Related papers: Detection of residual native state entropy changes…
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…
We study dynamical properties of systems with many interacting Fermi-particles under the influence of static imperfections. Main attention is payed to the time dependence of the Shannon entropy of wave packets, and to the fidelity of the…
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in folding nucleus and sequence conservation…
In the context of non-relativistic quantum mechanics, we investigated Shannon's entropy of a non-Hermitian system to understand how this quantity is modified with the cyclotron frequency. Subsequently, we turn our attention to the…
We carried out temperature and field dependent magnetic measurements to understand the evolution of magnetic non-collinearity near antiferromagnetic phase in conjunction with the evolution of magnetic entropy near phase transition. We…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
We apply a simulational proxy of the phi-value analysis and perform extensive mutagenesis experiments to identify the nucleating residues in the folding reactions of two small lattice Go polymers with different native geometries. These…
Iron-substitution in hexagonal YMnO3 causes isostructural intra-lattice changes exceeding those of the lattice cell, contrary to the effects of non-magnetic B-site dopants. Magnetization M(T) evidence antiferromagnetic (AFM) ordering of the…
The influence of high-enthalpy effects on hypersonic turbulent boundary layers is investigated by means of direct numerical simulations (DNS). A quasi-adiabatic flat-plate air flow at free-stream Mach number equal to 10 is simulated up to…
Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…
The Fenna Mathews Olson (FMO) complex of green sulphur bacteria is an example of a photosynthetic pigment protein complex, in which the electronic properties of the pigments are modified by the protein environment to promote efficient…
Structural changes in REMnO3 (RE= Y, Ho, Lu) under high pressure were examined by synchrotron x-ray diffraction methods at room temperature. Compression occurs more readily in the ab plane than along the c-axis. Under hydrostatic pressure…
The structural and magnetic properties of Zn/Al doped nickel ferrite thin films can be adjusted by changing the Zn and Al content. The films are epitaxially grown by reactive magnetron sputtering using a triple cluster system to sputter…
A systematic modification of the entropy trajectory $S_m(T)$ is observed at very low temperature in magnetically frustrated systems as a consequence of the constraint $S_m\geq 0$ imposed by the third law of thermodynamics. The lack of…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
Predicting the stability and fitness effects of amino acid mutations in proteins is a cornerstone of biological discovery and engineering. Various experimental techniques have been developed to measure mutational effects, providing us with…
Predicting the impact of single-point amino acid mutations on protein stability is essential for understanding disease mechanisms and advancing drug development. Protein stability, quantified by changes in Gibbs free energy ($\Delta\Delta…
Kerogen-rich shale reservoirs will play a key role during the energy transition, yet the effects of nano-confinement on the NMR relaxation of hydrocarbons in kerogen are poorly understood. We use atomistic MD simulations to investigate the…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…