Molecular dynamics simulation of oil displacement using surfactant in a nano-silica pore

This work was supported by National Natural Science Foundation of China (52074347) Open Access via the Elsevier agreementPeer reviewedPublisher PD

Nanotribology investigations with classical molecular dynamics

This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein: measuring the contact area in atomistic simulations, the applicability of continuum mechanics theories for describing nanocontacts, and the topography of rough surfaces at the atomic scale

Selective Removal of Hydrogen Sulphide from Industrial Gas Mixtures Using Zeolite NaA

Hydrogen sulphide removal from simple gas mixtures using a highly polar zeolite was studied by molecular simulation. The equilibrium adsorption properties of hydrogen sulphide, hydrogen, methane and their mixtures on dehydrated zeolite NaA were computed by Grand Canonical Monte Carlo simulations. Existing all-atom intermolecular potential models were optimized to reproduce the adsorption isotherms of the pure substances. The adsorption results of the mixture, also confirmed by IAST calculations, showed very high selectivities of hydrogen sulphide to the investigated non-polar gases, predicting an outstanding performance of zeolite NaA in technological applications that target hydrogen sulphide capture

The future of molecular dynamics simulations in drug discovery

Molecular dynamics simulations can now track rapid processes—those occurring in less than about a millisecond—at atomic resolution for many biologically relevant systems. These simulations appear poised to exert a significant impact on how new drugs are found, perhaps even transforming the very process of drug discovery. We predict here future results we can expect from, and enhancements we need to make in, molecular dynamics simulations over the coming 25 years, and in so doing set out several Grand Challenges for the field. In the context of the problems now facing the pharmaceutical industry, we ask how we can best address drug discovery needs of the next quarter century using molecular dynamics simulations, and we suggest some possible approaches

ADSORPTION OF CYCLOALKANES ON SURFACES WITH DIFFERENT SYMMETRY AND COMPOSITION

Adsorption of gas molecules on solid surfaces plays a major role in many physical and chemical processes involved in catalysis, surface wetting, lubrication, gas storage and separation. The homologous series of cycloalkane is an important group of compounds in petrochemical and synthetic industries. These molecules offer conformational varieties that change dramatically with the change in ring size. In this study the effect of surface and molecular symmetry on the physical adsorption properties of thin films of cycloalkanes on three different substrates were investigated. The changes in molecular configuration and dynamics within these films were studied using thermodynamic and molecular modeling methods. High-resolution volumetric adsorption isotherms of cycloalkane (C5- to C8-) on magnesium oxide (MgO) (100), graphite and hexagonal boron nitride (hBN) basal planes were recorded over a broad range of temperature (195K-263K). These isotherms were analyzed to determine the thermodynamics of adsorption (i.e. heats of adsorption, isosteric heats, differential enthalpy and entropy) and to identify regions of possible phase transitions. Molecular dynamics simulations of mono- and multilayers of cycloalkanes (C5- to C8-) on these surfaces were used to obtain binding energies, molecular trajectories, pair-correlation functions and molecular distribution perpendicular to the surface plane of the adsorbent substrate. These experimental and modeling results can serve as the prelude to elastic and inelastic neutron scattering experiments

Computational studies of protein-ligand recognition

Molecular recognition between biomolecules and ligands is very specific in living cells. The functions of all biochemical processes and cell mechanisms are dependent upon complex but specific non-covalent intermolecular interactions. As essential building blocks in protein and nucleic acid, phosphate groups are commonly found in nucleic acids, proteins, and lipids. Nearly half of known proteins have been shown to interact with ligands containing a phosphate group. Binding of a phosphoryl group is fundamental to a range of biological processes including metabolism, biosynthesis, gene regulation, signal transduction, muscle contraction, and antibiotic resistance. Phosphorylation is one of the most common forms of reversible posttranslational modification of protein and, nearly 30% of all proteins are phosphorylated on at least one residue in cells. However, phosphate binding sites are less well defined and fundamental principles of why and how proteins recognize phosphate groups are not yet fully understood. Molecular modeling is a common tool for studying biomolecular structure, dynamics, interaction and function. Due to the complex electrostatics, high concentration of ions and intricate interactions with environment, however, the modeling and designing of highly charged drug-like molecules and nucleic acid derivatives are extremely difficult. This thesis will focus on the highly charged phosphate, including its different protonation states, and energetic and thermodynamic driving forces behind protein-phosphate recognition. This thesis work will also discuss the development of more sophisticated computational models, AMOEBA+, that are necessary for a better understanding and prediction of the physical properties of small organic molecules. Four projects will be discussed in this dissertation: two projects on force field development, and two on applying molecular dynamic simulations to understand biological processes. These projects have led to new insights into understanding of physical and chemical principles and mechanisms underlying highly protein-phosphate binding and nucleic acid stability. In addition, this thesis work will enhance the capability to develop and apply computational and theoretical frameworks to model, predict and design proteins, therapeutics, and diagnostic strategies targeting phosphates, phosphate-containing biomoleculesBiomedical Engineerin

Computational modeling of thermal interfaces in graphene based nanostructures

L'abstract è presente nell'allegato / the abstract is in the attachmen

A Novel Approach to Design an Integrated Antenna-Battery System

In this study, an integrated antenna-battery was explored. Studying the systems separately allowed information to be obtained relating to the materials' performance and feasibility of an integrated system. Conducting polymers are promising in modern day lithium ion batteries. With high electrical conductivity as well as good ionic conductivity, they are now becoming more widely used. Here, we present a study of a co-block polymer (PEDOT-PEG) in which a polymer with high electrical conductivity is linked to a polymer with lithium ion conductivity, using a combination of atomistic simulations and experiments. Simulations showed that the diffusion and ionic conductivity for PEDOT-PEG agreed well with experiments. A trend was identified as a function of lithium salt concentration, in which the ionic conductivity decreased with increasing concentration. This was identified to be down to the significant ion pairing occurring in the system between lithium and the counterion. Requirements for the antenna were the ability to be mounted easily onto a battery substrate without a significant loss in efficiency and bandwidth. Studies were undertaken in which a slot dipole antenna was modified so as to incorporate properties more closely associated with battery materials i.e. permittivity and dielectric loss. An ultra-thin Mylar prototype was also synthesised and mounted onto a variety of surfaces, to assess how the antenna performed in different environments. Results for the antenna showed usable bandwidths and efficiencies when the antenna structure was modified to closely resemble a solid state battery. Despite a reduction seen in certain cases, these losses were not significant, and showed promise with regards to designing an integrated system. The Mylar prototype showed a good match between simulation and experiment in free space and when mounted on surfaces such as polymers, indicating that an ultra-thin antenna-battery is feasible