相关论文: On the Diffusion Time Evolution of Folding Chains …

We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…

In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…

We study the structural and dynamical behaviors of a diblock copolymer chain in a bath of active Brownian particles (ABPs) by extensive Brownian dynamics simulation in a two-dimensional model system. Specifically, the A block of chain is…

The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…

We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…

We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…

We study the formation and evolution of several molecules in a collapsing interstellar cloud using a reasonably large reaction network containing more then four hundred atomic and molecular species. We employ a time dependent, spherically…

Power law potentials dictate interactions across scales and matter, controlling the structure and dynamics of inanimate, and living systems. Though the equilibrium distributions of particles with a power law repulsion were extensively…

The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…

Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…

In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…

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…

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…

We consider an electrodiffusion model describing the evolution of $N$ ionic species in a three-dimensional fluid flowing through a porous medium and forced by added body charges. We address the global well-posedness and long-time dynamics…

Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native…

We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…

We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…

In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…