Related papers: Protein folding, anisotropic collapse and blue pha…
We develop a new quantitative molecular theory of liquid-phase dipolar polymer gels. We model monomer units of the polymer network as a couple of charged sites separated by a fluctuating distance. For the first time, within the random phase…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We study the effect of dielectric anisotropy of polymers on their equilibrium ordering within mean-field theory but with a formalism that takes into account the full n-body nature of van der Waals forces. Dielectric anisotropy within…
We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of…
Conformations of a single semiflexible polymer chain dissolved in a low molecular weight liquid crystalline solvents (nematogens) are examined by using a mean field theory. We takes into account a stiffness and partial orientational…
Spontaneous onset of a low temperature topologically ordered phase in a 2-dimensional (2D) lattice model of uniaxial liquid crystal (LC) was debated extensively pointing to a suspected underlying mechanism affecting the RG flow near the…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We explore the phase structure of a chiral model of constituent quarks and gluons implementing scale symmetry breaking at finite temperature and chemical potential. In this model the chiral dynamics is intimately linked to the trace anomaly…
We point out that the correlation between folding times and $\sigma = (T_{\theta } - T_{f})/T_{\theta }$ in protein-like heteropolymer models where $T_{\theta }$ and $T_{f}$ are the collapse and folding transition temperatures was already…
Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
We investigate in this paper the ground state and the nature of the transition from an orientational ordered phase at low temperature to the disordered state at high temperature in a molecular crystal. Our model is a Potts model which takes…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
We investigate the behavior of entanglement entropy in the holographic QCD model proposed by Gubser et al. By choosing suitable parameters of the scalar self-interaction potential, this model can exhibit various types of phase structures:…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is…
The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
We investigate the addition of stiffness to the lattice model of hydrogen-bonded polymers in two and three dimensions. We find that, in contrast to polymers that interact via a homogeneous short-range interaction, the collapse transition is…