Related papers: A microscopic description of acid-base equilibrium
Fluid phase equilibria involving nano-dispersed phases, where at least one of the coexisting phases is confined to a small volume, are investigated by molecular dynamics simulation. Complementing previous studies on nanoscopic droplets,…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
We investigate the quantum many-body dynamics of dissociation of a Bose-Einstein condensate of molecular dimers into pairs of constituent bosonic atoms and analyze the resulting atom-atom correlations. The quantum fields of both the…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
A combinative approach for chemical analysis makes it possible to distinguish a mixture of a large number of compounds from other mixtures in a single step. This work demonstrates a combinative analysis approach by using surface…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. Like in all first order first transitions there is an interplay between…
Cross-reactions and other systematic issues generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key…
The empirical laws of chemical kinetics are studied from a microscopic point of view. An analysis based on elementary probability theory and combinatorics is enough to explain the kinetics law observed in experiments. Thus, an out of…