Related papers: pH modulates friction memory effects in protein fo…
Proteins often exhibit subdiffusive configurational dynamics. The origins of this subdiffusion are still unresolved. We investigate the impact of non-Markovian friction and the free energy landscape on the dynamics of fast-folding proteins…
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…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
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…
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 introduce a generalized Langevin model system for different non-Markovian effects in the well and barrier regions of a potential, and use it to numerically study the dependence of the barrier-crossing time. In the appropriate limits, our…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
Memory effects arise in many complex systems, from protein folding, to the spreading of epidemics and financial decisions. While so-called non-Markovian dynamics is common in larger systems with interacting components, observations in…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Single-molecule experiments provide insight into the motion (conformational dynamics) of individual protein molecules. Usually, a well-defined but coarse-grained intramolecular coordinate is measured and subsequently analysed with the help…
This paper is concerned with correlation functions of stochastic systems with memory, a prominent example being a molecule or colloid moving through a complex (e.g., viscoelastic) fluid environment. Analytical investigations of such systems…
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…
Quantum information processing relies on how dynamics unfold in open quantum systems. In this work, we study the non-Markovian dynamics in the single mode spin-boson model at strong couplings. In order to apply perturbation theory, we…
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…
Non-Markovian dynamics is central to quantum information processing, as memory effects strongly influence coherence preservation, metrology, and communication. In this work, we investigate the role of stochastic system--bath couplings in…
The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable.…
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has…
We investigate memory effects in the spin-boson model using a recently proposed measure for non-Markovian behavior based on the information exchange between an open system and its environment. Employing the numerical exact multilayer…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…