Search NASA⌕ Search

SEARCH · Search NASA

Results for “permutation”

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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Permutable SOS (symmetry operational similarity)

Abstract Based on symmetry consideration, quasi-one-dimensional (1D) objects, relevant to numerous observables or phenomena, can be classified into eight different types. We provide various examples of each 1D type and discuss their symmetry operational similarity (SOS) relationships, which are often permutable. A number of recent experimental observations, including current-induced magnetization in polar or chiral conductors, non-linear Hall effect in polar conductors, spin-polarization of tunneling current to chiral conductors, and ferro-rotational domain imaging with linear gyration are discussed in terms of (permutable) SOS. In addition, based on (permutable) SOS, we predict a large number of new phenomena in low symmetry materials that can be experimentally verified in the future.

Materials Science↗
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 NTRS1986

Finite state model and compatibility theory - New analysis tools for permutation networks

A simple model to describe the fundamental operation theory of shuffle-exchange-type permutation networks, the finite permutation machine (FPM), is described, and theorems which transform the control matrix result to a continuous compatible vector result are developed. It is found that only 2n-1 shuffle exchange passes are necessary, and that 3n-3 passes are sufficient, to realize all permutations, reducing the sufficient number of passes by two from previous results. The flexibility of the approach is demonstrated by the description of a stack permutation machine (SPM) which can realize all permutations, and by showing that the FPM corresponding to the Benes (1965) network belongs to the SPM. The FPM corresponding to the network with two cascaded reverse-exchange networks is found to realize all permutations, and a simple mechanism to verify several equivalence relationships of various permutation networks is discussed.

Huang, S.-T.↗
DOE OSTI2023

Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables

The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques exist for data-driven discovery of CVs parameterizing the important large scale motions of the system. A challenge to CV discovery is learning CVs invariant to symmetries of the molecular system, frequently rigid translation, rigid rotation, and permutational relabeling of identical particles. Of these, permutational invariance has proved a persistent challenge in frustrating the data-driven discovery of multi-molecular CVs in systems of self-assembling particles and solvent-inclusive CVs for solvated systems. In this work, we integrate Permutation Invariant Vector (PIV) featurizations with autoencoding neural networks to learn nonlinear CVs invariant to translation, rotation, and permutation, and perform interleaved rounds of CV discovery and enhanced sampling to iteratively expand sampling of configurational phase space and obtain converged CVs and free energy landscapes. Here, we demonstrate the Permutationally Invariant Network for Enhanced Sampling (PINES) approach in applications to the self-assembly of a 13-atom Argon cluster, association/dissociation of a NaCl ion pair in water, and hydrophobic collapse of a C 45 H 92 n-pentatetracontane polymer chain. We make the approach freely available as a new module within the PLUMED2 enhanced sampling libraries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Permutation-adapted complete and independent basis for atomic cluster expansion descriptors

In many recent applications, particularly in the field of atom-centered descriptors for interatomic potentials, tensor products of spherical harmonics have been used to characterize complex atomic environments. When coupled with a radial basis, the atomic cluster expansion (ACE) basis is obtained. However, symmetrization with respect to both rotation and permutation results in an overcomplete set of ACE descriptors with linear dependencies occurring within blocks of functions corresponding to particular generalized Wigner symbols. All practical applications of ACE employ semi-numerical constructions to generate a complete, fully independent basis. While computationally tractable, the resultant basis cannot be expressed analytically, is susceptible to numerical instability, and thus has limited reproducibility. Here we present a procedure for generating explicit analytic expressions for a complete and independent set of ACE descriptors. The procedure uses a coupling scheme that is maximally symmetric w.r.t. permutation of the atoms, exposing the permutational symmetries of the generalized Wigner symbols, and yields a permutation-adapted rotationally and permutationally invariant basis (PA-RPI ACE). Theoretical support for the approach is presented, as well as numerical evidence of completeness and independence. A summary of explicit enumeration of PA-RPI functions up to rank 6 and polynomial degree 32 is provided. The PA-RPI blocks corresponding to particular generalized Wigner symbols may be either larger or smaller than the corresponding blocks in the simpler rotationally invariant basis. Finally, we demonstrate that basis functions of high polynomial degree persist under strong regularization, indicating the importance of not restricting the maximum degree of basis functions in ACE models a priori.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1972

Permutation codes for sources.

