Some aspects of grain boundary segregation (GBS) are discussed. This paper adds two new sprouts. The first is connected with formation of the atomic complexes in boundary region and their effect on grain boundary diffusion (GBD). The second – with a nonhomogeneity of energy distribution between boundary sites.

No / The conformational propensities of amino acids are an amalgamation of sequence effects, environmental effects and underlying intrinsic behavior. Many have attempted to investigate neighboring residue effects to aid in our understanding of protein folding and improve structure prediction efforts, especially with respect to difficult to characterize states, such as disordered or unfolded states. Host-guest peptide series are a useful tool in examining the propensities of the amino acids free from the surrounding protein structure. Here, we compare the distributions of the backbone dihedral angles (φ/ψ) of the 20 proteogenic amino acids in two different sequence contexts using the AAXAA and GGXGG host-guest pentapeptide series. We further examine their intrinsic behaviors across three environmental contexts: water at 298 K, water at 498 K, and 8 M urea at 298 K. The GGXGG systems provide the intrinsic amino acid propensities devoid of any conformational context. The alanine residues in the AAXAA series enforce backbone chirality, thereby providing a model of the intrinsic behavior of amino acids in a protein chain. Our results show modest differences in φ/ψ distributions due to the steric constraints of the Ala side chains, the magnitudes of which are dependent on the denaturing conditions. One of the strongest factors modulating φ/ψ distributions was the protonation of titratable side chains, and the largest differences observed were in the amino acid propensities for the rarely sampled αL region. / NIH

The size effect in the thermo-mechanical behavior of polymeric materials is a critically important phenomenon and has been the subject of many researches in past decades. For example, polystyrene (PS), a widely used polymeric material, is brittle at the bulk state. When the dimensions decreases to the nanoscale, such as PS in nanofibers, their ductility becomes orders higher than their bulk state. In recent years a number of diverse applications, such as scaffolds in tissue engineering, drug delivery devices, as well as soft robotics, are designed by utilizing the unique properties of polymers at nanoscale. However, the inside mechanism of the size dependency in polymeric materials are still not clear yet. In this dissertation, systematic computational and experimental studies are made in order to understand the origins of the size effect for one- and two-dimensional polymeric materials. This framework is also expanded to investigate the size-dependent multi-physics response of functional polymeric materials (shape memory polymers) which are actuated by high-intensity focused ultrasound (HIFU). Our computational studies are based on molecular dynamic (MD) simulations at the atomistic scale, and experimentally-validated finite element models at the bulk level. From bottom-up direction, molecular dynamics can reveal the mechanisms of the size effect in polymers at molecular level, and help predict properties of the bulk materials. In this research, MD simulations are performed to track the origins of the size-effect in the mechanical properties of PE and PS nanofibers. In addition, the size-dependent thermal response of functional polymeric films is also studied at the atomistic scale by utilizing molecular dynamics simulations to predict the thermal properties and actuation mechanisms in these materials when subjected to HIFU fields. From top-down direction, experiments and finite element analysis, are also conducted in this research. An experimentally-validated finite element framework is built to study the mechanical response of shape memory polymers (SMPs) triggered by HIFU. As an external trail towards application fields, a SMP composite with enhanced shape memory ability and also a two-way SMP are synthesized. A smart gripper and also a self-rolling structure are designed by using these SMPs, which approves that these SMPs are good components in designing soft robotics. Finally, The influence of evaporation during fiber forming process is investigated by molecular dynamics simulation. It is found that the formation of the microstructure of polymeric fibers at nanoscale depends on the balance of stretching force and evaporation rate when the fiber is forming. / Doctor of Philosophy / Thermomechanical properties of a thin fiber, a thin film and a cube made of a polymer are significantly different. Although, based on the extensive research that has been performed in recent years our understanding of this size-dependency is advanced to a great degree in the past decades, there are still many unanswered basic questions that can only be addressed by performing computational and experimental investigation at different length scales, from atomistic up to bulk level in polymers. In this research we target exploring some unknown aspects of the size dependency in the thermomechanical properties of polymers by investigating their deformation mechanisms at different length scales. As the first step, we will investigate the mechanical properties of polymeric fibers. For these fibers, the mechanical properties are strongly connected to the fiber's diameter. The prevailing hypothesis is that this size dependency is closely related to the thickness of the surface layer of the nanofibers. Our results show some unknown origins behind the size dependency of the mechanical properties in polyethylene (PE) and polystyrene (PS) nanofibers, which originate from the deformation mechanisms at the atomistic scale. In addition, not just the mechanical properties, the thermal properties and response of functional polymers subjected to an external stimulation are also related to their size. For example, the thermal conductivity of a fiber, a sheet and a cube may be significantly different. Our study shows the thermal responses of different polymers triggered by ultrasound are also different. The size and the type of the polymers will both have influence on the final temperature in the polymeric materials, when the polymeric materials are heated by same ultrasound source. We also have applied our computational and experimental frameworks to investigate this phenomenon. In addition, we also used a new shape memory polymer composite and a two-way shape memory polymer on designing soft robotics-like structures. Overall this research indicates that both mechanical response and thermal responses of polymers are highly related to their dimension. Taking advantage of these unique size effects, and by tailoring this property, diverse devices can be made for being used in a broad range of applications.

