Search NASA⌕ Search

SEARCH · Search NASA

Results for “minimum free energy secondary structure”

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.

3 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Dynamic programming algorithms within the NUPACK software suite enable analysis of equilibrium base-pairing properties for complex and test tube ensembles containing arbitrary numbers of interacting nucleic acid strands. Currently, calculations are limited to single-material systems that are either all-RNA or all-DNA. Here, to enable analysis of mixed-material systems that are critical for modern applications in vitro, in situ, and in vivo, we develop physical models and dynamic programming algorithms that allow the material of the system to be specified at nucleotide resolution. Free energy parameter sets are constructed for both RNA/DNA and RNA/2'OMe-RNA mixed-material systems by combining available empirical mixed-material parameters with single-material parameter sets to enable treatment of the full complex and test tube ensembles. New dynamic programming recursions account for the material of each nucleotide throughout the recursive process. For a complex with N nucleotides, the mixed-material dynamic programming algorithms maintain the O(N 3 ) time complexity of the single-material algorithms, enabling efficient calculation of diverse physical quantities over complex and test tube ensembles (e.g., complex partition function, equilibrium complex concentrations, equilibrium base-pairing probabilities, minimum free energy secondary structure(s), and Boltzmann-sampled secondary structures) at a cost increase of roughly 2.0-3.5×. The results of existing single-material algorithms are exactly reproduced when applying the new mixed-material algorithms to single-material systems. Accuracy is significantly enhanced using mixed-material models and algorithms to predict RNA/DNA and RNA/2'OMe-RNA duplex melting temperatures from the experimental literature as well as RNA/DNA melt profiles from new experiments. In conclusion, mixed-material analyses can be performed online using the NUPACK web app (www.nupack.org) or locally using the NUPACK Python module.

2′OMe-RNA↗
NASA NTRS2001

Shielded Heavy-Ion Environment Linear Detector (SHIELD): an experiment for the Radiation and Technology Demonstration (RTD) Mission

Radiological assessment of the many cosmic ion species of widely distributed energies requires the use of theoretical transport models to accurately describe diverse physical processes related to nuclear reactions in spacecraft structures, planetary atmospheres and surfaces, and tissues. Heavy-ion transport models that were designed to characterize shielded radiation fields have been validated through comparison with data from thick-target irradiation experiments at particle accelerators. With the RTD Mission comes a unique opportunity to validate existing radiation transport models and guide the development of tools for shield design. For the first time, transport properties will be measured in free-space to characterize the shielding effectiveness of materials that are likely to be aboard interplanetary space missions. Target materials composed of aluminum, advanced composite spacecraft structure and other shielding materials, helium (a propellant) and tissue equivalent matrices will be evaluated. Large solid state detectors will provide kinetic energy and charge identification for incident heavy-ions and for secondary ions created in the target material. Transport calculations using the HZETRN model suggest that 8 g cm -2 thick targets would be adequate to evaluate the shielding effectiveness during solar minimum activity conditions for a period of 30 days or more.

NASA Center LaRC↗
DOE OSTI2025

Diffusion Monte Carlo Study of the Structure and Spectroscopy of H 3 O –

A potential energy surface for H 3 O – has been developed based on the NN+(MOB-ML) approach we developed for studies of complexes of OH – with two or three water molecules. Unlike those systems, H 3 O – has two low-energy isomers, H – ·H 2 O and OH – ·H 2 , which differ in energy by less than 2.5 kcal mol –1 , and which are separated by a barrier of roughly 4.5 kcal mol –1 . We find that by training the NN+(MOB-ML) model using structures based on diffusion Monte Carlo (DMC) simulations initiated in the two potential minima, we are able to obtain a potential surface that describes both isomers. Using these potentials, the structure and spectra of H 3 O – and its deuterated analogues are investigated using DMC. These calculations show that the ground state wave function for H 3 O – is mainly localized in the H – ·H 2 O minimum in the potential, with a small amount of the probability amplitude (<5%) in the region of the OH – ·H 2 minimum. The delocalization of the wave function into the secondary minimum is lowered by deuteration of the water molecule, while replacing H – with D – increases the isomerization due to the shortening of the average distance between the hydride ion and the hydrogen atom in water to which it is bound. Introducing one quantum of excitation in the H – ···H 2 O stretching vibration increases the amount of isomerization, while the isomerization decreases with additional excitation of this mode. Excitation of the free OH stretch in the water molecule also increases the amount of isomerization, while excitation of the out-of-plane bending vibration suppresses the isomerization. Furthermore, the effects of partial deuteration on the frequencies for these vibrations are also explored.

Chemical structure↗