DOE Office of Scientific and Technical Information (OSTI.GOV)

Herman, D.

The Savannah River Site (SRS) Actinide Removal Process has been processing salt waste since 2008. This process includes a filtration step in the 512-S facility. Initial operations included the addition, or strike, of monosodium titanate (MST) to remove soluble actinides and strontium. The added MST and any entrained sludge solids were then separated from the supernate by cross flow filtration. During this time, the filter operations have, on many occasions, been the bottleneck process limiting the rate of salt processing. Recently, 512-S- has started operations utilizing “No-MST” where the MST actinide removal strike was not performed and the supernate wasmore » simply pre-filtered prior to Cs removal processing. Direct filtration of decanted tank supernate, as demonstrated in 512-S, is the proposed method of operation for the Hanford Low Activity Waste Pretreatment System (LAWPS) facility. Processing decanted supernate without MST solids has been demonstrated for cross flow filtration to provide a significant improvement in production with the SRS Salt Batches 8 and 9 feed chemistries. The average filtration rate for the first 512-S batch processing cycle using No-MST has increased filtrate production by over 35% of the historical average. The increase was sustained for more than double the amount of filtrate batches processed before cleaning of the filter was necessary. While there are differences in the design of the 512-S and Hanford filter systems, the 512-S system should provide a reasonable indication of LAWPS filter performance with similar feed properties. Based on the data from the 512-S facility and with favorable feed properties, the LAWPS filter, as currently sized at over twice the size of the 512-S filter (532 square feet filtration area versus 235 square feet), has the potential to provide sustained filtrate production at the upper range of the planned LAWPS production rate of 17 gpm.« less

LITERATURE REVIEWS TO SUPPORT ION EXCHANGE TECHNOLOGY SELECTION FOR MODULAR SALT PROCESSING

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, W

2007-11-30

This report summarizes the results of literature reviews conducted to support the selection of a cesium removal technology for application in a small column ion exchange (SCIX) unit supported within a high level waste tank. SCIX is being considered as a technology for the treatment of radioactive salt solutions in order to accelerate closure of waste tanks at the Savannah River Site (SRS) as part of the Modular Salt Processing (MSP) technology development program. Two ion exchange materials, spherical Resorcinol-Formaldehyde (RF) and engineered Crystalline Silicotitanate (CST), are being considered for use within the SCIX unit. Both ion exchange materials havemore » been studied extensively and are known to have high affinities for cesium ions in caustic tank waste supernates. RF is an elutable organic resin and CST is a non-elutable inorganic material. Waste treatment processes developed for the two technologies will differ with regard to solutions processed, secondary waste streams generated, optimum column size, and waste throughput. Pertinent references, anticipated processing sequences for utilization in waste treatment, gaps in the available data, and technical comparisons will be provided for the two ion exchange materials to assist in technology selection for SCIX. The engineered, granular form of CST (UOP IE-911) was the baseline ion exchange material used for the initial development and design of the SRS SCIX process (McCabe, 2005). To date, in-tank SCIX has not been implemented for treatment of radioactive waste solutions at SRS. Since initial development and consideration of SCIX for SRS waste treatment an alternative technology has been developed as part of the River Protection Project Waste Treatment Plant (RPP-WTP) Research and Technology program (Thorson, 2006). Spherical RF resin is the baseline media for cesium removal in the RPP-WTP, which was designed for the treatment of radioactive waste supernates and is currently under construction in Hanford, WA. Application of RF for cesium removal in the Hanford WTP does not involve in-riser columns but does utilize the resin in large scale column configurations in a waste treatment facility. The basic conceptual design for SCIX involves the dissolution of saltcake in SRS Tanks 1-3 to give approximately 6 M sodium solutions and the treatment of these solutions for cesium removal using one or two columns supported within a high level waste tank. Prior to ion exchange treatment, the solutions will be filtered for removal of entrained solids. In addition to Tanks 1-3, solutions in two other tanks (37 and 41) will require treatment for cesium removal in the SCIX unit. The previous SCIX design (McCabe, 2005) utilized CST for cesium removal with downflow supernate processing and included a CST grinder following cesium loading. Grinding of CST was necessary to make the cesium-loaded material suitable for vitrification in the SRS Defense Waste Processing Facility (DWPF). Because RF resin is elutable (and reusable) and processing requires conversion between sodium and hydrogen forms using caustic and acidic solutions more liquid processing steps are involved. The WTP baseline process involves a series of caustic and acidic solutions (downflow processing) with water washes between pH transitions across neutral. In addition, due to resin swelling during conversion from hydrogen to sodium form an upflow caustic regeneration step is required. Presumably, one of these basic processes (or some variation) will be utilized for MSP for the appropriate ion exchange technology selected. CST processing involves two primary waste products: loaded CST and decontaminated salt solution (DSS). RF processing involves three primary waste products: spent RF resin, DSS, and acidic cesium eluate, although the resin is reusable and typically does not require replacement until completion of multiple treatment cycles. CST processing requires grinding of the ion exchange media, handling of solids with high cesium loading, and handling of liquid wash and conditioning solutions. RF processing requires handling and evaporation of cesium eluates, disposal of spent organic resin, and handling of the various liquid wash and regenerate solutions used. In both cases, the DSS will be immobilized in a low activity waste form. It appears that both technologies are mature, well studied, and generally suitable for this application. Technology selection will likely be based on downstream impacts or preferences between the various processing options for the two materials rather than on some unacceptable performance property identified for one material. As a result, the following detailed technical review and summary of the two technologies should be useful to assist in technology selection for SCIX.« less

SLUDGE TREATMENT PROJECT ENGINEERED CONTAINER RETRIEVAL AND TRANSFER SYSTEM PRELMINARY DESIGN HAZARD AND OPERABILITY STUDY

DOE Office of Scientific and Technical Information (OSTI.GOV)

CARRO CA

2011-07-15

This Hazard and Operability (HAZOP) study addresses the Sludge Treatment Project (STP) Engineered Container Retrieval and Transfer System (ECRTS) preliminary design for retrieving sludge from underwater engineered containers located in the 105-K West (KW) Basin, transferring the sludge as a sludge-water slurry (hereafter referred to as 'slurry') to a Sludge Transport and Storage Container (STSC) located in a Modified KW Basin Annex, and preparing the STSC for transport to T Plant using the Sludge Transport System (STS). There are six, underwater engineered containers located in the KW Basin that, at the time of sludge retrieval, will contain an estimated volumemore » of 5.2 m{sup 3} of KW Basin floor and pit sludge, 18.4 m{sup 3} of 105-K East (KE) Basin floor, pit, and canister sludge, and 3.5 m{sup 3} of settler tank sludge. The KE and KW Basin sludge consists of fuel corrosion products (including metallic uranium, and fission and activation products), small fuel fragments, iron and aluminum oxide, sand, dirt, operational debris, and biological debris. The settler tank sludge consists of sludge generated by the washing of KE and KW Basin fuel in the Primary Clean Machine. A detailed description of the origin of sludge and its chemical and physical characteristics can be found in HNF-41051, Preliminary STP Container and Settler Sludge Process System Description and Material Balance. In summary, the ECRTS retrieves sludge from the engineered containers and hydraulically transfers it as a slurry into an STSC positioned within a trailer-mounted STS cask located in a Modified KW Basin Annex. The slurry is allowed to settle within the STSC to concentrate the solids and clarify the supernate. After a prescribed settling period the supernate is decanted. The decanted supernate is filtered through a sand filter and returned to the basin. Subsequent batches of slurry are added to the STSC, settled, and excess supernate removed until the prescribed quantity of sludge is collected. The sand filter is then backwashed into the STSC. The STSC and STS cask are then inerted and transported to T Plant.« less

Test Report for Cesium and Solids Removal from an 11.5L Composite of Archived Hanford Double Shell Tank Supernate for Off-Site Disposal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doll, Stephanie R.; Cooke, Gary A.

The 222-S Laboratory blended supernate waste from Hanford Tanks 241-AN-101, 241-AN- 106, 241-AP-105, 241-AP-106, 241-AP-107, and 241-AY-101 from the hot cell archive to create a bulk composite. The composite was blended with 600 mL 19.4 M NaOH, which brought the total volume to approximately 11.5 L (3 gal). The composite was filtered to remove solids and passed through spherical resorcinol-formaldehyde ion-exchange resin columns to remove cesium. The composite masses were tracked as a treatability study. Samples collected before, during, and after the ion-exchange process were characterized for a full suite of analytes (inorganic, organic, and radionuclides) to aid in themore » classification of the waste for shipping, receiving, treatment, and disposal determinations.« less

Test Report for Cesium and Solids Removal from an 11.5L Composite of Archived Hanford Double Shell Tank Supernate for Off-Site Disposal.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doll, S. R.; Cooke, G. A.

The 222-S Laboratory blended supernate waste from Hanford Tanks 241-AN-101, 241-AN- 106, 241-AP-105, 241-AP-106, 241-AP-107, and 241-AY-101 from the hot cell archive to create a bulk composite. The composite was blended with 600 mL 19.4 M NaOH, which brought the total volume to approximately 11.5 L (3 gal). The composite was filtered to remove solids and passed through spherical resorcinol-formaldehyde ion-exchange resin columns to remove cesium. The composite masses were tracked as a treatability study. Samples collected before, during, and after the ion exchange process were characterized for a full suite of analytes (inorganic, organic, and radionuclides) to aid inmore » the classification of the waste for shipping, receiving, treatment, and disposal determinations.« less

TANK 26 EVAPORATOR FEED PUMP TRANSFER ANALYSIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamburello, D; Si Lee, S; Richard Dimenna, R

2008-09-30

The transfer of liquid salt solution from Tank 26 to an evaporator is to be accomplished by activating the evaporator feed pump, located approximately 72 inches above the sludge layer, while simultaneously turning on the downcomer. Previously, activation of the evaporator feed pump was an isolated event without any other components running at the same time. An analysis of the dissolved solution transfer has been performed using computational fluid dynamics methods to determine the amount of entrained sludge solids pumped out of the tank to the evaporator with the downcomer turned on. The analysis results showed that, for the maximummore » and minimum supernate levels in Tank 26 (252.5 and 72 inches above the sludge layer, respectively), the evaporator feed pump will entrain between 0.05 and 0.1 wt% sludge solids weight fraction into the eductor, respectively. Lower tank liquid levels, with respect to the sludge layer, result in higher amounts of sludge entrainment due to the increased velocity of the plunging jets from the downcomer and evaporator feed pump bypass as well as decreased dissipation depth.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, Renee L.; Fiskum, Sandra K.; Smoot, Margaret R.

Washington River Protection Solutions (WRPS) is developing a Low-Activity Waste Pretreatment System (LAWPS) to provide low-activity waste (LAW) directly to the Hanford Tank Waste Treatment and Immobilization Plant (WTP) Low-Activity Waste Facility for immobilization. The pretreatment that will be conducted on tank waste supernate at the LAWPS facility entails filtration to remove entrained solids and cesium (Cs) ion exchange to remove Cs from the product sent to the WTP. Currently, spherical resorcinol-formaldehyde (sRF) resin (Microbeads AS, Skedsmokorset, Norway) is the Cs ion exchange resin of choice. Most work on Cs ion exchange efficacy in Hanford tank waste has been conductedmore » at nominally 5 M sodium (Na). WRPS is examining the possibility of processing supernatant at high Na concentrations—up to 8 M Na—to maximize processing efficiency through the LAWPS. Minimal Cs ion exchange work has been conducted at 6 M and 8 M Na concentrations..« less

Prediction of stress corrosion of carbon steel by nuclear process liquid wastes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ondrejcin, R.S.

1978-08-01

Radioactive liquid wastes are produced as a consequence of processing fuel from Savannah River Plant (SRP) production reactors. These wastes are stored in mild steel waste tanks, some of which have developed cracks from stress corrosion. A laboratory test was developed to determine the relative agressiveness of the wastes for stress corrosion cracking of mild steel. Tensile samples were strained to fracture in synthetic waste solutions in an electrochemical cell with the sample as the anode. Crack initiation is expected if total elongation of the steel in the test is less than its uniform elongation in air. Cracking would bemore » anticipated in a plant waste tank if solution conditions were equivalent to test conditions that cause a total elongation that is less than uniform elongation. The electrochemical tensile tests showed that the supernates in salt receiver tanks at SRP have the least aggressive compositions, and wastes newly generated during fuel repocessing have the most aggressive ones. Test data also verified that ASTM A 516-70 steel used in the fabrication of the later design waste tanks is less susceptible to cracking than the ASTM A 285-B steel used in earlier designs.« less

Method for processing aqueous wastes

DOEpatents

Pickett, John B.; Martin, Hollis L.; Langton, Christine A.; Harley, Willie W.

