Related papers: Hierarchical friction memory leads to subdiffusive…
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analyze both Markovian…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described…
We study the non-Markovian folding dynamics of the $\alpha$3D protein under low- and neutral-pH conditions. Recently published all-atom simulations of $\alpha$3D by the Shaw group reveal that lowering the pH significantly reduces both…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Friction is a phenomenon that manifests across all spatial and temporal scales, from the molecular to the macroscopic scale. It describes the dissipation of energy from the motion of particles or abstract reaction coordinates and arises in…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We investigate non-Markovian barrier-crossing kinetics of a massive particle in one dimension in the presence of a memory function that is the sum of two exponentials with different memory times $\tau_1$ and $\tau_2$. Our Langevin…
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…
We consider different Markovian embedding schemes of non-Markovian stochastic processes that are described by generalized Langevin equations (GLE) and obey thermal detailed balance under equilibrium conditions. At thermal equilibrium…
Non-Markovian transport equations for nuclear large amplitude motion are derived from the collisional kinetic equation. The memory effects are caused by the Fermi surface distortions and depend on the relaxation time. It is shown that the…
Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and…
We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…