. To address this knowledge gap, researchers at the NASA Glenn Research Center executed a multiphase study to better understand and mitigate seal dust-exposure risks. The focus of this report is on the second phase of that study, in which tests were conducted to evaluate the viability of seal cleaning methods for use in the lunar environment. Multiple methods for cleaning seals contaminated with lunar simulant were assessed for cleaning effectiveness and viability for use in the lunar environment. Leak tests were performed on seals after they were cleaned to determine whether leak rates could be brought back to acceptable levels, and cleaned seals were examined to determine whether their surfaces had been damaged by the cleaning processes. This phase of the study also investigated changes in the seals’ adhesion forces as a result of contamination and cleaning.
Components of an integrated system having all functions for model preparation and generation, image computation and scene generation, and collision detection and reporting for the visual simulation of space shuttle maneuvers and its interaction with the manipular arm and other objects, as well as during earth landing exercises are described. High surface solution by range priority allows for correct views of dynamically moving objects from any viewpoint. Smooth shading, anti-aliasing and edge smoothing techniques provide a high quality picture. The collision detection system allows for simulation of impenetrable objects and docking maneuvers, and the modeling systems permit production of new data bases for desired simulations.