Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Kinetic modeling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19

A Theoretical Study of NH 2 Radical Reactions with Propane and Its Kinetic Implications in NH 3 -Propane Blends’ Oxidation

The reaction of NH 2 radicals with C 3 H 8 is crucial for understanding the combustion behavior of NH 3 /C 3 H 8 blends. In this study, we investigated the temperature dependence of the rate coefficients for the hydrogen abstraction reactions of C 3 H 8 by NH 2 radicals using high-level theoretical approaches. The potential energy surface was constructed at the CCSD(T)/cc-pV(T, Q)//M06-2X/aug-cc-pVTZ level of theory, and the rate coefficients were computed using conventional transition state theory, incorporating the corrections for quantum tunneling and hindered internal rotors (HIR). The computed rate coefficients showed a strong curvature in the Arrhenius behavior, capturing the experimental literature data well at low temperatures. However, at T > 1500 K, the theory severely overpredicted the experimental data. The available theoretical studies did not align with the experiment at high temperatures, and the possible reasons for this discrepancy are discussed. At 300 K, the reaction of NH 2 with C 3 H 8 predominantly occurs at the secondary C-H site, which accounts for approximately 95% of the total reaction flux. However, the hydrogen abstraction reaction at the primary C-H site becomes the dominant reaction above 1700 K. A composite kinetic model was built, which incorporated the computed rate coefficients for NH 2 + C 3 H 8 reactions. The importance of NH 2 + C 3 H 8 reactions in predicting the combustion behavior of NH 3 /C 3 H 8 blends was demonstrated by kinetic modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oxidation and pyrolysis of methyl propyl ether

The ignition, oxidation, and pyrolysis chemistry of methyl propyl ether (MPE) was probed experimentally at several different conditions, and a comprehensive chemical kinetic model was constructed to help understand the observations, with many of the key parameters computed using quantum chemistry and transition state theory. Experiments were carried out in a shock tube measuring time variation of CO concentrations, in a flow tube measuring product concentrations, and in a rapid compression machine (RCM) measuring ignition delay times. The detailed reaction mechanism was constructed using the Reaction Mechanism Generator software. Sensitivity and flux analyses were used to identify key rate and thermochemical parameters, which were then computed using quantum chemistry to improve the mechanism. Validation of the final model against the 1-20 bar 600-1500 K experimental data is presented with a discussion of the kinetics. The model is in excellent agreement with most of the shock tube and RCM data. Strong non-monotonic variation in conversion and product distribution is observed in the flow-tube experiments as the temperature is increased, and unusually strong pressure dependence and significant heat release during the compression stroke is observed in the RCM experiments. These observations are largely explained by a close competition between radical decomposition and addition to O2 at different sites in MPE; this causes small shifts in conditions to lead to big shifts in the dominant reaction pathways. The validated mechanism was used to study the chemistry occurring during ignition in a diesel engine, simulated using Ignition Quality Test (IQT) conditions. At the IQT conditions, where the MPE concentration is higher, bimolecular reactions of peroxy radicals are much more important than in the RCM.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transport Modeling of Kinetically Limited Microscale Extraction Systems: Droplet and Supported Liquid Membrane Separations

Microfluidic droplet extraction devices can be used to efficiently measure solute phase transfer kinetics in liquid–liquid extraction systems. In this work, a droplet extraction apparatus was constructed using off-the-shelf and custom 3D printed parts for less than 110 USD. The interfacial kinetics of the transfer of Pu(IV) between an aqueous nitric acid phase and a 5 v/v% tridodecylamine (TDA) in toluene phase were characterized by determining the extent of Pu(IV) transfer between phases at different flow rates. Forward interfacial rate constants calculated from this data using an analytical model are 5.6 × 10 –3 mm s –1 under extraction (aqueous-to-organic solute transfer) conditions and 3.3 × 10 –3 mm s –1 under stripping (organic-to-aqueous solute transfer) conditions. The analytical model is valid when the rate of solute transfer across the interface between the two liquid phases has pseudo-first-order reversible reaction kinetics and is slow relative to the rate of solute transport to the interface. The change in the outlet concentration with residence time determined using the analytical model was compared with the results of a numerical model accounting for advection/diffusion to the interface in addition to kinetically limited interfacial solute transfer. These calculations revealed that for systems with forward interfacial rate constants greater than approximately 10 –2 mm s –1 , the analytical model must be supplemented with a numerical transport model accounting for an additional advection/diffusion mass transfer resistance. This threshold corresponds to a Damköhler number of one. The measured interfacial kinetic rate constants for Pu(IV)/TDA were used in a supported liquid membrane (SLM) numerical model, which showed that the Pu(IV) phase transfer kinetics are fast enough for use in a practical separation.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Automated identification and calculation of prompt effects in kinetic mechanisms using statistical models