Source encoding techniques based on permutation codes are investigated. For a broad class of distortion measures it is shown that optimum encoding of a source permutation code is easy to instrument even for very long block lengths. Also, the nonparametric nature of permutation encoding is well suited to situations involving unknown source statistics. For the squared-error distortion measure a procedure for generating good permutation codes of a given rate and block length is described. The performance of such codes for a memoryless Gaussian source is compared both with the rate-distortion function bound and with the performance of various quantization schemes. The comparison reveals that permutation codes are asymptotically ideal for small rates and perform as well as the best entropy-coded quantizers presently known for intermediate rates. They can be made to compare favorably at high rates, too, provided the coding delay associated with extremely long block lengths is tolerable.

Berger, T.↗
NASA NTRS2004

A Versatile Platform for Nanotechnology Based on Circular Permutation of a Chaperonin Protein

A number of protein complexes have been developed as nanoscale templates. These templates can be functionalized using the peptide sequences that bind inorganic materials. However, it is difficult to integrate peptides into a specific position within a protein template. Integrating intact proteins with desirable binding or catalytic activities is an even greater challenge. We present a general method for modifying protein templates using circular permutation so that additional peptide sequence can be added in a wide variety of specific locations. Circular permutation is a reordering of the polypeptide chain such that the original termini are joined and new termini are created elsewhere in the protein. New sequence can be joined to the protein termini without perturbing the protein structure and with minimal limitation on the size and conformation of the added sequence. We have used this approach to modify a chaperonin protein template, placing termini at five different locations distributed across the surface of the protein complex. These permutants are competent to form the double-ring structures typical of chaperonin proteins. The permuted double-rings also form the same assemblies as the unmodified protein. We fused a fluorescent protein to two representative permutants and demonstrated that it assumes its active structure and does not interfere with assembly of chaperonin double-rings.

Paavola, Chad↗
NASA NTRS2004

Circular Permutation of a Chaperonin Protein: Biophysics and Application to Nanotechnology

We have designed five circular permutants of a chaperonin protein derived from the hyperthermophilic organism Sulfolobus shibatae. These permuted proteins were expressed in E. coli and are well-folded. Furthermore, all the permutants assemble into 18-mer double rings of the same form as the wild-type protein. We characterized the thermodynamics of folding for each permutant by both guanidine denaturation and differential scanning calorimetry. We also examined the assembly of chaperonin rings into higher order structures that may be used as nanoscale templates. The results show that circular permutation can be used to tune the thermodynamic properties of a protein template as well as facilitating the fusion of peptides, binding proteins or enzymes onto nanostructured templates.

Paavola, Chad↗
DOE OSTI2024

Permutation-adapted complete and independent basis for atomic cluster expansion descriptors

Atomic cluster expansion (ACE) methods provide a systematic way to describe particle local environments of arbitrary body order. For practical applications it is often required that the basis of cluster functions be symmetrized with respect to rotations and permutations. Existing methodologies yield sets of symmetrized functions that are over-complete. These methodologies thus require an additional numerical procedure, such as singular value decomposition (SVD), to eliminate redundant functions. In this work, it is shown that analytical linear relationships for subsets of cluster functions may be derived using recursion and permutation properties of generalized Wigner symbols. From these relationships, subsets (blocks) of cluster functions can be selected such that, within each block, functions are guaranteed to be linearly independent. It is conjectured that this block-wise independent set of permutation-adapted rotation and permutation invariant (PA-RPI) functions forms a complete, independent basis for ACE. Along with the first analytical proofs of block-wise linear dependence of ACE cluster functions and other theoretical arguments, numerical results are offered to demonstrate this. The utility of the method is demonstrated in the development of an ACE interatomic potential for tantalum. Using the new basis functions in combination with Bayesian compressive sensing sparse regression, some high degree descriptors are observed to persist and help achieve high-accuracy models.

