Técnicas de injeção de traçadores são bastante utilizadas nos estudos de escoamentos em meios porosos heterogêneos, principalmente em problemas relacionados à simulação numérica de escoamentos miscíveis em reservatórios de petróleo e à dispersão de contaminantes em aqüíferos. Neste trabalho apresentamos novos algoritmos para a aproximação numérica do problema de injeção de traçadores. Apresentaremos desenvolvimentos recentes do método Forward Integral-Tube Tracking (FIT) que foi originalmente apresentado em Aquino et al. (2007a). O FIT é um método lagrangeano localmente conservativo utilizado na resolução de problemas de transporte linear. Este método não faz o uso de soluções de problemas de Riemann e baseia-se na construção dos tubos integrais introduzidas em Douglas Jr. et al. (2000b). Além disso, ele possui excelente eficiência computacional e é virtualmente livre de difusão numérica. Resultados numéricos são apresentados com o objetivo de comparar a precisão das soluções fornecidas por novas implementações do método FIT na resolução do problema do traçador em reservatórios de petróleo. / The injection of tracers are used in the investigation of flows in heterogeneous porous media, in studies related to the simulation of miscible dispacements in petroleum reservoirs and the dispersion of contaminants in aquifers. In this work we present new algorithms for the numerical approximation of tracer injection problems. We discuss recent developments of the Forward Integral-Tube Tracking (FIT) scheme which was introduced in Aquino et al. (2007a). The FIT is a locally conservative lagrangian scheme for the approximation of the linear transport problems. This scheme does not use analytic solutions of Riemann problems and is based on the construction of the integral tubes introduced in Douglas Jr. et al. (2000b). The FIT scheme is computationally very eficient and is virtually free of numerical diffusion. Numerical results are presented to compare the accuracy of the solutions provided by new implementation of the FIT scheme for the injection of tracers in petroleum reservoirs.

Formulamos um modelo simplificado para o estudo do processo de injeção de solvente em reservatórios de petróleo, onde o fluido injetado (um ácido) tem a capacidade de dissolver parcialmente a matriz sólida. Como hipóteses principais, consideramos que o solvente e o soluto (componente químico que constitui o meio poroso) são espécies totalmente miscíveis, a viscosidade da mistura solvente + soluto não varia com a concentração de soluto, há significativa transferência de massa entre as fases e a permeabilidade do meio poroso varia linearmente com a porosidade. O modelo é formado por duas Equações Diferenciais Parciais, uma do tipo Convecção-Difusão a outra é do tipo Convecção-Reação. Para resolução numérica, desenvolvemos uma metodologia que denominamos de EPEC (Explícita Porosidade e Explícita Concentração). Tal metodologia se baseia em um limitador de fluxo do tipo TVD e em diferenças finitas centradas de segunda ordem. Em adição, o EPEC emprega uma técnica de separação de operadores. Deste modo, em cada passo de tempo, realizamos inicialmente o cálculo explícito da porosidade seguido do cálculo explícito da concentração do solvente. Assim, obtemos um desacoplamento natural das equações que descrevem o problema. Resultados de simulações são apresentados para um meio poroso bidimensional, após sessenta dias de injeção de solvente. / We formulate a simplified Model to study the process of solvent injection in petroleum Reservoir, where the injected fluid (an acid) can partially dissolve a solid matrix. As prime hypotheses, we considered that solvent an soluble component are completely mixed, the viscosity of the fluid does not vary with the concentration of the soluble component, theres significant transfer of mass between the parts and, the permeability of media porous changes linearly with porosity. The model is formed by two Partial Differential Equation, one is convection-diffusion type and another is a convection-reaction type. The Numerical Resolution weve developed a method called EPEC (Explicit Porosity Explicit Concentration). Such methodology is based upon a Limiting of Flow of TVD type and, used Centered Finite Differences of second order. In addition, the EPEC use a operators separation technique. This way, every time, first we clearly calculate the porosity and then the concentration of solvent is calculated. Thus we obtain a natural decoupling of the equations that describe the problem. Simulation results are presented to a two dimensional media porous after sixty days of solvent injection.