Studies on nuclear technology have been ongoing since nuclear power became uniquely important to meet climate change goals while phasing out fossil fuels. Research on the fluoride salt cooled high temperature reactor (FHR), which is funded by the United States Department of Energy (DOE), has developed smoothly with the ultimate goal of a 2030 deployment. One challenge presented by FHR is that the primary coolant salt can acquire contamination from fuel failure and moisture leaking into the system. If contamination happens, it will result in a low concentration of fission products, fuel, transuranic materials and oxide impurities in the coolant. These impurities will then affect the properties of the molten salt in the long term and need to be removed without introducing new impurities. Most of the research conducted recently has focused on impurity separation in chloride molten salts. More research urgently needs to be conducted to study the impurity separation method for the fluoride molten salts. In this study, the La₂O₃-LiF-NaF-KF (La₂O₃-FLiNaK) system is used to demonstrate impurity separation in molten fluoride salt. Since lanthanum oxide needs to be dissolved in the fluoride molten salt and studies in this field are still not complete, the solubility of lanthanum oxide in FLiNaK have been measured at different temperatures to obtain the temperature-dependent solubility and understand the corresponding dissolution mechanisms first. In the solubility related experiments, Inductively Coupled Plasma Mass Spectrometry (ICP-MS) is utilized to analyze the concentration of lanthanum ions in the molten FLiNaK salt, while X-ray powder diffraction (XRD) was applied to determine the phase patterns of molten salt. Second, electrochemical experiments with tungsten and graphite as working electrodes were conducted individually to demonstrate the separation of the dissolved oxide from the salt. When the tungsten working electrode was applied, the lanthanum ions were reduced to lanthanum metal at the tungsten cathode, while the fluorine ions reacted with the tungsten anode to form tungsten fluoride. In the experiments, the production of tungsten fluoride could lead to increasing current in the cell, even overload. Moreover, theoretically, tungsten fluoride WF4 is soluble in the fluoride salt thus introducing new impurities. All these issues make tungsten not the best choice when applied to the separation of oxygen ions. Therefore, another common working electrode graphite is used. It not only has all the advantages of tungsten, but also has good performance on separation of oxygen ions. When the graphite electrode was applied, the lanthanum ions were separated in the form of lanthanum carbide (LaC₂), while the oxygen ions can be removed in the form of carbon dioxide (CO₂) or carbon monoxide (CO). In addition, only graphite was consumed during the whole separation process, which is why the graphite anode electrode is called the “sacrificial electrode”. Third, First Principle Molecular Dynamics (FPMD) simulations with Vienne Ab initio Simulation Package (VASP) was conducted to study the properties of the fluoride molten salt. In this study, the structure information and enthalpy of formation were obtained. Generally, the simulation process can be divided into four steps: (1) the simulation systems are prepared by packing ions randomly via Packmol package in the simulation cell; (2) an equilibrium calculation is performed to pre-equilibrate the systems; (3) FPMD simulations in an NVT ensemble are implemented in VASP; (4) based on the FPMD simulations results, the first peak radius and the first-shell coordination number were evaluated with partial radial distribution function (PRDF) analysis to determine the statistics of molten salt structure information, while the transport properties, e.g., the self-diffusion coefficient was calculated according to the function of mean square displacement (MSD) of time generated by the Einstein-Smoluchowshi equation. The viscosity and ionic conductivity were obtained by combining the self-distribution coefficient with the Einstein-Stokes formula and Nernst-Einstein equation. / Master of Science / With the fast development of modern society and economy, more and more energy is urgently needed to meet the growth of industry. Since the traditional energy, such as nature gas, coal, has limited storage and not sustainable, nuclear energy has attracted much attention in the past few decades. Although lots of study has been conducted by thousands of researchers which has attributed to application of nuclear power, there are still some concerns in this field, among which, impurities removal is the most difficult part. Fluoride salt cooled high temperature reactor (FHR) is one of the most promising Gen IV reactor types. As the name indicates, molten salt is the coolant to serve as the heat exchanger intermedium. In addition, it’s inevitable that fission products, i.e. lanthanum, moisture, would leak into the coolant pipe, thus affect the molten salt properties, even degrade reactor performance, therefore, those impurities must be removed without introducing new impurities. In this study, the La₂O₃-LiF-NaF-KF (La₂O₃-FLiNaK) system is used to demonstrate impurity separation into molten fluoride salt. First, solubility of lanthanum oxide in FLiNaK has been measured at different temperatures to understand its dissolution mechanisms. Then, electrochemical experiments with tungsten and graphite as working electrodes were conducted individually to demonstrate the separation of the dissolved oxide from the salt. It has been concluded that tungsten performed well to separate La3+, while failed in the separation of O2-. However, graphite working electrode has succeeded in the removal of La³⁺ and O²⁻. Finally, molecular dynamic simulation with first principle was also conducted to further understand the local structure and heat of formation in the molten FLiNaK and La₂O₃-FLiNaK salt.

