Related papers: Protein conformational dynamics and electronic str…
The chemical flexibility of metal-organic frameworks (MOFs) offers an ideal platform to tune structure and composition for specific applications, from gas sensing to catalysis and from photoelectric conversion to energy storage. This…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The dielectric properties of proteins, particularly in their hydrated state, have been extensively studied. Numerous theoretical and experimental investigations have reported values of both the permittivity and the intrinsic dipole moments…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
We construct an energy function that describes the crystallographic structure of spermwhale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature.…
In previous works it was shown that protein 3D-conformations could be encoded into discrete sequences called dominance partition sequences (DPS), that generated a linear partition of molecular conformational space into regions of molecular…
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…
We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition…
The conformational and electronic properties of conducting flexible random and self-avoiding walk polymer chains are under investigation. A Hamiltonian for conjugated flexible polymers is introduced and its physical consequences are…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by relatively slow changes in total concentrations (copy numbers) of interacting proteins. The second type, to which…
Introducing partial sum rules for the optical multiplet transitions, we outline a unified approach to magnetic and optical properties of strongly correlated transition metal oxides. On the example of LaVO$_3$ we demonstrate how the…
The physical basis for observed long-lived electronic coherence in photosynthetic light-harvesting systems is identified using an analytically soluble model. Three physical features are found to be responsible for their long coherence…
The energy and analytic gradient are developed for FMO combined with the Hartree-Fock method augmented with three empirical corrections (HF-3c). The auxiliary basis set approach to FMO is extended to perform pair interaction energy…
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…
The two-orbital degenerate Hubbard model with distinct hopping integrals is studied by combining dynamical mean-field theory with quantum Monte Carlo simulations. The role of orbital fluctuations for the nature of the Mott transition is…
Electronic structure of strongly correlated transition metal oxides (TMOs) is a complex phenomenon due to competing interaction among the charge, spin, orbital and lattice degrees of freedom. Often individual compounds are examined to…
The differential cross section of exclusive diffractive vector meson production in electron proton collisions carries important information on the geometric structure of the proton. More specifically, the coherent cross section as a…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…