Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Implementação de algoritmos genéticos paralelos em uma arquitetura MPSoC.

Essa dissertação apresenta a implementação de um algoritmo genético paralelo utilizando o modelo de granularidade grossa, também conhecido como modelo das ilhas, para sistemas embutidos multiprocessados. Os sistemas embutidos multiprocessados estão tornando-se cada vez mais complexos, pressionados pela demanda por maior poder computacional requerido pelas aplicações, principalmente de multimídia, Internet e comunicações sem fio, que são executadas nesses sistemas. Algumas das referidas aplicações estão começando a utilizar algoritmos genéticos, que podem ser beneficiados pelas vantagens proporcionadas pelo processamento paralelo disponível em sistemas embutidos multiprocessados. No algoritmo genético paralelo do modelo das ilhas, cada processador do sistema embutido é responsável pela evolução de uma população de forma independente dos demais. A fim de acelerar o processo evolutivo, o operador de migração é executado em intervalos definidos para realizar a migração dos melhores indivíduos entre as ilhas. Diferentes topologias lógicas, tais como anel, vizinhança e broadcast, são analisadas na fase de migração de indivíduos. Resultados experimentais são gerados para a otimização de três funções encontradas na literatura.

River Crake (at Bouthrey Bridge) freeze coring report

This is the River Crake (at Bouthrey Bridge) freeze coring report produced by Lancaster University in 1999. This study looks at fine materials in river Crake at Bouthrey Bridge that may have to be considered detrimental to successful salmonid spawning. Following an observed decline in quality of salmonid fisheries at the site an investigation was initiated to assess the extent of ingress of fine sediments into the spawning gravels. Fine sediments from one potential source, upstream riverbanks, are also compared to those isolated from the spawning gravels. The percentage by weight of fine sediments for the six freeze cores, was found to be lower than first expected, given the visual appearance of the reach. However the fines were found to be distributed evenly down the cores with a marked absence of an upper, coarse gravel armour layer. In addition the median grain size (D50) of the six samples was generally low, falling to 6mm for core 5. The low median grain size and the absence of coarse grained upper strata are considered detrimental to the success rate of salmonid spawning.

Thermodynamic formulation of flowing soft matter with transient forces

The Responsive Particle Dynamics model is a very efficient method to account for the transient forces present in complex fluids, such as solutions of entangled polymers. This coarse-grained model considers a solution of particles that are made of a core and a corona. The cores typically interact through conservative interactions, while the coronae transiently penetrate each other to form short-lived temporary interactions, typically of entropic origin. In this study, we reformulate the resulting rheological model within the general framework of nonequilibrium thermodynamics called General Equation for the Nonequilibrium Reversible-Irreversible Coupling. This allows us to determine the consistency of the model, from a mechanistic and thermodynamic point of view, and to isolate the reversible and irreversible contributions to the dynamics of the model system. © 2012 Springer-Verlag Berlin Heidelberg.

Sedimentary records of water environment in lake Chaohu in the Yangtze delta region, China

Three lacustrine core samples were collected from Chaohu lake in December 2002 in the Yangtze delta region. The grain sizes were analyzed using a Laser Analyzer to obtain grain-size parameters. Sediment geochronology was determined in radioisotopes Cs-137 and the average sedimentary rates are 0.29cm.a(-1), 0.35 cm.a(-1) and 0.24cm-a(-1) in Cores C 1, C2 and C3, respectively. The grain-size parameters of the deposits vary regularly with the fluctuation of hydrodynamics. From 1950s to the beginning of 20th century, coarse-grained sediment was deposited, suggesting strong hydraulic conditions and high water-level periods with much precipitation; from the start of 20(th) century to latter half of 18(th) century, fine-grained sediment was deposited, indicating that weak hydraulic conditions and low water-level periods with less precipitation; before the first half of 18(th) century, coarse-grained sediment was deposited, suggesting great velocity of flow and high water-level periods of more precipitation.