The kinetics of prompt dissociation involves rovibrationally excited species (generally formed by exothermic reactions) which may dissociate or isomerize prior to thermalization via collisions with the bath gas. Treating such rovibrationally excited species (so-called "hot" species) with standard kinetic phenomenology may result in incorrect macroscopic representation of their reactivity. Here this work presents the first fully automated methodology for the calculation of prompt effects of a chosen species in a kinetic mechanism, including (i) reaction selection; (ii) theoretical calculation of rate constants and prompt branching fractions; and (iii) final rate constant fitting. The energy partition between hot fragments is estimated using a variety of statistical models, including a new physically sound microcanonical statistical model based on the rovibrational density of states of the fragments. The methodology is validated against literature data for the prompt dissociations of HCO and C 3 H 7 radicals. The microcanonical statistical model is in better agreement with trajectory simulations for larger species and is thus applicable for practical systems that typically involve large molecules, for which direct dynamics calculations are impractical. The automated workflow is applied to the evaluation of the effects of prompt dissociation for two isomeric radicals C 4 H 7 1-3 (1-methylallyl) and C 4 H 7 1-4 (3-buten-1-yl). Twelve H-atom abstraction reactions are selected and the corresponding rate constants are computed with first principles theory. The microcanonical statistical model predicts that prompt dissociations of C 4 H 7 1-3 and C 4 H 7 1-4 are already significant at 1000K, resulting in differences of up to an order of magnitude at 2000K with respect to the phenomenological thermal rate constants. To illustrate the effects of prompt dissociation on simulations of experimental data, the calculated prompt rate constants are implemented in both CRECK and C3MechV3.3 kinetic mechanisms. Simulations of experimental flame data illustrate the noticeable impact of prompt dissociation kinetics on the high-temperature combustion reactivity of C 4 H 8 -1 and C 4 H 8 -2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Flow dynamics and bending of wide-angle tailed radio sources

The dynamics of tailed radio sources (WATs) is studied on the basis of VLA observations of 11 wide-angle WATs at 6 and 20 cm. These new images, in conjunction with optical and X-ray data, are used to describe the unifying characteristics of this class. WATs are found in centers of clusters without cooling cores, associated with galaxies of low space velocity. They are large sources, extending at least 50 kpc from the cluster center, and they have radio power close to the Fanaroff-Riley I/II break. The surface brightness and spectral distributions are used to model the flow fields and bending dynamics of the sources. Two limiting models are employed: the adiabatic model, in which no in situ energization takes place, and the kinetic model, in which all of the radio luminosity comes from in situ energization. It is found that the sources cannot be bent by the slow galaxy motion in the kinetic model. The sources can be bent by the ram pressure of a slowly moving central galaxy in the adiabatic model.

O'Donoghue, Aileen A.↗

Oxidation kinetics of model compounds of metabolic waste in supercritical water

In this NASA-funded study, the oxidation kinetics of methanol and ammonia in supercritical water have been experimentally determined in an isothermal plug flow reactor. Theoretical studies have also been carried out to characterize key reaction pathways. Methanol oxidation rates were found to be proportional to the first power of methanol concentration and independent of oxygen concentration and were highly activated with an activation energy of approximately 98 kcal/mole over the temperature range 480 to 540 C at 246 bar. The oxidation of ammonia was found to be catalytic with an activation energy of 38 kcal/mole over temperatures ranging from 640 to 700 C. An elementary reaction model for methanol oxidation was applied after correction for the effect of high pressure on the rate constants. The conversion of methanol predicted by the model was in good agreement with experimental data.

