Related papers: Optimized Baxter Model of Protein Solutions: Elect…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
Based on the notion of a construction process consisting of the stepwise addition of particles to the pure fluid, a discrete model for the apparent viscosity as well as for the maximum packing fraction of polydisperse suspensions of…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
We compute effective energies of thin bilayer structures composed by soft nematic elastic-liquid crystals in various geometrical regimes and functional configurations. Our focus is on order-strain interaction in elastic foundations composed…
Given a chain of viscoelastic spheres with fixed masses of the first and last particles. We raise the question: How to chose the masses of the other particles of the chain to assure maximal energy transfer? The results are compared with a…
Taking the cue from experiments on actin growth on spherical beads, we formulate and solve a model problem describing the accretion of an incompressible elastic solid on a rigid sphere due to attachment of diffusing free particles. One of…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We use virial series to study the equilibrium properties of confined soft-spheres fluids interacting through the inverse-power potentials. The confinement is induced by hard walls with planar, spherical and cylindrical shapes. We evaluate…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
Compressive mechanical stress exceeding a critical value leads to the formation of periodic surface buckling patterns in film-substrate systems. A comprehensive understanding of this buckling phenomenon is desired in applications where the…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
We introduce a simple spherical model whose structural properties are similar to the ones generated by models with directional interactions, by employing a binary mixture of large and small hard spheres, with a square-well attraction acting…
Starting from a general classical model of many interacting particles we present a well defined step by step procedure to derive the continuum-mechanics equations of nonlinear elasticity theory with fluctuations which describe the…
This paper consists of two parts. In the first part we prove the unique solvability for the abstract variational-hemivariational inequality with history-dependent operator. The proof is based on the existing result for the static…
The interplay of phase separation and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as hard and soft condensed matter physics, materials science, food engineering and…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
A two-dimensional free boundary transmission problem arising in the modeling of an electrostatically actuated plate is considered and a representation formula for the derivative of the associated electrostatic energy with respect to the…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
A collisional model of a confined quasi-two-dimensional granular mixture is considered to analyze homogeneous steady states. The model includes an effective mechanism to transfer the kinetic energy injected by vibration in the vertical…