相关论文: Topological complexity, contact order and protein …
Macromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of…
Correlation in two-dimensional soap froth is analysed with an effective potential for the first time. Cells with equal number of sides repel (with linear correlation) while cells with different number of sides attract (with NON-bilinear)…
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.…
We study structural phase transition of polymer-grafted colloidal particles by Monte Carlo simulations on hard spherical particles. The interaction potential, which has a weak repulsive step outside the hard core, was validated with use of…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
An order parameter, termed the maximal row correlation, is proposed for classical spin systems. Monte Carlo simulations on various Potts models suggest that this order parameter is applicable to a broad range of spin systems, including…
Many soft-matter and biophysical systems are composed of monomers which reversibly assemble into rod-like aggregates. The aggregates can then order into liquid-crystal phases if the density is high enough, and liquid-crystal ordering…
We study a one-dimensional extended Hubbard model with longer-range Coulomb interactions at quarter-filling in the strong coupling limit. We find two different charge-ordered (CO) ground states as the strength of the longer range…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
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…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
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…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
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…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…