Técnicas de injeção de traçadores são bastante utilizadas nos estudos de escoamentos em meios porosos heterogêneos, principalmente em problemas relacionados à simulação numérica de escoamentos miscíveis em reservatórios de petróleo e à dispersão de contaminantes em aqüíferos. Neste trabalho apresentamos novos algoritmos para a aproximação numérica do problema de injeção de traçadores. Apresentaremos desenvolvimentos recentes do método Forward Integral-Tube Tracking (FIT) que foi originalmente apresentado em Aquino et al. (2007a). O FIT é um método lagrangeano localmente conservativo utilizado na resolução de problemas de transporte linear. Este método não faz o uso de soluções de problemas de Riemann e baseia-se na construção dos tubos integrais introduzidas em Douglas Jr. et al. (2000b). Além disso, ele possui excelente eficiência computacional e é virtualmente livre de difusão numérica. Resultados numéricos são apresentados com o objetivo de comparar a precisão das soluções fornecidas por novas implementações do método FIT na resolução do problema do traçador em reservatórios de petróleo. / The injection of tracers are used in the investigation of flows in heterogeneous porous media, in studies related to the simulation of miscible dispacements in petroleum reservoirs and the dispersion of contaminants in aquifers. In this work we present new algorithms for the numerical approximation of tracer injection problems. We discuss recent developments of the Forward Integral-Tube Tracking (FIT) scheme which was introduced in Aquino et al. (2007a). The FIT is a locally conservative lagrangian scheme for the approximation of the linear transport problems. This scheme does not use analytic solutions of Riemann problems and is based on the construction of the integral tubes introduced in Douglas Jr. et al. (2000b). The FIT scheme is computationally very eficient and is virtually free of numerical diffusion. Numerical results are presented to compare the accuracy of the solutions provided by new implementation of the FIT scheme for the injection of tracers in petroleum reservoirs.

This thesis is an attempt to understand ways to improve thermo-mechanical and structural properties of nano-structured materials. A detailed study on computational design and analysis of metallic nanowires is carried out. Molecular dynamic simulation method is applied. In particular, FCC metallic nanowires, NiAl, and CuZr nanowires are studied. Various bottom-up approaches are suggested with improved structural and thermo¬mechanical properties. In the first part of the thesis, Cu nanowires are considered. Existence of a novel and stable pentagonal multi-shell nanobridge structure of Cu under high strain rate tensile loading is reported. Such a structure shows enhanced mechanical properties. A three-fold pseudo-elastic-plastic shape recovery mechanism in such nanowires is established. This study also shows that the length of the pentagonal nanobridge structures can be characterized by its inelastic strain. It is also reported that an initial FCC structure is transformed into a new HCP structure. The evidence of HCP structure is confirmed with the help of experimental data published in the literature. Subsequent to the above study, a novel mechanism involving coupled temperature-stress dependent reorientation in FCC nanowires is investigated. A detailed map is generated for size dependent stress-temperature induced solid-solid reorientation in Cu nanowires. In the second part of the thesis, deformation mechanisms in NiAl based intermetallic nanowires are studied. A novel mechanism of temperature and cross-section dependent pseudo-elastic/pseudo-plastic shape and strain recovery by an initial B2 phase of NiAl nanowire is reported. Such a recoverable strain, which is as high as ~ 30%, can potentially be utilized to realize various types of shape memory and strain sensing phenomena in nano-scale devices. An asymmetry in tensile and compressive yield strength behavior is also observed, which is due to the softening and hardening of the nanowires under tensile and compressive loadings, respectively. Two different deformation mechanisms dominated by twinning under tension and slip under compression are found. Most interestingly, a superplastic behavior with a failure strain of up to 700% in the intermetallic NiAl nanowires is found to exist at a temperature of 0.36Tm. Such superplastic behavior is attributed to the transformation of the nanowire from a crystalline phase to an amorphous phase after yielding of the nanowire. In the last part the work, another type of nanowires having Cu-Zr system is considered. A novel stress induced martensitic phase transformation from an initial B2 phase to BCT phase in a CuZr