Related papers: Dissecting Ubiquitin Folding Using the Self-Organi…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
We consider the motion of a harmonically trapped overdamped particle, which is submitted to a self-phoretic force, that is proportional to the gradient of a diffusive field for which the particle itself is the source. In agreement with…
We introduce a three-dimensional model for polyelectrolyte hydrogel filaments operating in a fluid environment under an electric field. The formulation builds on a morphoelastic framework for inextensible and unshearable rods, such that the…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
The electronic structure evolutions of few-layer black phosphorus (BP) under pressure shows a wealth of phenomena, such as the nonmonotonic change of direct gap at the {\Gamma} point, the layer-number dependence, and the distinct responses…
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…
Recent experiments revealed intriguing similarities in the $^{64}$Ni+$^{207}$Pb, $^{132}$Xe+$^{208}$Pb, and $^{238}$U+$^{238}$U reactions at energies around the Coulomb barrier. The experimental data indicate that for all systems…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
We present a study of the melting dynamics of a two-phase eutectic solid. In situ, thin-sample experiments using a transparent eutectic alloy and two-dimensional phase field simulations calibrated for the very same alloy are combined to…
Uranium is considered as a very important nuclear energy material because of the huge amount of energy released. As the main products of spontaneous decay of uranium, helium is difficult to react with uranium for its chemical inertness.…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
Over the past decade, autophoretic colloids have emerged as a prototypical system for studying self-propelled motion at microscopic scales, with promising applications in microfluidics, micromachinery, and therapeutics. Their motion in a…
Folding and unfolding of biopolymers are often manipulated in experiment by tuning pH, temperature, single-molecule force or shear field. Here we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in…
The low frequency lattice vibrations and relaxations are investigated in single crystals of the four 3D hybrid organolead perovskites, MAPbBr$_3$, FAPbBr$_3$, MAPbI$_3$, and $\alpha$-FAPbI$_3$, at the Brillouin zone center using Raman and…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…