Related papers: The dynamical transition in proteins and non-Gauss…
Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale…
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 paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…
The traditional picture of heat transfer in solids by atomic vibrations, also known as phonons, involves phonons scattering with each other like gas particles and is commonly referred to as the phonon gas model (PGM). This physical picture…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
The $\beta$-relaxation associated with the sub-glass transition temperature ($T_{\text{g},\beta}$) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature ($T_{g\alpha}$). Despite…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
A sharp change in apparent mobility at a characteristic temperature that depends on the observation time has been reported in experiments and simulations of hydrated proteins. Such behavior is often discussed in the context of the protein…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
It was shown recently that smooth and continuous "Matsubara" phase-space loops follow a quantum-Boltzmann-conserving classical dynamics when decoupled from non-smooth distributions, which was suggested as the reason that many dynamical…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
This work concerns the theoretical description of the quantum dynamics of molecular junctions with thermal fluctuations and probability losses To this end, we propose a theory for describing non-Hermitian quantum systems embedded in…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Vibrational energy transfer of the amide I mode of N-methylacetamide (NMA) is studied theoretically using the vibrational configuration interaction method. A quartic force field of NMA is constructed at the B3LYP/6-31G+(d) level of theory…
Since 2014 the layered semiconductor SnSe in the high-temperature Cmcm phase is known to be the most efficient thermoelectric material. Making use of first-principles calculations we show that its vibrational and thermal transport…