Related papers: H-bonds in Crambin: Coherence in an alpha helix
Using the molecular dynamics method, dynamics of hydrogen bond (HB) networks emerging on the surface of a graphene sheet during its functionalization with hydroxyl groups OH are simulated. It is demonstrated that two OH groups form an…
The first search for nonresonant production of Higgs boson pairs (HH) with one H decaying into four leptons and the other into a pair of b quarks is presented, using proton-proton collisions recorded at a center-of-mass energy of $\sqrt{s}$…
Profiling is a process that finds similarities between different RNA secondary structures by extracting signals from the Boltzmann sampling. The reproducibility of profiling can be identified by the standard deviation of number of features…
In this paper, we systematically investigate the structural and electronic properties of twisted h-BN bilayers to understand the role of the twisting angle. Using first-principles methods with relaxation taken into account, we simulate h-BN…
The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H$_2$) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or…
We propose the conformon as a quantum of conformational change for energy transfer in alpha-helical proteins. The underlying mechanism of interaction between the quantum of excitation and the conformational degrees of freedom is nonlinear…
Rydberg atoms excited by cold blackbody radiation are shown to display long-lived quantum coherences on timescales of tens of picoseconds. By solving non-Markovian equations of motion with no free parameters we obtain the time evolution of…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
We have performed a multi-species hydrodynamical simulation of the formation and evolution of Lyman alpha clouds in a flat CDM dominated universe with an external flux of ionizing radiation. We solve the fully coupled non-equilibrium rate…
We revisit here how Raman spectroscopy can be used to estimate the H content in hard hydrogenated amorphous carbon layers. The H content was varied from 2 at.% to 30 at.%, using heat treatments of a a-C:H, from room temperature to 1300 K…
We study electron decoherence by measuring the temperature dependence of Aharonov-Bohm (AB) oscillations in quasi-1D rings, etched in a high-mobility GaAs/GaAlAs heterostructure. The oscillation amplitude is influenced both by…
Analysis of the electron density distribution in clusters composed of hydrogen fluoride, water, and ammonia molecules, especially within the hydrogen-bond domains, reveals the existence of both \sigma- and \pi-binding between molecules. The…
We report a detailed study of high-order harmonic generation (HHG) in helium. When comparing predictions from a single-active-electron model with those from all-electron simulations, such as ATTOMESA and R-matrix with time-dependence, which…
We have studied hydrogen-hydrogen-alkali three-body systems in the adiabatic hyperspherical representation. For the spin-stretched case, there exists a single $X$H molecular state when $X$ is one of the bosonic alkali atoms: $^7$Li,…
The HII region oxygen abundance is a key observable for studying chemical properties of galaxies. Deriving oxygen abundances using optical spectra often relies on empirical strong-line calibrations calibrated to the direct method. Existing…
Smashing nuclei at ultrarelativistic speeds and analyzing the momentum distribution of outgoing debris provides a powerful method to probe the many-body properties of the incoming nuclear ground states. Within a perturbative description of…
Network coherence generally refers to the emergence of simple aggregated dynamical behaviours, despite heterogeneity in the dynamics of the subsystems that constitute the network. In this paper, we develop a general frequency domain…
We study the dynamical behaviour of the proton transfer in the hydrogen bonds in the base-pairs of the double helices of the DNA type. Under the assumption that the elastic and the tunnelling degrees of freedom may be coupled, we derive a…
The synthetic actin network arouses great interest as bio-material due to its soft and wet nature that mimics many biological scaffolding structures. Inside the cell, the actin network is regulated by tens of actin-binding proteins (ABP's),…
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…