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Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
High-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) is a vital tool for characterizing single-atom catalysts (SACs). However, reliable elemental identification of different atoms remains challenging because…
An analytical model of the electrostatic force between the tip of a non-contact Atomic Force Microscope (nc-AFM) and the (001) surface of an ionic crystal is reported. The model is able to account for the atomic contrast of the local…
Recent studies have utilized AC fields and electrochemical reactions in multicomponent electrolyte solutions to control colloidal assembly. However, theoretical investigations have thus far been limited to binary electrolytes and have…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones…
The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (80%), RNA (10%), and a number of different proteins (10%). These nucleoid proteins act as regulators of gene expression…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
A multiple-image method is developed to accurately calculate the electrostatic interaction between neutral dielectric particles and a uniformly charged dielectric substrate. The difference in dielectric constants between the particle and…
Using computer simulations, the electrophoretic motion of a positively charged colloid (macroion) in an electrolyte solution is studied in the framework of the primitive model. Hydrodynamic interactions are fully taken into account by…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Interparticle interactions and bulk properties of colloidal suspensions can be substantially modified by addition of nanoparticles. Extreme asymmetries in size and charge between colloidal particles and nanoparticles present severe…
We model the electron clouds of nucleic acids in DNA as a chain of coupled quantum harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. Crucial parameters in our model are…
Functionalizing colloids with reactive DNA linkers is a versatile way of programming self-assembly. DNA selectivity provides direct control over colloid-colloid interactions allowing the engineering of structures such as complex crystals or…
Dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D Fast Fourier…
We study the reduced Bogoliubov-Dirac-Fock (BDF) energy which allows to describe relativistic electrons interacting with the Dirac sea, in an external electrostatic potential. The model can be seen as a mean-field approximation of Quantum…
Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a…
Large-scale applications of energy density functional (EDF) methods depend on fast and reliable algorithms to solve the associated non-linear self-consistency problem. When dealing with large single-particle variational spaces, existing…
Rigid, cage-like molecules, like diamondoids, show unique self-assembly behavior, such as templating 1-D nanomaterial assembly via pathways that are typically blocked for such bulky substituents. We investigate molecular forces between…