Related papers: Backbone and Sidechain Ordering in a small Protein
High energy x-ray diffraction is used to investigate the bulk oxygen ordering properties of YBa_2Cu_3O_{6+x}. Superstructures of Cu-O chains aligned along the b axis and ordered with periodicity ma, along the a axis have been observed. For…
A hybrid phase transition (HPT) that exhibits properties of continuous and discontinuous phase transitions at the same transition point has been observed in diverse complex systems. Previous studies of the HPTs on complex networks mainly…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
Numerical modeling is used to investigate the dynamics of a polaron in a chain with small random Langevin-like perturbations which imitate the environmental temperature $T$ and under the influence of a constant electric field. In the…
We investigate the mechanism of heat conduction in ordered and disordered harmonic onedimensional chains within the quantum mechanical Langevin method. In the case of the disordered chains we find indications for normal heat conduction…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
Finite-temperature charge-ordering phase transition in quasi one-dimensional (1D) molecular conductors is investigated theoretically, based on a quasi 1D extended Hubbard model at quarter filling with interchain Coulomb repulsion $V_\perp$.…
The Hubbard model is known to accommodate various electronic orders, including stripes, which are important for understanding the physics of cuprates. We study spin-stripe order in the square lattice Hubbard model as a function of doping…
The properties of helical thin films have been thoroughly investigated by classical Monte Carlo simulations. The employed model assumes classical planar spins in a body-centered tetragonal lattice, where the helical arrangement along the…
The rigidity and flexibility of homologous psychrophilic(P), mesophilic(M) and thermophilic(T) proteins have been investigated at the global and local levels in terms of packing factor and atomic fluctuations obtained from B-factors. For…
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…
The front dynamics in the Harper (or Aubry-Andr\'e) model (which has a localization transition) is investigated using two different settings, particle number front where the system is at zero temperature, and initially, the particle numbers…
The theory of superstatistics, originally proposed for the study of complex nonequilibrium systems, has recently been extended to studies of small systems interacting with a finite environment, because such systems display interestingly…
Mesoscopic structure of the periodically alternating layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for the systems with both strong (ionic) and weak (hydrogen) interactions. We…
A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The…