Deformation behaviour of electrodeposited nanocrystalline Ni with broad grain size distribution

In the present work, nanocrystalline Ni (nc-Ni) with a broad grain size distribution (BGSD) of 5-120 nm and an average grain size of 27.2 nm was prepared. The BGSD nc-Ni sample shows a similar strength and good ductility in comparison with electrodeposited nc-Ni with a narrow grain size distribution. The intracrystalline dislocation network was observed in the post-deformed microstructure confirming the conventional intracrystalline dislocation sliding mechanism in BGSD nc-Ni. The uniaxial tensile loading-unloading-loading deformation shows BGSD nc-Ni has the capability to store dislocations in the grain interior, which is very limited compared with that of coarse grained metals. For BGSD nc-Ni, the strain rate sensitivity of flow stress m enhances with decreasing strain rate. At the strain rate of 5 x 10(-6) s(-1), m was estimated to be 0.055. At the corresponding strain rate, the enhanced ductility along with the decreased strength was achievable, indicating activation of other deformation mechanisms, e. g. grain boundary sliding or diffusion.

Low temperature heat capacity and thermal stability of nanocrystalline nickel

The heat capacity (C-p) of nanocrystalline nickel (nc-Ni, 40 mn crystallite size) has been measured over the temperature range of 78-370 K with a high-resolution automated adiabatic calorimeter. The measured results are compared with the C-p values of the corresponding coarse-grained crystal, and an enhancement of heat capacity of the nanocrystalline nickel was observed to be 2-4% in the temperature range between 100 and 370 K. The thermal stability of the nanocrystalline nickel sample was determined by a differential scanning calorimeter and a thermogravimetric system. The melting point of nc-Ni is the same as that of the corresponding coarse-grained crystalline nickel and the sample is stable at temperature lower than 500 K. (C) 2002 Elsevier Science B.V. All rights reserved.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Sedimentary changes during the Holocene in the Bohai Sea and its paleoenvironmental implication

Samples of two cores, Cores M5-5 and M7-4 in the Bohai Sea were analyzed in isotopes, grain size, heavy minerals, chemical compositions, and 14 C dating to reconstruct the sedimentation during the Holocene. Abrupt change in carbon and oxygen stable isotopes was recognized at Core M5-5 at about 6400 a BP, which was likely due to the intrusion of the Yellow Sea Warm Current (YSWC) extension into the Bohai Sea. At Core M7-4, sediments between 5900 and 6600 a BP (150-260 cm depth) became coarse-grained, containing rich garnet, high manganese content, and nil autogenic pyrite, indicating a very dynamic sedimentary event during which the ambience was transformed from reductive to oxidative, and sedimentation boosted. Meanwhile, the YSWC had invaded into the Bohai Sea indicated by rich planktonic foraminifera in this event. (c) 2008 Elsevier Ltd. All rights reserved.

Geochemical characteristics of nitrogen in the southern Yellow Sea surface sediments

Roles and distributions of various forms of nitrogen in biogeochemical cycling in the southern Yellow Sea surface sediments were investigated. The southern Yellow Sea could be divided into three regions (I, II and III) according to the proportion of fine-grained sediment in > 65%, 35-65% and < 35%, respectively. The ratios of different forms of nitrogen contents between each two of the three regions indicated that the nitrogen contents increased with the proportion of fine-grained sediment increasing. The quanta of exchangeable forms of nitrogen were similar in the three regions, while their releasing time increased from regions I to III, indicating that the cycle of nitrogen in fine-grained sediments was shorter than that in coarse-grained sediments. Nitrogen burial fluxes were also similar in these regions, while the burial efficiency increased from regions I to III. The highest burial efficiency was 30.21% in region III, indicating that more than 70% of nitrogen in the southern Yellow Sea surface sediments could be released to take part in biogeochemical recycling. When all the four forms of exchangeable nitrogen (nitrogen in ion exchangeable form (IEF-N), nitrogen in weak acid extractable form (WAEF-N), nitrogen in strong alkali extractable form (SAEF-N) and nitrogen in strong oxidant extractable form (SOEF-N)) were released to take part in recycling, their potential contributions were 80% (SOEF-N), 11% (IEF-N), 6% (SAEF-N), 3% (WAEF-N) respectively, which showed that SOEF-N was the predominant one, and its contribution to biogeochemical cycling was the highest. (c) 2004 Elsevier B.V. All rights reserved.

