Related papers: Protein conformational dynamics and electronic str…
Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is…
The thermoelectric response of molecular junctions exhibits large fluctuations, as observed in recent experiments [e.g. Malen J. A. {\sl et al.}, Nano Lett. {\bf 10}, 3406 (2009)]. These were attributed to fluctuations in the energy…
We develop a formalism to accurately account for the renormalization of electronic structure due to quantum and thermal nuclear motions within the Born-Oppenheimer approximation. We focus on the fundamental energy gap obtained from…
We develop a procedure to determine the portion of exact Hartree-Fock exchange interaction contained in a hybrid density functional to treat the range of electronic correlation governing the physics of a system as a function of a…
In this work we investigate doping and temperature dependences of electronic structure of system with strong electronic correlations and strong electron-phonon interaction modeling cuprates in the frameworks of the three-band p-d-Holstein…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Linear-scaling electronic structure methods based on the calculation of moments of the underlying electronic Hamiltonian offer a computationally efficient and numerically robust scheme to drive large-scale atomistic simulations, in which…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…
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…
We consider the consequences of the presence of metric fluctuations upon the properties of a hydrogen atom. Particularly, we introduce these metric fluctuations in the corresponding effective Schroedinger equation and deduce the…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
Inter- or intramolecular coupling processes between chromophores such as excimer formation or H- and J-aggregation are crucial to describing the photophysics of closely packed films of conjugated polymers. Such coupling is highly distance…
In this work electronic structures and optical properties of organic-inorganic exciton and polaritons in two-dimensional heterostructures combining both organic and semiconductor materials are studied. In those systems, Wannier-Frenkel…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
In a companion paper, we have developed a phase-space electronic structure theory of molecules in magnetic fields, whereby the electronic energy levels arise from diagonalizing a phase-space Hamiltonian $\hat H_{PS}(\bf{X},\bf{\Pi})$ that…
The elastic and $\gamma \to \pi$ transition form factors of the pion along with its usual static observables are calculated within a light-front field approach to the constituent quark model. The focus of this exercise in a simple model is…