nanowire under tensile loading is reported. It is further shown that such a stress induced martenistic phase transformation can be achieved under both tensile as well as compressive loadings. Tensile-compressive asymmetry in the stress-strain behavior is observed due to two different phase transformation mechanisms having maximum transformation strains of ~ 5% under compressive loading and ~ 20% under tensile loading. A size and temperature dependent tensile phase transformation in the nanowire is also observed. Small nanowires show a single step tensile phase transformation whereas the nanowires with larger size show a two step deformation mechanism via an intermediate R-phase hardening followed by R-phase yielding. A study of energetic behavior of these nanowires reveals uniform distribution of stress over the nanowire cross-section and such stress distribution can lead to a significant improvement in its thermo-mechanical properties. Similar improvement is demonstrated by designing the nanowires via manipulating the surface configuration of B2-CuZr system. It is found that the CuZr nanowires with Zr atoms at the surface sites are energetically more stable and also give a uniform distribution of stresses across the cross-section. This leads to the improvement in yield strength as well as failure strain. An approach to design energetically stable nano-structured materials via manipulating the surface configurations with improved thermo-mechanical properties is demonstrated which can help in fundamental understanding and development of similar structures with more stability and enhanced structural properties. Further ab-initio and experimental studies on the confirmation of the stability of the nanowires via manipulating the surface site is an open area of research and related future scopes are highlighted in the closure.

<p>This study is concerned with the predictive modeling of the machining and the mechanical behaviors of additive manufactured (AMed) Ti6AlV/TiC composites and Ti6Al4V, respectively, using microstructure-based hierarchical multiscale modeling. The predicted results could constitute as a basis for optimizing the parameters of machining and AM of the current materials.</p> <p>Through hierarchical flow of material behaviors from the atomistic, to the microscopic and the macroscopic scales, multiscale heterogeneous models (MHMs) coupled to the finite element method (FEM) are employed to simulate the conventional and the laser assisted machining (LAM) of Ti6AlV/TiC composites. In the atomistic level, molecular dynamics (MD) simulations are used to determine the traction-separation relationship for the cohesive zone model (CZM) describing the Ti6AlV/TiC interface. Bridging the microstructures across the scales in MHMs is achieved by representing the workpiece by macroscopic model with the microscopic heterogeneous structure including the Ti6Al4V matrix, the TiC particles, and their interfaces represented by the parameterized CZM. As a result, MHMs are capable of revealing the possible reasons of the peculiar high thrust forces behavior during conventional machining of Ti6Al4V/TiC composites, and how laser assisted machining can improve this behavior, which has not been conducted before.</p> <p>Extending MHMs to predict the mechanical behaviors of AMed Ti6Al4V would require including the heterogeneous microstructure at the grain level, which could be computational expensive. To solve this issue, the extended mechanics of structure genome (XMSG) is introduced as a novel multiscale homogenization approach to predict the mechanical behavior of AMed Ti6Al4V in a computationally efficient manner. This is realized by embedding the effects of microstructure heterogeneity, porosity growth, and crack propagation in the multiscale calculations of the mechanical behavior of the AMed Ti6Al4V using FEM. In addition, the XMSG can predict the asymmetry in the Young’s modulus of the AMed Ti6Al4V under tensile and compression loading as well as the anisotropy in the mechanical behaviors. The applicability of XMSG to fatigue life prediction with valid results is conducted by including the energy dissipations associated with cyclic loading/unloading in the calculations of the cyclic response of the material.</p>