1993-01-01

A method for treating waste water such as that from an industrial processing facility comprising the separation of the waste water into a dilute waste stream and a concentrated waste stream. The concentrated waste stream is treated chemically to enhance precipitation and then allowed to separate into a sludge and a supernate. The supernate is skimmed or filtered from the sludge and blended with the dilute waste stream to form a second dilute waste stream. The sludge remaining is mixed with cementitious material, rinsed to dissolve soluble components, then pressed to remove excess water and dissolved solids before being allowed to cure. The dilute waste stream is also chemically treated to decompose carbonate complexes and metal ions and then mixed with cationic polymer to cause the precipitated solids to flocculate. Filtration of the flocculant removes sufficient solids to allow the waste water to be discharged to the surface of a stream. The filtered material is added to the sludge of the concentrated waste stream. The method is also applicable to the treatment and removal of soluble uranium from aqueous streams, such that the treated stream may be used as a potable water supply.

Short communication: Improved method for centrifugal recovery of bacteria from raw milk applied to sensitive real-time quantitative PCR detection of Salmonella spp

USDA-ARS?s Scientific Manuscript database

Centrifugation of milk is widely used as a separation/concentration step in assays for pathogenic microorganisms. Separation of the cream and liquid supernate from the pellet containing sedimented solids, somatic cells and microorganisms eliminates many interfering substances, and resuspension of th...

Corrosion impact of reductant on DWPF and downstream facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mickalonis, J. I.; Imrich, K. J.; Jantzen, C. M.

2014-12-01

Glycolic acid is being evaluated as an alternate reductant in the preparation of high level waste for the Defense Waste Processing Facility (DWPF) at the Savannah River Site (SRS). During processing, the glycolic acid is not completely consumed and small quantities of the glycolate anion are carried forward to other high level waste (HLW) facilities. The impact of the glycolate anion on the corrosion of the materials of construction throughout the waste processing system has not been previously evaluated. A literature review had revealed that corrosion data in glycolate-bearing solution applicable to SRS systems were not available. Therefore, testing wasmore » recommended to evaluate the materials of construction of vessels, piping and components within DWPF and downstream facilities. The testing, conducted in non-radioactive simulants, consisted of both accelerated tests (electrochemical and hot-wall) with coupons in laboratory vessels and prototypical tests with coupons immersed in scale-up and mock-up test systems. Eight waste or process streams were identified in which the glycolate anion might impact the performance of the materials of construction. These streams were 70% glycolic acid (DWPF feed vessels and piping), SRAT/SME supernate (Chemical Processing Cell (CPC) vessels and piping), DWPF acidic recycle (DWPF condenser and recycle tanks and piping), basic concentrated recycle (HLW tanks, evaporators, and transfer lines), salt processing (ARP, MCU, and Saltstone tanks and piping), boric acid (MCU separators), and dilute waste (HLW evaporator condensate tanks and transfer line and ETF components). For each stream, high temperature limits and worst-case glycolate concentrations were identified for performing the recommended tests. Test solution chemistries were generally based on analytical results of actual waste samples taken from the various process facilities or of prototypical simulants produced in the laboratory. The materials of construction for most vessels, components and piping were not impacted with the presence of glycolic acid or the impact is not expected to affect the service life. However, the presence of the glycolate anion was found to affect corrosion susceptibility of some materials of construction in the DWPF and downstream facilities, especially at elevated temperatures. The following table summarizes the results of the electrochemical and hot wall testing and indicates expected performance in service with the glycolate anion present.« less

Hanford Waste Physical and Rheological Properties: Data and Gaps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wells, Beric E.; Kurath, Dean E.; Mahoney, Lenna A.

2011-08-01

The Hanford Site in Washington State manages 177 underground storage tanks containing approximately 250,000 m3 of waste generated during past defense reprocessing and waste management operations. These tanks contain a mixture of sludge, saltcake and supernatant liquids. The insoluble sludge fraction of the waste consists of metal oxides and hydroxides and contains the bulk of many radionuclides such as the transuranic components and 90Sr. The saltcake, generated by extensive evaporation of aqueous solutions, consists primarily of dried sodium salts. The supernates consist of concentrated (5-15 M) aqueous solutions of sodium and potassium salts. The 177 storage tanks include 149 single-shellmore » tanks (SSTs) and 28 double -hell tanks (DSTs). Ultimately the wastes need to be retrieved from the tanks for treatment and disposal. The SSTs contain minimal amounts of liquid wastes, and the Tank Operations Contractor is continuing a program of moving solid wastes from SSTs to interim storage in the DSTs. The Hanford DST system provides the staging location for waste feed delivery to the Department of Energy (DOE) Office of River Protection’s (ORP) Hanford Tank Waste Treatment and Immobilization Plant (WTP). The WTP is being designed and constructed to pretreat and then vitrify a large portion of the wastes in Hanford’s 177 underground waste storage tanks.« less

TANK 32 EVAPORATOR FEED PUMP TRANSFER ANALYSIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamburello, D; Richard Dimenna, R; Si Lee, S

2009-01-27

The transfer of liquid salt solution from Tank 32 to an evaporator is to be accomplished by activating the evaporator feed pump, with the supernate surface at a minimum height of approximately 74.4 inches above the sludge layer, while simultaneously turning on the downcomer with a flow rate of 110 gpm. Previously, activation of the evaporator feed pump was an isolated event without any other components running at the same time. An analysis of the dissolved solution transfer has been performed using computational fluid dynamics (CFD) methods to determine the amount of entrained sludge solids pumped out of the tankmore » toward the evaporator with the downcomer turned on. The analysis results shows that, for the minimum tank liquid level of 105 inches above the tank bottom (which corresponds to a liquid depth of 74.4 inches above the sludge layer), the evaporator feed pump will contain less than 0.1 wt% sludge solids in the discharge stream, which is an order of magnitude less than the 1.0 wt% undissolved solids (UDS) loading criteria to feed the evaporator. Lower liquid levels with respect to the sludge layer will result in higher amounts of sludge entrainment due to the increased plunging jet velocity from the downcomer disturbing the sludge layer.« less

SLUDGE WASHING AND DEMONSTRATION OF THE DWPF FLOWSHEET IN THE SRNL SHIELDED CELLS FOR SLUDGE BATCH 7A QUALIFICATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pareizs, J.; Billings, A.; Click, D.

2011-07-08

Waste Solidification Engineering (WSE) has requested that characterization and a radioactive demonstration of the next batch of sludge slurry (Sludge Batch 7a*) be completed in the Shielded Cells Facility of the Savannah River National Laboratory (SRNL) via a Technical Task Request (TTR). This characterization and demonstration, or sludge batch qualification process, is required prior to transfer of the sludge from Tank 51 to the Defense Waste Processing Facility (DWPF) feed tank (Tank 40). The current WSE practice is to prepare sludge batches in Tank 51 by transferring sludge from other tanks. Discharges of nuclear materials from H Canyon are oftenmore » added to Tank 51 during sludge batch preparation. The sludge is washed and transferred to Tank 40, the current DWPF feed tank. Prior to transfer of Tank 51 to Tank 40, SRNL simulates the Tank Farm and DWPF processes with a Tank 51 sample (referred to as the qualification sample). Sludge Batch 7a (SB7a) is composed of portions of Tanks 4, 7, and 12; the Sludge Batch 6 heel in Tank 51; and a plutonium stream from H Canyon. SRNL received the Tank 51 qualification sample (sample ID HTF-51-10-125) following sludge additions to Tank 51. This report documents: (1) The washing (addition of water to dilute the sludge supernate) and concentration (decanting of supernate) of the SB7a - Tank 51 qualification sample to adjust sodium content and weight percent insoluble solids to Tank Farm projections. (2) The performance of a DWPF Chemical Process Cell (CPC) simulation using the washed Tank 51 sample. The simulation included a Sludge Receipt and Adjustment Tank (SRAT) cycle, where acid was added to the sludge to destroy nitrite and reduce mercury, and a Slurry Mix Evaporator (SME) cycle, where glass frit was added to the sludge in preparation for vitrification. The SME cycle also included replication of five canister decontamination additions and concentrations. Processing parameters were based on work with a non-radioactive simulant. (3) Vitrification of a portion of the SME product and characterization and durability testing (as measured by the Product Consistency Test (PCT)) of the resulting glass. (4) Rheology measurements of the initial slurry samples and samples after each phase of CPC processing. This program was controlled by a Task Technical and Quality Assurance Plan (TTQAP), and analyses were guided by an Analytical Study Plan. This work is Technical Baseline Research and Development (R&D) for the DWPF. It should be noted that much of the data in this document has been published in interoffice memoranda. The intent of this technical report is bring all of the SB7a related data together in a single permanent record and to discuss the overall aspects of SB7a processing.« less

Experimental Determination and Thermodynamic Modeling of Electrical Conductivity of SRS Waste Tank Supernate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pike, J.; Reboul, S.

2015-06-01

SRS High Level Waste Tank Farm personnel rely on conductivity probes for detection of incipient overflow conditions in waste tanks. Minimal information is available concerning the sensitivity that must be achieved such that that liquid detection is assured. Overly sensitive electronics results in numerous nuisance alarms for these safety-related instruments. In order to determine the minimum sensitivity required of the probe, Tank Farm Engineering personnel need adequate conductivity data to improve the existing designs. Little or no measurements of liquid waste conductivity exist; however, the liquid phase of the waste consists of inorganic electrolytes for which the conductivity may bemore » calculated. Savannah River Remediation (SRR) Tank Farm Facility Engineering requested SRNL to determine the conductivity of the supernate resident in SRS waste Tank 40 experimentally as well as computationally. In addition, SRNL was requested to develop a correlation, if possible, that would be generally applicable to liquid waste resident in SRS waste tanks. A waste sample from Tank 40 was analyzed for composition and electrical conductivity as shown in Table 4-6, Table 4-7, and Table 4-9. The conductivity for undiluted Tank 40 sample was 0.087 S/cm. The accuracy of OLI Analyzer™ was determined using available literature data. Overall, 95% of computed estimates of electrical conductivity are within ±15% of literature values for component concentrations from 0 to 15 M and temperatures from 0 to 125 °C. Though the computational results are generally in good agreement with the measured data, a small portion of literature data deviates as much as ±76%. A simplified model was created that can be used readily to estimate electrical conductivity of waste solution in computer spreadsheets. The variability of this simplified approach deviates up to 140% from measured values. Generally, this model can be applied to estimate the conductivity within a factor of two. The comparison of the simplified model to pure component literature data suggests that the simplified model will tend to under estimate the electrical conductivity. Comparison of the computed Tank 40 conductivity with the measured conductivity shows good agreement within the range of deviation identified based on pure component literature data.« less

Lipoprotein Agarose Gel Electrophoresis. Application in HDL-Cholesterol Methodology.

DTIC Science & Technology

1985-06-01

on determination of high-density lipo- protein cholesterol by precipitation with sodium phosphotungstate- magnesium. Clin Chem 25(4):560 (1979). 6...determinations of cholesterol levels in supernates obtained after addition of various amounts of precipitants , lipo- protein electrophoresis can help to...plotted against the corresponding volumes of sodium phosphotungstate-MgCl2 (NAPT) precipitant added. 10 ’ ’’ ’i - n

Method for processing aqueous wastes

DOEpatents

Pickett, J.B.; Martin, H.L.; Langton, C.A.; Harley, W.W.

1993-12-28

A method is presented for treating waste water such as that from an industrial processing facility comprising the separation of the waste water into a dilute waste stream and a concentrated waste stream. The concentrated waste stream is treated chemically to enhance precipitation and then allowed to separate into a sludge and a supernate. The supernate is skimmed or filtered from the sludge and blended with the dilute waste stream to form a second dilute waste stream. The sludge remaining is mixed with cementitious material, rinsed to dissolve soluble components, then pressed to remove excess water and dissolved solids before being allowed to cure. The dilute waste stream is also chemically treated to decompose carbonate complexes and metal ions and then mixed with cationic polymer to cause the precipitated solids to flocculate. Filtration of the flocculant removes sufficient solids to allow the waste water to be discharged to the surface of a stream. The filtered material is added to the sludge of the concentrated waste stream. The method is also applicable to the treatment and removal of soluble uranium from aqueous streams, such that the treated stream may be used as a potable water supply. 4 figures.