Webley, Paul A.↗

Analysis of thermo-chemical nonequilibrium models for carbon dioxide flows

The aerothermodynamics of thermochemical nonequilibrium carbon dioxide flows is studied. The chemical kinetics models of McKenzie and Park are implemented in separate three-dimensional computational fluid dynamics codes. The codes incorporate a five-species gas model characterized by a translational-rotational and a vibrational temperature. Solutions are obtained for flow over finite length elliptical and circular cylinders. The computed flowfields are then employed to calculate Mach-Zehnder interferograms for comparison with experimental data. The accuracy of the chemical kinetics models is determined through this comparison. Also, the methodology of the three-dimensional thermochemical nonequilibrium code is verified by the reproduction of the experiments.

Rock, Stacey G.↗

An E and B gyrokinetic simulation model for kinetic Alfvén waves in tokamak plasmas

The gyrokinetic particle simulation is a powerful tool for studies of transport, nonlinear phenomenon, and energetic particle physics in tokamak plasmas. While most gyrokinetic simulations make use of the scalar and vector potentials, a new model (GK-E&B) has been developed by using the E and B field in a general form and has been implemented in simulating kinetic Alfvén waves in uniform plasma. In our work, the Chen et al. GK-E&B model has been expressed, in general, tokamak geometry using the local orthogonal coordinates and general tokamak coordinates. Its reduction for uniform plasma is verified, and the numerical results show good agreement with the original work. The theoretical dispersion relation and numerical results in the local model in screw pinch geometry are also in excellent agreement. Numerical results show excellent performance in a realistic parameter regime of burning plasmas with high values of β/(M e k$^{2}_{⊥}$ρ$^{2}_{i}$), which is a challenge for traditional methods due to the “cancellation” problem. As one application, the GK-E&B model is implemented with kinetic electrons in the local single flux surface limit. With the matched International Tokamak Physics Activity-Toroidicity-induced Alfvén Eigenmodes parameters adopted, numerical results show the capability of the GK-E&B in treating the parallel electron Landau damping for realistic tokamak plasma parameters. As another application, the global GK-E&B model has been implemented with the dominant electron contribution in the cold electron limit. Its capability in simulating the finite E || due to the finite electron mass is demonstrated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Explosive Soot Challenge (Final Report)

This project assembled a broad ensemble of modeling and experimentation tools to study the morphological and optical properties of detonation soots in explosive fireballs. A gram-scale hemispherical high explosive was studied in a low-pressure controlled environment using in-situ experimentation with diffusely illuminated visible absorption spectroscopy, particle sizing through light scattering techniques, and post-test collections with subsequent morphological analysis. Hydrocode modeling was performed to replicate the detonation flow observations, and subsequent aerosol kinetics models provided particle size distributions and extinction coefficients from the hydrocode results. Experimentally observed soot morphologies agreed with expectation from the literature - a bimodal distribution was found, brought upon by the particles growing to a size where their inertia and fluid wakes are non-negligible. The aerosol kinetics model did not replicate the observed bimodal size distribution for lack of a coagulation kernel to represent the behavior. To recover particulate optical properties, a spectrally resolved absorption spectroscopy method termed Spectral diffuse back-illuminated extinction imaging (SBI-EI) was developed and implemented on two explosive types. Inverting the absorption spectra using a Kramers-Kronig consistent method yielded the complex index of refraction for the soots produced by the explosives. This method resulted in an unrealistic index of refraction for one of the two explosives, and this is suspected to be due to the model neglecting scattering brought upon by the large particle sizes observed. In addition to the core work, three additional studies were performed in parallel. These investigated the impact of scattering on diffuse absorption spectroscopy, studied how soots oxidate and sublimate in a well-controlled shock tube, and laid the theoretical groundwork for a new collision kernel to replicate the bimodal size distribution from the observations. Summaries of these efforts are included at the end of this report.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Next-Generation Ion Thruster Design Tool

Computational tools that accurately predict the performance of electric propulsion devices are highly desirable and beneficial to NASA and the broader electric propulsion community. The current state of the art in electric propulsion modeling relies heavily on empirical data and numerous computational "knobs." In Phase I of this project, Tech-X Corporation developed the most detailed ion engine discharge chamber model that currently exists. This kinetic model simulates all particles in the discharge chamber along with a physically correct simulation of the electric fields. In addition, kinetic erosion models are included for modeling the ion-impingement effects on thruster component erosion. In Phase II, Tech-X developed a user-friendly computer program for NASA and other governmental and industry customers. Tech-X has implemented a number of advanced numerical routines to bring the computational time down to a commercially acceptable level. NASA now has a highly sophisticated, user-friendly ion engine discharge chamber modeling tool.

