Related papers: A simplified exactly solvable model for beta-amylo…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
A simple, dual-site model of bolaamphiphiles (bolaforms or bipolar amphiphiles) is developed based on an earlier single-site model of (monopolar) amphiphiles [S. Dey, J. Saha, Phys. Rev. E 95, 023315 (2017)]. The model incorporates aqueous…
We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. We find that in its low temperature phase…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
An analytical model based on variational principles for a thin-walled stiffened plate subjected to axial compression is presented. A system of nonlinear differential and integral equations is derived and solved using numerical continuation.…
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
We present a generic model to describe the fractal self-assembly of proteins in terms of electrostatic and hydrophobic interactions. The predictions of the model were correlated with the simulated fractals obtained using patchy…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
In this paper, we present an exactly solvable phase transition model in which the phase transition is purely statistically derived. The phase transition in this model is a generalized Bose-Einstein condensation. The exact expression of the…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein…
Simple application of the Einstein model combined with the elastic description of solid state is developed. The frequency of quantum oscillators has been assumed as volume dependent and, furthermore, elastic energy terms of static character…
Bilayer membranes self-assembled from amphiphilic molecules such as lipids, surfactants and block copolymers are ubiquitous in biological and physiochemical systems. The shape and structure of bilayer membranes depend crucially on their…
Prevention of protein aggregation and thus stabilization of proteins has large biological and biotechnological implications. Here, we show that inhibition of amyloid-like aggregates is possible in stoichiometric conjugates of polymer…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
In this paper we present a method to study the folding structure of a simple model consisting of two kinds of monomers, hydrophobic and hydrophilic. This method has three main steps: an efficient simulation method to bring an open sequence…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
The Leibler theory [L. Leibler, Macromolecules, v.13, 1602 (1980)] for microphase separation in AB block copolymer melts is generalized for systems with arbitrary topology of molecules. A diagrammatic technique for calculation of the…
We investigate thermal fluctuations in a smectic A phase of an amphiphile-solvent mixture with molecular dynamics simulations. We use an idealized model system, where solvent particles are represented by simple beads, and amphiphiles by…