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Employing a recently proposed measure for quantum non-Markovianity, we carry out a systematic study of the size of memory effects in the spin-boson model for a large region of temperature and frequency cutoff parameters. The dynamics of the…
Nonnative residual interactions have attracted increasing attention in recent protein folding researches. Experimental and theoretical investigations had been set out to catch nonnative contacts that might dominate key events in protein…
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also…
Water hydrating phospholipid membranes determine their stability and function, as well as their interaction with other molecules. In this article we study, using all-atom molecular dynamics simulations, the rotational and translational…
We measure the static frictional resistance and the real area of contact between two solid blocks subjected to a normal load. We show that following a two-step change in the normal load the system exhibits nonmonotonic aging and memory…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
The adhesive and frictional response of an AFM tip connected to a substrate through supramolecular host-guest complexes is investigated by dynamic Monte Carlo simulations. The variation of the pull-off force with the unloading rate recently…
The visible dynamics of small-scale systems are strongly affected by unobservable degrees of freedom, which can belong either to external environments or internal subsystems and almost inevitably induce memory effects. Formally, such…
Active gels perform key mechanical roles inside the cell, such as cell division, motion and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
The classical Hodgkin--Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
The friction coefficient of fluids may become a function of the velocity at increased external driving. This non-Newtonian behavior is of general theoretical interest as well as of great practical importance, e.g., for the design of…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
Non-Markovian evolution of an open quantum system can be induced by the memory effects of a reservoir. Although a reservoir with stronger memory effects may seem like it should cause stronger non-Markovian effects on the system of interest,…
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We investigated frictional effects on the folding rates of a human telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations of the Three Interaction Site (TIS) model for RNA. The heat…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Skeletal muscle modeling has a vital role in movement studies and the development of therapeutic approaches. In the current study, a Huxley-based model for skeletal muscle is proposed, which demonstrates the impact of impairments in muscle…