Related papers: Vibrational entropy and the structural organizatio…
We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…
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…
Protein function prediction is dominated by representations grounded in sequence and static structure, neither of which captures the collective vibrational dynamics through which proteins act. Here we introduce frequency-space mechanics, a…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…
Vibration signals have been increasingly utilized in various engineering fields for analysis and monitoring purposes, including structural health monitoring, fault diagnosis and damage detection, where vibration signals can provide valuable…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Calculating the vibrational entropy of an N-atom assembly in the harmonic approximation requires the diagonalisation of a large matrix. This operation becomes rapidly time consuming when increasing the dimensions of the simulation cell. In…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
We construct a new order parameter from the normal modes of vibration, based on the consideration of energy equipartition, to quantify the structural heterogeneity in disordered solids. The order parameter exhibits strong spatial…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
Modern engineering structures exhibit nonlinear vibration behavior as designs are pushed to reduce weight and energy consumption. Of specific interest here, joints in assembled structures introduce friction, hysteresis, and unilateral…
Collective protein modes are expected to be important for facilitating energy transfer in the Fenna-Matthews-Olson (FMO) complex, however to date little work has focussed on the microscopic details of these vibrations. The nonlinear network…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The vibrational behavior of molecules serves as a crucial fingerprint of their structure, chemical state, and surrounding environment. Neutron vibrational spectroscopy provides comprehensive measurements of vibrational modes without…
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
Structural Health Monitoring (SHM) plays an indispensable role in ensuring the longevity and safety of infrastructure. With the rapid growth of sensor technology, the volume of data generated from various structures has seen an…