相关论文: Proteins and polymers
We study a homopolymer model of a protein chain, where each monomer carries a dipole moment. To mimic the geometry of the peptidic bond, these dipoles are constrained to be locally perpendicular to the chain. The tensorial character of the…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
A simple analytic theory for mixtures of hard spheres and larger polymers with excluded volume interactions is developed. The mixture is shown to exhibit extensive immiscibility. For large polymers with strong excluded volume interactions,…
Ring, or cyclic, polymers have unique properties compared to linear polymers, due to their topologically closed structure that has no beginning or end. Experimental measurements on molecular ring polymers are challenging due to their…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
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…
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve…
Nanoscale and microscale confinement of biopolymers naturally occurs in cells and has been recently achieved in artificial structures designed for nanotechnological applications. Here, we present an extensive theoretical investigation of…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
We show that non-entangled polymers display an elastic-like behaviour at a macroscopic scale (probed at some 0.100 mm thickness) up to at least hundred degrees above the glass transition temperature. This observation, found under…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
Here, we provide an overview of theoretical approaches to semiflexible polymers and their networks. Such semiflexible polymers have large bending rigidities that can compete with the entropic tendency of a chain to crumple up into a random…