The release behavior of inorganic nitrogen and phosphorus in sediment during disturbance

Sediments and surface water were sampled in a tide flat in the Huiquan Bay, Qingdao, China in January 2004 to simulate the exchange of NH4-N/NO3-N/PO43- between sediments and surface water. A working system was designed with which samples were shaken at 60, 120 and 150 revolutions per minute (r/min). Experiment results show that NH4-N concentration in water at shaking rate of 60 r/min decreased gradually, while at 120 r/min increased gradually. In resuspension, fine-grained sediments contributed most NH4-N to the seawater, followed by medium-grained and coarse-grained sediments. The NO3-N concentration in water had a negative relation, with the shaking rate; the medium-grained sediments contributed more NO3-N to seawater than the coarse- and fine-grained sediments. The PO43- concentration is positively related with the shaking rate, the fine-grained sediments were the main N and P contributor to the seawater, followed by medium- and coarse-grained sediments.

芝麻坊石榴子石二辉橄榄岩多期变质演化及其地幔过程

Many garnet peridotite bodies are enclosed in ultrahigh-pressure (UHP) gneisses and/or migmatites in worldwide UHP terranes formed by subduction of continental crust. On the basis of petrochemical data, a group of garnet peridotites have been derived from depleted mantle and were subsequently metasomatized by melts and/or fluids derived from the subducted continental crust. However, their depletion and enrichment processes and tectonic evolutions are still in conflicts. New evidences for metamorphism of garnet lherzolite from Zhimafang, Donghai County, Sulu UHP terrane are reported. The garnet lherzolite have experienced a prolonged multistage metamorphic history. At least seven stages of recrystallization have been identified based on detailed analysis of reaction textures and mineral compositions. Stage I was a high-pressure and high-temperature enriched garnet lherzolite stage, which is inferred from the presence of high Ca-Cr core of garnet porphyroclast and inclusions of high-Mg clinopyroxene, high-Al-Cr orthopyroxene and high-Mg olivine. Stage II is a high-temperature and low-pressure depleted spinel-hurzbergite or spinel-dunite stage, as indicated by the presence of relict Al-rich spinel, very high-Mg and low-Ni olivine and high-Mg orthopyroxene included in the low-Cr mantle of the porphyroclastic garnet and core of fine-grained neoblastic garnet, clinopyroxene is absent in this stage. Stage III is an hydrous amphibole spinel-lherzolite stage, which recorded events of cooling and metasomatic re-enrichment, this stage is manifested by metasomatic origin of amphibole and phlogopite-bearing porphyroblastic clinopyroxene, and porphyroblastic orthopyroxene. Stage IV is a high-pressure amphibole garnet-lherzolite stage, which is indicated by the formation of low-Cr mantle of the porphyroclastic garnet and amphibole-bearing low-Cr core of neoblastic garnet. Stage V is an UHP metamorphic garnet-lherzolite stage, which is characterized by the formation of high-Cr rim of both porphyroclastic and neoblastic garnet and recrystallization of olivine, clinopyroxene and orthopyroxene in the matrix. During UHP metamorphism, the garnet lherzolite is dehydrated, hornblende decomposed to clinopyroxene and olivine. Stage VI is a high-pressure decompression amphibole garnet-lherzolite stage, indicated by formation of later coarse-grained pargasitic hornblende and phlogopite in the garnet stability field. Stage VII is a low-pressure decompression amphibole-chlorite spinel-lherzolite stage, indicated by replacement of garnet by kelyphite of high-Al orthopyroxene + aluminous spinel + tremolitic amphibole + chlorite + talc. The metamorphic evolutions of Zhimafang garnet lherzolite suggest that it displays progressive mantle wedge convection during the subduction of previous oceanic and subsequent continental slab. We propose that the Zhimafang garnet lherzolite were originated from enriched deep mantle wedge above the previously subducted oceanic slab, subduction of oceanic slab resulted in their convection to shallower back arc and sub-arc setting, decompressional melting transformed the enriched garnet-lherzolite to depleted spinel-hurzbergite or spinel-dunite, the spinel-hurzbergite or spinel dunite was then convected to the hydrous mantle wedge corner driven by corner flow and was cooled and metasomatized by slab-derived melts/fluids, and was transformed to enriched lherzolite. The lherzolites formed a downward mantle wedge layer above successively subducted continental crust. The peridotite subducted together with the underlying continental crust and suffered UHP metamorphism. Finally, the garnet-lherzolite exhumed to the earth surface together with the UHP terrane. Detailed analyses of reaction textures and mineral compositions revealed several stages of metasomatism related to continental subduction and exhumation.

