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Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)n (n = 30 and 31) show that the salt-dependent free energy gap, ΔGS, between the ground (perfect hairpin) and the excited state (slipped hairpin (SH) with one CAG overhang) of the monomer for (n even) is the primary factor that determines the rates and yield of self-assembly. For odd n, the free energy (GS) of the ground state, which is an SH, is used to predict the self-association kinetics. As the monovalent salt concentration, CS, increases, ΔGS and GS increase, which decreases the rates of dimer formation. In contrast, ΔGS for shuffled sequences, with the same length and sequence composition as (CAG)31, is larger, which suppresses their propensities to aggregate. Although demonstrated explicitly for (CAG) polymers, the finding of inverse correlation between the free energy gap and RNA aggregation is general.
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This content will become publicly available on December 1, 2025
Multisite gates for state preparation in quantum simulation of the Bose-Hubbard model
We construct a sequence of multisite gates which transform an easily constructed product state into an approx- imation to the superfluid ground state of the Bose-Hubbard model. The mapping is exact in the one-dimensional hard-core limit and for noninteracting particles in both one and two dimensions. The gate sequence has other applications, such as being used as part of a many-body interferometer which probes the existence of doublons.
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- Award ID(s):
- 2409403
- PAR ID:
- 10609834
- Publisher / Repository:
- American Physical Society
- Date Published:
- Journal Name:
- Physical Review A
- Volume:
- 110
- Issue:
- 6
- ISSN:
- 2469-9926
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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