Glycolic acid physical properties and impurities assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lambert, D. P.; Pickenheim, B. R.; Bibler, N. E.

This document has been revised due to recent information that the glycolic acid used in Savannah River National Laboratory (SRNL) experiments contains both formaldehyde and methoxyacetic acid. These impurities were in the glycolic acid used in the testing included in this report and in subsequent testing using DuPont (now called Chemours) supplied Technical Grade 70 wt% glycolic acid. However, these impurities were not reported in earlier revisions. Additional data concerning the properties of glycolic acid have also been added to this report. The Defense Waste Processing Facility (DWPF) is planning to implement a nitric-glycolic acid flowsheets to increase attainment tomore » meet closure commitment dates during Sludge Batch 9. In fiscal year 2009, SRNL was requested to determine the physical properties of formic and glycolic acid blends. Blends of formic acid in glycolic acid were prepared and their physical properties tested. Increasing amounts of glycolic acid led to increases in blend density, viscosity and surface tension as compared to the 90 wt% formic acid that is currently used at DWPF. These increases are small, however, and are not expected to present any difficulties in terms of processing. The effect of sulfur impurities in Technical Grade glycolic acid was studied for its impact on DWPF glass quality. While the glycolic acid specification allows for more sulfate than the current formic acid specification, the ultimate impact is expected to be on the order of 0.033 wt% sulfur in glass. Note that lower sulfur content glycolic acid could likely be procured at some increased cost if deemed necessary. A paper study on the effects of radiation on glycolic acid was performed. The analysis indicates that substitution of glycolic acid for formic acid would not increase the radiolytic production rate of H2 and cause an adverse effect in the Slurry Receipt and Adjustment Tank (SRAT) or Slurry Mix Evaporator (SME) process. It has been cited that glycolic acid solutions that are depleted of O2 when subjected to large radiation doses produced considerable quantities of a non-diffusive polymeric material. Considering a constant air purge is maintained in the SRAT and the solution is continuously mixed, oxygen depletion seems unlikely, however, if this polymer is formed in the SRAT solution, the rheology of the solution may be affected and pumping of the solution may be hindered. However, an irradiation test with a simulated SRAT product supernate containing glycolic acid in an oxygen depleted atmosphere found no evidence of polymerization.« less

Microdetermination of Sucrose in Plasma with the Anthrone Reagent.

DTIC Science & Technology

1979-11-01

polysaccharides . The initial attempts to use it for selective determinations of monosaccharides in a mixture, however, were frustrated by a mutual...disaccharides and polysaccharides are hydrolyzed to form monosaccharides . In addition, water is split off from the latter to form hydroxaldehyde...supernate were then concentrated to dryness at 80 C with a manifold evaporator after which endogenous monosaccharides were destroyed by the addition of

Description of Defense Waste Processing Facility reference waste form and canister. Revision 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baxter, R.G.

1983-08-01

The Defense Waste Processing Facility (DWPF) will be located at the Savannah River Plant in Aiken, SC, and is scheduled for construction authorization during FY-1984. The reference waste form is borosilicate glass containing approx. 28 wt % sludge oxides, with the balance glass frit. Borosilicate glass was chosen because of its high resistance to leaching by water, its relatively high solubility for nuclides found in the sludge, and its reasonably low melting temperature. The glass frit contains about 58% SiO/sub 2/ and 15% B/sub 2/O/sub 3/. Leachabilities of SRP waste glasses are expected to approach 10/sup -8/ g/m/sup 2/-day basedmore » upon 1000-day tests using glasses containing SRP radioactive waste. Tests were performed under a wide variety of conditions simulating repository environments. The canister is filled with 3260 lb of glass which occupies about 85% of the free canister volume. The filled canister will generate approx. 470 watts when filled with oxides from 5-year-old sludge and 15-year-old supernate from the sludge and supernate processes. The radionuclide content of the canister is about 177,000 ci, with a radiation level of 5500 rem/h at canister surface contact. The reference canister is fabricated of standard 24-in.-OD, Schedule 20, 304L stainless steel pipe with a dished bottom, domed head, and a combined lifting and welding flange on the head neck. The overall canister length is 9 ft 10 in. with a 3/8-in. wall thickness. The 3-m canister length was selected to reduce equipment cell height in the DWPF to a practical size. The canister diameter was selected as an optimum size from glass quality considerations, a logical size for repository handling and to ensure that a filled canister with its double containment shipping cask could be accommodated on a legal-weight truck. The overall dimensions and weight appear to be compatible with preliminary assessments of repository requirements. 10 references.« less

Induction, transcription, synthesis, and adsorption of interleukin-1 by dialyzer membranes.

PubMed

Vaziri, N D; Wang, J; Cesario, T; Yousefi, S; Valenzuela, R; Carandang, G

1994-05-01

This study was designed to dissect the direct effect of dialyzer membrane on interleukin-1 (IL-1) induction from those of complement activation, mechanical stimulation, acetate/bicarbonate and endotoxin diffusion, and cell type interactions. To this end, a suspension of P388D1 murine macrophages in a complement-free culture medium containing 10% heat-inactivated serum, a closed-loop system consisting of tubing alone or with a hollow-fiber cuprammonium cellulose (CU) or polyacrylonitrile (PAN) dialyzer, and a roller pump were used. The dialysate compartment was filled with the same medium and capped. Cell suspension was recirculated at 300 mL/min for 3 h. Cells and supernates were separated, and adhering proteins were eluted. All samples tested negative for endotoxin. IL-1 mRNA was greatest with CU, followed by PAN and tubing alone. IL-1 in the supernate was greater with CU than with either tubing alone or PAN (P < 0.005; analysis of variance), which showed comparable values. IL-1 eluted from loops was greatest with PAN dialyzers, followed by sets with CU dialyzers and tubing alone (P < 0.001; analysis of variance). Thus, both CU and PAN membranes directly induce IL-1. However, avid adsorption by PAN attenuates the rise in circulating IL-1.

Dose potential of sludge contaminated and/or TRU contaminated waste in B-25s for tornado and straight wind events

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aponte, C.I.

F and H Tank Farms generate supernate and sludge contaminated Low-Level Waste. The waste is collected, characterized, and packaged for disposal. Before the waste can be disposed of, however, it must be properly characterized. Since the radionuclide distribution in typical supernate is well known, its characterization is relatively straight forward and requires minimal effort. Non-routine waste, including potentially sludge contaminated, requires much more effort to effectively characterize. The radionuclide distribution must be determined. In some cases the waste can be contaminated by various sludge transfers with unique radionuclide distributions. In these cases, the characterization can require an extensive effort. Evenmore » after an extensive characterization effort, the container must still be prepared for shipping. Therefore a significant amount of time may elapse from the time the waste is generated until the time of disposal. During the time it is possible for a tornado or high wind scenario to occur. The purpose of this report is to determine the effect of a tornado on potential sludge contaminated waste, or Transuranic (TRU) waste in B-25s [large storage containers], to evaluate the potential impact on F and H Tank Farms, and to help establish a B-25 control program for tornado events.« less

Low melting high lithia glass compositions and methods

DOEpatents

Jantzen, Carol M.; Pickett, John B.; Cicero-Herman, Connie A.; Marra, James C.

2004-11-02

The invention relates to methods of vitrifying waste and for lowering the melting point of glass forming systems by including lithia formers in the glass forming composition in significant amounts, typically from about 0.16 wt % to about 11 wt %, based on the total glass forming oxides. The lithia is typically included as a replacement for alkali oxide glass formers that would normally be present in a particular glass forming system. Replacement can occur on a mole percent or weight percent basis, and typically results in a composition wherein lithia forms about 10 wt % to about 100 wt % of the alkali oxide glass formers present in the composition. The present invention also relates to the high lithia glass compositions formed by these methods. The invention is useful for stabilization of numerous types of waste materials, including aqueous waste streams, sludge solids, mixtures of aqueous supernate and sludge solids, combinations of spent filter aids from waste water treatment and waste sludges, supernate alone, incinerator ash, incinerator offgas blowdown, or combinations thereof, geological mine tailings and sludges, asbestos, inorganic filter media, cement waste forms in need of remediation, spent or partially spent ion exchange resins or zeolites, contaminated soils, lead paint, etc. The decrease in melting point achieved by the present invention desirably prevents volatilization of hazardous or radioactive species during vitrification.

Low melting high lithia glass compositions and methods

DOEpatents

Jantzen, Carol M.; Pickett, John B.; Cicero-Herman, Connie A.; Marra, James C.

2003-10-07

The invention relates to methods of vitrifying waste and for lowering the melting point of glass forming systems by including lithia formers in the glass forming composition in significant amounts, typically from about 0.16 wt % to about 11 wt %, based on the total glass forming oxides. The lithia is typically included as a replacement for alkali oxide glass formers that would normally be present in a particular glass forming system. Replacement can occur on a mole percent or weight percent basis, and typically results in a composition wherein lithia forms about 10 wt % to about 100 wt % of the alkali oxide glass formers present in the composition. The present invention also relates to the high lithia glass compositions formed by these methods. The invention is useful for stabilization of numerous types of waste materials, including aqueous waste streams, sludge solids, mixtures of aqueous supernate and sludge solids, combinations of spent filter aids from waste water treatment and waste sludges, supernate alone, incinerator ash, incinerator offgas blowdown, or combinations thereof, geological mine tailings and sludges, asbestos, inorganic filter media, cement waste forms in need of remediation, spent or partially spent ion exchange resins or zeolites, contaminated soils, lead paint, etc. The decrease in melting point achieved by the present invention desirably prevents volatilization of hazardous or radioactive species during vitrification.

Low melting high lithia glass compositions and methods

DOEpatents

Jantzen, Carol M.; Pickett, John B.; Cicero-Herman, Connie A.; Marra, James C.

2000-01-01

The invention relates to methods of vitrifying waste and for lowering the melting point of glass forming systems by including lithia formers in the glass forming composition in significant amounts, typically from about 0.16 wt % to about 11 wt %, based on the total glass forming oxides. The lithia is typically included as a replacement for alkali oxide glass formers that would normally be present in a particular glass forming system. Replacement can occur on a mole percent or weight percent basis, and typically results in a composition wherein lithia forms about 10 wt % to about 100 wt % of the alkali oxide glass formers present in the composition. The present invention also relates to the high lithia glass compositions formed by these methods. The invention is useful for stabilization of numerous types of waste materials, including aqueous waste streams, sludge solids, mixtures of aqueous supernate and sludge solids, combinations of spent filter aids from waste water treatment and waste sludges, supernate alone, incinerator ash, incinerator offgas blowdown, or combinations thereof, geological mine tailings and sludges, asbestos, inorganic filter media, cement waste forms in need of remediation, spent or partially spent ion exchange resins or zeolites, contaminated soils, lead paint, etc. The decrease in melting point achieved by the present invention desirably prevents volatilization of hazardous or radioactive species during vitrification.

Methods of vitrifying waste with low melting high lithia glass compositions

DOEpatents

Jantzen, Carol M.; Pickett, John B.; Cicero-Herman, Connie A.; Marra, James C.

2001-01-01

The invention relates to methods of vitrifying waste and for lowering the melting point of glass forming systems by including lithia formers in the glass forming composition in significant amounts, typically from about 0.16 wt % to about 11 wt %, based on the total glass forming oxides. The lithia is typically included as a replacement for alkali oxide glass formers that would normally be present in a particular glass forming system. Replacement can occur on a mole percent or weight percent basis, and typically results in a composition wherein lithia forms about 10 wt % to about 100 wt % of the alkali oxide glass formers present in the composition. The present invention also relates to the high lithia glass compositions formed by these methods. The invention is useful for stabilization of numerous types of waste materials, including aqueous waste streams, sludge solids, mixtures of aqueous supernate and sludge solids, combinations of spent filter aids from waste water treatment and waste sludges, supernate alone, incinerator ash, incinerator offgas blowdown, or combinations thereof, geological mine tailings and sludges, asbestos, inorganic filter media, cement waste forms in need of remediation, spent or partially spent ion exchange resins or zeolites, contaminated soils, lead paint, etc. The decrease in melting point achieved by the present invention desirably prevents volatilization of hazardous or radioactive species during vitrification.

