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PubblicazioneUnique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA( 2025)Adenosine-to-inosine (A-to-I) editing is a highly abundant modification of double-stranded RNA (dsRNA) and plays an important role in posttranscriptional gene regulation. Editing of multiple inosines by the ADAR1 enzyme leads to A-to-I hyper-editing of non-coding dsRNA, such as 3'UTRs, transposable elements, or foreign pathogenic RNAs, and is implicated in immune response and human diseases including cancer. The structural consequences of hyper-editing and its role in protein binding are poorly understood. Here, we combine solution nuclear magnetic resonance spectroscopy (NMR), biophysical methods such as small-angle X-ray scattering, and molecular dynamics simulations to study the sequence-dependent effects on conformation and dynamics of A-to-I hyper-editing for a 20-mer dsRNA and recognition of such RNAs by Endonuclease V. By comparing non-edited, single-edited, and hyper-edited dsRNA, we identify unique conformational features and extensive dynamics associated with hyper-editing, resulting in significantly increased base-pair opening. Hyper-edited dsRNA is more extended and adopts a highly dynamic ensemble of canonical and non-canonical conformations, which lead to preferential binding by Endonuclease V. Our integrated experimental and computational analysis identifies unique structural and dynamic features that are likely linked to specific protein recognition and the unique biological consequences of hyper-editing.
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PubblicazioneAn observation on the existence of stable generalized complex structures on ruled surfaces( 2025)We point out that any stable generalized complex structure on a sphere bundle over a closed surface of genus at least two must be of constant type.
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PubblicazioneClifford-dressed variational principles for precise Loschmidt echoes( 2025)We extend the recently introduced Clifford-dressed time-dependent variational principle (TDVP) to efficiently compute many-body wave-function amplitudes in the computational basis. This advancement enhances the study of Loschmidt echoes, which generally require accurate calculations of the overlap between the evolved state and the initial wave function. By incorporating Clifford-disentangling gates during TDVP evolution, our method effectively controls entanglement growth while keeping the computation of these amplitudes accessible. Specifically, it reduces the problem to evaluating the overlap between a matrix product state (MPS) and a stabilizer state, a task that remains computationally feasible within the proposed framework. To demonstrate the effectiveness of this approach, we first benchmark it on the one-dimensional transverse-field Ising model. We then apply it to more challenging scenarios, including a nonintegrable next-to-nearest-neighbor Ising chain and a two-dimensional Ising model. Our results highlight the versatility and efficiency of the Clifford-augmented MPS, showcasing its capability to go beyond the evaluation of simple expectation values. This makes it a powerful tool for exploring various aspects of many-body quantum dynamics.
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PubblicazioneExploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations( 2025): Biomolecular condensates are currently recognized to play a key role in organizing cellular space and in orchestrating biochemical processes. Despite an increasing interest in characterizing their internal organization at the molecular scale, not much is known about how the densely crowded environment within these condensates affects the structural properties of recruited macromolecules. Here, we adopted explicit-solvent all-atom simulations based on a combination of enhanced sampling approaches to investigate how the conformational ensemble of an RNA hairpin is reshaped in a highly concentrated peptide solution that mimics the interior of a biomolecular condensate. Our simulations indicate that RNA structure is greatly perturbed by this distinctive physico-chemical environment, which weakens RNA secondary structure and promotes extended nonnative conformations. The resulting high-resolution picture reveals that RNA unfolding is driven by the effective solvation of nucleobases through hydrogen bonding and stacking interactions with surrounding peptides. This solvent effect can be modulated by the amino acid composition of the model condensate as proven by the differential RNA behavior observed in the case of arginine-rich and lysine-rich peptides.
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PubblicazioneVisuo-spatial reasoning in the human brain(SISSA, 2024-11-25)This thesis explores the brain correlates and contextual factors influencing visuo-spatial reasoning through Mental Rotation (MR) tasks in men and women. Visuo-spatial reasoning, a critical cognitive function, underpins everyday activities and is often assessed through MR tasks, where previous studies have shown gender differences favoring men. The research addresses the ongoing nature-nurture debate by examining the contributions of top-down (strategy-related), bottom-up (stimulus-related), and cognitive traits to MR performance and neural activation. Four experiments are conducted to: (1) investigate gender-specific strategy preferences in MR tasks; (2) characterize the neural correlates of MR and their modulation by imagery strategies; (3) compare brain activations related to different MR stimuli (abstract, manipulable, and bodily); and (4) assess the impact of individual cognitive traits on MR performance and brain activity. This comprehensive approach aims to provide deeper insights into the cognitive and neural mechanisms underlying gender differences in MR, with implications for understanding disparities in STEM-related fields.