相关论文: Polymer uncrossing and knotting in protein folding…

We consider the minimum spanning tree problem with predictions, using the weight-arrival model, i.e., the graph is given, together with predictions for the weights of all edges. Then the actual weights arrive one at a time and an…

A well-known algorithm for unknotting knots involves traversing a knot diagram and changing each crossing that is first encountered from below. The minimal number of crossings changed in this way across all diagrams for a knot is called the…

Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…

A protein structure is represented as a network of residues whereby edges are determined by intra-molecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino-acid pair…

The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…

The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…

A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…

Native shortcut networks (SCN0) are sub-graphs of native protein residue networks (PRN0). In this paper, we propose the Network Dynamics (ND) model, which reconstructs a PRN0 by adding back its edges according to some recipe, while its…

A method that reconstructs protein residue networks using suitable node selection and edge recovery policies produced numerical observations that correlate strongly (Pearson's correlation coefficient < -0.83) with published folding rates…

We introduce a two-dimensional lattice model for the description of knotted polymer rings. A polymer configuration is modeled by a closed polygon drawn on the square diagonal lattice, with possible crossings describing pairs of strands of…

Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…

Minimum spanning trees and forests are powerful sparsification techniques that remove cycles from weighted graphs to minimize total edge weight while preserving node connectivity. They have applications in computer science, network science,…

Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…

The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in which almost all instances have no…

The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…

External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High throughput experiments identify numerous molecular…

For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…

Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…

The viscous flow of polymer chains in dense melts is dominated by topological constraints whenever the single chain contour length, N, becomes larger than the characteristic scale Ne, defining comprehensively the macroscopic rheological…