Preliminary technical data summary No. 3 for the Defense Waste Processing Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Landon, L.F.

1980-05-01

This document presents an update on the best information presently available for the purpose of establishing the basis for the design of a Defense Waste Processing Facility. Objective of this project is to provide a facility to fix the radionuclides present in Savannah River Plant (SRP) high-level liquid waste in a high-integrity form (glass). Flowsheets and material balances reflect the alternate CAB case including the incorporation of low-level supernate in concrete. (DLC)

THE HYDROTHERMAL REACTIONS OF MONOSODIUM TITANATE, CRYSTALLINE SILICOTITANATE AND SLUDGE IN THE MODULAR SALT PROCESS: A LITERATURE SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fondeur, F.; Pennebaker, F.; Fink, S.

2010-11-11

The use of crystalline silicotitanate (CST) is proposed for an at-tank process to treat High Level Waste at the Savannah River Site. The proposed configuration includes deployment of ion exchange columns suspended in the risers of existing tanks to process salt waste without building a new facility. The CST is available in an engineered form, designated as IE-911-CW, from UOP. Prior data indicates CST has a proclivity to agglomerate from deposits of silica rich compounds present in the alkaline waste solutions. This report documents the prior literature and provides guidance for the design and operations that include CST to mitigatemore » that risk. The proposed operation will also add monosodium titanate (MST) to the supernate of the tank prior to the ion exchange operation to remove strontium and select alpha-emitting actinides. The cesium loaded CST is ground and then passed forward to the sludge washing tank as feed to the Defense Waste Processing Facility (DWPF). Similarly, the MST will be transferred to the sludge washing tank. Sludge processing includes the potential to leach aluminum from the solids at elevated temperature (e.g., 65 C) using concentrated (3M) sodium hydroxide solutions. Prior literature indicates that both CST and MST will agglomerate and form higher yield stress slurries with exposure to elevated temperatures. This report assessed that data and provides guidance on minimizing the impact of CST and MST on sludge transfer and aluminum leaching sludge.« less

Tank 26 Evaporator Feed Pump Transfer Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamburello, David; Dimenna, Richard; Lee, Si

2009-02-11

The transfer of liquid salt solution from Tank 26 to an evaporator is to be accomplished by activating the evaporator feed pump, located approximately 72 inches above the sludge layer, while simultaneously turning on the downcomer. Previously, activation of the evaporator feed pump was an isolated event without any other components running at the same time. An analysis of the dissolved solution transfer has been performed using computational fluid dynamics methods to determine the amount of entrained sludge solids pumped out of the tank to the evaporator with the downcomer turned on. The analysis results showed that, for the maximummore » and minimum supernate levels in Tank 26 (252.5 and 72 inches above the sludge layer, respectively), the evaporator feed pump will entrain between 0.03 and 0.1 wt% sludge undissolved solids weight fraction into the eductor, respectively, and therefore are an order of magnitude less than the 1.0 wt% undissolved solids loading criteria to feed the evaporator. Lower tank liquid levels, with respect to the sludge layer, result in higher amounts of sludge entrainment due to the increased velocity of the plunging jets from the downcomer and evaporator feed pump bypass as well as decreased dissipation depth. Revision 1 clarifies the analysis presented in Revision 0 and corrects a mathematical error in the calculations for Table 4.1 in Revision 0. However, the conclusions and recommendations of the analysis do not change for Revision 1.« less

Nuclear criticality safety bounding analysis for the in-tank-precipitation (ITP) process, impacted by fissile isotopic weight fractions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bess, C.E.

The In-Tank Precipitation process (ITP) receives High Level Waste (HLW) supernatant liquid containing radionuclides in waste processing tank 48H. Sodium tetraphenylborate, NaTPB, and monosodium titanate (MST), NaTi{sub 2}O{sub 5}H, are added for removal of radioactive Cs and Sr, respectively. In addition to removal of radio-strontium, MST will also remove plutonium and uranium. The majority of the feed solutions to ITP will come from the dissolution of supernate that had been concentrated by evaporation to a crystallized salt form, commonly referred to as saltcake. The concern for criticality safety arises from the adsorption of U and Pt onto MST. If sufficientmore » mass and optimum conditions are achieved then criticality is credible. The concentration of u and Pt from solution into the smaller volume of precipitate represents a concern for criticality. This report supplements WSRC-TR-93-171, Nuclear Criticality Safety Bounding Analysis For The In-Tank-Precipitation (ITP) Process. Criticality safety in ITP can be analyzed by two bounding conditions: (1) the minimum safe ratio of MST to fissionable material and (2) the maximum fissionable material adsorption capacity of the MST. Calculations have provided the first bounding condition and experimental analysis has established the second. This report combines these conditions with canyon facility data to evaluate the potential for criticality in the ITP process due to the adsorption of the fissionable material from solution. In addition, this report analyzes the potential impact of increased U loading onto MST. Results of this analysis demonstrate a greater safety margin for ITP operations than the previous analysis. This report further demonstrates that the potential for criticality in the ITP process due to adsorption of fissionable material by MST is not credible.« less

Titration of Serum Lipoproteins with Lipoprotein Precipitants.

DTIC Science & Technology

1981-12-01

Lipid Res 11:583 (1970). 6. Grove, T. H. Effect of reagent pH on determination of high-density lipo- protein cholesterol by precipitation with sodium ...of choles- terol in the supernate plateaued at 43 mg/dl after the beta and prebeta lipo- proteins had been precipitated . The intensities of the two...AD-A113 370 SCHOOL OF AEROSPACE MEDICINE BROOKS AFS TX F/S 6/1 TITRATION OF SERU’LIPOPROTEINS WITH LIPOPROTEIN PRECIPITANTS .(Ul DEC 81 0 A CLARK. J A

Safety of Immunogenicity Testing of a Pilot Polysaccharide Vaccine Preparation to Pseudomonas aeruginosa.

DTIC Science & Technology

1980-09-01

Pilot Polysaccharide Vaccine Preparation to Pseudomonas Aeruginosa .°’. SafGetad uoenct Testin ofaPio.PDsa.ard e(For p ri d 16 August 1979 to 15 August...Immunogenicity Testing of a Pilot Annual Report Polysaccharide Vaccine Preparation to (16 Aug. 79 - 15 Auj. 80) Pseudomonas Aeruginosa 6. PERFORMING ORG. REPORT...qiit polysaccharide (PS) maLerial isolated from Lhe ouit e _l Aace or, cultural supernates of P. ae ruginosa (i) . in it tyl , ; I m W" "des have

Technologies of stage magic: Simulation and dissimulation.

PubMed

Smith, Wally

2015-06-01

The craft of stage magic is presented in this article as a site to study the interplay of people and technology. The focus is on conjuring in the 19th and early 20th centuries, a time when magicians eagerly appropriated new optical, mechanical and electrical technologies into their acts. Also at this time, a modern style of conjuring emerged, characterized by minimal apparatus and a natural manner of performance. Applying Lucy Suchman's perspective of human-machine reconfigurations, conjuring in this modern style is interpreted as an early form of simulation, coupled with techniques of dissimulation. Magicians simulated the presence of supernational agency for public audiences, while dissimulating the underlying methods and mechanisms. Dissimulation implies that the secret inner workings of apparatus were not simply concealed but were rendered absent. This, in turn, obscured the production of supernatural effects in the translation of agencies within an assembly of performers, assistants, apparatus, apparatus-builders, and so on. How this was achieved is investigated through an analysis of key instructional texts written by and for magicians working in the modern style. Techniques of dissimulation are identified in the design of apparatus for three stage illusions, and in the new naturalness of the performer's manner. To explore the significance of this picture of stage magic, and its reliance on techniques of dissimulation, a parallel is drawn between conjuring and recent performances of computerized life forms, especially those of social robotics. The paper concludes by considering what is revealed about the production of agency in stage magic's peculiar human-machine assemblies.

MST Filterability Tests

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poirier, M. R.; Burket, P. R.; Duignan, M. R.

2015-03-12

The Savannah River Site (SRS) is currently treating radioactive liquid waste with the Actinide Removal Process (ARP) and the Modular Caustic Side Solvent Extraction Unit (MCU). The low filter flux through the ARP has limited the rate at which radioactive liquid waste can be treated. Recent filter flux has averaged approximately 5 gallons per minute (gpm). Salt Batch 6 has had a lower processing rate and required frequent filter cleaning. Savannah River Remediation (SRR) has a desire to understand the causes of the low filter flux and to increase ARP/MCU throughput. In addition, at the time the testing started, SRRmore » was assessing the impact of replacing the 0.1 micron filter with a 0.5 micron filter. This report describes testing of MST filterability to investigate the impact of filter pore size and MST particle size on filter flux and testing of filter enhancers to attempt to increase filter flux. The authors constructed a laboratory-scale crossflow filter apparatus with two crossflow filters operating in parallel. One filter was a 0.1 micron Mott sintered SS filter and the other was a 0.5 micron Mott sintered SS filter. The authors also constructed a dead-end filtration apparatus to conduct screening tests with potential filter aids and body feeds, referred to as filter enhancers. The original baseline for ARP was 5.6 M sodium salt solution with a free hydroxide concentration of approximately 1.7 M.3 ARP has been operating with a sodium concentration of approximately 6.4 M and a free hydroxide concentration of approximately 2.5 M. SRNL conducted tests varying the concentration of sodium and free hydroxide to determine whether those changes had a significant effect on filter flux. The feed slurries for the MST filterability tests were composed of simple salts (NaOH, NaNO 2, and NaNO 3) and MST (0.2 – 4.8 g/L). The feed slurry for the filter enhancer tests contained simulated salt batch 6 supernate, MST, and filter enhancers.« less

Influence of tube type, storage time, and temperature on the total and free concentration of valproic acid.

PubMed

Tarasidis, C G; Garnett, W R; Kline, B J; Pellock, J M

1986-01-01

The influence of storage conditions on the total and free concentration of valproic acid (VPA) was studied in six normal male subjects who ingested 750 mg of VPA (3 X 250 mg Depakene capsules; Abbott Laboratories). Blood samples were collected in various types of Vacutainer tubes (red top, no additives; green top, sodium heparin; blue top, sodium citrate; and purple top, EDTA) 2 h post administration of VPA. Either these samples were centrifuged immediately or stored for various periods of time at room temperature or refrigerated, or the supernate was frozen prior to analysis. Free VPA samples were obtained utilizing the Amicon ultrafiltration system. All VPA samples were analyzed by gas-liquid chromatography. Total VPA concentrations obtained from plasma collected with sodium citrate were lower (p less than 0.05) than either serum or plasma collected with other anticoagulants. There were no differences (p greater than 0.05) in total or free VPA concentrations between samples collected in serum or in plasma collected with heparin or EDTA. Storing samples for 96 h at room temperature did not alter the total VPA concentrations but was found to increase the free fraction of VPA (p less than 0.05). The refrigeration or freezing of the supernate from the blood samples for 7 days did not alter (p greater than 0.05) the total or the free fraction of VPA. The results of this study demonstrate that total and/or free VPA may be collected from either serum or plasma, provided sodium citrate is not used to collect plasma.(ABSTRACT TRUNCATED AT 250 WORDS)

Investigation of Plutonium and Uranium Precipitation Behavior with Gadolinium as a Neutron Poison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Visser, A.E.

