Related papers: Dissecting Ubiquitin Folding Using the Self-Organi…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
The response of underwater structures to a near-field explosion is coupled with the dynamics of the explosion bubble and the surrounding water. This multiphase fluid-structure interaction process is investigated using a model problem that…
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
In the present paper we revisit, theoretical and experimentally, the fall of a folded U-chain and of a pile-chain. The model calculation implies the division of the whole system into two subsystems of variable mass, allowing to explore the…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…
The qualitative behavior of a recently formulated ODE model for the dynamics of heterogenous aggregates is analyzed. Aggregates contain two types of particles, oligomers and cross-linkers. The motivation is a preparatory step of cellular…
The microscopic mechanisms involved in the formation/dissociation of methane hydrate confined at the nanometer scale are unraveled using advanced molecular modeling techniques combined with a mesoscale thermodynamic approach. By means of…
Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding molecules are free to diffuse and rearrange on the surface, giving rise to spontaneous control over the…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
We investigate the Yb valence instabilities in the strongly correlated YbPd compound using resonant X-ray emission spectroscopy as a function of pressure across the charge-order (CO) transition. At a low temperature (T = 30 K) in the CO…
We develop a hybrid oscillator-qubit processor framework for quantum simulation of strongly correlated fermions and bosons that avoids the boson-to-qubit mapping overhead encountered in qubit hardware. This framework gives exact…
We present results of molecular dynamics simulations of the electron system on the surface of liquid helium. The simulations are done for 1600 electrons with periodic boundary conditions. Electron scattering by capillary waves and phonons…
Utilizing single-photon photoassociation, we have achieved ultracold rubidium molecules with a high number density that provides a new efficient approach toward molecular quantum degeneracy. A new detection mechanism for ultracold molecule…