In this paper a new particle wall boundary condition to replace explicit solid walls in molecular dynamics (MD) simulations is proposed. This new wall potential reduces the computational complexity considerably and allows the investigation of larger channels without compromising macroscopic quantities, such as density, temperature, pressure and heat flux. Since it is common practice in MD to truncate pair interaction potentials, an alternative and explicit derivation of the wall potential is possible, which is in contrast to previous work. Moreover, different types of crystal lattices can be included in the new potential. To demonstrate the applicablity of the method, MD simulations of a gas between two parallel plates at different temperatures and densities have been performed. The results of these simulations are compared to explicit wall simulations and previously proposed wall potentials. Although differences with other wall potentials are minor, some superior aspects of the new potential are addressed.
Very low calorie diets (VLCD) with and without exercise programs lead to major metabolic improvements in obese type 2 diabetes patients. The mechanisms underlying these improvements have so far not been elucidated fully. To further investigate the mechanisms of a VLCD with or without exercise and to uncover possible biomarkers associated with these interventions, blood samples were collected from 27 obese type 2 diabetes patients before and after a 16-week VLCD (Modifast ∼450 kcal/day). Thirteen of these patients followed an exercise program in addition to the VCLD. Plasma was obtained from 27 lean and 27 obese controls as well. Proteomic analysis was performed using mass spectrometry (MS) and targeted multiple reaction monitoring (MRM) and a large scale isobaric tags for relative and absolute quantitation (iTRAQ) approach. After the 16-week VLCD, there was a significant decrease in body weight and HbA1c in all patients, without differences between the two intervention groups. Targeted MRM analysis revealed differences in several proteins, which could be divided in diabetes-associated (fibrinogen, transthyretin), obesity-associated (complement C3), and diet-associated markers (apolipoproteins, especially apolipoprotein A-IV). To further investigate the effects of exercise, large scale iTRAQ analysis was performed. However, no proteins were found showing an exercise effect. Thus, in this study, specific proteins were found to be differentially expressed in type 2 diabetes patients versus controls and before and after a VLCD. These proteins are potential disease state and intervention specific biomarkers. Trial Registration Controlled-Trials.com ISRCTN76920690
The understanding of multi-component mixtures of self-assembling molecules under thermodynamic equilibrium can only be advanced by a combined experimental and theoretical approach. In such systems, small differences in association energy between the various components can be significantly amplified at the supramolecular level via intricate nonlinear effects. Here we report a theoretical investigation of two-component, self-assembling systems in order to rationalize chiral amplification in cooperative supramolecular copolymerizations. Unlike previous models based on theories developed for covalent polymers, the models presented here take into account the equilibrium between the monomer pool and supramolecular polymers, and the cooperative growth of the latter. Using two distinct methodologies, that is, solving mass-balance equations and stochastic simulation, we show that monomer exchange accounts for numerous unexplained observations in chiral amplification in supramolecular copolymerization. In analogy with asymmetric catalysis, amplification of chirality in supramolecular polymers results in an asymmetric depletion of the enantiomerically related monomer pool. In multi-component mixtures of self-assembling molecules, small differences in association energy between components can be amplified by nonlinear effects. This theoretical investigation of self-assembling systems rationalizes chiral amplification in cooperative supramolecular copolymerizations.
Abstract Chiral amplification in molecular self-assembly has profound impact on the recognition and separation of chiroptical materials, biomolecules, and pharmaceuticals. An understanding of how to control this phenomenon is nonetheless restricted by the structural complexity in multicomponent self-assembling systems. Here, we create chiral octahedra incorporating a combination of chiral and achiral vertices and show that their discrete nature makes these octahedra an ideal platform for in-depth investigation of chiral transfer. Through the construction of dynamic combinatorial libraries, the unique possibility to separate and characterise each individual assembly type, density functional theory calculations, and a theoretical equilibrium model, we elucidate that a single chiral unit suffices to control all other units in an octahedron and how this local amplification combined with the distribution of distinct assembly types culminates in the observed overall chiral amplification in the system. Our combined experimental and theoretical strategy can be applied generally to quantify discrete multi-component self-assembling systems.
Significance The molecular organization of semiconducting molecules is extremely important for the performance of functional organic materials in electronic devices. The processing of these materials often leads to multiple assembly pathways toward different types of molecular organizations. Hence, directing the assembly process toward the desired type of organization requires many trial-and-error optimization steps. In this paper, we introduce an approach to optimize these self-assembly processes. Based on experiments with a system that assembles into 1D helices in solution, we have developed models to describe the dynamics of multicomponent self-assembly processes. These models simulate the experimental data very well and allow us to understand and avoid, or alternatively attenuate, the entrapment of materials in nonequilibrium assemblies.
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