相关论文: Conformational Biases of {\alpha}-Synuclein and Fo…
Natively unstructured proteins defy the classical "one sequence-one structure" paradigm of protein science. Monomers of these proteins in pathological conditions can aggregate in the cell, a process that underlies socially relevant…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
Macroscopic properties and shapes of biological tissues depend on the remodelling of cell-cell junctions at the microscopic scale. We propose a theoretical framework that couples a vertex model of solid confluent tissues with the dynamics…
It is well-known that localized topological defects (solitons) experience recoil when they suffer an impact by incident particles. Higher-dimensional topological defects develop distinctive wave patterns propagating along their worldvolume…
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…
We have investigated the role that different connectivity regimes play on the dynamics of a network of Hodgkin-Huxley neurons by computer simulations. The different connectivity topologies exhibit the following features: random connectivity…
We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
Within cells, vesicles and proteins are actively transported several micrometers along the cytoskeletal filaments. The transport along microtubules is propelled by dynein and kinesin motors, which carry the cargo in opposite directions.…
Using numerical simulations of the full nonlinear equations of motion we investigate topological solitons of a modified O(3) sigma model in three space dimensions, in which the solitons are stabilized by the Hopf charge. We find that for…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using $\beta$-lactoglobulin fibrils as a model, that semiflexible…
We study a model of an active gel of cross-linked semiflexible filaments with additional active linkers such as myosin II clusters. We show that the coupling of the elasticity of the semiflexible filaments to the mechanical properties of…
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate…
Superconducting cosmic strings (SCSs) have received revived interests recently. In this paper we treat closed SCSs as oriented knotted line defects, and concentrate on their topology by studying the Hopf topological invariant. This…
Complex networks have certain properties that distinguish them from their respective uniform or regular counterparts. One of these properties is the variation of topological properties along different hierarchical levels. In this work, we…
The actin cytoskeleton in living cells generates forces in conjunction with myosin motor proteins to directly and indirectly drive essential cellular processes. The semiflexible filaments of the cytoskeleton can respond nonlinearly to the…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…