Dendrimer-Guest Interactions: Challenging Conventional Wisdom

Solutions to many future challenges - including water purification, drug delivery, and energy storage - will require innovative new materials. Dendrimers are a class of materials with wide-ranging applications whose behavior is not fully understood. In many potential applications, dendrimers interact with small molecules. Our work focuses on describing the fundamental mechanisms governing the interactions between dendrimers and hydrocarbons using molecular modeling and computer simulations. A common view of dendrimer host-guest interactions is that the guest molecules are encapsulated in protected interior voids within the dendrimer structure. Our results present an alternative picture and show that the association of a model aromatic hydrocarbon, naphthalene (NPH), involves temporary pockets formed by the dendrimer branches and interactions between the NPH molecules themselves

Large-scale Molecular Dynamics Simulation with Forward Flux Sampling on Hadoop

Simulating rare events is extremely difficulty and requires massive computational resources and complex data processing workflow, which is determined by the nature of stochastic systems. To help computational scientists discover hard scientific problems in this area, we built a large-scale molecular dynamics simulation framework integrated with forward flux sampling (FFS) technique on Hadoop ecosystem. In this project, we port the customized FFS workflow to underlying MapReduce-based computing pipeline by using dataflow-driven design pattern and Gromacs application. The early works show that our framework is able to provide a scalable, fault-tolerance and efficient rare events simulation environment over varieties of computing infrastructures, while preserving the flexibility of the original scientific application

Dendrimers for Water Purification Applications: Molecular Dynamics Studies

In this project, we use molecular dynamics simulations to study the behavior of dendrimers, a class of branched polymers, in an aqueous solution of hydrocarbons. Previous experimental studies have suggested that dendrimers can be used for oil spill remediation and water purification. Both these applications depend on how the dendrimers interact with the hydrocarbons present in the oil spill as well as the water contaminants. In our study, we focus on elucidating the molecular mechanisms through which the dendrimers associate with different types of hydrocarbons. Specifically, we use all-atom and coarse-grained models to study the association of dendrimers with aromatic hydrocarbons like naphthalene and linear hydrocarbons like octane. We have investigated the effect of dendrimer size, and hydrocarbon concentration on the association behavior. Our studies reveal new pictures of dendrimer-hydrocarbon association and provide insights that can be used to engineer dendrimers for effective use in water purification applications

Water Structure and Its Correlation to Heterogeneous Ice Nucleation

Clouds, a mixture of water vapor, condensed liquid droplets, solid crystals and aerosol particles, exert an importance on weather and climate via controlling the amount of precipitation and transportation of radiative fluxes. One of the major processes involved in clouds is heterogeneous ice nucleation, which is nucleation facilitated by the presence of mineral substrates. Understanding the role played by solid surfaces in influencing the structure and dynamics of water and thus regulating ice nucleation paves the road for forecasting long-term climate change and designing surfaces with customer-specified ice nucleation properties. The goal of our research is to be able to predict the nucleating ability of a surface based on the interfacial water structure and dynamics. To investigate this problem, we focus on mica, which has a molecularly smooth nature to begin with, thus eases out the complexity of dealing with surface defects. By combining molecular dynamics (MD) simulations with Fourier-transform infrared spectroscopy (FTIR), we probe the change in interfacial water arrangement, spatial correlation and dynamics on mica surface. The interplay of ion-water, ion-surface, and surface-water interactions affect the interfacial water arrangement along with the hydrogen bond network, which is found to be the crucial part in altering surface nucleating ability

Proceedings of the SC15 Workshop on Producing High Performance and Sustainable Software for Molecular Simulation

These are the proceedings of the SC15 Workshop on Producing High Performance and Sustainable Software for Molecular Simulation, which was organised as part of the APES project. Please see the Introduction and Table of Contents for more details

Effect of Surface Parameters on Interfacial Water Film Behavior

Vapor-to-liquid and liquid-to-solid transitions on mineral surfaces are the primary pathways for phase transitions in atmospheric water. These phase transitions affect the microphysics of clouds and have significant effects on the weather and climate. Our overall goal is to elucidate the mechanisms through which surfaces affect these transitions, and develop predictive abilities to correlate surface properties to the thermodynamics and kinetics of the phase transitions. In this work, we use molecular dynamics simulations to study the structure, and dynamics of water near kaolinite-like surfaces. Kaolinite is the most abundant mineral dust in the atmosphere. We specifically investigate the effect of lattice spacing on water structure in water films of varying thicknesses. Our results will help us ascertain the properties important to promote ice nucleation. The insights gained also have implications in designing materials that can prevent ice nucleation in applications such as power-lines, car windshields, and computer chips

Heterogeneous Ice Nucleation: Interplay of Surface Properties and Their Impact on Water Orientations

Ice is ubiquitous in nature, and heterogeneous ice nucleation is the most common pathway of ice formation. How surface properties affect the propensity to observe ice nucleation on that surface remains an open question. We present results of molecular dynamics studies of heterogeneous ice nucleation on model surfaces. The models surfaces considered emulate the chemistry of kaolinite, an abundant component of mineral dust. We investigate the interplay of surface lattice and hydrogen bonding properties in affecting ice nucleation. We find that lattice matching and hydrogen bonding are necessary but not sufficient conditions for observing ice nucleation at these surfaces. We correlate this behavior to the orientations sampled by the metastable supercooled water in contact with the surfaces. We find that ice is observed in cases where water molecules not only sample orientations favorable for bilayer formation but also do not sample unfavorable orientations. This distribution depends on both surface-water and water–water interactions and can change with subtle modifications to the surface properties. Our results provide insights into the diverse behavior of ice nucleation observed at different surfaces and highlight the complexity in elucidating heterogeneous ice nucleation

Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

We compare the free energies of adsorption (∆Aads) and the structural preferences of amino acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force fields, the trends in the free energy of adsorption with amino acids are similar across the studied force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with graphene–water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption of proteins and peptides would be described consistently across different force fields, the structural preferences of peptides and proteins on graphene will be force field dependent. </div