Related papers: Side-chain and backbone ordering in Homopolymers
Dynamics of a polymer chain in solution gets significantly affected by the temperature and the frictional forces arising due to solvent viscosity. Here, using an explicit solvent framework for polymer simulation with the liberty to tune the…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
The study of protein interactions has generated great interest in the food industry. Therefore, research on new supramolecular structures shows promise. Supramolecular structures of the whey proteins {\alpha}-lactalbumin and…
We present photoluminescence studies as a function of temperature from a series of conjugated polymers and a conjugated molecule with distinctly different backbone conformations. The organic materials investigated here are: planar…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
Planar/flat configurations of fixed-angle chains and trees are well studied in the context of polymer science, molecular biology, and puzzles. In this paper, we focus on a simple type of fixed-angle linkage: every edge has unit length…
Extensive molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20 and 30 mol % of the alcohol, at temperatures between room temperature and…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
We present a combined x-ray diffraction and infrared spectroscopy study on the phase behavior and molecular dynamics of n-hexadecanol in its bulk state and confined in an array of aligned nanochannels of 8 nm diameter in mesoporous silicon.…
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple…
The phase structure of a homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence…
We study long polymer chains in a poor solvent, confined to the space between two parallel hard walls. The walls are energetically neutral and pose only a geometric constraint which changes the properties of the coil-globule (or…
We study one-dimensional sideband cooling of Cesium atoms strongly confined in a far-detuned optical lattice. The Lamb-Dicke regime is achieved in the lattice direction whereas the transverse confinement is much weaker. The employed…
We present several ordering mechanisms in diblock copolymers. For temperatures above the order-disorder temperature and in the weak segregation regime, a linear response theory is presented which gives the polymer density in the vicinity of…
A coarse-grained molecular dynamics model of linear polyethylene-like polymer chain system was built to investigate the responds of structure and mechanical properties during uniaxial deformation. The influence of chain length, temperature,…
Focusing on a small set of proteins that i) fold in a concerted, all-or-none fashion and ii) do not contain knots or slipknots, we show that the Gauss linking integral, the torsion and the number of sequence-distant contacts provide…
Using thermodynamics integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarity, ranging from the most polar water to the most non-polar cyclohexane. The amino acid side chain…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…