相关论文: Conformational Biases of {\alpha}-Synuclein and Fo…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
We study the equilibrium shapes of prime and composite knots confined to two dimensions. Using rigorous scaling arguments we show that, due to self-avoiding effects, the topological details of prime knots are localised on a small portion of…
The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime…
Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel…
Six sets of Navier-Stokes trefoil vortex knots in $(2\pi)^3$ domains show how the shape of the initialprofile influences the evolution of the enstrophy $Z$, helicity ${\cal H}$ and dissipation-scale. Significant differences develop even…
Nonequilibrium active polymers provide a minimal framework to investigate biopolymers such as DNA and chromatin under the action of molecular motors. Here we study active ring polymers with controlled topology and show that knot type…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…
The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands of proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these…
Optical knots and links, consisting of trajectories of phase or polarisation singularities, are intriguing nontrivial three-dimensional topologies. They are theoretically predicted and experimentally observed in paraxial and non-paraxial…
We investigate the nucleation and propagation of cracks in self-assembled viscoelastic fluids, which are made of surfactant micelles reversibly linked by telechelic polymers. The morphology of the micelles can be continuously tuned, from…
The reorientation dynamics of local tangent vectors of chains in isotropic amorphous melts containing semiflexible model polymers was studied by molecular dynamics simulations. The reorientation is strongly influenced both by the local…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
Helices are the quintessential geometric motif of the microscale, from alpha-helices in proteins to double helices in DNA. Assembly of the helical geometry of biopolymers is a foundational step in a hierarchy of structure that eventually…
Molecular dynamics studies within a coarse-grained structure based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects in the native structure of a knot. The first protein, N-acetylornithine…
How molecular motors like Kinesin regulates the affinity to the rail protein in the process of ATP hydrolysis remains to be uncovered. To understand the regulation mechanism, we investigate the structural fluctuation of KIF1A in different…
Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Topological nodal-line semimetals are characterized by one-dimensional lines of band crossing in the Brillouin zone. In contrast to nodal points, nodal lines can be in topologically nontrivial configurations. In this paper, we study the…
We use computer simulations to compare the dynamical behaviour of torus and even-twist knots in polymers under tension. The knots diffuse through a mechanism similar to reptation. Their friction coefficients grow linearly with average knot…