Vor dem Hintergrund zukünftiger Sensoren, basierend auf dem piezoresistiven Effekt von einwandigen Kohlenstoffnanoröhren (SWCNT), werden in dieser Arbeit umfangreiche Ergebnisse zum mechanischen Verhalten von Grenzflächen zwischen SWCNTs und edlen Metallen am Beispiel von Pd und Au präsentiert. Im Fokus steht dabei die Synergie von rechnerischen und experimentellen Methoden Molekulardynamik (MD), nanoskalige Tests und Analytik , um (1) mit guter Genauigkeit maximale Kräfte von gezogenen SWCNTs, welche in Metall eingebettet sind, vorauszuberechnen und (2) einen wertvollen Beitrag zum Verständnis der zu Grunde liegenden Fehlermechanismen zu liefern. Es wurde ein MDModell eines in eine einkristalline Matrix eingebetteten SWCNTs mit Randbedingen eines Auszugsversuchs entwickelt. Mit diesem Modell können Kraft-Weg-Beziehungen und Energieverläufe für einen quasistatischen verschiebungsgesteuerten Auszugsversuch errechnet werden. Das Modell liefert kritische Kräfte bei Versagen des Systems. Des Weiteren können mit diesem Modell der Einfluss des SWCNT-Typus, der Einbettungslänge, der Temperatur, von intrinsischen Defekten und Oberflächengruppen (SFGs) auf das Grenzflächenverhalten untersucht werden. Zum Vergleich wurden kritische Kräfte experimentell durch in situ Auszugsversuche in einem Rasterelektronenmikroskop bestimmt. Es wurde eine sehr gute Übereinstimmung von rechnerischen und experimentellen Daten festgestellt. Der vorherrschende Fehler im Experiment ist der SWCNT-Bruch, jedoch wurden auch einige SWCNT-Auszüge beobachtet. Mit Hilfe der MD-Simulationen wurde gefunden, dass die SFGs als kleine Anker in der umgebenden metallischen Matrix wirken und somit die maximalen Kräfte signifikant erhöhen. Diese Grenzflächenverstärkung kann Zugspannungen verursachen, die genügend hoch sind, so dass SWCNT-Bruch initiert wird. Im Gegensatz dazu zeigten Simulationen von Auszugstests mit idealen SWCNTs nur kleine Auszugskräfte, welche meistens unabhängig von der Einbettungslänge des SWCNTs sind. Dieses Verhalten wird mit einer inkommensurablen Konfiguration der Kristallstrukturen an der Grenzfläche von SWCNTs und der einbettenden Edelmetalle interpretiert. Zur Qualifizierung der Existenz von carboxylatischen Oberflächengruppen auf dem genutzten SWCNT-Material wurden analytische Untersuchungen mittels Fluoreszenzmarkierung von Oberflächengruppen durchgeführt. In Übereinstimmung mit Literaturstellen zum gesicherten Nachweis von SFGs, bedingt durch technologische Behandlungen, weisen diese Experimente stark auf das Vorhandensein von carboxylatischen Oberflächengruppen auf dem genutzten SWCNT-Material hin. Demnach kann der dominante SWCNT-Bruch Fehler durch die Grenzflächenverstärkung auf Grund von SFGs erklärt werden. / In the light of future sensors, that are based upon the piezoresistive effect of singlewalled carbon nanotubes (SWCNTs), this work presents comprehensive results of studies on the mechanical behavior of interfaces between SWCNTs and noble metals using the examples of Pd and Au. With this contribution, the focus is on a synergy between computational and experimental approaches involving molecular dynamics (MD) simulations, nanoscale testing, and analytics (1) to predict to a good degree of accuracy maximum forces of pulled SWCNTs embedded in a noble metal matrix and (2) to provide valuable input to understand the underlying mechanisms of failure. A MD model of a SWCNT embedded in a single crystalline matrix with pull-out test boundary conditions was developed. With this model, force-displacement relations and energy evolutions for a quasi-static displacement controlled test can be computed. The model provides critical forces for failure of the system. Furthermore, the influence of SWCNT type, embedding length, temperature, intrinsic defects and surface functional groups (SFGs) on the interface behavior can be studied using this model. For comparison, critical forces were experimentally determined by conducting pull-out tests in situ, inside a scanning electron microscope. A very good agreement of computational and experimental values was discovered. The dominant failure mode in the experiment was a SWCNT rupture, although several pull-out failures were also observed. From MD simulations, it was found that SFGs act as small anchors in the metal matrix and significantly enhance the maximum forces. This interface reinforcement can lead to tensile stresses sufficiently high to initiate SWCNT rupture. In contrast, pull-out test simulations of ideal SWCNTs show only small pull-out forces, which are mostly independent on SWCNT embedding length. This behavior is interpreted with an incommensurate configuration of crystal structures at the interface between SWCNTs and embedding noble metals. To qualify the existence of carboxylic SFGs on the used SWCNT material, an analytical investigation by means of fluorescence labeling of surface species was performed. In agreement with literature reports on the secured verification of SFGs due to necessary technological treatments, these experiments strongly indicate the presence of carboxylic SFGs on the used SWCNT material. Thus, the dominant SWCNT rupture failure is explained with an interface reinforcement by SFGs.

<p>Subcutaneous administration has become a common approach for drug delivery of biotherapeutics, such as monoclonal antibodies, which is achieved mainly by absorption through the lymphatic system. This dissertation focuses on the computational modeling of the fluid flow and solute transport in the skin tissue and the quantitative investigation of lymphatic uptake. First, the various mechanisms governing drug transport and lymphatic uptake of biotherapeutics through subcutaneous injection are investigated quantitatively through high-fidelity numerical simulations, including lymphatic drainage, blood perfusion, binding, and metabolism. The tissue is modeled as a homogeneous porous medium using both a single-layered domain and a multi-layered domain, which includes the epidermis, dermis, hypodermis (subcutaneous tissue), and muscle layers. A systematic parameter study is conducted to understand the roles of different properties of the tissue in terms of permeability, porosity, and vascular permeability. The role of binding and metabolism on drug absorption is studied by varying the binding parameters for different macromolecules after coupling the transport equation with a pharmacokinetic equation. The interstitial pressure plays an essential role in regulating the absorption of unbound drug proteins during the injection, while the binding and metabolism of drug molecules reduce the total free drugs. </p> <p>  </p> <p>The lymphatic vessel network is essential to achieve the functions of the lymphatic system. Thus, the drug transport and lymphatic uptake through a three-dimensional hybrid discrete-continuum vessel network in the skin tissue are investigated through high-fidelity numerical simulations. The explicit heterogeneous vessel network is embedded into the continuum model to investigate the role of explicit heterogeneous vessel network in drug transport and absorption. The solute transport across the vessel wall is investigated under various transport conditions. The diffusion of the drug solutes through the explicit vessel wall affects the drug absorption after the injection, while the convection under large interstitial pressure dominates the drug absorption during the injection. The effect of diffusion cannot be captured by the previously developed continuum model. Furthermore, the effects of injection volume and depth on the lymphatic uptake are investigated in a multi-layered domain. The injection volume significantly affects lymphatic uptake through the heterogeneous vessel network, while the injection depth has little influence. At last, the binding and metabolism of drug molecules are studied to bridge the simulation to the experimentally measured drug clearance. </p> <p><br></p> <p>Convective transport of drug solutes in biological tissues is regulated by the interstitial fluid pressure, which plays a crucial role in drug absorption into the lymphatic system through the subcutaneous (SC) injection.  An approximate continuum poroelasticity model is developed to simulate the pressure evolution in the soft porous tissue during an SC injection. This poroelastic model mimics the deformation of the tissue by introducing the time variation of the interstitial fluid pressure. The advantage of this method lies in its computational time efficiency and simplicity, and it can accurately model the relaxation of pressure. The interstitial fluid pressure obtained using the proposed model is validated against both the analytical and the numerical solution of the poroelastic tissue model. The decreasing elasticity elongates the relaxation time of pressure, and the sensitivity of pressure relaxation to elasticity decreases with the hydraulic permeability, while the increasing porosity and permeability due to deformation alleviate the high pressure. </p> <p><br></p> <p>At last, an improved Kedem-Katchalsky model is developed to study solute transport across the lymphatic vessel network, including convection and diffusion in the multi-layered poroelastic tissue with a hybrid discrete-continuum vessel network embedded inside. The effect of different drug solutes with different Stokes radii and different structures of the lymphatic vessel network, such as fractal trees and Voronoi structure, on the lymphatic uptake is investigated. The drug solute with a small size has a larger partition coefficient and diffusivity across the openings of the lymphatic vessel wall, which favors drug absorption. The Voronoi structure is found to be more efficient in lymphatic uptake. </p> <p><br></p> <p>The systematic and quantitative investigation of subcutaneous absorption based on high-fidelity numerical simulations can provide guidance on the optimization of drug delivery systems and is valuable for the translation of bioavailability from the pre-clinical species to humans. We provide a novel approach to studying the diffusion and convection of drug molecules into the lymphatic system by developing the hybrid discrete-continuum vessel network. The study of the solute transport across the discrete lymphatic vessel walls further improves our understanding of lymphatic uptake. The novel and time-efficient computational model for solute transport across the lymphatic vasculature connects the microscopic properties of the lymphatic vessel membrane to macroscopic drug absorption. The comprehensive hybrid vessel network model developed here can be further used to improve our understanding of the diseases caused by the disturbed lymphatic system, such as lymphedema, and provide insights into the treatment of diseases caused by the malfunction of lymphatics.</p>

<p>Thorium dioxide (ThO₂) and metallic uranium (alpha-U) represent important alternative nuclear fuels. Investigating the behavior of defects introduced into these materials in an irradiation environment is critical for understanding microstructure evolution and property changes. The objective of this dissertation is to investigate the clustering of point defects in ThO₂ and alpha-U under irradiation, into voids and prismatic dislocation loops as a function of irradiation dose rate and temperature. To achieve this, we have developed a mean-field cluster dynamics (CD) model based on reaction rate theory to predict the evolution of self-interstitial atom (SIA) and vacancy loops in neutron-irradiated alpha-U. Detailed atomistic simulations have been carried out using molecular dynamics (MD) to study the configuration of such loops and compute their energetics, which are essential parameters of the CD model. Bond-boost hyper-MD simulations have been performed to compute the diffusivity of uranium SIA and vacancies, which govern the kinetics of the clustering phenomenon. Another CD model has been demonstrated for proton-irradiated ThO₂, considering the clustering of Th and O SIA and vacancies into SIA loops and voids, respectively, with varying sizes and stoichiometry. The compositions of all SIA loops and voids dictated by crystallography of ThO₂ in its fluorite structure have been presented in their respective cluster composition space (CCS). The CD model solves the density evolution of off-stoichiometric loops and voids, with irradiation, in their respective CCS. MD simulations have been performed to compute the energetics of different clusters in their CCS, as parameters of the CD model. Temperature-accelerated MD simulations have been performed to compute the diffusivity of Th and O point defects, that dictates the kinetics of defect clustering on irradiation. In alpha-U, the CD predictions show an accumulation of small sized vacancy loops and the growth of SIA loops with irradiation dose, which closely fits the reported size distribution of loops in neutron-irradiated alpha-U by Hudson and coworkers. The CD predicted density of defect clusters in proton-irradiated ThO₂, shows the evolution of near-stoichiometric SIA loops in their CCS. The size distribution of SIA loops at high irradiation doses closely corresponds to the transmission electron microscopy (TEM) observations reported in the literature. Also, the CD model did not predict the growth of voids and vacancy clusters, which is consistent with findings in literature. The model was further used to predict the density of sub-nanometric defect clusters and point defects, on low-dose irradiation, that significantly impairs the thermal conductivity of ThO₂. An extensive TEM and CD investigation has also been carried out to study the growth and coarsening of SIA loop and voids during post-irradiation isochronal annealing of ThO₂ at high temperatures.</p>

