相关论文: Molecular recognition in a lattice model: An enume…
On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact…
The emergence of scanning probe and electron beam imaging techniques have allowed quantitative studies of atomic structure and minute details of electronic and vibrational structure on the level of individual atomic units. These microscopic…
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…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
In the monomer-polymer model, a linear rigid polymer covers $k$ adjacent lattice sites, with no lattice site occupied by more than one polymer. The polymers are called $k$-mers, and those unoccupied lattice sites are called monomers. The…
Machine learning has transformed material discovery for inorganic compounds and small molecules, yet polymers remain largely inaccessible to these methods. While data scarcity is often cited as the primary bottleneck, we demonstrate that…
Mixture quality plays a crucial role in the physical properties of multi-component immiscible polymer mixtures including nanocomposites and polymer blends. Such complex mixtures are often characterized by hierarchical internal structures,…
Polymers, integral to advancements in high-tech fields, necessitate the study of their thermal conductivity (TC) to enhance material attributes and energy efficiency. The TC of polymers obtained by molecular dynamics (MD) calculations and…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the adsorption energy for an…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
We investigate a modified version of the $AB$ random sequential adsorption model. Specifically, this model involves the deposition of two distinct types of particles onto a lattice, with the constraint that different types cannot occupy…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
The adsorption of polymer and surfactant molecules onto colloidal particles or droplets in solution can be characterized non-destructively by scattering techniques. In a first part, the general framework of Dynamic Light Scattering, Small…
Background: Understanding the relationship between the Omics and the phenotype is a central problem in precision medicine. The high dimensionality of metabolomics data challenges learning algorithms in terms of scalability and…
We analyze response of a macromolecule near to a substrate; the substrate is tiled in the sequential and specific manner so that repeat units of the macromolecule may have different response on its adsorption in different directions onto…
Despite the long-recognized fact that chemical structure and specific interactions greatly influence the thermodynamic properties of polymer systems, a predictive molecular theory that enables systematically addressing the role of chemical…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
A main goal of data-driven materials research is to find optimal low-dimensional descriptors, allowing us to predict a physical property, and to interpret them in a human-understandable way. In this work, we advance methods to identify…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…