Related papers: Ion Binding Sites and their Representations by Qua…

The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…

This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…

Correlated anion and cation motion can significantly reduce the overall ion conductivity in electrolytes versus the ideal conductivity calculated based on the diffusion constants alone. Using coarse-grained molecular dynamics simulations,…

We overview the current status of theoretical approaches for heavy-ion fusion reactions at subbarrier energies. We particularly discuss theoretical challenges in the coupled-channels approach, that include i) a description of deep…

A number of basic scientific questions relating to ion conduction in homogeneously disordered solids are discussed. The questions deal with how to define the mobile ion density, what can be learned from electrode effects, what is the ion…

Ion channels are protein structures that facilitate the selective passage of ions across the membrane cells of living organisms. They are known for their high conductance and high selectivity. The precise mechanism between these two…

The exploration of complex physical or technological processes usually requires exploiting available information from different sources: (i) physical laws often represented as a family of parameter dependent partial differential equations…

The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…

Small-world networks provide an interesting framework for studying the interplay between regular and random graphs, where links are located in a regular and random way, respectively. On one hand, the random links make the model to obey some…

Polymer electrolytes typically exhibit diminished ionic conductivity due to the presence of correlation effects between the cations and anions. Microscopically, transient ionic aggregates, e.g. {\it ion-pairs}, {\it ion-triplets} or higher…

Uncompensated charges do not occur in Nature and any local charge should be a result of charge separation. Dissociable chemical groups at interfaces in contact with ions in solution, whose chemical equilibrium depends both on short-range…

Fluctuations in the statistical model of heavy ion collisions are studied. The role of statistics, relativity, constraints, decaying resonances and branching processes are investigated using this model. Also studied are thermodynamic…

I review recent selected developments in the theory and modeling of ultrarelativistic heavy-ion collisions. I explain why relativistic viscous hydrodynamics is now used to model the expansion of the matter formed in these collisions. I give…

We study the ionic distribution near a charged surface. A new method for performing Monte Carlo simulations in this geometry is discussed. A theory is then presented that allows us to accurately reproduce the density profiles obtained in…

To construct models of large, multivariate complex systems, such as those in biology, one needs to constrain which variables are allowed to interact. This can be viewed as detecting "local" structures among the variables. In the context of…

Understanding the electrodes' surface morphology influence on the ions' distribution is essential for designing the supercapacitors with enhanced energy density characteristics. We develop a model for the structure of electrolytes near the…

The spectral statistics of complex networks are numerically studied. The features of the Anderson metal-insulator transition are found to be similar for a wide range of different networks. A metal-insulator transition as a function of the…

Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate…

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Based on the postulates of quantum mechanics, we introduce a hierarchy of representations which meet…

Molecular representation learning is pivotal for various molecular property prediction tasks related to drug discovery. Robust and accurate benchmarks are essential for refining and validating current methods. Existing molecular property…