The depletion of conventional oil reservoirs forced companies and consequently researchers to pursue alternatives such as resources that in the past were considered not economically viable, in consequence of the high depth, low porosity and permeability of the play zone. The exploration challenges were overcome mainly by the development of horizontal drilling and hydraulic fracturing. However, the extremely high temperatures and pressures, in association to a complex nanopore structure, in which reservoir fluids are now encountered, instigate further investigation of fluid phase behavior and composition, and challenge conventional macroscale reservoir simulation predictions. Moreover, the unusual high temperatures and pressures have increased the cost as well as the hazardous level for reservoir analyzes by lab experiments. Molecular Dynamics (MD) simulation of reservoirs can be a safe and inexpensive alternative tool to replicate reservoir pore and fluid conditions, as well as to monitor fluid behavior. In this study, a MD simulation of nanoconfinement effect on hydrocarbon fluid phase and compositional behavior in organic shale rocks is presented. Chapter 1 reviews and discusses previous works on MD simulations of geological resources. With the knowledge acquired, a fully atomistic squared graphite pore is proposed and applied to study hydrocarbon fluid phase and compositional behavior in organic shale rocks in Chapter 2. Results demonstrate that nano-confinement increases fluid mass density, which can contribute to phase transition, and heptane composition inside studied pores. The higher fluid density results in an alteration of oil in place (OIP) prediction by reservoir simulations, when nano-confinement effect is not considered. / Master of Science / Petroleum sub products are present in the day to day life of almost any human. The list include gasoline, plastics, perfumes, medications, polyester for clothing. Petroleum is naturally encountered in the void space, known as pores, inside rocks at reservoirs thousands of feet underground. In the past, the pores of oil reservoirs in development were larger and interconnected, which facilitates its extraction and reserve predictions. Most of reservoirs being developed nowadays have pores in the nanoscale and with poor interconnection as well as higher reservoir temperatures and pressure. These "new conditions", instigates further investigation of fluid phase behavior and composition, and challenge macroscale reservoir simulation predictions. In this study, the effect of decrease in pore size, as well as higher temperature and pressure conditions, in fluid behavior and composition is studied. Chapter 1 reviews and discusses previous works on geological resources modeling and simulation. With the knowledge acquired, a fully squared shale pore is proposed and applied to study hydrocarbon fluid phase and compositional behavior in organic shale rocks in Chapter 2. Results demonstrate that pores in the nanoscale region tend to increase fluid mass density, which can contribute to phase transition, and heptane composition inside studied pores. The higher fluid density results in an underestimation of reserves prediction by reservoir simulations, when the change in density is not considered.

No / Martensitic transformations are of considerable technological importance, a particularly promising application being the possibility of using martensitic materials, possibly proteins, as tiny machines. For organic crystals, however, a molecular level understanding of such transformations is lacking. We have studied a martensitic-type transformation in crystals of the amino acid DL-norleucine using molecular dynamics simulation. The crystal structures of DL-norleucine comprise stacks of bilayers (formed as a result of strong hydrogen bonding) that translate relative to each other on transformation. The simulations reveal that the transformation occurs by concerted molecular displacements involving entire bilayers rather than on a molecule-by-molecule basis. These observations can be rationalized on the basis that at sufficiently high excess temperatures, the free energy barriers to concerted molecular displacements can be overcome by the available thermal energy. Furthermore, in displacive transformations, the molecular displacements can occur by the propagation of a displacement wave (akin to a kink in a carpet), which requires the molecules to overcome only a local barrier. Concerted molecular displacements are therefore considered to be a significant feature of all displacive transformations. This finding is expected to be of value toward developing strategies for controlling or modulating martensitic-type transformations.

Yes / The structure and dynamics of a single molecule of the nonionic surfactant polysorbate 80 (POE (20) sorbitan monooleate; Tween 80 ) as well as a micelle of polysorbate 80 in water have been investigated by molecular dynamics simulation. In its free state in water the polysorbate 80 molecule samples almost its entire conformational space. The micelle structure is compact and exhibits a prolate ellipsoid shape, with the surface being dominated by the polar terminal groups of the POE chains. The radius of gyration of the micelle was 26.2 A. The physical radius, determined from both the radius of gyration and atomic density, was about 35 A. The estimated diffusion constants for the free molecule (1.8 10 6 cm2 s 1) and the micelle (1.8 10 7 cm2 s 1) were found to be remarkably close to the respective experimental values. The lateral diffusion of the molecules on the micelle surface was estimated to be 1.7 10 7 cm2 s 1, which confirms the highly dynamic nature of the micelle structure. / Tehran University of Medical Sciences & Health Services

No / We address the problem of recognition and growth of ice nuclei in simulation of supercooled bulk water. Bond orientation order parameters based on the spherical harmonics analysis are shown to be ineffective when applied to ice nucleation. Here we present an alternative method which robustly differentiates between hexagonal and cubic ice forms. The method is based on accumulation of the maximum projection of bond orientations onto a set of predetermined vectors, where different terms can contribute with opposite signs with the result that the irrelevant or incompatible molecular arrangements are damped out. We also introduce an effective cluster size by assigning a quality weight to each molecule in an ice-like cluster. We employ our cluster analysis in Monte Carlo simulation of homogeneous ice formation. Replica-exchange umbrella sampling is used for biasing the growth of the largest cluster and calculating the associated free energy barrier. Our results suggest that the ice formation can be seen as a two-stage process. Initially, short tetrahedrally arranged threads and rings are present; these become correlated and form a diffuse ice-genic network. Later, hydrogen bond arrangements within the amorphous ice-like structure gradually settle down and simultaneously `tune-up¿ nearby water molecules. As a result, a well-shaped ice core emerges and spreads throughout the system. The process is very slow and diverse owing to the rough energetic landscape and sluggish molecular motion in supercooled water, while large configurational fluctuations are needed for crystallization to occur. In the small systems studied so far the highly cooperative molecular rearrangements eventually lead to a relatively fast percolation of the forming ice structure through the periodic boundaries, which inevitably affects the simulation results. / EPSRC

No / There is considerable interest, both fundamental and technological, in understanding how additives and impurities influence crystal nucleation, and in the modulation of nucleation in a predictable way by using designer additives. An appropriate additive can promote, retard, or inhibit crystal nucleation and growth, assist in the selective crystallization of a particular enantiomer or polymorphic form, or enable crystals of a desired habit to be obtained.[1¿3] Applications involving additives include the control of the nucleation of proteins,[4] the inhibition of urinary-stone formation[5] and of ice formation in living tissues during cryoprotection,[6] their use as antifreeze agents in Antarctic fish,[7,8] the prevention of blockages in oil and gas pipelines as a result of wax precipitation[9] and gas-hydrate formation,[10] crystal-twin formation,[11] and as a possible basis for the antimalarial activity of some drugs.[12]We report herein the mode of action and explicit (apparently intuitive) rules for designing additive molecules for the modulation of crystal nucleation. The mode of action and the design features have been derived from molecular-dynamics simulations involving simple models.[13] These findings will help to rationalize how known nucleation inhibitors and modulators exert their effect and aid in the identification or design of new additives for the inhibition or promotion of nucleation in specific systems.

No / Most rotamer libraries are generated from subsets of the PDB and do not fully represent the conformational scope of protein side chains. Previous attempts to rectify this sparse coverage of conformational space have involved application of weighting and smoothing functions. We resolve these limitations by using physics-based molecular dynamics simulations to determine more accurate frequencies of rotameric states. This work forms part of our Dynameomics initiative and uses a set of 807 proteins selected to represent 97% of known autonomous protein folds, thereby eliminating the bias toward common topologies found within the PDB. Our Dynameomics derived rotamer libraries encompass 4.8 × 10(9) rotamers, sampled from at least 51,000 occurrences of each of 93,642 residues. Here, we provide a backbone-dependent rotamer library, based on secondary structure ϕ/ψ regions, and an update to our 2011 backbone-independent library that addresses the doubling of our dataset since its original publication. / NIH