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Besides direct molecular interactions, proteins and nanoparticles embedded in or adsorbed to membranes experience indirect interactions that are mediated by the membranes. These membrane-mediated interactions arise from the membrane…
Nucleic acids such as mRNA have emerged as a promising therapeutic modality with the capability of addressing a wide range of diseases. Lipid nanoparticles (LNPs) as a delivery platform for nucleic acids were used in the COVID-19 vaccines…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…
Aqueous two-phase systems (ATPSs), that is, phase-separating solutions of water soluble but mutually immiscible molecular species, offer fascinating prospects for selective partitioning, purification, and extraction. Here, we formulate a…
The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…
The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its monomers. In particular, interactions mediated by counterions play a significant role, and are affected by both specific molecular…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its…
This paper reviews the status of molecular dynamics as a method in describing solid-solid phase transitions, and its relationship to continuum approaches. Simulation work done in NiTi and Zr using first principles and semi-empirical…
Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified…
We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems in a Quantum Chemistry perspective, one has to take into account that…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano et al, J. Chem. Phys. 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles…
Functionalized metal nanoparticles (NPs) have been proposed as promising radiosensitizing agents for more efficient radiotherapy treatment using photons and ion beams. Radiosensitizing properties of NPs may depend on many different…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…