矾山杂岩体成因及其与磷（铁）矿的成矿关系

The Fanshan complex consists of layered potassic ultramafic-syenite intrusions. The Fanshan apatite (-magnetite) deposit occurs in the Fanshan complex, and is an important style of phosphorus deposit in China. The Fanshan complex consists of three (First- to Third-) Phases of intrusion, and then the dikes. The First-Phase Intrusive contains ten typical layered rocks: clinopyroxenite, biotite clinopyroxenite, coarse-grained biotite clinopyroxenite, pegmatitic orthoclase-biotite clinopyroxenite, variegated orthoclase clinopyroxenite, interstitial orthoclase clinopyroxenite, biotite rock, biotite-apatite rock, biotite rock and magnetite-apatite rock. This layered intrusive consists of nine rhythmic units. Each rhythmic unit essentially comprises a pair of layers: clinopyroxenite at the bottom and biotite clinopyroxenite at the top. The apatite (-magnetite) deposit is situated near the top of rhythmic Unit no. 6 of the First-Phase Intrusive. The Second-Phase Intrusive contains three typical rocks: coarse-grained orthoclase clinopyroxenite, . coarse-grained salite syenite and schorlomite-salite syenite. The Third-Phase Intrusive includes pseudo-trachytic salite syenite, porphyritic augite syenite, fine-grained orthoclase clinopyroxenite and fine-grained salite syenite. The origin of the Fanshan complex is always paid attention to it in China. Because most layered igneous intrusion in the world not only have important deposit in it, but also carry many useful information for studying the formation of the intrusion and the evolvement of magma. Two sketch maps were drawn through orebodies along no. 25 cross-cut on 425 mL and no. 1 cross-cut on 491 mL in the Fanshan mine. Through this mapping, a small-scaled rhythmic layering (called sub-rhythmic layering in the present study) was newly found at the top of the rhythmic Unit no. 6. The concept of sub-rhythmic layering is defined in this article. The sub-rhythmic layering is recognized throughout this apatite-rich part, except for magnetite-apatite rock. Presence of the layered magnetite-apatite rock is one of the characteristics of the Fanshan apatite (-magnetite) deposit. Thus, from this layer downwards six units of sub-rhythmic layering are recognized in the present study. Each unit consists of biotite clinopyroxenite (or biotite rock and biotite-apatite rock) layer at the bottom and apatite rock layer at the top. To study this feature in detail is an important work for understanding the origin of the Fanshan complex and apatite (-magnetite) deposit. The origin of the Fanshan complex and the relation of the formation of the apatite(-magnetite)deposit will be interpreted by the study of sub-rhythmic layering on the basis of previous research works. The magma formed the Fanshan complex was rich in K2O, early crystallized pyroxene, and after this phase more biotite crystallized, but no amphibole appeared. This indicated that the activity of H2O in the magma was low. Major element compositions of biotite and clinopyroxene (on thin sections) in the sub-rhythmic layering were analyzed using electron microprobe analyzer. The analytical results indicate Mg/(Mg+Fe*+Mn) atomic ratios (Fe*, total iron) of these two minerals rhythmically changed in sub-rhythmic layering. The trends of Mg/(Mg+Fe*+Mn) atomic ratio (Fe*, total iron) of biotite and clinopyroxene indicate that the magma evolved markedly from relatively magnesian bottom layer to less magnesian top layer in each sub-rhythmic unit. A general trend through the sub-rhythmic layering sequence is both minerals becoming relatively magnesian upwards. The formation temperatures for sub-rhythmic layering yield values between 