Related papers: Molecular dynamics simulation analysis of structur…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
The standard model for molecular recognition of an odorant is that receptor sites discriminate by molecular geometry as evidenced that two chiral molecules may smell very differently. However, recent studies of isotopically labeled…
Path-integral molecular dynamics simulations and electronic structure-based energy decomposition analysis (EDA) are employed to connect hydrogen bond (H-bond) strength, its asymmetry, and the total delocalization energy at the water/air…
Selectivity of olfactory receptor neuron (ORN) is compared with that of its receptor proteins (R) with fluctuations of odor binding-releasing process taken into account. The binding-releasing process is modeled as N Bernoulli trials, where…
In order to understand the nature and dynamics of interfacial water molecules on the surface of complex systems, large scale molecular dynamics simulations of an aqueous micelle of cesium perfluorooctanoate surfactant molecules have been…
New analysis methods for the vibrational dynamics from molecular dynamics are proposed and applied to liquid H$_{2}$O. The internal modes of H$_{2}$O are amplitude-modulated by Langevin dynamics with the frequency of the H$_{2}$O libration…
A basic model of hydrogen bonds related to $\rm{H}_2\rm{O}$, which is adapted from the Jaynes--Cummings model, is suggested, and its different dynamic features are studied theoretically. In this model, the making and breaking of hydrogen…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Aromatic compounds form an unusual kind of hydrogen bond with water and ammonia molecules, known as the $\pi$-hydrogen bond. In this work, we report ab initio path integral molecular dynamics simulations enhanced by machine-learning…
Understanding how molecular structure gives rise to odor perception remains a long-standing challenge, with ongoing debate over whether olfaction is primarily governed by molecular shape, vibrational properties, or their interplay at the…
In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried…
We propose a mechanism for binding of diatomic ligands to heme based on a dynamical orbital selection process. This scenario may be described as bonding determined by local valence fluctuations. We support this model using linear-scaling…
The dynamics of water molecules plays a vital role in understanding water. We combined computer simulation and deep learning to study the dynamics of H-bonds between water molecules. Based on ab initio molecular dynamics simulations and a…
We present a hybrid method based on a combination of quantum/classical molecular dynamics (MD) simulations and a mod el Hamiltonian approach to describe charge transport through bio-molecular wires with variable lengths in presence o f a…
The hydrogen-bonded structure of methanol-water mixtures is investigated over the entire alcohol concentration range (from $x_{\mathrm{Methanol}}=$ 0.1 to 1.0) at several temperatures, from 300 K down to the freezing point of the given…
Hypothesis: The structural details, viscosity trends and dynamic phenomena in t-butanol/water solutions are closely related on the molecular scales across the entire composition range. Utilizing the experimental small- and wide-angle x-ray…
Recordings from neurons in the insects' olfactory primary processing center, the antennal lobe (AL), reveal that the AL is able to process the input from chemical receptors into distinct neural activity patterns, called olfactory neural…
Hydrogen bonding is essential in electron transfer processes at water-electrode interfaces. We study the impact of the H-bonding of water as a solvent molecule on real-time electron transfer dynamics across a Cs+-Cu(111) ion-metal interface…
Mean square displacements of hydrogen atoms in glass-forming materials and proteins, as reported by incoherent elastic neutron scattering, show kinks in their temperature dependence. This crossover, known as the dynamical transition,…
Hybrid QM(DFT)/MM molecular dynamics simulations have been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. Trajectories are analyzed putting…