Related papers: Stacking and Hydrogen Bonding. DNA Cooperativity a…
Residential electric water heaters have significant load shifting capabilities due to their thermal heat capacity and large energy consumption. Model predictive control (MPC) has been shown to be an effective control strategy to enable…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
Performing molecular dynamics simulations for all-atom models, we characterize the conformational and structural relaxations of poly(ethylene oxide) and poly(propylene oxide) melts. The temperature dependence of these relaxation processes…
Cells contain multiple condensates which spontaneously form due to the heterotypic interactions between their components. Although the proteins and disordered region sequences that are responsible for condensate formation have been…
Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid state packing and polymer-electrolyte…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
Research on conjugated polymers for thermoelectric applications has made tremendous progress in recent years, which is accompanied by surging interest in molecular doping as a means to achieve the high electrical conductivities that are…
Homogenization protocols model the quantum mechanical evolution of a system to a fixed state independently from its initial configuration by repeatedly coupling it with a collection of identical ancillas. Here we analyze these protocols…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
We study phase behaviours of lipid--bilayer vesicles functionalised by ligand--receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo…
Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with different types of intrinsic stiffness. Important static observables of the single chain such as gyration radius or persistence length are…
Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules e.g.…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
The supercooled state of bulk water is largely hidden by unavoidable crystallization, which creates an experimentally inaccessible temperature regime - a 'no man's land'. We address this and circumvent the crystallization problem by…
Stacking fault energy dictates phase stability and deformation behavior in Co alloys and WC-Co cemented carbides, yet a quantitative assessment of alloying effects at finite temperatures remains poorly established. By integrating…
Associative polymers (APs) with reversible, specific interactions between ``sticker'' sites exhibit a phase behavior that depends on a delicate balance between distinct contributions controlling the binding. For highly-bonded systems, it is…
In this study, a versatile methodology for initiating polymerization from monomers in highly cross-linked materials is investigated. As polymerization progresses, force-field parameters undergo continuous modification due to the formation…