600 and 800 ℃, were calculated using the ratio of Mg/(Mg+Fe+Mn) in the salite and biotite assemblage. The equilibrium pressures in the rhythmic layers calculated using the contents of Al in the salite were plotted in the section map, shown a concave curve. This indicates that the magma formed the First-Phase Intrusive crystallized by two vis-a-vis ways, from its bottom and top to its centre, and the magnetite-apatite rock was crytallized in the latest stage. The values of equilibrium pressures in the sub-rhythmic layering were 3.6-6.8(xlO8) Pa with calculated using the contents of Al in the salite. The characteristics of geochemistry in various intrusive rocks and the rocks or apatite of sub-rhythmic layers indicated that the Fanshan complex formed by the comagmatic crystallization. The contents of immiscible elements and REEs of apatite rock at the top of one sub-rhythmic unit are more than biotite clinopyroxenite at the bottom. The contents of immiscible elements and REEs of apatite of biotite clinopyroxenite at the bottom of one sub-rhythmic unit are higher than apatite rock at the top. The curves of rocks (or apatite) in the upper sub-rhythmic units are between two curves of the below sub-rhythmic unit in the primitive mantle-normalized trace element abundance spider diagram and the primitive mantle-normalized REE pattern. The trend for the contents of immiscible elements and REEs inclines to the same contents from the bottom to the top in sub-rhythmic layering. These characteristics of geochemistry of rocks or apatites from sub-rhythmic layering indicate that the latter sub-rhythmic unit was produced by the residual magma after crystallization of the previous sub-rhythmic unit. The characteristics of petrology, petrochemistry, geochemistry in the Fanshan complex and sub-rhythmic layers and the trends of Mg/(Mg+Fe+Mn) atomic ratio of biotite and clinopyroxene in sub-rhytmic layering rejected the hypotheses, such as magma immiscibility, ravitational settling and multiple and pulse supplement of magma. The hypothesis of differentiation by crystallization lacks of evidences of field and excludes by this study. On the base of the trends of formation temperatures and pressures, the characteristics of petrology, petrochemistry, geochemistry for the Fanshan complex and the characteristics of geochemistry for the rocks (or apatites), the trends of Mg/(Mg+Fe+Mn) atomic ratio of biotite and clinopyroxene in sub-rhytmic layering, and the data of oxygen, hydrogen, strontium and neodymium isotopes, this study suggests that the magma formed the Fanshan complex was formed by low degree partial melting of mantle at a low activity of H2O, and went through the differentiation at the depth of mantle, then multiply intruded and crystallized. The rhythmic layers of the First-Phase Intrusive formed by the magma fractional crystallized in two vis-a-vis ways, from the bottom and top to the centre in-situ fractional crystallization. The apatite (-magnetite) deposit of the Fanshan complex occurs in sub-rhythmic layering sequence. The the origin of the sub-rhythmic layering is substantially the origin of the Fanshan apatite (-magnetite) deposit. The magma formed the rhythmic layers of First-Phase Intrusive was rich in H2O, F and P at the later stage of its in-situ fractional crystallization. The Fanshan apatite (-magnetite) deposit was formed by this residual magma in-situ fractional crystallization. The magnetite-apatite rock was crystallized by two vis-a-vis ways at the latest stage in-situ fractional crystallization in the rhythmic layers. The result was light apatite layer below heavy the magnetite-apatite layer, formed an "inversion" phenomenon.

