Related papers: Ion Binding Sites and their Representations by Qua…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
We study two designed and one natural zinc-finger peptide each with the Cys2His2 (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue…
We use the Quantum Hypernetted Chain Approximation (QHNC) to calculate the ion-ion and electron-ion correlations for liquid metallic Li, Be, Na, Mg, Al, K, Ca, and Ga. We discuss trends in electron-ion structure factors and radial…
This paper introduces a new representation method that is mainly based on chemical bonds among atoms in materials. Each chemical bond and its surrounded atoms are considered as a unified unit or a local structure that is expected to reflect…
We analyze the effect of an external electric field on the electronic structure of molecules which have been recently studied as molecular wires or diodes. We use a self-consistent tight binding technique which provides results in good…
Physicochemical models can be powerful tools to trace the chemical evolution of a protostellar system and allow to constrain its physical conditions at formation. The aim of this work is to assess whether source-tailored modelling is needed…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
In this paper we develop a simple theory to study the effects of ionic size on ionic distributions around a charged spherical particle. We include a correction to the regular Poisson-Boltzmann equation in order to take into account the size…
Within the quasichemical approach, the hydration free energy of an ion is decomposed into a chemical term accounting for ion specific ion-water interactions within the coordination sphere and nonspecific contributions accounting for packing…
We present a theoretical description of the effect of polyvalent ions on the interaction between titratable macro-ions. The model system consists of two point-like macro-ions with dissociable sites, immersed in an asymmetric ionic mixture…
Recent work has provided the means to rigorously determine properties of super-hadronic matter from experimental data through the application of broad scale modeling of high-energy nuclear collisions within a Bayesian framework. These…
Transition metal complexes for photochemical applications often feature a high density of electron-vibrational states characterized by nonadiabatic and spin-orbit couplings. Overall, the dynamics after photoexcitation is shaped by rapid…
Coordination chemistry relies on harnessing active metal sites within organic matrices. Polynuclear complexes - consisting of organic ligands binding to clusters of several metal atoms are of particular interest, owing to their…
The integration of machine learning (ML) into chemistry offers transformative potential in the design of molecules with targeted properties. However, the focus has often been on creating highly efficient predictive models, sometimes at the…
Simplified representations of macromolecules help in rationalising and understanding the outcome of atomistic simulations, and serve to the construction of effective, coarse-grained models. The number and distribution of coarse-grained…
Macromolecules can form regular structures on inert surfaces. We have developed a combined empirical and modeling approach to derive the bonding. From experimental scanning tunneling microscopy (STM) images of structures formed on Au(111)…
Physics-based electrochemical battery models derived from porous electrode theory are a very powerful tool for understanding lithium-ion batteries, as well as for improving their design and management. Different model fidelity, and thus…
Covalent molecules are characterized by directed bonds, which provide stability-of-form to the molecules relative atomic positions. In contrast, bulk metals are characterized by delocalized bonds, where a large number of resonance…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…