相关论文: Side-chain and backbone ordering in Homopolymers

A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…

Using transfer operator and fundamental measure theories, we examine the structural and thermodynamic properties of hard rectangles confined between two parallel hard walls. The side lengths of the rectangle ($L$ and $D$, $L>D$) and the…

We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…

In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory…

We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…

We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…

Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the…

We present the results of a quantitative study of the phase behavior of a model polymer chain with side spheres using two independent computer simulation techniques. We find that the mere addition of side spheres results in key…

The present work continues our previous studies of pom-pom molecule [K. Haydukivska, O. Kalyuzhnyi, V. Blavatska, and J. Ilnytskyi, J. Mol. Liq. 328, 115456 (2021); Condens. Matter Phys. 25, 23302 (2022)]. The molecule consists of a linear…

The phase behavior of a cross-linked polymer blend made of two incompatible species, $A$ and $B$, of different chemical nature is analyzed. Besides a homogeneous phase, this system also exhibits two microphases and a phase of total…

Using first-principles approaches we investigate local heating and the inelastic contribution to the current for various alkanethiols sandwiched between metal electrodes. In the absence of good heat dissipation into the bulk electrodes, we…

The consequences of recent experimental finding that hydrogen bonds of the anti-parallel $\beta $-sheet in nonspecific binding site of serine proteases become significantly shorter and stronger synchronously with the catalytic act are…

Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…

We propose a model describing the phase behavior of two-component membranes consisting of binary mixtures of electrically charged and neutral lipids. We take into account the structural phase transition (main-transition) of the hydrocarbon…

To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…

The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences,…

In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…

The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not…

Halide perovskites are known for their rich phase diagram and superior performance in diverse optoelectronics applications. The latter property is often attributed to the long electron-hole recombination time, whose underlying physical…

Lithium and sodium are the only solids that are known to lose crystalline order upon cooling. The seemingly-disordered low-temperature phase shows signatures of various close-packed structures. The lack of order has been attributed to a…