Stolz, Peter↗

Data for Selective Oxidation of 3-Hydroxypropionic Acid to Malonic Acid over Pd/C: Mechanistic and Kinetic Study

Malonic acid (MA) is a high-value dicarboxylic acid with strong industrial demand, yet its current production heavily relies on petrochemical feedstocks. Here, we report the first systematic study for the sustainable production of MA via oxidation of 3-hydroxypropionic acid (3-HP) with a Pd/Carbon catalyst. The effects of oxidant type (O2 and H2O2), pH, and temperature on the reaction chemistry were comprehensively evaluated. Guided by experimental observation and DFT-calculated thermochemical energetics, reaction networks for 3-HP oxidation with both oxidants are proposed and validated through kinetic modeling. MA was identified as the primary oxidation product, while further oxidation yields acetic acid and oxalic acid. The kinetic model validated the network, displaying excellent agreement (R2 > 0.95). Kinetic observations also enabled a direct comparison between O2 and H2O2 and revealed their distinct behaviors. The model was further developed into a temperature-time map, providing insight into conditions that maximize MA production. Malonic acid selectivity of 56.9 % and yield of 50.5 % were achieved at 3 bar oxygen, equimolar NaOH:3-HP ratio, and 50 °C.

Bioproducts↗

Application of NEAMS Codes to Capture MSR Phenomena

This report documents work completed in FY21 under the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program’s Molten Salt Reactor (MSR) Application Drivers activity at Argonne. The common focus was on identifying the modeling and simulation functional requirements for designing, licensing, and operating MSRs and applying those capabilities already developed in NEAMS tools to example problems of interest. The four main parts of this report each focuses on a specific area of simulation physics as it relates to MSR phenomena: fuel evolution, chemistry, computational fluid dynamics (CFD), and systems analysis. In terms of fuel evolution, which includes depletion, decay, on-line separations, and transmutation, the current state of computational capabilities for modeling this behavior in liquid-fueled molten salt reactor is discussed. Some of the functional requirements to accomplish the various applications of MSR fuel depletion modeling are highlighted, followed by a summary of recent approaches and code development activities. The chemistry functional requirements were discussed in the context of several applications of high importance for MSRs, such as corrosion, salt chemistry, and species transport. Each of these types of chemistry modeling have considerable impact on various aspects of reactor applications, including informing on reactor designs, improving operational efficiencies, analyzing safety and reactivity concerns, and estimating the mechanistic source term of the reactor. A brief overview is also provided on code development activities ongoing under NEAMS relevant to chemistry modeling of MSRs. In terms of CFD applications, the state-of-the-art spectral element code, Nek5000 was used to model the fluid dynamics within a full core of the Molten Salt Fast Reactor (MSFR) concept designed as part of the Euratom EVOL project. This concept was selected as the challenge problem because of its similar features to several U.S. industry concepts. The goal was to model some of the fast MSR design challenges, including potential large internal re-circulations, the need of accurate tracking of delayed neutron precursors (DNP), and the lack of relevant thermal-hydraulics models/correlations, etc. Therefore, a series of CFD models were created for the MSFR core cavity using a k – τ model two-equation model for the turbulence. These first full core results demonstrated that any potential recirculation zones could be properly identified with the current NEAMS CFD capabilities. The development of these models will also set the stage for future testing of Nek5000’s functionalities to model other MSR thermal-fluid phenomena. Lastly, the validation of SAM against experimental data from the Molten Salt Reactor Experiment, which started in FY19, continues with the inclusion of modeling the reactivity insertion tests. This involved using SAM and its point kinetics model for flowing fuel salt to recreate the time dependent power changes and response after positive reactivity insertions at the 1, 5, and 8 MWt power levels. Through these exercises, several code modifications were suggested to the SAM development team and accommodated to enable closer agreement with solid technical and physical justifications. These include adding a moderator reactivity feedback coefficient as an available input and modifying the solution approach for the point kinetics model. Additional SAM development suggestions for flowing fuel MSRs include adding the capability to allow the moderator power change proportionally with the reactor power and enabling specification of the power and DNP distributions separately.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Uncertainty Quantification and Error Propagation in the Enthalpy and Entropy of Surface Reactions Arising from a Single DFT Functional

