Related papers: Insights into DNA-mediated interparticle interacti…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
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…
The computational study of the interaction between charged, ligand-protected metal nanoparticles and model lipid membranes has been recently addressed both at atomistic and coarse grained level. Here we compare the performance of three…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers.…
Patchy particles have received great attention due to their ability to develop directional and selective interactions and serve as building units for the self-assembly of innovative colloidal molecules and crystalline structures. Although…
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The…
Electroporation is a physical method to induce the uptake of therapeutic drugs and DNA, by eukaryotic cells and tissues. The phenomena behind electro-mediated membrane permeabilization to plasmid DNA have been shown to be significantly more…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
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…
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…