Related papers: Deriving molecular bonding from macromolecular sel…
We use ab initio density functional calculations to study the formation and structural as well as thermal stability of cellular foam-like carbon nanostructures. These systems with a mixed $sp^2/sp^3$ bonding character may be viewed as…
This paper proposes a machine learning (ML) method to predict stable molecular geometries from their chemical composition. The method is useful for generating molecular conformations which may serve as initial geometries for saving time…
As an extension of the former study on 2-dimensional systems, we simulate phase behavior of polymer-grafted colloidal particles in 3 dimensions by molecular Monte Carlo technique in the canonical ensemble. We use a spherically symmetric…
To insight the relationships between the self-organizing structures of cells, such as the cell clusters, and the properties of biotissues is helpful in revealing the function and designing biomaterial. Traditional random foam model neglects…
Molecular nanowires in which a single molecule bonds chemically to two metal electrodes and forms a stable electrically conducting bridge between them have been studied intensively for more than a decade. However the experimental…
We develop a graph-based model of the hydrogen bond network in water, with a view towards quantitatively modeling the molecular-level correlational structure of the network. The networks are formed are studied by the constructing the model…
A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance…
Although common in nature, the self-assembly of small molecules at sold-liquid interfaces is difficult to control in artificial systems. The high mobility of dissolved small molecules limits their residence at the interface, typically…
We develop a mesoscopic lattice model to study the morphology formation in interacting ternary mixtures with evaporation of one component. As concrete application of our model, we wish to capture morphologies as they are typically arising…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
Development of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo…
We present a simple model which allows to investigate equilibrium aspects of molecular recognition between rigid biomolecules on a generic level. Using a two-stage approach, which consists of a design and a testing step, the role of…
An important yet challenging aspect of atomistic materials modeling is reconciling experimental and computational results. Conventional approaches involve generating numerous configurations through molecular dynamics or Monte Carlo…
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…
Unraveling the relation between the chemical structure of small drug-like compounds and their rate of passive permeation across lipid membranes is of fundamental importance for pharmaceutical applications. The elucidation of a comprehensive…
Molecular self-assembly plays a very important role in various aspects of technology as well as in biological systems. Governed by the covalent, hydrogen or van der Waals interactions - self-assembly of alike molecules results in a large…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
We report theoretical investigations on the role of interfacial bonding mechanism and its resulting structures to quantum transport in molecular wires. Two bonding mechanisms for the Au-S bond in an Au(111)/1,4-benzenedithiol(BDT)/Au(111)…
The first off-lattice Monte Carlo kinetics model of interstellar dust-grain surface chemistry is presented. The positions of all surface particles are determined explicitly, according to the local potential minima resulting from the…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…