相关论文: Sidechain Dynamics and Protein Folding
The excitation-chain theory of the glass transition, proposed in an earlier publication, predicts diverging, super-Arrhenius relaxation times and, {\it via} a similarly diverging length scale, suggests a way of understanding the relations…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
We study the relaxation process in a two-dimensional lattice gas model, where the interactions come from the excluded volume. In this model particles have three arms with an asymmetrical shape, which results in geometrical frustration that…
A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the…
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
The structure of the self-cleaving hairpin ribozyme is well characterized, and its folding has been examined in bulk and by single-molecule fluorescence, establishing the importance of cations, especially magnesium in the stability of the…
Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
We study the relaxational dynamics of flux lines in high-temperature superconductors with random pinning using Langevin dynamics. At high temperatures the dynamics is stationary and the fluctuation dissipation theorem (FDT) holds. At low…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^\lambda$ at temperature of fastest folding.…
Ultracold dipolar particles pinned in optical lattices or tweezers provide an excellent platform for studying out-of-equilibrium quantum magnetism with dipole-mediated couplings. Starting with an initial state with spins of opposite…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
We combine the swap Monte Carlo algorithm to long multi-CPU molecular dynamics simulations to analyse the equilibrium relaxation dynamics of model supercooled liquids over a time window covering ten orders of magnitude for temperatures down…