Related papers: Dissecting Ubiquitin Folding Using the Self-Organi…
Using Langevin dynamics complemented by Wang-Landau Monte Carlo simulations, we study the phase behavior of single and multiple semiflexible polymer chains in solution under poor-solvent conditions. In the case of a single chain, we obtain…
We present results of molecular simulations of a model protein whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
The growing trend towards engineering interfacial complexion (or phase) transitions has been seen in the grain boundary and solid surface systems.Meanwhile, little attention has been paid to the chemically heterogeneous solid/liquid…
A mathematical model for the evolution of, and deposition from, a thin particle-laden droplet on an infinitely thick, isotropic, flooded, porous substrate with interconnected pores undergoing simultaneous evaporation and imbibition is…
We present a method for density-functional modeling of metallic overlayers grown on metallic supports. It offers a tool to study nanostructures and combines the power of self-consistent pseudopotential calculations with the simplicity of a…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…
Hybrid ion-atom systems provide an excellent platform for studies of state-resolved quantum chemistry at low temperatures, where quantum effects may be prevalent. Here we study theoretically the process of vibrational relaxation of an…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly…
Eukaryotic cells maintain their inner order by a hectic process of distillation of molecular factors taking place on the surface of their lipid membranes. To understand the properties of this molecular sorting process, a physical model of…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on a metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
We discuss the microscopic mechanisms by which low-temperature amorphous states, such as ultrastable glasses, transform into equilibrium fluids, after a sudden temperature increase. Experiments suggest that this process is similar to the…