Home

Publication

First-order coil-globule transition driven by vibrational entropy

About
Privacy
Disclaimer

Graph Chatbot

Related publications (35)

Page 2 of 2

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

Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications

Che Yang

Evolution has created, selected and evolved large repertoires of proteins that operate in various biological systems. Nowadays biotechnological needs are coming up orders of magnitude faster than proteins naturally evolve. The emergence of de novo protein ...

EPFL2020

Structural and Dynamical Properties of Potassium Dodecahydro-monocarba-closo-dodecaborate: KCB11H12

Mirjana Dimitrievska

MCB11H12 (M: Li, Na) dodecahydro-monocarba-closo-dodecaborate salt compounds are known to have stellar superionic Li+ and Na+ conductivities in their high-temperature disordered phases, making them potentially appealing electrolytes in all-solid-state batt ...

AMER CHEMICAL SOC2020

From the Principle of Inertia to the Death Drive: The Influence of the Second Law of Thermodynamics on the Freudian Theory of the Psychical Apparatus

Pierre Magistretti, Jean-Philippe Ansermet

In the Freudian theory of the psychical apparatus, the introduction from the 1920s onward of the second drive dualism appears as a major turning point. The idea of a "death drive," first expressed in Beyond the Pleasure Principle (Freud, 1920), is generall ...

Frontiers Media2020

Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?

Matteo Dal Peraro, Luciano Andres Abriata

Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) h ...

AMER CHEMICAL SOC2020

Room-temperature skyrmion phase in bulk Cu2OSeO3 under high pressures

Helmuth Berger

A skyrmion state in a noncentrosymmetric helimagnet displays topologically protected spin textures with profound technological implications for high-density information storage, ultrafast spintronics, and effective microwave devices. Usually, its equilibri ...

National Academy of Sciences2020

Entropy production in master equations and Fokker-Planck equations: facing the coarse-graining and recovering the information loss

Daniel Maria Busiello, Amos Maritan

Systems operating out of equilibrium exchange energy and matter with the environment, thus producing entropy in their surroundings. Since the entropy production depends on the current flowing throughout the system, its quantification is affected by the lev ...

2019

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

Laura Piveteau, Claudia Esther Avalos

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

Determination and evaluation of the nonadditivity in wetting of molecularly heterogeneous surfaces

Francesco Stellacci, Michele Ceriotti, Sylvie Roke, Halil Ibrahim Okur, Quy Ong Khac, David Mark Wilkins, Zhi Luo, Anna Murello, Filip Kovacik

The interface between water and folded proteins is very complex. Proteins have "patchy" solvent-accessible areas composed of domains of varying hydrophobicity. The textbook understanding is that these domains contribute additively to interfacial properties ...

National Academy of Sciences2019

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

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck

BackgroundLarge-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological data at an unprecedented rate. The deta ...

2019

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

Entropy production for coarse-grained dynamics

Daniel Maria Busiello, Amos Maritan

Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master equation (ME) that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We show that the ...

2019