Angular momentum↗
DOE OSTI2024

Efficient Unitary Designs from Random Sums and Permutations

A unitary k-design is an ensemble of unitaries that matches the first k moments of the Haar measure. In this work, we provide two efficient constructions of k-designs on n-qubits using new random matrix theory techniques. Our first construction is based on exponentiating sums of random i.i.d. Hermitian matrices and uses O(k2n2)-many gates. In the spirit of central limit theorems, we show that this random sum approximates the Gaussian Unitary Ensemble (GUE). We then show that the product of just two exponentiated GUE matrices is already approximately Haar random. Our second construction is based on products of exponentiated sums of random permutations and uses Õ(k poly (n)) many gates. The k dependence is optimal (up to polylogarithmic factors) and is inherited from the efficiency of existing k-wise independent permutations. Furthermore, replacing random permutations with quantum-secure pseudorandom permutations (PRPs), we also obtain a pseudorandom unitary (PRU) ensemble that is secure under nonadaptive queries. A central feature of both proofs is a new connection between the polynomial method in quantum query complexity and the large-dimension (N) expansion in random matrix theory. In particular, the first construction uses the polynomial method to control high moments of certain random matrix ensembles without requiring delicate Weingarten calculations. In doing so, we define and solve a moment problem on the unit circle, asking whether a finite number of equally weighted points can reproduce a given set of moments. In our second construction, the key step is to exhibit an orthonormal basis for irreducible representations of the partition algebra that has a low-degree large-N expansion. This allows us to show that the distinguishing probability is a low-degree rational polynomial of the dimension N.

algebra↗
DOE OSTI2025

Semi-supervised permutation invariant particle-level anomaly detection

The development of analysis methods to distinguish potential beyond the Standard Model phenomena in a model-agnostic way can significantly enhance the discovery reach in collider experiments. However, the typical machine learning (ML) algorithms employed for this task require fixed length and ordered inputs that break the natural permutation invariance in collision events. To address this, a semi-supervised anomaly detection tool is presented that takes a variable number of particle-level inputs and leverages a signal model to encode this information into a permutation invariant, event-level representation via supervised training with a Particle Flow Network (PFN). Data events are then encoded into this representation and given as input to an autoencoder for unsupervised ANomaly deTEction on particLe flOw latent sPacE (ANTELOPE), classifying anomalous events based on a low-level and permutation invariant input modeling. Performance of the ANTELOPE architecture is evaluated on simulated samples of hadronic processes in a high energy collider experiment, showing good capability to distinguish disparate models of new physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Permutationally Invariant Polynomial Expansions with Unrestricted Complexity

A general strategy is presented for constructing and validating permutationally invariant polynomial (PIP) expansions for chemical systems of any stoichiometry. Demonstrations are made for three categories of gas-phase dynamics and kinetics: collisional energy-transfer trajectories for predicting pressure-dependent kinetics, three-body collisions for describing transient van der Waals adducts relevant to atmospheric chemistry, and nonthermal reactivity via quasiclassical trajectories. In total, 30 systems are considered with up to 15 atoms and 39 degrees of freedom. Permutational invariance is enforced in PIP expansions with as many as 13 million terms and 13 permutationally distinct atom types by taking advantage of petascale computational resources. The quality of the PIP expansions is demonstrated through the systematic convergence of in-sample and out-of-sample errors with respect to both the number of training data and the order of the expansion, and these errors are shown to predict errors in the dynamics for both reactive and nonreactive applications. Here, the parallelized code distributed as part of this work enables the automation of PIP generation for complex systems with multiple channels and flexible user-defined symmetry constraints and for automatically removing unphysical unconnected terms from the basis set expansions, all of which are required for simulating complex reactive systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Five-point functions and the permutation group 𝑆 5

Five-point functions and five-body wave functions play an important role in many areas of nuclear and particle physics, e.g., in 2 →3 scattering processes, in the five-gluon vertex, or in the study of pentaquarks. In this work we consider the permutation group 𝑆 5 to facilitate the description of such objects. We work out the multiplets transforming under irreducible representations of 𝑆 5 and provide compact formulas allowing one to cast the permutations of an object 𝑓 12345 into combinations with definite permutation symmetry. We also give the explicit expressions for the irreducible multiplet products. We consider several practical applications as examples: We arrange the four-momenta and Lorentz invariants of a five-point function into the multiplet structure, we work out the color tensors of the five-gluon vertex in the multiplet notation, and we discuss applications for five-body wave functions like those of pentaquarks.

