Related papers: Helix vs. Sheet Formation in a Small Peptide
We investigate the swelling and shrinking of L_beta lamellar gel phases composed of surfactant and fatty alcohol after contact with aqueous poly(ethylene-glycol) solutions. The height change $\Delta h(t)$ is diffusion-like with a swelling…
A $\beta$-skeleton, $\beta \geq 1$, is a planar proximity undirected graph of an Euclidean points set, where nodes are connected by an edge if their lune-based neighbourhood contains no other points of the given set. Parameter $\beta$…
The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide…
Short-period sub-Neptunes are common in extrasolar systems. These sub-Neptunes are generally thought to have primary atmospheres of protoplanetary-disk gas origin. However, atmospheric escape followed by degassing from their interiors can…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…
The study of the structural behaviour of pure and multi-component lipids at various temperatures and the interaction of these multi-component lipids with pharmaceutically important drugs carry huge importance. Here, we investigated the…
We consider a model of lipids in which a head group, characterized by its volume, is attached to two flexible tails of equal length. The phase diagram of the anhydrous lipid is obtained within self-consistent field theory, and displays, as…
Impacts of individual slow highly charged ions on alkaline earth halide and alkali halide surfaces create nano-scale surface modifications. For different materials and impact energies a wide variety of topographic alterations have been…
Inspired by recent experiments and simulations on pattern formation in biomolecules by optical tweezers, a theoretical description based on reference interaction site model (RISM) integral equation method is developed to calculate the…
The confinement of silver selenide was investigated using mesoporous silica. Results from x-ray diffraction and electron microscopy show that the confined material still exhibits a \beta to \alpha transition similar to the one that takes…
We propose a method for predicting helical membrane protein structures by computer simulations. Our method consists of two parts. In the first part, amino-acid sequences of the transmembrane helix regions are obtained from one of existing…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
A direct observation of nucleation of Ge hut clusters formed by ultrahigh vacuum molecular beam epitaxy is reported for the first time. The nuclei of the pyramidal and wedge-like clusters have been observed on the wetting layer blocks and…
Helical motifs are ubiquitious in macromolecular systems. The mechanism of spontaneous emergence of helicity is unknown, especially in cases where torsional interactions are absent. Emergence of helical order needs coordinated organization…
Shape transformations of flat bilayer membranes and vesicles induced by hydrolysis and condensation reactions of amphiphilic molecules are studied using coarse-grained molecular dynamics simulations. The hydrolysis and condensation…
The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, helix has a unique position. Helical structures are ubiquitous in nature and a helical shape…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…
Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of…
The self-assembly of proteins into $\beta$-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to…