Related papers: Electrostatic considerations affecting the calcula…
We recently developed a generalization of the halo model in order to describe the spatial clustering properties of each mass component in the Universe, including hot gas and stars. In this work we discuss the complementarity of the model…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
We explore the impact of a LWDM cosmological scenario on the clustering properties of large-scale structure in the Universe. We do this by extending the halo model. The new development is that we consider two components to the mass density:…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
While in principle exact, Kohn-Sham density functional theory -- the workhorse of computational chemistry -- must rely on approximations for the exchange-correlation functional. Despite staggering successes, present-day approximations still…
In this study, internal energy (U), electric field (E) and particle number (N) which specify the system quantities i.e. thermodynamical quantities for the proteins. In the frame of thermodynamical formalism, the relation between the heat…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
In this Letter, we investigate how changes in the system entropy influence the characteristic time scale of the system molecular dynamics near the glass transition. Independently of any model of thermodynamic evolution of the time scale,…
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different…
A generalization of the Kohn--Sham approach is derived where the correlation-energy functional depends on the one-particle density matrix of noninteracting states and on the external potential from the interacting target-state. The…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
In transitions between different environmental settings, a molecular system inevitably undergoes a range of detectable changes, and the ability to accurately simulate such responses, e.g., in the form of shifts to molecular energies,…
In biological and synthetic materials, many important processes involve charges that are present in a medium with spatially varying dielectric permittivity. To accurately understand the role of electrostatic interactions in such systems, it…
An open quantum system refers to a system that is further coupled to a bath system consisting of surrounding radiation fields, atoms, molecules, or proteins. The bath system is typically modeled by an infinite number of harmonic…
Within the Halo Model of large scale structure, all matter is contained in dark matter halos. This simple yet powerful framework has been broadly applied to multiple data sets and enriched our comprehension of how matter is distributed in…
Quantum gas microscopes, which image the atomic occupations in an optical lattice, have opened a new avenue to the exploration of many-body lattice systems. Imaging trapped systems after freezing the density distribution by ramping up a…
We report on a methodology for the treatment of the Coulomb energy and potential in Kohn-Sham density functional theory that is free from self-interaction effects. Specifically, we determine the Coulomb potential given as the functional…
We present an alternative to the Kohn-Sham formulation of density functional theory for the ground-state properties of strongly interacting electronic systems. The idea is to start from the limit of zero kinetic energy and systematically…