Related papers: The protein dynamical transition is independent of…
The energy transfer processes and coherent phenomena in the fucoxanthin-chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional…
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…
We study processes at the transition region between hot (rare) and cold (dense) plasma in the collisionless regime. We use a 3-dimensional electromagnetic particle-in-cell (3-D PIC) relativistic code. Motivated by the transition region in…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence…
Experiments in bulk water confirm the existence of two local arrangements of water molecules with different densities, but, because of inevitable freezing at low temperature $T$, can not ascertain whether the two arrangements separate in…
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 this study, the additional heat capacity which appear during the water dissociation of the proteins that are one of the soft materials, have been considered by the statistical mechanical methods. For this purpose, taking the electric…
Using an activation mechanism reproducing facilitation, a dynamic phase transition triggered by a few active molecules was recently found in a supercooled model liquid. Prompted by this finding we investigate the presence of a similar…
The time evolution of anharmonic molecular wave packets is investigated under the influence of the environment consisting of harmonic oscillators. These oscillators represent photon or phonon modes and assumed to be in thermal equilibrium.…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
We present photoluminescence studies as a function of temperature from a series of conjugated polymers and a conjugated molecule with distinctly different backbone conformations. The organic materials investigated here are: planar…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We study the temperature and pressure dependence of the structural and electronic properties of the iron pnictide superconductor BaFe2As2. We use density functional theory based Born-Oppenheimer molecular dynamics simulations to investigate…
We present the self-dynamics of protein amino acids of hydrated lysozyme powder around the physiological temperature by means of molecular dynamics (MD) simulations. The self-intermediate scattering functions (SISF) of the amino acid…
We use recently introduced three-point dynamic susceptibilities to obtain an experimental determination of the temperature evolution of the number of molecules, N_corr, that are dynamically correlated during the structural relaxation of…
The vibrational dynamics of protein folding is analyzed in the framework of Tsallis thermostatistics. The generalized partition functions, internal energies, free energies and temperature factor (or Debye-Waller factor) are calculated. It…
Electron paramagnetic resonance signal parameters of TEMPO dichlorotriazine and TEMPO maleimide spin labels attached to protein human serum albumin molecules have been monitored at various temperatures, salts and sucrose concentrations. The…
Collapsin response mediator protein CRMP2 (gene: DPYSL2) is crucial for neuronal development. The homotetrameric CRMP2 complex is regulated via two mechanisms, first by phosphorylation at, and second by reduction and oxidation of the Cys504…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…