Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequence design”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

Impact of restructuring on Space Station Freedom assembly sequence

The Space Station Freedom program and the process used to develop an assembly sequence are overviewed, with special attention given to the outcome of the recent restructuring activity and the positive impact it had on the Space Station design and the assembly sequence. The many technically complex and challenging aspects of the assembly sequence planning are examined, including the launch vehicle integration, the spacecraft systems capability development, and the availability of resources. It is shown that the restructuring reduced the size and the complexity of the Space Station, while the increase of ground integration through the use of preintegrated truss and shortened modules offers a reduced program risk and reduced demands on the STS.

Chung, Steven Y.↗
DOE OSTI2021

Neural networks to learn protein sequence–function relationships from deep mutational scanning data

Understanding the relationship between protein sequence and function is necessary to design new and useful proteins with applications in bioenergy, medicine, and agriculture. The mapping from sequence to function is tremendously complex because it involves thousands of molecular interactions that are coupled over multiple lengths and timescales. We show that neural networks can learn the sequence–function mapping from large protein datasets. Neural networks are appealing for this task because they can learn complicated relationships from data, make few assumptions about the nature of the sequence–function relationship, and can learn general rules that apply across the length of the protein sequence. We demonstrate that learned models can be applied to design new proteins with properties that exceed natural sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development of a Systematic and Extensible Force Field for Peptoids (STEPs)

Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. In conclusion, equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1984

Modular design attitude control system

A sequence of single axismodels and a series of reduced state linear observers of minimum order are used to reconstruct inaccessible variables pertaining to the modular attitude control of a rigid body flexible suspension model of a flexible spacecraft. The single axis models consist of two, three, four, and five rigid bodies, each interconnected by a flexible shaft passing through the mass centers of the bodies. Modal damping is added to each model. Reduced state linear observers are developed for synthesizing the inaccessible modal state variables for each modal model.

Chichester, F. D.↗
NASA NTRS1995

Cascade Optimization Strategy Maximizes Thrust for High-Speed Civil Transport Propulsion System Concept

The design of a High-Speed Civil Transport (HSCT) air-breathing propulsion system for multimission, variable-cycle operations was successfully optimized through a soft coupling of the engine performance analyzer NASA Engine Performance Program (NEPP) to a multidisciplinary optimization tool COMETBOARDS that was developed at the NASA Lewis Research Center. The design optimization of this engine was cast as a nonlinear optimization problem, with engine thrust as the merit function and the bypass ratios, r-values of fans, fuel flow, and other factors as important active design variables. Constraints were specified on factors including the maximum speed of the compressors, the positive surge margins for the compressors with specified safety factors, the discharge temperature, the pressure ratios, and the mixer extreme Mach number. Solving the problem by using the most reliable optimization algorithm available in COMETBOARDS would provide feasible optimum results only for a portion of the aircraft flight regime because of the large number of mission points (defined by altitudes, Mach numbers, flow rates, and other factors), diverse constraint types, and overall poor conditioning of the design space. Only the cascade optimization strategy of COMETBOARDS, which was devised especially for difficult multidisciplinary applications, could successfully solve a number of engine design problems for their flight regimes. Furthermore, the cascade strategy converged to the same global optimum solution even when it was initiated from different design points. Multiple optimizers in a specified sequence, pseudorandom damping, and reduction of the design space distortion via a global scaling scheme are some of the key features of the cascade strategy. HSCT engine concept, optimized solution for HSCT engine concept. A COMETBOARDS solution for an HSCT engine (Mach-2.4 mixed-flow turbofan) along with its configuration is shown. The optimum thrust is normalized with respect to NEPP results. COMETBOARDS added value in the design optimization of the HSCT engine.

