相关论文: Ideal Glasses and Protein Network Dynamics

We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…

Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…

The interplay of slow dynamics and thermodynamic features of dense liquids is studied by examinining how the glass transition changes depending on the presence or absence of Lennard-Jones-like attractions. Quite different thermodynamic…

A comparative study of the dynamics of inherent structures at low temperatures is performed on different models of glass formers: a three dimensional Lennard-Jones binary mixture (LJBM), facilitated spin models (either symmetrically…

We propose a connection between self-similar, focusing dynamics in nonlinear partial differential equations (PDEs) and macroscopic dynamic features of the glass transition. In particular, we explore the divergence of the appropriate…

A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…

This paper gives an introduction and brief overview of some of our recent work on the equilibrium thermodynamics of glasses. We have focused onto first principle computations in simple fragile glasses, starting from the two body interatomic…

Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…

Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…

Many modern-day applications require the development of new materials with specific properties. In particular, the design of new glass compositions is of great industrial interest. Current machine learning methods for learning the…

Inorganic glasses, produced by the melt-quenching of a concoction of minerals, compounds, and elements, can possess unique optical and elastic properties along with excellent chemical, and thermal durability. Despite the ubiquitous use of…

Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…

The usefulness of glasses, and particularly of metallic glasses, in technological applications is often limited by their toughness, which is defined as the area under the stress vs. strain curve before plastic yielding. Recently toughness…

The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…

Vibrational spectra of proteins and topologically disordered solids display a common anomaly at low frequencies, known as Boson peak. We show that such feature in globular proteins can be deciphered in terms of an energy landscape picture,…

We provide a theoretical perspective on the glass transition in molecular liquids at thermal equilibrium, on the spatially heterogeneous and aging dynamics of disordered materials, and on the rheology of soft glassy materials. We start with…

Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…

connected spin-glass models with a discontinuous transition. In the thermodynamic limit the equilibrium properties in the high temperature phase are described by the schematic Mode Coupling Theory of super-cooled liquids. We show that {\it…

We analyse the relationship between dynamics and configuration space structure of Ising spin glass systems. The exact knowledge of the structure of the low--energy landscape is used to study the relaxation of the system by random walk in…

We present a detailed analysis of the ion hopping dynamics and the related nearby oxygen dynamics in a lithium meta silicate glass via molecular dynamics simulation. For this purpose we have developed numerical techniques to identify ion…