2003-10-17

The caustic precipitation of plutonium (Pu)-containing solutions has been investigated to determine whether the presence of 3:1 uranium (U):Pu in solutions stored in the H-Canyon Facility at the U.S. Department of Energy's (DOE) Savannah River Site (SRS) would adversely impact the use of gadolinium nitrate (Gd(NO3)3) as a neutron poison. In the past, this disposition strategy has been successfully used to discard solutions containing approximately 100 kg of Pu to the SRS high level waste (HLW) system. In the current experiments, gadolinium (as Gd(NO3)3) was added to samples of a 3:1 U:Pu solution, a surrogate 3 g/L U solution, andmore » a surrogate 3 g/L U with 1 g/L Pu solution. A series of experiments was then performed to observe and characterize the precipitate at selected pH values. Solids formed at pH 4.5 and were found to contain at least 50 percent of the U and 94 percent of the Pu, but only 6 percent of the Gd. As the pH of the solution increased (e.g., pH greater than 14 with 1.2 or 3.6 M sodium hydroxide (NaOH) excess), the precipitate contained greater than 99 percent of the Pu, U, and Gd. After the pH greater than 14 systems were undisturbed for one week, no significant changes were found in the composition of the solid or supernate for each sample. The solids were characterized by X-ray diffraction (XRD) which found sodium diuranate (Na2U2O7) and gadolinium hydroxide (Gd(OH)3) at pH 14. Thermal gravimetric analysis (TGA) indicated sufficient water molecules were present in the solids to thermalize the neutrons, a requirement for the use of Gd as a neutron poison. Scanning electron microscopy (SEM) was also performed and the accompanying back-scattering electron analysis (BSE) found Pu, U, and Gd compounds in all pH greater than 14 precipitate samples. The rheological properties of the slurries at pH greater than 14 were also investigated by performing precipitate settling rate studies and measuring the viscosity and density of the materials. Based on the results of these experiments, poisoning the Pu-U solutions with Gd and subsequent neutralization is a viable process for discarding the Pu to the SRS HLW system.« less

Efficacy and mechanisms of non-antibacterial, chemical plaque control by dentifrices--an in vitro study.

PubMed

Busscher, Henk J; White, Don J; Atema-Smit, Jelly; van der Mei, Henny C

2007-04-01

The provision of antiplaque benefits to dentifrices assists patients in improving hygiene and reducing susceptibility to gingivitis and caries. Chemical plaque control involves different mechanisms and is mostly associated with antibacterial effects, but also includes effects on pellicle surface chemistry to improve cleansing or discourage renewed plaque formation. It is the aim of this paper to analyze in vitro detachment of co-aggregating oral actinomyces and streptococci from pellicle surfaces by dentifrice supernates and to study subsequent de novo streptococcal deposition. Detachment by dentifrices of a co-adhering bacterial pair was studied in the parallel plate flow chamber on a 16 h pellicle coated surface. After detachment by perfusing the chamber with a dentifrice, re-deposition was initiated by flowing with a fresh streptococcal suspension. The dentifrices included both a regular, SLS-fluoride based formulation as well a pyrophosphate, anticalculus and antimicrobial formulations. All dentifrice supernates containing SLS were effective in detaching co-adhering bacteria from pellicles surfaces, except in combination with SnF(2). When hexametaphosphate was added immediate detachment was relatively low, but continued even during re-deposition. The re-deposition of streptococci after detachment by other, NaF containing dentifrices involved relatively few large aggregates, presumably because fluoride was able to block bi-dentate calcium binding sites on the bacterial cell surfaces, mediating co-adhesion. When pyrophosphate was present in addition to NaF, re-deposition involved significantly more large aggregates, likely because pyrophosphate served as a bi-dentate bridge between calcium bound on the bacterial cell surfaces. Commercially available dentifrice formulations differ in their ability to stimulate bacterial detachment from pellicles and dependent on their composition yield the formation of large co-adhering aggregates of actinomyces and streptococci in de novo deposition.

Comparison of in vitro and in vivo methods to study stability of PLGA microencapsulated tetanus toxoid vaccines.

PubMed

Sasiak, A B; Bolgiano, B; Crane, D T; Hockley, D J; Corbel, M J; Sesardic, D

2000-11-22

The purpose of this study was to investigate the utility of various in vitro and in vivo methods to assess the stability of experimental vaccines containing tetanus toxoid (TT) within PLGA microspheres. In vitro, the breakdown of the encapsulating polymers into their acid components led to changes in the structure of TT, as determined by the physico-chemical methods, rendering it undetectable by capture ELISA and altering its structural integrity. The changes in TT were directly related to increasing acidity of the vaccine supernate. Purified toxoid (not encapsulated) exposed to low pH (2.5) underwent similar changes but re-neutralisation of buffer containing free toxoid, even after one week at pH 2.5 led to some re-folding of protein as determined by fluorescence spectroscopy and gel filtration chromatography. The microencapsulated vaccines were still able to generate an antibody response in mice even after prolonged pre-incubation at 37 degrees C and the apparent absence of detectable toxoid in the vaccine supernate. Electron microscopy demonstrated differences in the amount of degradation between different formulations of microspheres. Vaccines that had retained their spherical morphology after incubation in vitro for up to 28 days were able to induce protective antibodies response equal to that of freshly prepared vaccines, which indicates that the toxoid within intact microspheres remained immunogenic. Immunochemical and physico-chemical detection methods, performed on antigen released from PLGA vaccines in vitro, are valuable in providing information on product characteristics but may not be able to predict effectiveness and should be used with in vivo methods to evaluate the stability of such formulations.

Lysis of Chlamydomonas reinhardtii by high-intensity focused ultrasound as a function of exposure time.

PubMed

Bigelow, Timothy A; Xu, Jin; Stessman, Dan J; Yao, Linxing; Spalding, Martin H; Wang, Tong

2014-05-01

Efficient lysis of microalgae for lipid extraction is an important concern when processing biofuels. Historically, ultrasound frequencies in the range of 10-40 kHz have been utilized for this task. However, greater efficiencies might be achievable if higher frequencies could be used. In our study, we evaluated the potential of using 1.1 MHz ultrasound to lyse microalgae for biofuel production while using Chlamydomonas reinhardtii as a model organism. The ultrasound was generated using a spherically focused transducer with a focal length of 6.34 cm and an active diameter of 6.36 cm driven by 20 cycle sine-wave tone bursts at a pulse repetition frequency of 2 kHz (3.6% duty cycle). The time-average acoustic power output was 26.2 W while the spatial-peak-pulse-average intensity (ISPPA) for each tone burst was 41 kW/cm(2). The peak compressional and rarefactional pressures at the focus were 102 and 17 MPa, respectively. The exposure time was varied for the different cases in the experiments from 5s to 9 min and cell lysis was assessed by quantifying the percentage of protein and chlorophyll release into the supernate as well as the lipid extractability. Free radical generation and lipid oxidation for the different ultrasound exposures were also determined. We found that there was a statistically significant increase in lipid extractability for all of the exposures compared to the control. The longer exposures also completely fragmented the cells releasing almost all of the protein and chlorophyll into the supernate. The cavitation activity did not significantly increase lipid oxidation while there was a minor trend of increased free radical production with increased ultrasound exposure. Copyright © 2013 Elsevier B.V. All rights reserved.

Support for HLW Direct Feed - Phase 2, VSL-15R3440-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matlack, K. S.; Pegg, I.; Joseph, I.

This report describes work performed to develop and test new glass and feed formulations originating from a potential flow-sheet for the direct vitrification of High Level Waste (HLW) with minimal or no pretreatment. In the HLW direct feed option that is under consideration for early operations at the Hanford Tank Waste Treatment and Immobilization Plant (WTP), the pretreatment facility would be bypassed in order to support an earlier start-up of the vitrification facility. For HLW, this would mean that the ultrafiltration and caustic leaching operations that would otherwise have been performed in the pretreatment facility would either not be performedmore » or would be replaced by an interim pretreatment function (in-tank leaching and settling, for example). These changes would likely affect glass formulations and waste loadings and have impacts on the downstream vitrification operations. Modification of the pretreatment process may result in: (i) Higher aluminum contents if caustic leaching is not performed; (ii) Higher chromium contents if oxidative leaching is not performed; (iii) A higher fraction of supernate in the HLW feed resulting from the lower efficiency of in-tank washing; and (iv) A higher water content due to the likely lower effectiveness of in-tank settling compared to ultrafiltration. The HLW direct feed option has also been proposed as a potential route for treating HLW streams that contain the highest concentrations of fast-settling plutoniumcontaining particles, thereby avoiding some of the potential issues associated with such particles in the WTP Pretreatment facility [1]. In response, the work presented herein focuses on the impacts of increased supernate and water content on wastes from one of the candidate source tanks for the direct feed option that is high in plutonium.« less

CESIUM REMOVAL FROM TANKS 241-AN-103 & 241-SX-105 & 241-AZ-101/102 COMPOSITE FOR TESTING IN BENCH SCALE STEAM REFORMER

DOE Office of Scientific and Technical Information (OSTI.GOV)

DUNCAN JB; HUBER HJ

2011-06-08

This report documents the preparation of three actual Hanford tank waste samples for shipment to the Savannah River National Laboratory (SRNL). Two of the samples were dissolved saltcakes from tank 241-AN-103 (hereafter AN-103) and tank 241-SX-105 (hereafter SX-105); one sample was a supernate composite from tanks 241-AZ-101 and 241-AZ-102 (hereafter AZ-101/102). The preparation of the samples was executed following the test plans LAB-PLAN-10-00006, Test Plan for the Preparation of Samples from Hanford Tanks 241-SX-105, 241-AN-103, 241-AN-107, and LAB-PLN-10-00014, Test Plan for the Preparation of a Composite Sample from Hanford Tanks 241-AZ-101 and 241-AZ-102 for Steam Reformer Testing at the Savannahmore » River National Laboratory. All procedural steps were recorded in laboratory notebook HNF-N-274 3. Sample breakdown diagrams for AN-103 and SX-105 are presented in Appendix A. The tank samples were prepared in support of a series of treatability studies of the Fluidized Bed Steam Reforming (FBSR) process using a Bench-Scale Reformer (BSR) at SRNL. Tests with simulants have shown that the FBSR mineralized waste form is comparable to low-activity waste glass with respect to environmental durability (WSRC-STI-2008-00268, Mineralization of Radioactive Wastes by Fluidized Bed Steam Reforming (FBSR): Comparisons to Vitreous Waste Forms and Pertinent Durability Testing). However, a rigorous assessment requires long-term performance data from FB SR product formed from actual Hanford tank waste. Washington River Protection Solutions, LLC (WRPS) has initiated a Waste Form Qualification Program (WP-S.2.1-20 1 0-00 1, Fluidized Bed Steam Reformer Low-level Waste Form Qualification) to gather the data required to demonstrate that an adequate FBSR mineralized waste form can be produced. The documentation of the selection process of the three tank samples has been separately reported in RPP-48824, 'Sample Selection Process for Bench-Scale Steam Reforming Treatability Studies Using Hanford Waste Samples.'« less

CESIUM REMOVAL FROM TANKS 241-AN-103 & 241-SX-105 & 241-AZ-101 & 241AZ-102 COMPOSITE FOR TESTING IN BENCH SCALE STEAM REFORMER

DOE Office of Scientific and Technical Information (OSTI.GOV)

DUNCAN JB; HUBER HJ

2011-04-21

This report documents the preparation of three actual Hanford tank waste samples for shipment to the Savannah River National Laboratory (SRNL). Two of the samples were dissolved saltcakes from tank 241-AN-103 (hereafter AN-103) and tank 241-SX-105 (hereafter SX-105); one sample was a supernate composite from tanks 241-AZ-101 and 241-AZ-102 (hereafter AZ-101/102). The preparation of the samples was executed following the test plans LAB-PLAN-10-00006, Test Plan for the Preparation of Samples from Hanford Tanks 241-SX-105, 241-AN-103, 241-AN-107, and LAB-PLN-l0-00014, Test Plan for the Preparation of a Composite Sample from Hanford Tanks 241-AZ-101 and 241-AZ-102 for Steam Reformer Testing at the Savannahmore » River National Laboratory. All procedural steps were recorded in laboratory notebook HNF-N-274 3. Sample breakdown diagrams for AN-103 and SX-105 are presented in Appendix A. The tank samples were prepared in support of a series of treatability studies of the Fluidized Bed Steam Reforming (FBSR) process using a Bench-Scale Reformer (BSR) at SRNL. Tests with simulants have shown that the FBSR mineralized waste form is comparable to low-activity waste glass with respect to environmental durability (WSRC-STI-2008-00268, Mineralization of Radioactive Wastes by Fluidized Bed Steam Reforming (FBSR): Comparisons to Vitreous Waste Forms and Pertinent Durability Testing). However, a rigorous assessment requires long-term performance data from FBSR product formed from actual Hanford tank waste. Washington River Protection Solutions, LLC (WRPS) has initiated a Waste Form Qualification Program (WP-5.2.1-2010-001, Fluidized Bed Steam Reformer Low-level Waste Form Qualification) to gather the data required to demonstrate that an adequate FBSR mineralized waste form can be produced. The documentation of the selection process of the three tank samples has been separately reported in RPP-48824, Sample Selection Process for Bench-Scale Steam Reforming Treatability Studies Using Hanford Waste Samples.« less

Effect of residual ascorbate on determination of nitrite in commercial cured meat products.

