Related papers: Protein conformational dynamics and electronic str…
Having established the fact that interacting classical kicked rotor systems exhibit long-lived prethermal phase with quasi-conserved average Hamiltonian before entering into chaotic heating regime, we use spatio-temporal fluctuation…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the…
The two-dimensional nature of engineered transition-metal ultra-thin oxide films offers a large playground of yet to be fully understood physics. Here, we study pristine SrVO$_3$ monolayers that have recently been predicted to display a…
In this paper, a simple geometric structure is shown, which underlies the interaction Hamiltonian of quantum electrodynamics. Specifically, eight parts of the interaction Hamiltonian, corresponding to eight basic Feynman diagrams, are found…
The extended SSH model and Bogoliubov-de Gennes(BdeG) formalism are applied to investigate the electronic properties and stable lattice configurations of C$_{36}$. We focus the problem on the molecule's unusual $D_{6h}$ symmetry. The…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
Optical reflectivity measurements were performed on a single crystal of the d-electron heavy-fermion (HF) metal LiV2O4. The results evidence the highly incoherent character of the charge dynamics for all temperatures above T^* \approx 20 K.…
Series of molecular dynamics simulations for 2-propanol-water mixtures, as a function of temperature (between freezing and room temperature) and composition (xip= 0, 0.5, 0.1 and 0.2) have been performed for temperatures reported in the…
We constrain the amount of event-by-event fluctuations of the proton by comparing with the HERA coherent and incoherent diffractive $J/\Psi$ production data. We find that the HERA measurements prefer large geometric fluctuations. We then…
In 2D electronic spectroscopy studies, long-lived quantum beats have recently been observed in photosynthetic systems, and it has been suggested that the beats are produced by quantum mechanically mixed electronic and vibrational states.…
The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed…
We study the long time coherence dynamics of a two-mode Bose-Hubbard model in the Josephson interaction regime, as a function of the relative phase and occupation imbalance of an arbitrary coherent preparation. We find that the variance of…
We investigate the detailed electronic structure of PrCoO$_3$ and its temperature evolution using state-of-the-art photoemission spectroscopy and ab initio band structure calculations. We observe that in addition to the correlation effect,…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…
Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Go model with binary variables. The exponential dependence of the time constants on the force is verified, and folding and unfolding lengths are…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
In this review, we discuss the electronic structure of finite quantal systems on the nanoscale. After a few general remarks on the many-particle physics of the harmonic oscillator -- likely being the most studied example for the many-body…
We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem…