Related papers: Molecular recognition in a lattice model: An enume…
We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength $\kappa$ of the local…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
In this paper, we study the role of surface of the globule and the role of interactions with the solvent for designed sequence heteropolymers using random energy model (REM). We investigate the ground state energy and surface monomer…
Structure of monolayers built during adsorption process is strongly related to the properties of adsorbed particles. The most important factor is their shape. For example, adsorption of elongated molecules on patterned surfaces may produce…
Recent decades have seen the discovery of numerous complex materials. At the root of the complexity underlying many of these materials lies a large number of possible contending atomic- and larger-scale configurations and the intricate…
Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…
We introduce a framework for adsorption of a single polymer in which the topology of the polymer is quenched before adsorption, in contrast to more standard adsorption models having annealed topology. Our "topology" refers either to the…
We examine a two-dimensional nonequilibrium lattice model where particles adsorb at empty sites and desorb when the number of neighbouring particles is greater than a given threshold. In a certain range of parameters the model exhibits…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
Determining the stability of molecules and condensed phases is the cornerstone of atomistic modelling, underpinning our understanding of chemical and materials properties and transformations. Here we show that a machine learning model,…
The tools and technology that are currently used to analyze chemical compound structures that identify polymer types in microplastics are not well-calibrated for environmentally weathered microplastics. Microplastics that have been degraded…
An infinite hierarchy of layering transitions exists for model polymers in solution under poor solvent or low temperatures and near an attractive surface. A flat histogram stochastic growth algorithm known as FlatPERM has been used on a…
We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…
In this paper I describe the computer simulations that I have performed to critically examine the Lauritzen-Hoffman and the Sadler-Gilmer theories of polymer crystallization. In particular, I have computed the free energy profile for…
The adsorption of a single multi-block $AB$-copolymer on a solid planar substrate is investigated by means of computer simulations and scaling analysis. It is shown that the problem can be mapped onto an effective homopolymer adsorption…
Progress in functional materials discovery has been accelerated by advances in high throughput materials synthesis and by the development of high-throughput computation. However, a complementary robust and high throughput structural…
Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method…
Selective targeting of membranes with a specific receptor profile is an ongoing challenge in targeted drug delivery. We investigate the adsorption of copolymers on a multicomponent receptor-covered surface using grand-canonical Monte Carlo…
Transformers generate valid and diverse chemical structures, but little is known about the mechanisms that enable these models to capture the rules of molecular representation. We present a mechanistic analysis of autoregressive…