PubMed

Fox, J B; Doerr, R C; Gates, R

1984-01-01

Residual ascorbate in cured meat slurries results in different amounts of pigment being produced from different Griess reagent combinations. The phenomenon was used to study residual ascorbate in commercial cured meat products which had a variety of textures, acidities, moisture and meat content, fat, homogeneity, initial nitrite, and processing conditions. Diluting and heating the samples according to the AOAC procedure did not completely eliminate the ascorbate interference, but making the sample alkaline did. Determining nitrite separately in supernate and precipitate from the first dilution showed the effect of heating to be the elimination of interferences and solubilization or extraction of nitrite from the precipitate.

EVALUATION OF ALTERNATIVE STRONIUM AND TRANSURANIC SEPARATION PROCESSES

DOE Office of Scientific and Technical Information (OSTI.GOV)

SMALLEY CS

2011-04-25

In order to meet contract requirements on the concentrations of strontium-90 and transuranic isotopes in the immobilized low-activity waste, strontium-90 and transuranics must be removed from the supernate of tanks 241-AN-102 and 241-AN-107. The process currently proposed for this application is an in-tank precipitation process using strontium nitrate and sodium permanganate. Development work on the process has not proceeded since 2005. The purpose of the evaluation is to identify whether any promising alternative processes have been developed since this issue was last examined, evaluate the alternatives and the baseline process, and recommend which process should be carried forward.

DWPF DECON FRIT: SUMP AND SLURRY SOLIDS ANALYSIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, C.; Peeler, D.; Click, D.

The Savannah River National Laboratory (SRNL) has been requested to perform analyses on samples of the Defense Waste Processing Facility (DWPF) decon frit slurry (i.e., supernate samples and sump solid samples). Four 1-L liquid slurry samples were provided to SRNL by Savannah River Remediation (SRR) from the 'front-end' decon activities. Additionally, two 1-L sump solids samples were provided to SRNL for compositional and physical analysis. In this report, the physical and chemical characterization results of the slurry solids and sump solids are reported. Crawford et al. (2010) provide the results of the supernate analysis. The results of the sump solidsmore » are reported on a mass basis given the samples were essentially dry upon receipt. The results of the slurry solids were converted to a volume basis given approximately 2.4 grams of slurry solids were obtained from the {approx}4 liters of liquid slurry sample. Although there were slight differences in the analytical results between the sump solids and slurry solids the following general summary statements can be made. Slight differences in the results are also captured for specific analysis. (1) Physical characterization - (a) SEM/EDS analysis suggested that the samples were enriched in Li and Si (B and Na not detectable using the current EDS system) which is consistent with two of the four principle oxides of Frit 418 (B{sub 2}O{sub 3}, Na{sub 2}O, Li{sub 2}O and SiO{sub 2}). (b) SEM/EDS analysis also identified impurities which were elementally consistent with stainless steel (i.e., Fe, Ni, Cr contamination). (c) XRD results indicated that the sump solids samples were amorphous which is consistent with XRD results expected for a Frit 418 based sample. (d) For the sump solids, SEM/EDS analysis indicated that the particle size of the sump solids were consistent with that of an as received Frit 418 sample from a current DWPF vendor. (e) For the slurry solids, SEM/EDS analysis indicated that the particle size range of the slurry solids was much broader than compared to the sump solids. More specifically, there were significantly more fines in the slurry solids as compared to the sump solids. (f) PSD results indicated that > 99% of both the sump and slurry solids were less than 350 microns. The PSD results also supported SEM/EDS analysis that there were significantly more fines in the slurry solids as compared to the sump solids. (2) Weight Percent Solids - Based on the measured supernate density and mass of insoluble solids (2.388 grams) filtered from the four liters of liquid slurry samples, the weight percent insoluble solids was estimated to be 0.060 wt%. This level of insoluble solids is higher than the ETP WAC limit of 100 mg/L, or 0.01 wt% which suggests a separation technology of some type would be required. (3) Chemical Analysis - (a) Elemental results from ICP-ES analysis indicated that the sump solids and slurry were very consistent with the nominal composition of Frit 418. There were other elements identified by ICP analysis which were either consistent with the presence of stainless steel (as identified by SEM/EDS analysis) or impurities that have been observed in 'as received' Frit 418 from the vendor. (b) IC anion analysis of the sump solids and slurry solids indicated all of the species were less than detection limits. (c) Radionuclide analysis of the sump solids also indicated that most of the analytes were either at or below the detection limits. (d) Organic analysis of the sump solids and slurry solids indicated all of the species were less than detection limits. It should be noted that the results of this study may not be representative of future decon frit solutions or sump/slurry solids samples. Therefore, future DWPF decisions regarding the possible disposal pathways for either the aqueous or solid portions of the Decon Frit system need to factor in the potential differences. More specifically, introduction of a different frit or changes to other DWPF flowsheet unit operations (e.g., different sludge batch or coupling with other process streams) may impact not only the results but also the conclusions regarding acceptability with respect to the ETF WAC limits or other alternative disposal options.« less

[Effect of haw leaf extract and its preparation on polymorphonuclear leucocyte adhesion during HUVEC anoxia/reoxygenation injury].

PubMed

Li, Peng; Fu, Jian-hua; Li, Xin-zhi

2008-08-01

To study the effect and molecular mechanism of two haw leaf extracts, Vitexin-rhamnoside (VR) and Vitexin-glucoside (VG), and their preparation, Aoshaen injection (AI), on the polymorphonuclear leucocyte (PMN) adhesion during human umbilical vein endothelial cell (HUVEC) anoxia/reoxygenation (A/R) injury. The cell model of A/R injury duplicated by breaking off the oxygen supplying of HUVEC for 60 min followed with reoxygenating for 30 min (phase 1) or 240 min (phase 2) was taken as the experimental objective. The effects of testing drugs (VR, VG and AI) on PMN adhesion in the model cells were measured by enzyme immunoassay, and their effects on PMN superficial adhesion molecule CD11/CD18 expression were measured by flow cytometer respectively. After 60 min of anoxia, HUVEC was shrunk and deformed. The adhesion between PMN and HUVEC significantly revealed at phase 1 in the model group, but it was fewer in the normal cell group, and also lesser in the groups treated with various drugs. The condition of cell adhesion revealed at phase 2 was the similar to that at phase 1. All testing drugs, VR, VG and AI, showed inhibitory effect on the cell adhesion at either phase 1 or phase 2, showing a certain dose-effect relationship. The expression of CD11/ CD18 was also inhibited by the testing drugs, and a good dose-effect relation was shown by VG and AI. At the resting condition, there are almost no expression of CD11/CD18 molecule, but it could be enhanced by incubating PMN with supernate of A/R injured HUVEC culture, and more marked at phase 1. Adding the test drugs into the supernate could inhibit the enhancing of CD11/CD18 molecule expression and reduce the PMN-HUVEC adhesion, which may be one of the molecular mechanisms of haw leaf extracts and their preparation in protecting heart against A/R injury.

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

Development and validation of a liquid chromatography-tandem mass spectrometry method for the determination of pyridostigmine bromide from guinea pig plasma.

PubMed

Needham, Shane R; Ye, Binying; Smith, J Richard; Korte, William D

2003-11-05

An HPLC/MS/MS method was validated for the low level analysis of pyridostigmine bromide (PB) from guinea pig plasma. An advantage of this strong-cation exchange HPLC/MS/MS method was the enhancement of the ESI-MS signal by providing good retention and good peak shape of PB with a mobile phase of 70% acetonitrile. In addition, the use of 70% acetonitrile in the mobile phase allowed the direct injection of the supernant from the protein precipitated extracted sample. The assay was linear from the range of 0.1 to 50 ng/ml using only 25 microl of sample. The precision and accuracy of the assay was better than 9.1 and 113%, respectively.

Studies on the mechanism of endogenous pyrogen production. III. Human blood monocytes.

PubMed

Bodel, P

1974-10-01

The characteristics of pyrogen production and release by human blood monocytes were investigated. A dose-response assay of monocyte pyrogen in rabbits indicated a linear relationship of temperature elevation to dose of pyrogen at lower doses. Monocytes did not contain pyrogen when first obtained, nor did they release it spontaneously even after 5 days of incubation in vitro. Pyrogen production was apparent 4 h after stimulation by endotoxin or phagocytosis, and continued for 24 h or more. Puromycin, an inhibitor of protein synthesis, prevented both initiation and continuation of pyrogen production and release. Pyrogen-containing supernates retained most pyrogenic activity during overnight incubation even in the presence of activated cells. Lymphocytes appeared to play no role in either initiation or continuation of pyrogen production in these studies.

Simulation of water-quality data at selected stream sites in the Missouri River Basin, Montana

USGS Publications Warehouse

Knapton, J.R.; Jacobson, M.A.

1980-01-01

Modification of sampling programs at some water-quality stations in the Missouri River basin in Montana has eliminated the means by which solute loads have been directly obtained in past years. To compensate for this loss, water-quality and streamflow data were statistically analyzed and solute loads were simulated using computer techniques.Functional relationships existing between specific conductance and solute concentration for monthly samples were used to develop linear regression models. The models were then used to simulate daily solute concentrations using daily specific conductance as the independent variable. Once simulated, the solute concentrations, in milligrams per liter, were transformed into daily solute loads, in tons, using mean daily streamflow records.Computer output was formatted into tables listing simulated mean monthly solute concentrations, in milligrams per liter, and the monthly and annual solute loads, in tons, for water years 1975-78.

Test Report for Permanganate and Cold Strontium Strike for Tank 241-AN-102

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duncan, James B.; Huber, Heinz J.; Smalley, Colleen S.

Tanks 241-AN-102 and 241-AN-107 supernatants contain soluble Sr-90 and transuranic elements that require removal prior to vitrification to comply with the Waste Treatment and Immobilization Plant immobilized low-activity waste specification (WTP Contract, DE-AC27-01RV 14136, Specification 2.2.2.8, "Radionuclide Concentration Limitations") and the U.S. Nuclear Regulatory Commission provisional agreement on waste incidental to reprocessing (letter, Paperiello, C. J., "Classification of Hanford Low-Activity Tank Waste Fraction"). These two tanks have high concentrations of organics and organic complexants and are referred to as complexant concentrate tanks. A precipitation process using sodium permanganate (NaMnO{sub 4}) and strontium nitrate (Sr(NO{sub 3}){sub 2}) was developed and testedmore » with tank waste samples to precipitate Sr-90 and transuranic elements from the supernate (PNWD-3141, Optimization of Sr/TRU Removal Conditions with Samples of AN-102 Tank Waste). Testing documented in this report was conducted to further evaluate the use of the strontium nitrate/sodium permanganate process in tank farms with a retention time of up to 12 months. Previous testing was focused on developing a process for deployment in the ultrafiltration vessels in the Waste Treatment and Immobilization Plant. This environment is different from tank farms in two important ways: the waste is diluted in the Waste Treatment and Immobilization Plant to ~5.5 M sodium, whereas the supernate in the tank farms is ~9 M Na. Secondly, while the Waste Treatment and Immobilization Plant allows for a maximum treatment time of hours to days, the in-tank farms treatment of tanks 241-AN102 and 241-AN-107 will result in a retention time of months (perhaps up to12 months) before processing. A comparative compilation of separation processes for Sr/transuranics has been published as RPP-RPT-48340, Evaluation of Alternative Strontium and Transuranic Separation Processes. This report also listed the testing needs for the permanganate precipitation process to be field-deployable. A more comprehensive listing of future testing needs to allow the process to be field deployable are contained in RPP-PLAN-51288, Development Test Plan for Sr/TRU Precipitation Process.« less

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

NASA Astrophysics Data System (ADS)

Ahlstrand, Emma; Zukerman Schpector, Julio; Friedman, Ran

2017-11-01

When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions are available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li+ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.

