Related papers: Protein conformational dynamics and electronic str…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
We have carried out a comparative study of the electronic specific heat and electronic structure of $\alpha$ and $\delta$-plutonium using dynmical mean field theory (DMFT). We use the perturbative T-matrix and fluctuating exchange (T-matrix…
We have performed momentum dependent electron energy-loss studies of the electronic excitations in sexithiophene and compared the results to those from parent oligomers. Our experiment probes the dynamic structure factor S(q,omega)and we…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
We study the coupling of internal electronic excitations to vibrational modes of the external motion of ultracold atoms in an optical lattice. For different ground and excited state potentials the on-site coupling of excitations and…
Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…
Native extracellular matrices (ECMs), such as those of the human brain and other neural tissues, exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Domain motions involved in the function of proteins can often be well described as a combination of motions along a handfull of low-frequency modes, that is, with the values of a few normal coordinates. This means that, when the functional…
We showed that quantum mechanical superposition can sustain in the process of ion transfer in protein membrane for a substantial period, in spite of the presence of the interactions with environmental modes of molecular vibration. The…
We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron…
The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. Local fluctuations are known to initiate biologically relevant pathways as they cooperatively enhance the dynamics in…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…
The dynamics of quasicrystals is characterized by the existence of phason excitations in addition to the usual phonon modes. In order to investigate their interplay on an elementary level we resort to various one-dimensional model systems.…
Using a diverse set of 100 oligothiophenes, extrapolated oligomer and polymer HOMO, LUMO and HOMO-LUMO gaps are shown to be accurately estimated from the computed values of the trimer HOMO, trimer LUMO and trimer HOMO-LUMO gaps. These…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
Several experimental studies have reported thermally activated behavior of the mechanical response of solid Helium-4 which does not fit into the model of thermally activated Frenkel pairs in an ideal crystal. The purpose of the present work…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
Quantum fluctuation of the energy is studied for an ultracold gas of interacting fermions trapped in a three-dimensional potential. Periodic-orbit theory is explored, and energy fluctuations are studied versus particle number for generic…