Related papers: Ion Binding Sites and their Representations by Qua…
The experimentally observed swelling and collapse response of weakly charged polymers to the addition of specific salts displays quite convoluted behavior that is not easy to categorize. Here we use a minimalistic implicit solvent /…
An elementary understanding of the relevant length, mass and energy scales at the molecular level can be used to explain the order of magnitude of material properties such as mass density, latent heat, surface tension, elastic moduli and…
The quasiparticle method, which has achieved a great success in solid state electronics and crystal lattice vibration, is adopted to study the solid state ion transport. A general recipe is put forward to map the classical solid state ion…
The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic…
Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with…
Two-particle correlation measurements and analysis are an important component of the relativistic heavy-ion physics program. In particular, particle pair-number correlations on two-dimensional transverse momentum ($p_t$) allow unique access…
Electron capture processes for low energy Ar9+ ions colliding on Ar2 dimer targets are investigated, focusing attention on charge sharing as a function of molecule orientation and impact parameter. A preference in charge-asymmetric…
A model system of highly asymmetric polyelectrolyte with directional short-range attractive interactions was studied by canonical Monte Carlo computer simulations. Comparison of MC data with previously published theoretical results shows…
Quasi-static models of barrier suppression have played a major role in our understanding of the ionization of atoms and molecules in strong laser fields. Despite their success, in the case of diatomic molecules these studies have so far…
We consider geometries and possible physical models for weak low ionization absorbers based on the relative incidence of low and high ionization absorption systems. We found a total of 16 metal-line systems, with low and/or high ionization…
Bimolecular binding rate constants are often used to describe the association of large molecules, such as proteins. In this paper, we analyze a model for such binding rates that includes the fact that pairs of molecules can bind only in…
Potassium (K-) channels catalyze K+ ion permeation across cellular membranes while simultaneously discriminating their permeation over Na+ ions by more than a factor of a thousand. Structural studies show bare K+ ions occupying the…
Small-molecule foundation models are typically pretrained on standalone molecular data, unlike vision and language models that often benefit from cross-modal or relational supervision. Protein-ligand co-folding provides a molecular analogue…
We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition. The mode-coupling theory (MCT) originally formulated to study the slow relaxation in simple…
Biomolecular binding kinetics including the association (kon) and dissociation (koff) rates are critical parameters for therapeutic design of small-molecule drugs, peptides and antibodies. Notably, drug molecule residence time or…
X-ray crystallography rarely captures chemical bonding between atoms of a structure in question. Most of the time distance-based heuristics are applied to establish the pairs of bonded atoms. One class of such heuristics depends on a set of…
Relativistic heavy-ion collisions suggest that low momentum regions of the observed particle spectra are thermal and hydrodynamic, while medium-high momentum regions are non-thermal and perturbative. In this study, I construct a…
The formal link between the linear combination of atomic orbitals approach to density functional theory and two-center Slater-Koster tight-binding models is used to derive an orthogonal $d$-band tight-binding model for iron with only two…
A theoretical framework for studying strong-field ionization of aligned molecules is presented, and alignment-dependent ionization yields are computed for CO2. Our calculations are in unprecedented agreement with recent experiments. We find…
Trapped atomic ions are among the most advanced platforms for quantum simulation, computation, and metrology, offering long coherence times and precise, individual control over both internal and motional degrees of freedom. In this review,…