Molecular simulations of diffusion in electrolytes

NASA Astrophysics Data System (ADS)

Wheeler, Dean Richard

This work demonstrates new methodologies for simulating multicomponent diffusion in concentrated solutions using molecular dynamics (MD). Experimental diffusion data for concentrated multicomponent solutions are often lacking, as are accurate methods of predicting diffusion for nonideal solutions. MD can be a viable means of understanding and predicting multicomponent diffusion. While there have been several prior reports of MD simulations of mutual diffusion, no satisfactory expressions for simulating Stefan-Maxwell diffusivities for an arbitrary number of species exist. The approaches developed here allow for the computation of a full diffusion matrix for any number of species in both nonequilibrium and equilibrium MD ensembles. Our nonequilibrium approach is based on the application of constant external fields to drive species diffusion. Our equilibrium approach uses a newly developed Green-Kubo formula for Stefan-Maxwell diffusivities. In addition, as part of this work, we demonstrate a widely applicable means of increasing the computational efficiency of the Ewald sum, a technique for handling long-range Coulombic interactions in simulations. The theoretical development is applicable to any solution which can be simulated using MD; nevertheless, our primary interest is in electrochemical applications. To this end, the methods are tested by simulations of aqueous salt solutions and lithium-battery electrolytes. KCl and NaCl aqueous solutions were simulated over the concentration range 1 to 4 molal. Intermolecular-potential models were parameterized for these transport-based simulations. This work is the first to simulate all three independent diffusion coefficients for aqueous NaCl and KCl solutions. The results show that the nonequilibrium and equilibrium methods are consistent with each other, and in moderate agreement with experiment. We simulate lithium-battery electrolytes containing LiPF6 in propylene carbonate and mixed ethylene carbonate-dimethyl carbonate solvents. As with the aqueous-solution work, potential parameters were generated for these molecules. These nonaqueous electrolytes demonstrate rich transport behavior, which the simulations are able to reproduce qualitatively. In a mixed-solvent simulation we regress all six independent transport coefficients. The simulations show that strong ion pairing is responsible for the increase in viscosity and maximum in conductivity as ion concentrations are increased.

An atomistic simulation scheme for modeling crystal formation from solution.

PubMed

Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk

2006-01-14

We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.

Sensitivity analysis of conservative and reactive stream transient storage models applied to field data from multiple-reach experiments

USGS Publications Warehouse

Gooseff, M.N.; Bencala, K.E.; Scott, D.T.; Runkel, R.L.; McKnight, Diane M.

2005-01-01

The transient storage model (TSM) has been widely used in studies of stream solute transport and fate, with an increasing emphasis on reactive solute transport. In this study we perform sensitivity analyses of a conservative TSM and two different reactive solute transport models (RSTM), one that includes first-order decay in the stream and the storage zone, and a second that considers sorption of a reactive solute on streambed sediments. Two previously analyzed data sets are examined with a focus on the reliability of these RSTMs in characterizing stream and storage zone solute reactions. Sensitivities of simulations to parameters within and among reaches, parameter coefficients of variation, and correlation coefficients are computed and analyzed. Our results indicate that (1) simulated values have the greatest sensitivity to parameters within the same reach, (2) simulated values are also sensitive to parameters in reaches immediately upstream and downstream (inter-reach sensitivity), (3) simulated values have decreasing sensitivity to parameters in reaches farther downstream, and (4) in-stream reactive solute data provide adequate data to resolve effective storage zone reaction parameters, given the model formulations. Simulations of reactive solutes are shown to be equally sensitive to transport parameters and effective reaction parameters of the model, evidence of the control of physical transport on reactive solute dynamics. Similar to conservative transport analysis, reactive solute simulations appear to be most sensitive to data collected during the rising and falling limb of the concentration breakthrough curve. ?? 2005 Elsevier Ltd. All rights reserved.

Investigation of Tank 241-AW-104 Composite Floating Layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meznarich, H. K.; Bolling, S. D.; Lachut, J. S.

Seven grab samples and one field blank were taken from Tank 241-AW-104 (AW-104) on June 2, 2017, and received at 222-S Laboratory on June 5, 2017. A visible layer with brown solids was observed floating on the top of two surface tank waste samples (4AW-17-02 and 4AW 17 02DUP). The floating layer from both samples was collected, composited, and submitted for chemical analyses and solid phase characterization in order to understand the composition of the floating layer. Tributyl phosphate and tridecane were higher in the floating layer than in the aqueous phase. Density in the floating layer was slightly lowermore » than the mean density of all grab samples. Sodium nitrate and sodium carbonate were major components with a trace of gibbsite and very small size agglomerates were present in the solids of the floating layer. The supernate consisted of organics, soluble salt, and particulates.« less

Rotating black hole solutions in relativistic analogue gravity

NASA Astrophysics Data System (ADS)

Giacomelli, Luca; Liberati, Stefano

2017-09-01

Simulation and experimental realization of acoustic black holes in analogue gravity systems have lead to a novel understanding of relevant phenomena such as Hawking radiation or superradiance. We explore here the possibility of using relativistic systems for simulating rotating black hole solutions and possibly get an acoustic analogue of a Kerr black hole. In doing so, we demonstrate a precise relation between nonrelativistic and relativistic solutions and provide a new class of vortex solutions for relativistic systems. Such solutions might be used in the future as a test bed in numerical simulations as well as concrete experiments.

System Simulation by Recursive Feedback: Coupling A Set of Stand-Alone Subsystem Simulations

NASA Technical Reports Server (NTRS)

Nixon, Douglas D.; Hanson, John M. (Technical Monitor)

2002-01-01

Recursive feedback is defined and discussed as a framework for development of specific algorithms and procedures that propagate the time-domain solution for a dynamical system simulation consisting of multiple numerically coupled self-contained stand-alone subsystem simulations. A satellite motion example containing three subsystems (other dynamics, attitude dynamics, and aerodynamics) has been defined and constructed using this approach. Conventional solution methods are used in the subsystem simulations. Centralized and distributed versions of coupling structure have been addressed. Numerical results are evaluated by direct comparison with a standard total-system simultaneous-solution approach.

A dual-porosity model for simulating solute transport in oil shale

USGS Publications Warehouse

Glover, K.C.

1987-01-01

A model is described for simulating three-dimensional groundwater flow and solute transport in oil shale and associated geohydrologic units. The model treats oil shale as a dual-porosity medium by simulating flow and transport within fractures using the finite-element method. Diffusion of solute between fractures and the essentially static water of the shale matrix is simulated by including an analytical solution that acts as a source-sink term to the differential equation of solute transport. While knowledge of fracture orientation and spacing is needed to effectively use the model, it is not necessary to map the locations of individual fractures. The computer program listed in the report incorporates many of the features of previous dual-porosity models while retaining a practical approach to solving field problems. As a result the theory of solute transport is not extended in any appreciable way. The emphasis is on bringing together various aspects of solute transport theory in a manner that is particularly suited to the unusual groundwater flow and solute transport characteristics of oil shale systems. (Author 's abstract)

On the first crossing distributions in fractional Brownian motion and the mass function of dark matter haloes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiotelis, Nicos; Popolo, Antonino Del, E-mail: adelpopolo@oact.inaf.it, E-mail: hiotelis@ipta.demokritos.gr

We construct an integral equation for the first crossing distributions for fractional Brownian motion in the case of a constant barrier and we present an exact analytical solution. Additionally we present first crossing distributions derived by simulating paths from fractional Brownian motion. We compare the results of the analytical solutions with both those of simulations and those of some approximated solutions which have been used in the literature. Finally, we present multiplicity functions for dark matter structures resulting from our analytical approach and we compare with those resulting from N-body simulations. We show that the results of analytical solutions aremore » in good agreement with those of path simulations but differ significantly from those derived from approximated solutions. Additionally, multiplicity functions derived from fractional Brownian motion are poor fits of the those which result from N-body simulations. We also present comparisons with other models which are exist in the literature and we discuss different ways of improving the agreement between analytical results and N-body simulations.« less

Tank 40 Final SB7b Chemical Characterization Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bannochie, C. J.

2012-11-06

A sample of Sludge Batch 7b (SB7b) was taken from Tank 40 in order to obtain radionuclide inventory analyses necessary for compliance with the Waste Acceptance Product Specifications (WAPS). The SB7b WAPS sample was also analyzed for chemical composition including noble metals and fissile constituents. At the Savannah River National Laboratory (SRNL) the 3-L Tank 40 SB7b sample was transferred from the shipping container into a 4-L high density polyethylene bottle and solids were allowed to settle over the weekend. Supernate was then siphoned off and circulated through the shipping container to complete the transfer of the sample. Following thoroughmore » mixing of the 3-L sample, a 558 g sub-sample was removed. This sub-sample was then utilized for all subsequent analytical samples. Eight separate aliquots of the slurry were digested, four with HNO{sub 3}/HCl (aqua regia) in sealed Teflon vessels and four with NaOH/Na{sub 2}O{sub 2} (alkali or peroxide fusion) using Zr crucibles. Two Analytical Reference Glass ? 1 (ARG-1) standards were digested along with a blank for each preparation. Each aqua regia digestion and blank was diluted to 1:100 mL with deionized water and submitted to Analytical Development (AD) for inductively coupled plasma ? atomic emission spectroscopy (ICP-AES) analysis, inductively coupled plasma ? mass spectrometry (ICP-MS) analysis, atomic absorption spectroscopy (AA) for As and Se, and cold vapor atomic absorption spectroscopy (CV-AA) for Hg. Equivalent dilutions of the alkali fusion digestions and blank were submitted to AD for ICP-AES analysis. Tank 40 SB7b supernate was collected from a mixed slurry sample in the SRNL Shielded Cells and submitted to AD for ICP-AES, ion chromatography (IC), total base/free OH{sup -}/other base, total inorganic carbon/total organic carbon (TIC/TOC) analyses, and Cs-137 gamma scan. Weighted dilutions of slurry were submitted for IC, TIC/TOC, and total base/free OH-/other base analyses. Activities for U-233, U-235, and Pu-239 were determined from the ICP-MS data for the aqua regia digestions of the Tank 40 WAPS slurry using the specific activity of each isotope. The Pu-241 value was determined from a Pu-238/-241 method.« less

Method and system for fault accommodation of machines

NASA Technical Reports Server (NTRS)

Goebel, Kai Frank (Inventor); Subbu, Rajesh Venkat (Inventor); Rausch, Randal Thomas (Inventor); Frederick, Dean Kimball (Inventor)

2011-01-01

A method for multi-objective fault accommodation using predictive modeling is disclosed. The method includes using a simulated machine that simulates a faulted actual machine, and using a simulated controller that simulates an actual controller. A multi-objective optimization process is performed, based on specified control settings for the simulated controller and specified operational scenarios for the simulated machine controlled by the simulated controller, to generate a Pareto frontier-based solution space relating performance of the simulated machine to settings of the simulated controller, including adjustment to the operational scenarios to represent a fault condition of the simulated machine. Control settings of the actual controller are adjusted, represented by the simulated controller, for controlling the actual machine, represented by the simulated machine, in response to a fault condition of the actual machine, based on the Pareto frontier-based solution space, to maximize desirable operational conditions and minimize undesirable operational conditions while operating the actual machine in a region of the solution space defined by the Pareto frontier.

Corrosion property of 9Cr-ODS steel in nitric acid solution for spent nuclear fuel reprocessing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takeuchi, M.; Koizumi, T.; Inoue, M.

2013-07-01

Corrosion tests of oxide dispersion strengthened with 9% Cr (9Cr-ODS) steel, which is one of the desirable materials for cladding tube of sodium-cooled fast reactors, in pure nitric acid solution, spent FBR fuel solution, and its simulated solution were performed to understand the corrosion behavior in a spent nuclear fuel reprocessing. In this study, the 9Cr-ODS steel with lower effective chromium content was evaluated to understand the corrosion behavior conservatively. As results, the tube-type specimens of the 9Cr-ODS steels suffered severe weight loss owing to active dissolution at the beginning of the immersion test in pure nitric acid solution inmore » the range from 1 to 3.5 M. In contrast, the weight loss was decreased and they showed a stable corrosion in the higher nitric acid concentration, the dissolved FBR fuel solution, and its simulated solution by passivation. The corrosion rates of the 9Cr-ODS steel in the dissolved FBR fuel solution and its simulated solution were 1-2 mm/y and showed good agreement with each other. The passivation was caused by the shift of corrosion potential to noble side owing to increase in nitric acid concentration or oxidative ions in the dissolved FBR fuel solution and the simulated spent fuel solution. (authors)« less

Steady and Unsteady Nozzle Simulations Using the Conservation Element and Solution Element Method

NASA Technical Reports Server (NTRS)

Friedlander, David Joshua; Wang, Xiao-Yen J.

