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First-order coil-globule transition driven by vibrational entropy

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Tensor network investigation of frustrated Ising models

Jeanne Colbois

In spin systems, geometrical frustration describes the impossibility of minimizing simultaneously all the interactions in a Hamiltonian, often giving rise to macroscopic ground-state degeneracies and emergent low-temperature physics. In this thesis, combin ...

EPFL2022

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

PUBLIC LIBRARY SCIENCE2022

Second harmonic scattering of water in a biological context

Tereza Schönfeldová

Water is one of the most abundant molecules in the universe. It forms a hydrogen bond network with unique structure and dynamics. Hydrogen bonding is highly relevant to many biological processes including membrane formation, protein folding, adsorption, an ...

EPFL2022

Enhanced Room-Temperature Ionic Conductivity of NaCB11H12 via High-Energy Mechanical Milling

Laura Piveteau, Claudia Esther Avalos, Radovan Cerny, Matteo Brighi

The body-centered cubic (bcc) polymorph of NaCB11H12 has been stabilized at room temperature by highenergy mechanical milling. Temperature-dependent electrochemical impedance spectroscopy shows an optimum at 45-min milling time, leading to an rt conductivi ...

AMER CHEMICAL SOC2021

Control and Characterization of the Compactness of Single-Chain Nanoparticles

Francesco Stellacci, Luciano Andres Abriata, Lixia Wei, Suiyang Liao

Polymers when self-cross-linked into single-chain nanoparticles bear some resemblance to folded proteins; yet proteins have clear energy landscapes that determine precisely folded structures, while single-chain polymer nanoparticles (SCNPs) have more undef ...

American Chemical Society2021

Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization

Matteo Dal Peraro, Luciano Andres Abriata

Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...

2021

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Jaume Bonet Martinez

BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...

2021

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...

OXFORD UNIV PRESS2021

Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

David Lyndon Emsley, Jayasubba Reddy Yarava, Andrea Bertarello, Baptiste Busi, François Freymond

Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R-1) measurements to determine the hierarchical activation energies of motions of fou ...

AMER CHEMICAL SOC2021

Invariance principles in the theory and computation of transport coefficients

Federico Grasselli

In this work, we elaborate on two recently discovered invariance principles, according to which transport coefficients are, to a large extent, independent of the microscopic definition of the densities and currents of the conserved quantities being transpo ...

2021

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Tensor network investigation of frustrated Ising models

Jeanne Colbois

EPFL2022

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

PUBLIC LIBRARY SCIENCE2022

Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization

Matteo Dal Peraro, Luciano Andres Abriata

2021

Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

David Lyndon Emsley, Jayasubba Reddy Yarava, Andrea Bertarello, Baptiste Busi, François Freymond

AMER CHEMICAL SOC2021

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

OXFORD UNIV PRESS2021