Combining Enhanced Sampling with Experiment Directed Simulation of the GYG peptide

Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics simulations of large systems. This work combines experiment directed simulation with both the parallel-tempering and parallel-tempering well-tempered ensemble replica-exchange methods to enhance sampling of experiment directed simulations. These methods are demonstrated on the GYG tripeptide in explicit water. The collective variables biased by experiment directed simulation are chemical shifts, where the set-points are determined by NMR experiments. The results show that it is possible to enhance sampling with either parallel-tempering and parallel-tempering well-tempered ensemble in the experiment directed simulation method. This combination of methods provides a novel approach for both accurately and exhaustively simulating biological systems

A First Approach on Modelling Staff Proactiveness in Retail Simulation Models

There has been a noticeable shift in the relative composition of the industry in the developed countries in recent years; manufacturing is decreasing while the service sector is becoming more important. However, currently most simulation models for investigating service systems are still built in the same way as manufacturing simulation models, using a process-oriented world view, i.e. they model the flow of passive entities through a system. These kinds of models allow studying aspects of operational management but are not well suited for studying the dynamics that appear in service systems due to human behaviour. For these kinds of studies we require tools that allow modelling the system and entities using an object-oriented world view, where intelligent objects serve as abstract \'actors\' that are goal directed and can behave proactively. In our work we combine process-oriented discrete event simulation modelling and object-oriented agent based simulation modelling to investigate the impact of people management practices on retail productivity. In this paper, we reveal in a series of experiments what impact considering proactivity can have on the output accuracy of simulation models of human centric systems. The model and data we use for this investigation are based on a case study in a UK department store. We show that considering proactivity positively influences the validity of these kinds of models and therefore allows analysts to make better recommendations regarding strategies to apply people management practices.Retail Performance, Management Practices, Proactive Behaviour, Service Experience, Agent-Based Modelling, Simulation

Characterization, modeling, and simulation of multiscale directed-assembly systems

Nanoscience is a rapidly developing field at the nexus of all physical sciences which holds the potential for mankind to gain a new level of control of matter over matter and energy altogether. Directed-assembly is an emerging field within nanoscience in which non-equilibrium system dynamics are controlled to produce scalable, arbitrarily complex and interconnected multi-layered structures with custom chemical, biologically or environmentally-responsive, electronic, or optical properties. We construct mathematical models and interpret data from direct-assembly experiments via application and augmentation of classical and contemporary physics, biology, and chemistry methods. Crystal growth, protein pathway mapping, LASER tweezers optical trapping, and colloid processing are areas of directed-assembly with established experimental techniques. We apply a custom set of characterization, modeling, and simulation techniques to experiments to each of these four areas. Many of these techniques can be applied across several experimental areas within directed-assembly and to systems featuring multiscale system dynamics in general. We pay special attention to mathematical methods for bridging models of system dynamics across scale regimes, as they are particularly applicable and relevant to directed-assembly. We employ massively parallel simulations, enabled by custom software, to establish underlying system dynamics and develop new device production methods