Insights into the Kinetics of Supramolecular Comonomer Incorporation in Water

Multicomponent supramolecular polymers are a versatile platform to prepare functional architectures, but a few studies have been devoted to investigate their noncovalent synthesis. Here, we study supramolecular copolymerizations by examining the mechanism and time scales associated with the incorporation of new monomers in benzene-1,3,5-tricarboxamide (BTA)-based supramolecular polymers. The BTA molecules in this study all contain three tetra(ethylene glycol) chains at the periphery for water solubility but differ in their alkyl chains that feature either 10, 12 or 13 methylene units. C(10)BTA does not form ordered supramolecular assemblies, whereas C(12)BTA and C(13)BTA both form high aspect ratio supramolecular polymers. First, we illustrate that C(10)BTA can mix into the supramolecular polymers based on either C(12)BTA or C(13)BTA by comparing the temperature response of the equilibrated mixtures to the temperature response of the individual components in water. Subsequently, we mix C(10)BTA with the polymers and follow the copolymerization over time with UV spectroscopy and hydrogen/deuterium exchange mass spectrometry experiments. Interestingly, the time scales obtained in both experiments reveal significant differences in the rates of copolymerization. Coarse-grained simulations are used to study the incorporation pathway and kinetics of the C(10)BTA monomers into the different polymers. The results demonstrate that the kinetic stability of the host supramolecular polymer controls the rate at which new monomers can enter the existing supramolecular polymers

Morphology of proliferating epithelial cellular tissue

We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective division and division plane orientation. The model is applied to a bimodal mixture of stiff cells with a low growth potential and soft cells with a high growth potential. In an even mixture, the soft cells develop into a tissue matrix and the stiff cells into a dendrite-like network structure. For soft cell inclusion in a stiff cellular matrix, the soft cells develop to a fast growing tumour like structure that gradually evacuates the stiff cell matrix. With increasing inter-cell friction, the tumour growth slows down and parts of it is driven to self-inflicted cell death

CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions

We present a new open source software package \textit{CellSim3D} for computer simulations of cell division in three dimensions. The code is based on a previously \u3cbr/\u3eintroduced two dimensional mechanical model for cell division which is extended to full 3D. CellSim3D is written in C/C++ and CUDA and allows for simulations of 100,000 cells using standard desktop computers

Electronic excitations in complex molecular environments:Many-body Green's functions theory in votca-XTP

\u3cp\u3eMany-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identity techniques, the code is designed specifically for nonperiodic systems. Application to a small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2 to 8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a binucleobase CT exciton. The results show that VOTCA-XTP's GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments.\u3c/p\u3