Related papers: Discrete breathers in protein secondary structure
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
We investigate one-dimensional harmonically trapped two-component systems for repulsive interaction strengths ranging from the non-interacting to the strongly interacting regime for Fermi-Fermi mixtures. A new and powerful mapping between…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
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…
We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…
In this work, we study the dynamics of an infinite array of nonlinear dimer oscillators which are linearly coupled as in the classical model of Su, Schrieffer and Heeger (SSH). The ratio of in-cell and out-of-cell couplings of the SSH model…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Cell cortex contraction is essential for shaping cells, enabling movement, ensuring proper division, maintaining tissue integrity, guiding development, and responding to mechanical signals - all critical for the life and health of…
Qualitative information about breather initial profiles in the weak coupling limit of a chain of identical one-dimensional anharmonic oscillators is found by studying the linearized equations of motion at a one-site breather. In particular,…
We have carried out experiments to probe the static and dynamic interfacial properties of $\beta$--casein monolayers spread at the air-buffer interface, and analysed these results in the context of models of weak polyampholytes.…
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
A quasi-one-dimensional Bose-Einstein condensate loaded into a quasi-periodic potential created by two sub-lattices of comparable amplitudes and incommensurate periods is considered. Although the conventional tight-binding approximation is…
In this work the observational constraints on interaction coupling parameter between dynamical dark energy and cold dark matter were obtained using CMB, BAO and SN Ia data. The dark energy in considered models is dynamical and evolution of…