相关论文: Redox Entropy of Plastocyanin: Developing a Micros…
We present a novel discontinuous Galerkin finite element method for numerical simulations of the rotating thermal shallow water equations in complex geometries using curvilinear meshes, with arbitrary accuracy. We derive an entropy…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the…
We develop a relativistic multifluid dynamics appropriate for describing neutron star cores at finite temperatures based on Carter's convective variational procedure. The model includes seven fluids, accounting for both normal and…
The methodology proposed in this paper bridges the gap between entropy stable and positivity-preserving discontinuous Galerkin (DG) methods for nonlinear hyperbolic problems. The entropy stability property and, optionally, preservation of…
The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
We have recently developed a breakthrough methodology for rapidly computing entropy in both solids and liquids by integrating a multiscale entropy approach (known as zentropy theory) with molecular dynamics (MD) simulations. This approach…
We show that macroscopic irreversible thermodynamics for viscous fluids can be derived from exact information-theoretic thermodynamic identities valid at the microscale. Entropy production, in particular, is a measure of the loss of…
Entropy is a fundamental thermodynamic quantity that is a measure of the accessible microstates available to a system, with the stability of a system determined by the magnitude of the total entropy of the system. This is valid across truly…
Molecular Dynamics (MD) simulations are a powerful tool for studying matter at the atomic scale. However, to simulate solids, an initial atomic structure is crucial for the successful execution of MD simulations, but can be difficult to…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
Two-dimensional polar liquid crystals have been discovered recently in monolayers of anisotropic molecules. Here, we provide a systematic theoretical description of liquid-crystalline phases for polar particles in two spatial dimensions.…
To calculate the solvation of hydrophobic solutes we have developed the method based on the fundamental measure treatment of the density functional theory. This method allows us to carry out calculations of density profiles and the…
We employ a mesoscopic model for studying aggregation processes of protein-like hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase…
The first paper of this series presents a discretely entropy stable discontinuous Galerkin (DG) method for the resistive magnetohydrodynamics (MHD) equations on three-dimensional curvilinear unstructured hexahedral meshes. Compared to other…
We study model protein solutions and colloidal suspensions in the temperature range whereupon the nature of the system changes from a homogeneous fluid to a "cluster fluid". It is commonly assumed - as deduced by the behavior of the…
The continuum dislocation dynamics framework for mesoscale plasticity is intended to capture the dislocation density evolution and the deformation of crystals when subjected to mechanical loading. It does so by solving a set of transport…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…