Related papers: Quanta of Local Conformational Change: Conformons …
We examine the impact of the intrinsic molecular reorganization energy on switching in two-state quantum-dot cellular automata (QCA) cells. Switching a bit involves an electron transferring between charge centers within the molecule. This…
The hyperfine structure (HFS) of a bound electron is modified by the self-interaction of the electron with its own radiation field. This effect is known as the self-energy correction. In this work, we discuss the evaluation of higher-order…
We describe a model of electron transfer reactions affected by local binding to the donor or acceptor sites of a particle in equilibrium with the solution. The statistics of fluctuations of the donor-acceptor energy gap caused by…
Quantum phase transitions between competing equilibrium shapes of nuclei with an odd number of nucleons are explored using a microscopic framework of nuclear energy density functionals and a particle-boson core coupling model. The boson…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
Quantum phase transitions between competing ground-state shapes of atomic nuclei with an odd number of protons or neutrons are investigated in a microscopic framework based on nuclear energy density functional theory and the…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
We studied the thermodynamic behaviors of non-interacting bosons and fermions trapped by a scale-invariant branching structure of adjustable degree of heterogeneity. The full energy spectrum in tight-binding approximation was analytically…
Local scale transformations are made to vary the long range properties of harmonic oscillator orbitals conventionally used in model structure calculations of nuclear systems. The transformations ensure that those oscillator states…
A minimal model for coherent transport through a donor/acceptor molecular junction is presented. The two donor and acceptor sites are described by single levels energetically separated by an intramolecular tunnel barrier. In the limit of…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Structural phase transitions are accompanied by a movement of one nucleus (or a few) in the crystallographic unit cell. If the nucleus movement is continuous, a second order phase transition without latent heat results, whereas an abrupt…
We use a tight-binding Hamiltonian and Green functions methods to calculate the quantum transmission through single-wall fullerenes and bilayered and trilayered onions of icosahedral symmetry attached to metallic leads. The electronic…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
To investigate the effect of quantum coherence on electronic energy transfer, which is the subject of current interest in photosynthesis, we solve the problem of transport for the simplest model of an aggregate of monomers interacting…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
The low-energy effective quantum field theory of the edge excitations of a fully-gapped bulk topological phase corresponding to a local interaction Hamiltonian must be local and unitary. Here it is shown that whenever all the edge…
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…