Related papers: SAMPLE: Surface structure search enabled by coarse…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Molecular discovery within the vast chemical space remains a significant challenge due to the immense number of possible molecules and limited scalability of conventional screening methods. To approach chemical space exploration more…
We introduce and analyze numerical companion matrix methods for the reconstruction of hypersurfaces with crossings from smooth interpolants given unordered or, without loss of generality, value-sorted data. The problem is motivated by the…
The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
Much of our understanding of complex structures is based on simplification: for example, metal-organic frameworks are often discussed in the context of "nodes" and "linkers", allowing for a qualitative comparison with simpler inorganic…
A thorough in situ characterization of materials at extreme conditions is challenging, and computational tools such as crystal structural search methods in combination with ab initio calculations are widely used to guide experiments by…
Controlling the properties of organic/inorganic materials requires detailed knowledge of their molecular adsorption geometries. This is often unattainable, even with current state-of-the-art tools. Visualizing the structure of complex…
Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
The intentional growth of metastable surface structures of organic molecules adsorbed on inorganic substrates is a challenging task. It is usually unclear which kinetic mechanism leads to the metastable surface polymorph after a deposition…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…