Source record↗
NASA NTRS1968

A Computer Program for Simplifying Incompletely Specified Sequential Machines Using the Paull and Unger Technique

This report presents a description of a computer program mechanized to perform the Paull and Unger process of simplifying incompletely specified sequential machines. An understanding of the process, as given in Ref. 3, is a prerequisite to the use of the techniques presented in this report. This process has specific application in the design of asynchronous digital machines and was used in the design of operational support equipment for the Mariner 1966 central computer and sequencer. A typical sequential machine design problem is presented to show where the Paull and Unger process has application. A description of the Paull and Unger process together with a description of the computer algorithms used to develop the program mechanization are presented. Several examples are used to clarify the Paull and Unger process and the computer algorithms. Program flow diagrams, program listings, and a program user operating procedures are included as appendixes.

Ebersole, M. M.↗
NASA NTRS1985

Design of suboptimal regulators for nonlinear systems

An optimal feedback control law is preferred for the regulation of a deterministic nonlinear system. In this paper, a practical, iterative design method leading to a sequence of suboptimal control laws with successively improved performance is presented. The design method requires the determination of an upper bound to the performance of each successive control law. This is obtained by solving a partial differential inequality by means of a linear programming technique. Robustness properties and the application of the design method to the control of a robot manipulator arm are also presented.

Balaram, J.↗
DOE OSTI2024

Design of intrinsically disordered protein variants with diverse structural properties

Intrinsically disordered proteins (IDPs) perform a broad range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Computational design of IDPs with specific conformational properties has, however, been difficult because of their substantial dynamics and structural complexity. We describe a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs that differ in compaction, long-range contacts, and propensity to phase separate. We experimentally tested and validated our designs and analyzed the sequence features that determine conformations. We show how our results are captured by a machine learning model, enabling us to speed up the algorithm. Our work expands the toolbox for computational protein design and will facilitate the design of proteins whose functions exploit the many properties afforded by protein disorder.

Science & Technology - Other Topics↗
DOE OSTI2026

DIVA/DeviceEditor v6.1.2

DIVA is an end-to-end DNA design and construction management platform that streamlines how researchers design, build, and receive sequence-verified DNA constructs. Through a web-based BioCAD interface (DeviceEditor), researchers independently design DNA constructs and submit them to a centralized queue with a single action. Designs progress transparently through standardized states which allow researchers to track status and access finished constructs via a central DNA repository. Submitted designs are reviewed by dedicated staff for feasibility and optimization, reducing costly failures and improving downstream execution. Automated DNA assembly software optimizes construction strategies by reusing existing parts where possible and sourcing synthetic DNA only when needed. Standardized, sequence-agnostic assembly methods enable many independent constructs to be built in parallel using lab automation, dramatically increasing throughput. High-throughput next-generation sequencing is used to verify construct accuracy, with flexible platforms selected based on task requirements. Throughout the process, detailed success and failure data are captured and analyzed, enabling continuous improvement of assembly protocols. Compared to traditional, manual DNA construction workflows, DIVA offers higher scalability, transparency, reproducibility, and data-driven optimization.

Plahar, Hector [Lawrence Berkeley National Laborat↗
NASA NTRS1992

Stacking sequence optimization of simply supported laminates with stability and strain constraints

An integer programming formulation for the design of symmetric and balanced rectangular composite laminates with simply supported boundary conditions subject to buckling and strain constraints is presented. The design variables that define the stacking sequence of the laminate are ply-identity zero-one integers. The buckling constraint is linear in terms of the ply-identity design variables, but strains are nonlinear functions of these variables. A linear approximation is developed for the strain constraints so that the problem can be solved by sequential linearization using the branch and bound algorithm. Examples of graphite-epoxy plates under biaxial compression are presented. Optimum stacking sequences obtained using the linear approximation are compared with global optimum designs obtained using a genetic search procedure.