Accounting for parametric uncertainty in models is essential for quantifying the models’ predictive ability. Recently, approaches have been introduced to estimate parametric uncertainty in kinetic models while accounting for correlations among energy parameters. However, correlations have been estimated indirectly and correlations in entropies have not been accounted for. For surface-catalyzed microkinetic models of >C2 (more than two carbon-containing) molecules, which consist of thousands of reaction steps and intermediate surface species, first-principles density functional theory (DFT) is costly, and thus, estimation of thermochemistry and reaction barriers requires surrogate methods of DFT, such as group additivity and Brønsted–Evans–Polanyi relationships, respectively. For such parametrization, model uncertainty is unclear. This work develops a framework to overcome these gaps using group additivity and a single DFT functional. We estimate correlations in parameters of kinetic models and quantify uncertainty for thermochemistry, reaction barriers, reaction paths, and ultimately reaction rates, accounting also for the contribution of entropic uncertainty. Furthermore, the approach is illustrated on propane combustion and ethane oxidative dehydrogenation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Heterogeneous Combustion of Porous Graphite Particles in Microgravity

Recent theoretical investigations on graphite particle combustion have employed several levels of heterogeneous reaction models, ranging from global to elementary models, to describe the oxidation of carbon to gaseous products. Unlike the counterpart homogeneous reaction models, these heterogeneous reaction models are not well developed because of the difficulties associated with decoupling the physical characteristics of the solid (e.g. surface area taking part in combustion) from the chemical kinetic data. This is certainly true for porous graphite particle combustion, where heterogeneous and homogeneous reactions occur within the pores and play an important role in the overall oxidation process. As a result, there are considerable uncertainties of physical phenomena predicted using different heterogeneous kinetic models available in the literature. A good example, discussed later in this paper, is the predicted critical particle size below which the mass burning rate becomes exponentially small. The main goal of this study is to understand the basic mechanism controlling such rapid changes in burning rates, by developing a model where physical contributions are decoupled from chemical rate constants in a consistent manner. Another important goal of the proposed study is to develop a truly intrinsic, detailed heterogeneous reaction model for porous graphite combustion at high-temperatures, and to derive a systematically reduced heterogeneous reaction model in terms of the elementary reaction rate constants of the detailed model. The validation of chemical kinetic models describing the heterogeneous and homogeneous combustion in and around a spherically symmetric porous graphite particle can be considerably simplified by experimental measurements obtained under microgravity conditions. A vital component of this study is to conduct such supporting experiments on particle burning rate and surface temperature using NASA microgravity facilities, in close coordination with the theoretical effort. The basic understanding obtained and models developed as part of this project will be useful for optimal design of coal combustion devices. These models can also be extended to investigate the role of heterogeneous chemistry on pollutant formation pathways in combustion devices. The theoretical approach developed here, with pore diffusion effects decoupled from the chemical effects, can also be extended to understand the heterogeneous combustion of other porous fuels, for example, combustion of magnesium in a CO2 environment for propulsion in the Martian atmosphere.

Chelliah, Harsha K.↗

Compositional patterning in irradiated alloys: Effective potentials and effective interfacial energy

