Search NASA⌕ Search

SEARCH · Search NASA

Results for “dynamic simulations”

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 109 records · Page 6

Investigation of the iodate sorption mechanism by CoAl LDH through experiments and ab initio molecular dynamics simulations

Radioiodine released during the nuclear-fuel cycle constitutes a persistent radiological hazard. In this study, the IO 3 – uptake mechanism of CoAl LDH was resolved by combining pH-controlled sorption experiments, synchrotron XAFS, and DFT-based AIMD simulations. At pH close to 6, approximately 90% of IO 3 – was removed, and the equilibrium distribution coefficient reached about 1.7 × 10 4 mL g –1 . EXAFS analysis indicated an average iodine–oxygen bond length of 1.81 Å and a coordination number near 3, with the fit R-factor equal to 0.002. The simulations faithfully reproduced the experimental spectrum and revealed transient proton hopping events that generated metastable I–O–H species inside the interlayer, thereby confirming nitrate-to-iodate exchange as the controlling capture pathway. Atomic density profiles and radial distribution functions further showed that IO 3 – adopt an end-on orientation perpendicular to the hydroxide sheets, while water molecules mediate proton migration without disturbing the host lattice. In conclusion, the integrated experimental–computational evidence demonstrates that CoAl LDH can rapidly and selectively sequester IO 3 – under near-neutral conditions, offering atomic scale guidance for the rational engineering of layered sorbents for advanced radioactive-waste treatment.

Kang, Jaehyuk [Jeju National Univ. (Korea, Republi↗

Improved Treatment of 1–4 Interactions in Force Fields for Molecular Dynamics Simulations

Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled nonbonded interactions to capture 1-4 energies and forces of atoms separated by three bonds in a molecule. While this approach can yield accurate torsional energy barriers, it often leads to inaccurate forces and erroneous geometries and creates an interdependence between dihedral terms and nonbonded interactions, complicating parametrization and reducing transferability. Here, in this paper, we demonstrate that 1-4 interactions can be accurately modeled using only bonded coupling terms, eliminating the need for arbitrarily scaled nonbonded interactions altogether. Furthermore, by leveraging the automated parametrization capabilities of the Q-Force toolkit, we efficiently determine the necessary coupling terms without the need for manual adjustment. Our approach is first validated on a range of small molecule systems, encompassing both flexible and rigid structures, and shows a significant improvement in force field accuracy, obtaining subkcal/mol mean absolute error for every molecule tested. We further extend the bonded-only model for 1-4 interactions to Amber ff14sb, CHARMM36, and OPLS-AA force fields to reproduce ab initio gas and implicit solvent ϕ,ψ surfaces of alanine dipeptide.

Abdullah, Aalim S. [University of California, Berk↗

Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations

We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.

Do, Hung Nguyen↗

Summary of Jefferson Lab LDRD on FFA@CEBAF Beam Dynamics Simulations

As Thomas Jefferson National Accelerator Facility (Jefferson Lab) looks toward the future, we are considering expanding our energy reach by using Fixed-Field Alternating Gradient (FFA) technology. Significant efforts have been made to design a hybrid accelerator which combines conventional recirculating electron LINAC design with permanent magnet-based FFA technology to increase the number of beam recirculations, and thus the energy. In an effort to further this progress, Jefferson Lab awarded a Laboratory Directed Research and Development (LDRD) grant to focus not on the design, but on detailed simulations of the designs created by the larger collaboration. This document will summarize the work performed during this LDRD, and direct the reader to other proceedings which describe elements of the work in greater detail.

Deitrick, K.↗