Related papers: Polarisable force fields: What do they add in biom…
The electrostatic force is described in this model by the action of electric dipole distributions on charged particles. The individual hypothetical dipoles are propagating at the speed of light in vacuum transferring momentum and energy…
Classical empirical force fields have dominated biomolecular simulation for over 50 years. Although widely used in drug discovery, crystal structure prediction, and biomolecular dynamics, they generally lack the accuracy and transferability…
Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental…
The Poisson-Boltzmann mean-field description of ionic solutions has been successfully used in predicting charge distributions and interactions between charged macromolecules. While the electrostatic model of charged fluids, on which the…
We develop a direct derivation for the primary contribution to the vibrational polarizability for molecules, clusters and other finite systems. The vibrational polarizability is then calculated within the generalized gradient approximation…
Solids facing a plasma are a common situation in many astrophysical systems and laboratory setups. Moreover, many plasma technology applications rely on the control of the plasma-surface interaction. However, presently often a fundamental…
We study conformal field theories describing two massless one-dimensional fields interacting at a single spatial point. The interactions we include are periodic functions of the bosonized fields separately plus a ``magnetic'' interaction…
Friction is one of the fundamental issues in physics, mechanics and material science with lots of practical applications. However, the understanding of macroscopic friction phenomena from microscopic aspect is still on the way. In this…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
Molecular dynamics simulations are used to study the local dynamics of counterion-charged polymer association at charge densities above and below the counterion condensation threshold. Surprisingly, the counterions form weakly-interacting…
Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
The article provides a brief general introduction into the concepts of scaling, universality, and crossover scaling, plus the blob concept that provides an intuitive picture of crossover phenomena. We present the most important static and…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
The real and imaginary parts of the susceptibility are fundamentally associated with the molecular dispersion and absorption, respectively. Measurement of the molecular dispersion has given insight into underlying molecular dynamics such as…
With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…
In this paper we have derived explicitly computable bounds on the error in energy norms for the fully nonlinear Poisson-Boltzmann equation. Together with the computable bounds, we have also obtained efficient error indicators which can…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
There are many astrophysical and laboratory scenarios where kinetic effects play an important role. These range from astrophysical shocks and plasma shell collisions, to high intensity laser-plasma interactions, with applications to fast…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…