Related papers: BondMatcher: H-Bond Stability Analysis in Molecula…
In all standard force field-based simulations of organic, bio-molecules, polymers; the torsion angle based Hamiltonian has been an indispensable term to set up molecular simulation. Torsion often termed as a dihedral angle, the coordinate…
An effective Hamiltonian is considered for hydrogen bonding between two molecules due to the quantum mechanical interaction between the orbitals of the H-atom and the donor and acceptor atoms in the molecules. The Hamiltonian acts on two…
The local structure of liquid water plays a key role in determining the anomalous properties of water. We run all-atom simulations for three microscopic water models, and use multiple order parameters to analyse the local structure of…
We review recently introduced numerical methods for the unbiased detection of the order parameter and/or dominant correlations, in many-body interacting systems, by using reduced density matrices. Most of the paper is devoted to the…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…
Water is necessary both for the evolution of life and its continuance. It possesses particular properties that cannot be found in other materials and that are required for life-giving processes. These properties are brought about by the…
Geopolymers are an emerging class of binding materials used in sustainable cements, concretes, and composites. However, despite growing research, the lack of standardised processes and stability analyses for formulating activator solutions…
Recently, a hydrodynamic description of local equilibrium dynamics in quantum integrable systems was discovered. In the diffusionless limit, this is equivalent to a certain "Bethe-Boltzmann" kinetic equation, which has the form of an…
Recently, the progression toward more exact density functional theory has been questioned, implying a need for more formal ways to systematically measure progress, i.e. a path. Here I use the Hohenberg-Kohn theorems and the definition of…
Band alignment, namely the prediction of band-edge positions of semiconductors and insulators in aqueous solutions, is an important problem in physics and chemistry. Such a prediction is especially challenging for structurally and…
We introduce a vector-based interpretation of the chemical bond within the quantum theory of atoms in molecules (QTAIM), the bond-path framework set $\mathbb{B} = \{p, q, r\}$, to follow variations in the 3-D morphology of all bonds for the…
The local arrangement of atoms is one of the most important predictors of mechanical and functional properties of materials. However, algorithms for identifying the geometrical arrangements of atoms in complex materials systems are lacking.…
We predict large regions of the charge stability diagram using a multi-band and multi-electron configuration interaction model of a double quantum dot system. We account for many-body interactions within each quantum dot using full…
In models of Pt 111 and Pt 100 surfaces in water, motions of molecules in the first hydration layer are spatially and temporally correlated. To interpret these collective motions, we apply quantitative measures of dynamic heterogeneity that…
The formation and properties of a supersolid structure in a three-component ultracold Bose gas mixture at T=0 are investigated theoretically. The system consists of 23Na, 39K, and 41K atomic species, in which the binary mixtures of…
Adiabatic mixed quantum/classical molecular dynamics simulations were used to generate snapshots of the hydrated electron (e-) in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the e- were…
A new approach to computing the equilibria and steady-states of biomolecular systems modelled by bond graphs is presented. The approach is illustrated using a model of a biomolecular cycle representing a membrane transporter and a model of…
Polymer electrolytes are critical for safe, high-energy-density solid-state batteries, yet discovering candidates that balance high ionic conductivity with high transference numbers remains a significant challenge. In this work, we develop…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
Beam stability and halo formation in high-intensity axisymmetric 2D beams in a uniform focusing channel are analyzed using particle-in-cell simulations. The tune depression - mismatch space is explored for the uniform (KV) distribution of…