Related papers: Side chain and backbone ordering in a polypeptide
Extensive Monte Carlo simulations were carried out to investigate the nature of the ordering transition of a model of adsorbed self-assembled rigid rods on the bonds of a square lattice [Tavares et. al., Phys. Rev E 79, 021505 (2009)]. The…
Specific interactions between cations and proteins have a strong impact on peptide and protein structure. We here shed light on the nature of the underlying interactions, especially regarding the effects on the polyamide backbone structure.…
Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes,…
Methods of local topology are introduced to the field of protein physics. This is achieved by explaining how the folding and unfolding processes of a globular protein alter the local topology of the protein's C-alpha backbone through…
The microcanonical analysis is shown to be a powerful tool to characterize the protein folding transition and to neatly distinguish between good and bad folders. An off-lattice model with parameter chosen to represent polymers of these two…
An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent…
The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive…
We analyze the freezing and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer models in…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
Under an external field a double-stranded peptide chain can separate in a fragile or ductile transition. It is usually believed that these two regimes are driven either by chemical and thermal fields, or through non-local mechanical…
Experimental investigations of the phase transition in GeTe provide contradictory conclusions regarding the nature of the phase transition. Considering growing interest in technological applications of GeTe, settling these disputes is of…
As an example for the interplay of structure, dynamics, and phase behavior of macromolecular systems, this article focuses on the problem of bottle-brush polymers with either rigid or flexible backbones. On a polymer with chain length…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
We investigate the build-up of quasi-long-range order in the XX chain with transverse magnetic field at finite size. As the field is varied, the ground state of the system displays multiple level crossings producing a sequence of…
We characterize the order-disorder transition in a model lipid bilayer using molecular dynamics simulations. We find that the ordered phase is hexatic. In particular, in-plane structures possess a finite concentration of 5-7 disclination…
The $2$d orders are a sub class of causal sets, which is especially amenable to computer simulations. Past work has shown that the $2$d orders have a first order phase transition between a random and a crystalline phase. When coupling the…
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,…
Electronic structures of undoped and doped cyclic polythiophene (PT) are studied using modified $\sigma$-bond compressibility model. Cyclic PT doped with odd number of bipolarons creates an aromatic polyene backbone containing (4$n$+2)…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…