arXiv subjects

Paolo Rissone

Publications and source records attributed to Paolo Rissone.

8 recordsLinked to original sources

arXiv2026

Cluster-based Message-Passing (CluMP) Optimization for Complex QUBO Problems

Quadratic Unconstrained Boolean Optimization (QUBO) problems are widespread in both industrial applications and scientific studies. A QUBO problem corresponds to the optimization of a system of Ising spins defined on a generally sparse and heterogeneous graph. When the QUBO problem contains conflicting requests, the corresponding Ising system is frustrated, generating a complex energy landscape, which is hard to explore and optimize. Despite extensive algorithmic and hardware developments, finding low-energy configurations in these systems remains challenging (e.g., local-update heuristics typically become trapped in metastable states), especially when the (possibly frustrated) interactions generate extended correlated domains. We introduce CluMP (Cluster-based Message-Passing), an algorithm that performs collective updates on connected clusters of spins using information from Belief Propagation (BP). By controlling the amount of frustration within clusters, CluMP enables BP convergence on large subgraphs and proposes nonlocal rearrangements involving up to hundreds of spins in a single move. We benchmark CluMP against state-of-the-art local-update heuristics on spin-glass models defined on several graph topologies, including random regular graphs and lattice regular graphs in two and three dimensions. Cluster moves consistently bypass local trapping and reach lower energies with fewer effective operations than single-spin dynamics. These results demonstrate that frustration-tolerant cluster updates can be implemented efficiently on sparse graphs. The CluMP framework provides a scalable strategy for large-scale combinatorial optimization and inference problems, where exploiting medium- and long-range correlations is key to navigating complex energy landscapes.

cond-mat.dis-nn↗

arXiv2024

DNA Calorimetric Force Spectroscopy at Single Base Pair Resolution

DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have been done in melting experiments in bulk, of limited resolution due to ensemble averaging. In contrast, single-molecule methods have reached the maturity to derive DNA thermodynamics with unprecedented accuracy. We combine single-DNA mechanical unzipping experiments using a temperature jump optical trap with machine learning methods and derive the temperature-dependent DNA energy parameters of the NN model. In particular, we measure the previously unknown ten heat-capacity change parameters $ΔC_p$, relevant for thermodynamical predictions throughout the DNA stability range. Calorimetric force spectroscopy establishes a groundbreaking methodology to accurately study nucleic acids, from chemically modified DNA to RNA and DNA/RNA hybrid structures.

q-bio.BM↗

arXiv2024

Universal Cold RNA Phase Transitions

RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick RNA hairpins, the most basic secondary structure elements, undergo a glass-like transition below $\mathbf{T_G\sim 20 ^{\circ}}$C where the heat capacity abruptly changes and the RNA folds into a diversity of misfolded structures. We hypothesize that an altered RNA biochemistry, determined by sequence-independent ribose-water interactions, outweighs sequence-dependent base pairing. The ubiquitous ribose-water interactions lead to universal RNA phase transitions below $\mathbf{T_G}$, such as maximum stability at $\mathbf{T_S\sim 5 ^{\circ}}$C where water density is maximum, and cold denaturation at $\mathbf{T_C\sim-50^{\circ}}$C. RNA cold biochemistry may have a profound impact on RNA function and evolution.

q-bio.BM↗

arXiv2023

Experimental test of Sinai's model in DNA unzipping

The experimental measurement of correlation functions and critical exponents in disordered systems is key to testing renormalization group (RG) predictions. We mechanically unzip single DNA hairpins with optical tweezers, an experimental realization of the diffusive motion of a particle in a one-dimensional random force field, known as the Sinai model. We measure the unzipping forces $F_w$ as a function of the trap position $w$ in equilibrium and calculate the force-force correlator $Δ_m(w)$, its amplitude, and correlation length, finding agreement with theoretical predictions. We study the universal scaling properties since the effective trap stiffness $m^2$ decreases upon unzipping. Fluctuations of the position of the base pair at the unzipping junction $u$ scales as $u \sim m^{-ζ}$, with a roughness exponent $ ζ=1.34\pm0.06$, in agreement with the analytical prediction $ζ= \frac{4}{3}$. Our study provides a single-molecule test of the functional RG approach for disordered elastic systems in equilibrium.

cond-mat.dis-nn↗

arXiv2023

Unraveling RNA by Mechanical Unzipping

We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying experimental conditions. Energy measurements permit us to characterize the thermodynamics of RNA hybridization (base pairing and stacking), the dynamics of the formation of native and kinetic (intermediates and misfolded) molecular states, and interactions with metallic ions. This paper introduces basic concepts and reviews recent developments related to RNA force thermodynamics, native and barrier RNA energy landscapes, and RNA folding dynamics. We emphasize the implications of mechanical unzipping experiments to understand non-coding RNAs and RNAs in extreme environments.

cond-mat.soft↗

arXiv2022

Stem-loop formation drives RNA folding in mechanical unzipping experiments

Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force-distance curves (FDCs) exhibit strong irreversible effects with hysteresis and several intermediates, precluding the extraction of the NNBP energies with currently available methods. The combination of a suitable RNA synthesis with a tailored pulling protocol allowed us to obtain the fully reversible FDCs necessary to derive the NNBP energies. We demonstrate the equivalence of sodium and magnesium free-energy salt corrections at the level of individual NNBP. To characterize the irreversibility of the unzipping-rezipping process, we introduce a barrier energy landscape of the stem-loop structures forming along the complementary strands, which compete against the formation of the native hairpin. This landscape correlates with the hysteresis observed along the FDCs. RNA sequence analysis shows that base stacking and base pairing stabilize the stem-loops that kinetically trap the long-lived intermediates observed in the FDC. Stem-loops formation appears as a general mechanism to explain a wide range of behaviors observed in RNA folding.

q-bio.BM↗

arXiv2021

Long-Range Anomalous Decay of the Correlation in Jammed Packings

We numerically study the structure of the interactions occurring in three-dimensional systems of hard spheres at jamming, focusing on the large-scale behavior. Given the fundamental role they play in the configuration of jammed packings, we analyze the propagation through the system of the weak forces and of the variation of the coordination number with respect to the isostaticity condition $ΔZ$. We show that these correlations can be successfully probed by introducing a correlation function weighted on the density-density fluctuations. The results of this analysis can be further improved by introducing a representation of the system based on the contact points between particles. In particular, we find evidence that the weak forces and the $ΔZ$ fluctuations support the hypothesis of randomly jammed packings of spherical particles being hyperuniform by exhibiting an anomalous long-range decay. Moreover, we find that the large-scale structure of the density-density correlation exhibits a complex behavior due to the superimposition of two exponentially damped oscillating signals propagating with linearly depending frequencies.

cond-mat.soft↗

arXiv2019

Efficient methods for determining folding free energies in single-molecule pulling experiments

The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in nonequilibrium pulling experiments has become a benchmark in modern biophysics. In practice, the use of fluctuation relations to determine free energies requires a thorough evaluation of the usually large energetic contributions caused by the elastic deformation of the different elements of the experimental setup (such as the optical trap, the molecular linkers and the stretched-unfolded polymer). We review and describe how to optimally estimate such elastic energy contributions to extract folding free energies, using DNA and RNA hairpins as model systems pulled by laser optical tweezers. The methodology is generally applicable to other force-spectroscopy techniques and molecular systems.

q-bio.BM↗