Related papers: Molecular recognition in a lattice model: An enume…
We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed…
The detection and classification of microplastics in water remain a significant challenge due to their diverse properties and the limitations of traditional optical methods. Standard spectroscopic techniques often suffer from the strong…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
Powdered materials of sizes ranging from nanometers to microns are widely used in materials science and are carefully selected to enhance the performance of a matrix. Fillers have been used in order to improve, among the others, mechanical,…
Polymer bottlebrushes provide intriguing features being relevant both in nature and in synthetic systems. While their presence in the articular cartilage optimizes synovial joint lubrication, bottlebrushes offer pathways for fascinating…
We propose the use of topographic modulation of surfaces to select and localize particles in nematic colloids. By considering convex and concave deformations of one of the confining surfaces we show that the colloid-flat surface repulsion…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
We describe a class of "bare bones" models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the…
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…
We present two recent applications of lattice-gas modeling techniques to electrochemical adsorption on catalytically active metal substrates: urea on Pt(100) and (bi)sulfate on Rh(111). Both involve the specific adsorption of small…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
Microplastics (MPs) are ubiquitous pollutants with demonstrated potential to impact ecosystems and human health. Their microscopic size complicates detection, classification, and removal, especially in biological and environmental samples.…
We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of $N$ distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical…
We consider a linearly elastic composite medium, which consists of a homogeneous matrix containing a statistically homogeneous set of multimodal spherical inclusions modeling the morphology of heterogeneous solid propellants (HSP).…
The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time…
The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealised coarse-grained lattice models.…
Given the ubiquity of lattice models in physics, it is imperative for researchers to possess robust methods for quantifying clusters on the lattice --- whether they be Ising spins or clumps of molecules. Inspired by biophysical studies, we…