<p>Protein malfunction can cause human diseases, which makes the protein a target in the process of drug discovery. In-depth knowledge of how protein functions can widely contribute to the understanding of the mechanism of these diseases. Protein functions are determined by protein structures and their dynamic properties. Protein dynamics refers to the constant physical movement of atoms in a protein, which may result in the transition between different conformational states of the protein. These conformational transitions are critically important for the proteins to function. Understanding protein dynamics can help to understand and interfere with the conformational states and transitions, and thus with the function of the protein. If we can understand the mechanism of conformational transition of protein, we can design molecules to regulate this process and regulate the protein functions for new drug discovery. Protein Dynamics can be simulated by Molecular Dynamics (MD) Simulations.</p> <p>The MD simulation data generated are spatial-temporal and therefore very high dimensional. To analyze the data, distinguishing various atomic interactions within a protein by interpreting their 3D coordinate values plays a significant role. Since the data is humongous, the essential step is to find ways to interpret the data by generating more efficient algorithms to reduce the dimensionality and developing user-friendly visualization tools to find patterns and trends, which are not usually attainable by traditional methods of data process. The typical allosteric long-range nature of the interactions that lead to large conformational transition, pin-pointing the underlying forces and pathways responsible for the global conformational transition at atomic level is very challenging. To address the problems, Various analytical techniques are performed on the simulation data to better understand the mechanism of protein dynamics at atomic level by developing a new program called Probing Long-distance interactions by Tapping into Paired-Distances (PLITIP), which contains a set of new tools based on analysis of paired distances to remove the interference of the translation and rotation of the protein itself and therefore can capture the absolute changes within the protein.</p> <p>Firstly, we developed a tool called Decomposition of Paired Distances (DPD). This tool generates a distance matrix of all paired residues from our simulation data. This paired distance matrix therefore is not subjected to the interference of the translation or rotation of the protein and can capture the absolute changes within the protein. This matrix is then decomposed by DPD</p> <p>using Principal Component Analysis (PCA) to reduce dimensionality and to capture the largest structural variation. To showcase how DPD works, two protein systems, HIV-1 protease and 14-3-3 σ, that both have tremendous structural changes and conformational transitions as displayed by their MD simulation trajectories. The largest structural variation and conformational transition were captured by the first principal component in both cases. In addition, structural clustering and ranking of representative frames by their PC1 values revealed the long-distance nature of the conformational transition and locked the key candidate regions that might be responsible for the large conformational transitions.</p> <p>Secondly, to facilitate further analysis of identification of the long-distance path, a tool called Pearson Coefficient Spiral (PCP) that generates and visualizes Pearson Coefficient to measure the linear correlation between any two sets of residue pairs is developed. PCP allows users to fix one residue pair and examine the correlation of its change with other residue pairs.</p> <p>Thirdly, a set of visualization tools that generate paired atomic distances for the shortlisted candidate residue and captured significant interactions among them were developed. The first tool is the Residue Interaction Network Graph for Paired Atomic Distances (NG-PAD), which not only generates paired atomic distances for the shortlisted candidate residues, but also display significant interactions by a Network Graph for convenient visualization. Second, the Chord Diagram for Interaction Mapping (CD-IP) was developed to map the interactions to protein secondary structural elements and to further narrow down important interactions. Third, a Distance Plotting for Direct Comparison (DP-DC), which plots any two paired distances at user’s choice, either at residue or atomic level, to facilitate identification of similar or opposite pattern change of distances along the simulation time. All the above tools of PLITIP enabled us to identify critical residues contributing to the large conformational transitions in both HIV-1 protease and 14-3-3σ proteins.</p> <p>Beside the above major project, a side project of developing tools to study protein pseudo-symmetry is also reported. It has been proposed that symmetry provides protein stability, opportunities for allosteric regulation, and even functionality. This tool helps us to answer the questions of why there is a deviation from perfect symmetry in protein and how to quantify it.</p>

No description available.