Nagendra, S.↗
NASA NTRS1972

Analytical design and performance studies of the nuclear light bulb engine

Analytical studies were conducted to investigate in detail the heat balance characteristics of the nuclear light bulb engine. Distributions of energy deposition to all engine components from the fission process, conduction and convection, and thermal radiation were considered. Where uncertainties in basic data or heat transfer characteristics were encountered, ranges of heat loads were calculated and reference values were selected. The influence of these heat loads on engine performance, space radiator requirements, and cooling sequence and cooling circuit designs was determined. The analyses resulted in revisions to the previously reported reference engine characteristics, principally in the heat loads to some engine components and in the cooling sequence. These revisions were incorporated in the engine dynamics digital computer simulation program. No significant changes occurred in the dynamic response of the engine to perturbations in fuel injection rate, reactivity or exhaust nozzle area.

Rodgers, R. J.↗
DOE OSTI2022

Comprehensive view of microscopic interactions between DNA-coated colloids

Abstract The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic understanding of DNA-mediated colloidal interactions. Here we use total internal reflection microscopy to measure in situ the interaction potential between DNA-coated colloids with nanometer resolution and the macroscopic melting behavior. The range and strength of the interaction are measured and linked to key material design parameters, including DNA sequence, polymer length, grafting density, and complementary fraction. We present a first-principles model that screens and combines existing theories into one coherent framework and quantitatively reproduces our experimental data without fitting parameters over a wide range of DNA ligand designs. Our theory identifies a subtle competition between DNA binding and steric repulsion and accurately predicts adhesion and melting at a molecular level. Combining experimental and theoretical results, our work provides a quantitative and predictive approach for guiding material design with DNA-nanotechnology and can be further extended to a diversity of colloidal and biological systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1991

Stacking-sequence optimization for buckling of laminated plates by integer programming

Integer-programming formulations for the design of symmetric and balanced laminated plates under biaxial compression are presented. Both maximization of buckling load for a given total thickness and the minimization of total thickness subject to a buckling constraint are formulated. The design variables that define the stacking sequence of the laminate are zero-one integers. It is shown that the formulation results in a linear optimization problem that can be solved on readily available software. This is in contrast to the continuous case, where the design variables are the thicknesses of layers with specified ply orientations, and the optimization problem is nonlinear. Constraints on the stacking sequence such as a limit on the number of contiguous plies of the same orientation and limits on in-plane stiffnesses are easily accommodated. Examples are presented for graphite-epoxy plates under uniaxial and biaxial compression using a commercial software package based on the branch-and-bound algorithm.

Haftka, Raphael T.↗
NASA NTRS2004

Polymorphic Electronic Circuits

Polymorphic electronics is a nascent technological discipline that involves, among other things, designing the same circuit to perform different analog and/or digital functions under different conditions. For example, a circuit can be designed to function as an OR gate or an AND gate, depending on the temperature (see figure). Polymorphic electronics can also be considered a subset of polytronics, which is a broader technological discipline in which optical and possibly other information- processing systems could also be designed to perform multiple functions. Polytronics is an outgrowth of evolvable hardware (EHW). The basic concepts and some specific implementations of EHW were described in a number of previous NASA Tech Briefs articles. To recapitulate: The essence of EHW is to design, construct, and test a sequence of populations of circuits that function as incrementally better solutions of a given design problem through the selective, repetitive connection and/or disconnection of capacitors, transistors, amplifiers, inverters, and/or other circuit building blocks. The evolution is guided by a search-and-optimization algorithm (in particular, a genetic algorithm) that operates in the space of possible circuits to find a circuit that exhibits an acceptably close approximation of the desired functionality. The evolved circuits can be tested by computational simulation (in which case the evolution is said to be extrinsic), tested in real hardware (in which case the evolution is said to be intrinsic), or tested in random sequences of computational simulation and real hardware (in which case the evolution is said to be mixtrinsic).

