Related papers: On Heteropolymer Shape Dynamics
We investigate by Molecular Dynamics simulation a system of $N$ particles moving on the surface of a two-dimensional sphere and interacting by a Lennard-Jones potential. We detail the way to account for the changes brought by a nonzero…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
We investigate the spread of correlations carried by an excitation in a 1-dimensional lattice system with high on-site energy disorder and long-range couplings with a power-law dependence on the distance ($\propto r^{-\mu}$). The increase…
These notes are devoted to the statistical mechanics of directed polymers interacting with one-dimensional spatial defects. We are interested in particular in the situation where frozen disorder is present. These polymer models undergo a…
Scaling law for geometrical and dynamical quantities of biological molecules is an interesting topic. According to Flory's theory, a power law between radius of gyration and the length of homopolymer chain is found, with exponent 3/5 for…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
We derive the stochastic equations of motion for a tracer that is tightly attached to a semiflexible polymer and confined or agitated by an externally controlled potential. The generalised Langevin equation, the power spectrum, and the…
The unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ is studied using Monte Carlo simulations. We obtain the dynamical order parameter, $Q$, defined as…
Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Unfolded protein aggregation in cellular system is a problem causing various types of diseases depending on which type unfolded proteins aggregate. This phenomenon of aggregation may take place during production, storage, shipment or…
We consider a system of two coupled particles evolving in a periodic and spatially symmetric potential under the influence of external driving and damping. The particles are driven individually in such a way that in the uncoupled regime,…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
We investigate the time evolution towards the asymptotic steady state of a one dimensional interacting system after a quantum quench. We show that at finite time the latter induces entanglement between right- and left- moving density…
We study an influence of the quenched extended defects on the critical dynamics of the d=3-dimensional systems with m-component non-conserved order parameter (model A dynamics). Considering defects to be correlated in \epsilon_d dimensions…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…