Related papers: The Role of Structure in the Protein Dynamical Tra…
A model for the processive movement of dynein is presented based on experimental observations available. In the model, the change from strong microtubule-binding to weak binding of dynein is determined naturally by the variation of the…
Many proteins undergo conformational changes during their activity. A full understanding of the function of these proteins can only be obtained if different conformations and transitions between them can be monitored in aqueous solution,…
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.…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The glass transition temperature $T_{\rm g}$ and the temperature $T_{\alpha}$ corresponding to the peak in the dielectric loss due to the $\alpha$-process have been simultaneously determined as functions of film thickness d through…
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 couple the recently developed self-learning metabasin escape algorithm, which enables efficient exploration of the potential energy surface (PES), with shear deformation to elucidate strain-rate and temperature effects on the shear…
Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former),…
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and…
Density-functional theory may be used to predict both the frequency and the dipole moment of the fundamental oscillations of molecular crystals. Suitably polarized photons at those frequencies excite such oscillations. Thus, in principle,…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…
Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature…
A hallmark of a thermodynamic phase transition is the qualitative change of system thermodynamic properties such as energy and heat capacity. On the other hand, no phase transition is thought to operate in the supercritical state of matter…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
In this work, we present a new model for the interpretation of the local dynamic behavior and the mechanical reinforcement mechanism in polymer nanocomposites. The temperature dependence of the dynamics in the glassy region is described by…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…