Compositional patterning (CP) in binary alloys during energetic particle irradiation is studied using a kinetic model that considers two competing kinetic processes, a thermally activated one promoting macroscopic phase separation (MPS) of the concentration field c(r,t) and a forced one resulting in finite-range random atomic mixing. The forced mixing is modeled by a Gaussian relocation distribution with a characteristic distance R. A series of approximate kinetic models are introduced by expanding the mixing function into a series of n terms, thus replacing the non-local evaluations of the concentration field c(r'-r,t) by local derivatives of c(r,t). This approach makes it possible to obtain exact effective potentials and build steady-state diagrams for each order-n model. Phase field (PF) simulations using these order-n models reveal that near the onset of patterning, phase evolution is accurately described using an order-3 model, which changes smoothly from an extended Cahn-Hilliard free energy in the MPS regime to a one-mode Swift-Hohenberg functional in the CP regime. Deeper into the patterning regime, higher-order models are required to achieve convergence, yielding square-like concentration profiles characteristic of a strong segregation regime. These higher-order effective free energies are analogous to multimodal Swift-Hohenberg functionals. Here, a new definition for the effective interfacial energy is proposed in the CP regime, since the interfacial area is no longer an excess quantity in that regime, precluding the use of the standard thermodynamic definition of interfacial energy.

36 MATERIALS SCIENCE↗

Investigating Kinetic Mechanisms of Soot Formation in Plasma Pyrolysis of Methane via Active Learning (Final Technical Report)

Plasma pyrolysis of methane is an effective route for zero-carbon hydrogen production. Yet, soot generated from pyrolysis of hydrocarbons is detrimental to the climate and human health. There is ample experimental and theoretical evidence that suggests polycyclic aromatic hydrocarbons (PAHs) are the molecular precursors to soot particles. The reaction pathways of PAH formation are intricately dependent on a multitude of process parameters, whose kinetic mechanisms are not well-understood in plasma pyrolysis. This project aims to leverage advances in the kinetic modeling of soot formation in combustion, as well as in surrogate modeling and active learning, to systematically investigate the effects of process parameter on the kinetics of PAH formation in plasma pyrolysis of methane. To this end, we propose to use the PAH formation kinetics model developed by the PPPL/PU group based on the well-established ABF and HACA mechanisms, coupled with low-temperature plasma models. We will develop an active learning (AL) framework based on Bayesian optimization to systematically and data-efficiently explore the complex and multivariable parameter space of plasma pyrolysis in order to quantify the effects of plasma and feed parameters on the ABF and HACA kinetic pathways. AL is the branch of machine learning concerned with systematically querying samples from a system (experimental or computational) to train a data-driven model that maps design parameters to a performance criterion. We will use the data generated via AL to perform global sensitivity analysis, combined with uncertainty quantification, to elucidate the impact of different reaction pathways on minimizing formation of soot precursors. This study will result in an improved understanding of kinetics of PAH formation in plasma pyrolysis and can pave the way for more advanced mechanistic studies (e.g., soot nucleation mechanisms). Additionally, the findings will be useful for establishing practical strategies for increasing the pyrolysis efficiency and producing high-grade carbon for synthesis of nanomaterials.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Vertical effective stress and temperature as controls of quartz cementation in sandstones: Evidence from North Sea Fulmar and Gulf of Mexico Wilcox sandstones

Here we present quantitative petrographic data, high spatial resolution oxygen isotope analyses of quartz cement, basin modelling and a kinetic model for quartz precipitation for two Paleocene-Eocene Wilcox Group sandstones from Texas and two Jurassic Fulmar Formation sandstones from the Central North Sea. At each location, one sandstone has been buried to ca. 145 °C and one to ca. 185 °C. A key difference between the Wilcox and Fulmar burial histories is that the Wilcox sandstones are currently at higher vertical effective stresses and, from basin modelling studies, have been subjected to generally higher vertical effective stresses through their burial history. The amounts of quartz cement in the Wilcox sandstones are between 12 and 18%, and between 2 and 6% in the Fulmar sandstones. High-spatial-resolution oxygen isotope data obtained from the quartz cements suggest temperature ranges for quartz precipitation from 60 to 80 °C to values approaching maximum burial temperature. Factors such as grain coatings or the timing of petroleum emplacement cannot explain the differences in the amounts of quartz cement. Petrographic data show that most of the silica for quartz cement can be derived from intergranular pressure dissolution. Although the sample set is small, we interpret the results to suggest that the differences in quartz cementation in Fulmar and Wilcox sandstones can be explained better by differences in their vertical effective stress history than their temperature history; in this case, the supply of silica rather than the precipitation of quartz becomes an important control on the rate and extent of cementation.

58 GEOSCIENCES↗

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called “lag time”). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5–10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