Related papers: Quanta of Local Conformational Change: Conformons …
To understand the mechanism of TATA-box conformational transformations we model structure mobility and find the types of conformational excitations of DNA macromolecule in heteronomous conformation. We have constructed the two-component…
When canonical Hamiltonians of local quantum field theories are transformed using a renormalization group procedure for effective particles, the resulting interaction terms are non-local. The range of their non-locality depends on the…
Coherent responses of resonance atom layer to short optical pulse excitation are numerically considered. The inhomogeneous broadening of one-photon transition, the local field effect, and the substrate dispersion are involved into analysis.…
The interplay of geometric randomness and strong quantum fluctuations is an exciting topic in quantum many-body physics, leading to the emergence of novel quantum phases in strongly correlated electron systems. Recent investigations have…
We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to…
Hidden symmetries of non-relativistic $\mathfrak{so} (2,1)\cong \mathfrak{sl}(2, {\mathbb R})$ invariant systems in a cosmic string background are studied using the conformal bridge transformation. Geometric properties of this background…
Qualitatively different systems of molecular energy bands are studied on example of a parametric family of effective Hamiltonians describing rotational structure of triply degenerate vibrational state of a cubic symmetry molecule. The…
"Alchemical" interpolation paths, i.e.~coupling systems along fictitious paths that without realistic correspondence, are frequently used within materials and molecular modeling and simulation protocols for the estimation of relative…
We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are…
We calculate the correlation energy of a two-dimensional homogeneous electron gas using several available approximations for the exchange-correlation kernel $f_{\rm xc}(q,\omega)$ entering the linear dielectric response of the system. As in…
The performance of several common approximations for the exchange-correlation kernel within time-dependent density-functional theory is tested for elementary excitations in the homogeneous electron gas. Although the adiabatic local-density…
There has been disagreement in the literature on whether the hydrogen atom spectrum receives any tree-level correction due to noncommutativity. Here we shall clarify the issue and show that indeed a general argument on the structure of…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We investigate the role of quantum coherence in modulating the energy transfer rate between two independent energy donors and a single acceptor participating in an excitonic energy transfer process. The energy transfer rate depends…
I investigate energy transfer in a donor-acceptor pair beyond weak system-bath coupling. I identify a transition from coherent to incoherent dynamics with increasing temperature, due to multi-phonon effects not captured by a standard…
How do protons and neutrons bind to form nuclei? This is the central question of ab initio nuclear structure theory. While the answer may seem as simple as the fact that nuclear forces are attractive, the full story is more complex and…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
We show that a protein can be trained to recognise multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield…
Electronic coherences are key to understanding and controlling photo-induced molecular transformations. We identify a crucial quantum-mechanical feature of electron-nuclear correlation, the projected nuclear quantum momenta, essential to…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…