Related papers: Folding thermodynamics of model four-strand antipa…
Production of heat shock proteins are induced when a living cell is exposed to a rise in temperature. The heat shock response of protein DnaK synthesis in E.coli for temperature shifts from temperature T to T plus 7 degrees, respectively to…
Starting from a Huxley-type model for an agitated vibrational mode, we propose an embedding of standard active particle models in terms of two-temperature processes. One temperature refers to an ambient thermal bath, and the other…
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 thermodynamics of phase transitions between phases that are size-mismatched but coherent differs from conventional stress-free thermodynamics. Most notably, in open systems such phase transitions are always associated with hysteresis.…
We consider thermodynamic and dynamic phase transitions in plaquette spin models of glasses. The thermodynamic transitions involve coupled (annealed) replicas of the model. We map these coupled-replica systems to a single replica in a…
We present results from Molecular Dynamics simulations of the thermal glass transition in a dense polymer melt. In previous work we compared the simulation data with the idealized version of mode coupling theory (MCT) and found that the…
We study the finite-temperature dynamics of thin elastic sheets in a single-clamped cantilever configuration. This system is known to exhibit a tilt transition at which the preferred mean plane of the sheet shifts from horizontal to a plane…
The glass transition temperature and its connection to statistical properties of confined and free-standing polymer films of varying thickness containing unentangled to highly entangled bead-spring chains are studied by molecular dynamics…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
In view of the important role helix-sheet transitions play in protein aggregation, we introduce a simple model to study secondary structural transitions of helix-coil-sheet systems using a Potts model starting with an effective Hamiltonian.…
This article demonstrates that flexible and statistically tractable multi-modal diffusion models can be attained by transformation of simple well-known diffusion models such as the Ornstein-Uhlenbeck model, or more generally a Pearson…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
By use of the conservation laws a four-site Hubbard model coupled to a particle bath within an external magnetic field in z-direction was diagonalized. The analytical dependence of both the eigenvalues and the eigenstates on the interaction…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
Experimental realizations of a variety of atomic binary Bose-Fermi mixtures have brought opportunities for studying composite quantum systems with different spin-statistics. The binary atomic mixtures can exhibit a structural transition…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
We present extensive molecular dynamics simulations of a liquid of symmetric dumbbells, for constant packing fraction, as a function of temperature and molecular elongation. For large elongations, translational and rotational degrees of…