Bethe-Salpeter equation↗
DOE OSTI2024

High-dimensional and permutation invariant anomaly detection

Methods for anomaly detection of new physics processes are often limited to low-dimensional spaces due to the difficulty of learning high-dimensional probability densities. Particularly at the constituent level, incorporating desirable properties such as permutation invariance and variable-length inputs becomes difficult within popular density estimation methods. In this work, we introduce a permutation-invariant density estimator for particle physics data based on diffusion models, specifically designed to handle variable-length inputs. We demonstrate the efficacy of our methodology by utilizing the learned density as a permutation-invariant anomaly detection score, effectively identifying jets with low likelihood under the background-only hypothesis. To validate our density estimation method, we investigate the ratio of learned densities and compare to those obtained by a supervised classification algorithm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1989

A family of permutations for concurrent factorization of block tridiagonal matrices

The inherent strong seriality of closely coupled systems is circumvented by defining a family of permutations for reordering equation sets whose matrix of coefficients is Hermitian block tridiagonal. The authors show how these permutations can be used to achieve relatively high concurrency in the Cholesky factorization of banded systems at the expense of introducing limited extra computations due to fill-in terms in the factors. Directed graphs are developed for the concurrent factorization of the transformed matrix of coefficients by the Cholesky algorithm. Expressions for speedup and efficiency are derived in terms of parameters of the permutation, set of equations, and machine architecture.

Utku, Senol↗
DOE OSTI2019

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification

The ability to engineer natural proteins is pivotal to a future, pragmatic biology. CRISPR proteins have revolutionized genome modification, yet the CRISPR-Cas9 scaffold is not ideal for fusions or activation by cellular triggers. Here in this paper, we show that a topological rearrangement of Cas9 using circular permutation provides an advanced platform for RNA-guided genome modification and protection. Through systematic interrogation, we find that protein termini can be positioned adjacent to bound DNA, offering a straightforward mechanism for strategically fusing functional domains. Additionally, circular permutation enabled protease-sensing Cas9s (ProCas9s), a unique class of single-molecule effectors possessing programmable inputs and outputs. ProCas9s can sense a wide range of proteases, and we demonstrate that ProCas9 can orchestrate a cellular response to pathogen-associated protease activity. Together, these results provide a toolkit of safer and more efficient genome-modifying enzymes and molecular recorders for the advancement of precision genome engineering in research, agriculture, and biomedicine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Developing a circularly permuted variant of Renilla luciferase as a bioluminescent sensor for measuring Caspase-9 activity in the cell-free and cell-based systems

Highlights: • A luciferase based biosensor for measuring caspase-9 activity has been constructed using circular permutation strategy. • The designed biosensor detects the caspase-9 activity in a cell-free coupled assay system. • The designed biosensor can be implemented as a cell-based biosensor to detect cellular caspase-9 activity and apoptosis. Biosensors and whole cell biosensors consisting of biological molecules and living cells can sense a special stimulus on a living system and convert it to a measurable signal. A major group of them are the bioluminescent sensors derived from luciferases. This type of biosensors has a broad application in molecular biology and imaging systems. In this project, a luciferase-based biosensor for detecting and measuring caspase-9 activity is designed and constructed using the circular permutation strategy. The spectroscopic method results reveal changes in the biosensor structure. Additionally, its activity is examined in a cell-free coupled assay system. Afterward, the biosensor is utilized for measuring the cellular caspase-9 activity upon apoptosis induction in a cancer cell line. In following the gene of biosensor is sub-cloned into a eukaryotic vector and transfected to HEK293T cell line and then its activity is measured upon apoptosis induction in the presence and absence of a caspase-9 inhibitor. The obtained results show that the designed biosensor detects the caspase-9 activity in the cell-free and cell-based systems.

60 APPLIED LIFE SCIENCES↗