Related papers: The protein dynamical transition is independent of…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Possible variations in the dynamical behaviour of LiYF$_{4}$ due to its several structural changes under pressure are examined by making use of the complementary techniques of quasi-harmonic lattice dynamics and molecular dynamics…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Under natural conditions, excitation of biological molecules, which display non-unitary open system dynamics, occurs via incoherent processes such as temperature changes or irradiation by sunlight/moonlight. The dynamics of such processes…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Novel physical mechanism is proposed for explanation of temperature-independent transition reactions in molecular systems. The mechanism becomes effective in the case of conformation transitions between quasi-isoenergetic molecular states.…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on…
In the present chapter, we discuss an approach for transition from discrete to continuum description of thermomechanical behavior of solids. The transition is carried out for several anharmonic systems: one-dimensional crystal,…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
In the theory of open quantum systems, spectral densities are key quantities for modeling the dynamics and spectroscopic properties of the system under investigation. In the case of light-harvesting complexes, they encode the…
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the…
A theory of radiation absorption by dielectric mixtures is presented. The coarse-grained formulation is based on the wavevector-dependent correlation functions of molecular dipoles of the host polar liquid and a density-density structure…
Recent experiments suggest that atomic disordering dynamics are more universal than conventional coherent processes in photoinduced phase transitions (PIPTs), yet its mechanism remains unclear. Using real-time time-dependent density…