Stoica, Adrian↗
NASA NTRS2004

Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

interferometer↗
NASA NTRS1995

Weight distributions for turbo codes using random and nonrandom permutations

This article takes a preliminary look at the weight distributions achievable for turbo codes using random, nonrandom, and semirandom permutations. Due to the recursiveness of the encoders, it is important to distinguish between self-terminating and non-self-terminating input sequences. The non-self-terminating sequences have little effect on decoder performance, because they accumulate high encoded weight until they are artificially terminated at the end of the block. From probabilistic arguments based on selecting the permutations randomly, it is concluded that the self-terminating weight-2 data sequences are the most important consideration in the design of constituent codes; higher-weight self-terminating sequences have successively decreasing importance. Also, increasing the number of codes and, correspondingly, the number of permutations makes it more and more likely that the bad input sequences will be broken up by one or more of the permuters. It is possible to design nonrandom permutations that ensure that the minimum distance due to weight-2 input sequences grows roughly as the square root of (2N), where N is the block length. However, these nonrandom permutations amplify the bad effects of higher-weight inputs, and as a result they are inferior in performance to randomly selected permutations. But there are 'semirandom' permutations that perform nearly as well as the designed nonrandom permutations with respect to weight-2 input sequences and are not as susceptible to being foiled by higher-weight inputs.

Dolinar, S.↗
NASA NTRS2015

Attitude Design for the LADEE Mission

The Lunar Atmosphere and Dust Environment Explorer (LADEE) satellite successfully completed its 148-day science investigation in a low-altitude, near-equatorial lunar orbit on April 18, 2014. The LADEE spacecraft was built, managed and operated by NASA's Ames Research Center (ARC). The Mission Operations Center (MOC) was located at Ames and was responsible for activity planning, command sequencing, trajectory and attitude design, orbit determination, and spacecraft operations. The Science Operations Center (SOC) was located at Goddard Space Flight Center and was responsible for science planning, data archiving and distribution. This paper details attitude design and operations support for the LADEE mission. LADEE's attitude design was shaped by a wide range of instrument pointing requirements that necessitated regular excursions from the baseline one revolution per orbit "Ram" attitude. Such attitude excursions were constrained by a number of flight rules levied to protect instruments from the Sun, avoid geometries that would result in simultaneous occlusion of LADEE's two star tracker heads, and maintain the spacecraft within its thermal and power operating limits. To satisfy LADEE's many attitude requirements and constraints, a set of rules and conventions was adopted to manage the complexity of this design challenge and facilitate the automation of ground software that generated pointing commands spanning multiple days of operations at a time. The resulting LADEE Flight Dynamics System (FDS) that was developed used Visual Basic scripts that generated instructions to AGI's Satellite Tool Kit (STK) in order to derive quaternion commands at regular intervals that satisfied LADEE's pointing requirements. These scripts relied heavily on the powerful "align and constrain" capability of STK's attitude module to construct LADEE's attitude profiles and the slews to get there. A description of the scripts and the attitude modeling they embodied is provided. One particular challenge analysts faced was in the design of LADEE maneuver attitudes. A flight rule requiring pre-maneuver verification of in-flight maneuver conditions by ground operators prior to burn execution resulted in the need to accommodate long periods in the maneuver attitude. This in turn complicated efforts to satisfy star tracker interference and communication constraints in lunar orbit. In response to this challenge, a graphical method was developed and used to survey candidate rotation angles about the thrust vector. This survey method is described and an example of its use on a particular LADEE maneuver is discussed. Finally, the software and methodology used to satisfy LADEE's attitude requirements are also discussed in the context of LADEE's overall activity planning effort. In particular, the way in which strategic schedules of instrument and engineering activities were translated into actual attitude profiles at the tactical level, then converted into precise quaternion commands to achieve those pointing goals is explained. In order to reduce the risk of time-consuming re-planning efforts, this process included the generation of long-term projections of constraint violation predictions for individual attitude profiles that could be used to establish keep-out time-frames for particular attitude profiles. The challenges experienced and overall efficacy of both the overall LADEE ground system and the attitude components of the Flight Dynamics System in meeting LADEE's varied pointing requirements are discussed.

LADEE↗
DOE OSTI2025

Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers

Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.

Disulfides↗