Related papers: Analysis of Two-State Folding Using Parabolic Appr…
In this paper, we suppose a possible extension of Gibbs ensemble theory so that it can provide a reasonable description to phase transitions and spontaneous symmetry breaking. The extension is founded on three hypotheses, and can be…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
Variational calculations of excited electronic states are carried out by finding saddle points on the surface that describes how the energy of the system varies as a function of the electronic degrees of freedom. This approach has several…
In generic classical and quantum many-body systems, where typically energy and particle number are the only conserved quantities, stationary states are described by thermal equilibrium. In contrast, integrable systems showcase an infinite…
This article studies the interrelation between the determining modes property in the two-dimensional (2D) Navier-Stokes equations (NSE) of incompressible fluids and the reconstruction property of two filtering algorithms for continuous data…
Using well-known mathematical foundations of the elasticity theory, a mathematical model for two solutes transport in a poroelastic material (soft tissue is a typical example) is suggested. It is assumed that molecules of essentially…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective…
We study a class of exactly solvable models for strongly correlated electrons, defined on a set of N cells, and with infinite on-site repulsion on part of the sites of each cell. For 2N or more electrons the exact ground state is known. We…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
A thermodynamic model of formation of multi-component solid solutions as a thermodynamic mixture of their binary components, is proposed. There are obtained expressions for the effective temperature of the equilibrium state of the solid…
When a quantum system is placed in thermal environments, we often assume that the system relaxes to the Gibbs state in which decoherence takes place in the system energy eigenbasis. However, when the coupling between the system and the…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
A possible way to extract information about the reversible dissociation of a molecular adhesion bond from force fluctuations observed in force ramp experiments is discussed. For small loading rates the system undergoes a limited number of…
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…
The structure of the state-vector space for the two-mode parabose system is investigated and a complete set of state-vectors is constructed. The basis vectors are orthonormal in order $p=2$. In order $p=2$, conserved-charge parabose…