黄骅坳陷高尘头地区储层非均质性及成藏研究

Gaochentou region is located in the southwest direction of Gaochentou village in Huanghua city of Hebei province. In regionally structural position, It lies in Qikou sag In the middle part of Huanghua depression, which belongs to the east part of the south Dagang structure zone in the middle part of Huanghua depression. Its' very beneficial at regional structure in Gaochentou , and It becomes the advantage area for oil and gas gathered and preserved, Sandstone reservoir of Dongying Formation is main bearing bed .Dongying Formation in Gaochentou region of Huanghua depression is consisted of set of mudstone and sandstone interbeds by deposited delta fades . Dongying Formation can be divided into 3 members from above to below: the first member of Dongying Formation (FMDF), the second member of Dongying Formation (SMDF), and third member of Dongying Formation (TMDF). The lithology of the upper part of FMDF was consisted of mostly middle-grained and fine-grained sandstone, and it is small for the oil-bearing area of the sand bodies .The lithology of the lower part is coarse-grained sandstone bodies which are well connected between sandstone bodies of wells, and the lower part was main bed of oil production in Dongying Formation; SMDF and TMDF are consisted of larger scale set of mudstone, in which the sandbodies are lenticular and pinch out quickly, and the lithology was mostly fine sandstone and silt stone, in which there are little oil and gas .Because the reservoirs in this area are largely influenced by the factors such as lithology, fault and others, and the reservoirs have the strong,heterogeneity , there exists the problem of oil-down and water-up for vertical distribution of oil and gas bearing. It is not very clearly for the three dimension distribution of sandstone , and the geology researchs is not enough. So, it can't satisfy the need of further development and production for Gaochentou oilfield.Having the key problem of oil-down and water-up and the mechanism of the reservoir for Gaochentou area, There are as follow study works, the first, is study of the high-resolution correlation of sequence stratigraphy and sedimentary microfacies. Dongying Formation was divided into three parasequence sets and each parasequence set was divided into different amount of parasequences. FMDF, as the main oil and gas producing bed, can be divided into seven parasequences. Oil and gas are discovered in six parasequences except the seventh. On the basis of study of sedimentary microfacies, the sediments of Dongying Formation are considered deposited mainly in delta front subfacies. The microfacies types of Dongying Formation are sub-water distirbutary channel, sub-water natural bank, inter distributary channel bay, distributary channel mouth dam, and delta front mat sand.Seismic facies analysis and logging-constrained inversion technique were applied by Author for transverse prediction of sandstone reservoir. Having 4 modes of interwell single sandbodies correlation technique, Author have described distribution characteristics of sandbodies, and established geological reservoir model of Gaochentou reservoir.Author presented that the reservoirs characteristic have very strong heterogeneity ,and In the section of sandstone interlayed with mudstone,the folium sandstone interlayed with each other, and the wedge shaped sandbodies pinched out in the mudstone. So the pinch-out up sandstone trap and lenticular sandstone trap are easily formed. They are most small scale overlying pinches out in the place of slope. This article applies the concept of deep basin oil to resolve reasonably the problem of which the oil is below the water in Gaochentou area. Combined with the study of sedimentary facies, reservoir and other aspects, the mechanism and patterns of deep basin oil are studied on the basis of characteristics in Gaochentou area.On the basis of the above study, the mechanism of the oil and gas' migration and accumulation in isotropic sandstone and heterogeneous sandstone are thoroughly analyzed through experiments on physical modeling. Experiments on physical modeling show that the discrepancy between sand layers with different permeability and thickness has important influence on the direction, path, and injection layer of oil's migration. At the beginning of the injection of oil and gas in high permeability sand layer, the pressure is low, the migration resistance is small, and the oil and gas are more easily displacing the water in sand. So it can act as good transformation layer or reservoir. But at the beginning of the injection of oil and gas in sand layer with low permeability, the pressure is high, the migration resistance is big, and the oil and gas are more difficultly displacing the water in sand. So it can only act as bad or worse transformation layer or reservoir. Even if it cannot act as transformation layer or reservoir, it can act as water layer or dry layer. The discrepancy between sand layers on permeability and thickness can make discrepancy in injection of oil and gas between different layers. Consequently it leads to small amount of oil and gas injection in sand layers with low permeability. Ultimately it affects the oil's accumulation and distribution in different sand layers.At Last, combining analysis of the structure and pool forming condition, The thesis has established models of reservoir formation to predict the advantage distribution of oil and gas bearing , and put forward the prospective target It is not only of theoretical signification for explosion and importance, but also has realistic value in guiding the progressive petroleum exploration and exploitation.