2014-01-01

This paper presents results from computational fluid dynamic (CFD) simulations of a three-stream plug nozzle. Time-accurate, Euler, quasi-1D and 2D-axisymmetric simulations were performed as part of an effort to provide a CFD-based approach to modeling nozzle dynamics. The CFD code used for the simulations is based on the space-time Conservation Element and Solution Element (CESE) method. Steady-state results were validated using the Wind-US code and a code utilizing the MacCormack method while the unsteady results were partially validated via an aeroacoustic benchmark problem. The CESE steady-state flow field solutions showed excellent agreement with solutions derived from the other methods and codes while preliminary unsteady results for the three-stream plug nozzle are also shown. Additionally, a study was performed to explore the sensitivity of gross thrust computations to the control surface definition. The results showed that most of the sensitivity while computing the gross thrust is attributed to the control surface stencil resolution and choice of stencil end points and not to the control surface definition itself.Finally, comparisons between the quasi-1D and 2D-axisymetric solutions were performed in order to gain insight on whether a quasi-1D solution can capture the steady and unsteady nozzle phenomena without the cost of a 2D-axisymmetric simulation. Initial results show that while the quasi-1D solutions are similar to the 2D-axisymmetric solutions, the inability of the quasi-1D simulations to predict two dimensional phenomena limits its accuracy.

Cellulose Nanofibrils and Mechanism of their Mineralization in Biomimetic Synthesis of Hydroxyapatite/Native Bacterial Cellulose Nanocomposites: Molecular Dynamics Simulations.

PubMed

Lukasheva, N V; Tolmachev, D A

2016-01-12

Molecular dynamics (MD) simulation of a nanofibril of native bacterial cellulose (BC) in solutions of mineral ions is presented. The supersaturated calcium-phosphate (CP) solution with the ionic composition of hydroxyapatite and CaCl2 solutions with the concentrations below, equal to, and above the solubility limits are simulated. The influence of solvation models (TIP3P and TIP4P-ew water models) on structural characteristics of the simulated nanofibril and on the crystal nucleation process is assessed. The structural characteristics of cellulose nanofibrils (in particular, of the surface layer) are found to be nearly independent of the solvation models used in the simulation and on the presence of ions in the solutions. It is shown that ionic clusters are formed in the solution rather than on the fibril surface. The cluster sizes are slightly different for the two water models. The effect of the ion-ion interaction parameters on the results is discussed. The main conclusion is that the activity of hydroxyl groups on the BC fibril surface is not high enough to cause adsorption of Ca(2+) ions from the solution. Therefore, the nucleation of CP crystals takes place initially in solution, and then the crystallites formed can be adsorbed on BC nanofibril surfaces.

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal.

PubMed

Neale, Chris; Madill, Chris; Rauscher, Sarah; Pomès, Régis

2013-08-13

All molecular dynamics simulations are susceptible to sampling errors, which degrade the accuracy and precision of observed values. The statistical convergence of simulations containing atomistic lipid bilayers is limited by the slow relaxation of the lipid phase, which can exceed hundreds of nanoseconds. These long conformational autocorrelation times are exacerbated in the presence of charged solutes, which can induce significant distortions of the bilayer structure. Such long relaxation times represent hidden barriers that induce systematic sampling errors in simulations of solute insertion. To identify optimal methods for enhancing sampling efficiency, we quantitatively evaluate convergence rates using generalized ensemble sampling algorithms in calculations of the potential of mean force for the insertion of the ionic side chain analog of arginine in a lipid bilayer. Umbrella sampling (US) is used to restrain solute insertion depth along the bilayer normal, the order parameter commonly used in simulations of molecular solutes in lipid bilayers. When US simulations are modified to conduct random walks along the bilayer normal using a Hamiltonian exchange algorithm, systematic sampling errors are eliminated more rapidly and the rate of statistical convergence of the standard free energy of binding of the solute to the lipid bilayer is increased 3-fold. We compute the ratio of the replica flux transmitted across a defined region of the order parameter to the replica flux that entered that region in Hamiltonian exchange simulations. We show that this quantity, the transmission factor, identifies sampling barriers in degrees of freedom orthogonal to the order parameter. The transmission factor is used to estimate the depth-dependent conformational autocorrelation times of the simulation system, some of which exceed the simulation time, and thereby identify solute insertion depths that are prone to systematic sampling errors and estimate the lower bound of the amount of sampling that is required to resolve these sampling errors. Finally, we extend our simulations and verify that the conformational autocorrelation times estimated by the transmission factor accurately predict correlation times that exceed the simulation time scale-something that, to our knowledge, has never before been achieved.

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

PubMed

Xiao, Li; Luo, Ray

2017-12-07

We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

Application of an interactive water simulation model in urban water management: a case study in Amsterdam.

PubMed

Leskens, J G; Brugnach, M; Hoekstra, A Y

2014-01-01

Water simulation models are available to support decision-makers in urban water management. To use current water simulation models, special expertise is required. Therefore, model information is prepared prior to work sessions, in which decision-makers weigh different solutions. However, this model information quickly becomes outdated when new suggestions for solutions arise and are therefore limited in use. We suggest that new model techniques, i.e. fast and flexible computation algorithms and realistic visualizations, allow this problem to be solved by using simulation models during work sessions. A new Interactive Water Simulation Model was applied for two case study areas in Amsterdam and was used in two workshops. In these workshops, the Interactive Water Simulation Model was positively received. It included non-specialist participants in the process of suggesting and selecting possible solutions and made them part of the accompanying discussions and negotiations. It also provided the opportunity to evaluate and enhance possible solutions more often within the time horizon of a decision-making process. Several preconditions proved to be important for successfully applying the Interactive Water Simulation Model, such as the willingness of the stakeholders to participate and the preparation of different general main solutions that can be used for further iterations during a work session.

A modified dynamical model of drying process of polymer blend solution coated on a flat substrate

NASA Astrophysics Data System (ADS)

Kagami, Hiroyuki

2008-05-01

We have proposed and modified a model of drying process of polymer solution coated on a flat substrate for flat polymer film fabrication. And for example numerical simulation of the model reproduces a typical thickness profile of the polymer film formed after drying. Then we have clarified dependence of distribution of polymer molecules on a flat substrate on a various parameters based on analysis of numerical simulations. Then we drove nonlinear equations of drying process from the dynamical model and the fruits were reported. The subject of above studies was limited to solution having one kind of solute though the model could essentially deal with solution having some kinds of solutes. But nowadays discussion of drying process of a solution having some kinds of solutes is needed because drying process of solution having some kinds of solutes appears in many industrial scenes. Polymer blend solution is one instance. And typical resist consists of a few kinds of polymers. Then we introduced a dynamical model of drying process of polymer blend solution coated on a flat substrate and results of numerical simulations of the dynamical model. But above model was the simplest one. In this study, we modify above dynamical model of drying process of polymer blend solution adding effects that some parameters change with time as functions of some variables to it. Then we consider essence of drying process of polymer blend solution through comparison between results of numerical simulations of the modified model and those of the former model.

Super-rogue waves in simulations based on weakly nonlinear and fully nonlinear hydrodynamic equations.

PubMed

Slunyaev, A; Pelinovsky, E; Sergeeva, A; Chabchoub, A; Hoffmann, N; Onorato, M; Akhmediev, N

2013-07-01

The rogue wave solutions (rational multibreathers) of the nonlinear Schrödinger equation (NLS) are tested in numerical simulations of weakly nonlinear and fully nonlinear hydrodynamic equations. Only the lowest order solutions from 1 to 5 are considered. A higher accuracy of wave propagation in space is reached using the modified NLS equation, also known as the Dysthe equation. This numerical modeling allowed us to directly compare simulations with recent results of laboratory measurements in Chabchoub et al. [Phys. Rev. E 86, 056601 (2012)]. In order to achieve even higher physical accuracy, we employed fully nonlinear simulations of potential Euler equations. These simulations provided us with basic characteristics of long time evolution of rational solutions of the NLS equation in the case of near-breaking conditions. The analytic NLS solutions are found to describe the actual wave dynamics of steep waves reasonably well.

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

Evaluation of unsaturated-zone solute-transport models for studies of agricultural chemicals

USGS Publications Warehouse

Nolan, Bernard T.; Bayless, E. Randall; Green, Christopher T.; Garg, Sheena; Voss, Frank D.; Lampe, David C.; Barbash, Jack E.; Capel, Paul D.; Bekins, Barbara A.

2005-01-01

Of the models tested, RZWQM, HYDRUS2D, VS2DT, GLEAMS and PRZM had graphical user interfaces. Extensive documentation was available for RZWQM, HYDRUS2D, and VS2DT. RZWQM can explicitly simulate water and solute flux in macropores, and both HYDRUS2D and VS2DT can simulate water and solute flux in two dimensions. The version of RZWQM tested had a maximum simulation depth of 3 meters. The complex models simulate the formation, transport, and fate of degradates of up to three to five compounds including the parent, with the exception of VS2DT, which simulates the transport and fate of a single compound.

Nonisothermal Analysis of Solution Kinetics by Spreadsheet Simulation

ERIC Educational Resources Information Center

de Levie, Robert

2012-01-01

A fast and generally applicable alternative solution to the problem of determining the useful shelf life of medicinal solutions is described. It illustrates the power and convenience of the combination of numerical simulation and nonlinear least squares with a practical pharmaceutical application of chemical kinetics and thermodynamics, validated…

Theory and Simulation of Multicomponent Osmotic Systems

PubMed Central

Karunaweera, Sadish; Gee, Moon Bae; Weerasinghe, Samantha; Smith, Paul E.

2012-01-01

Most cellular processes occur in systems containing a variety of components many of which are open to material exchange. However, computer simulations of biological systems are almost exclusively performed in systems closed to material exchange. In principle, the behavior of biomolecules in open and closed systems will be different. Here, we provide a rigorous framework for the analysis of experimental and simulation data concerning open and closed multicomponent systems using the Kirkwood-Buff (KB) theory of solutions. The results are illustrated using computer simulations for various concentrations of the solutes Gly, Gly2 and Gly3 in both open and closed systems, and in the absence or presence of NaCl as a cosolvent. In addition, KB theory is used to help rationalize the aggregation properties of the solutes. Here one observes that the picture of solute association described by the KB integrals, which are directly related to the solution thermodynamics, and that provided by more physical clustering approaches are different. It is argued that the combination of KB theory and simulation data provides a simple and powerful tool for the analysis of complex multicomponent open and closed systems. PMID:23329894

Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations.

PubMed

Liao, Chenyi; Esai Selvan, Myvizhi; Zhao, Jun; Slimovitch, Jonathan L; Schneebeli, Severin T; Shelley, Mee; Shelley, John C; Li, Jianing

2015-08-20

Melittin is a natural peptide that aggregates in aqueous solutions with paradigmatic monomer-to-tetramer and coil-to-helix transitions. Since little is known about the molecular mechanisms of melittin aggregation in solution, we simulated its self-aggregation process under various conditions. After confirming the stability of a melittin tetramer in solution, we observed—for the first time in atomistic detail—that four separated melittin monomers aggregate into a tetramer. Our simulated dependence of melittin aggregation on peptide concentration, temperature, and ionic strength is in good agreement with prior experiments. We propose that melittin mainly self-aggregates via a mechanism involving the sequential addition of monomers, which is supported by both qualitative and quantitative evidence obtained from unbiased and metadynamics simulations. Moreover, by combining computer simulations and a theory of the electrical double layer, we provide evidence to suggest why melittin aggregation in solution likely stops at the tetramer, rather than forming higher-order oligomers. Overall, our study not only explains prior experimental results at the molecular level but also provides quantitative mechanistic information that may guide the engineering of melittin for higher efficacy and safety.

Modeling crystal growth from solution with molecular dynamics simulations: approaches to transition rate constants.

PubMed

Reilly, Anthony M; Briesen, Heiko

2012-01-21

The feasibility of using the molecular dynamics (MD) simulation technique to study crystal growth from solution quantitatively, as well as to obtain transition rate constants, has been studied. The dynamics of an interface between a solution of Lennard-Jones particles and the (100) face of an fcc lattice comprised of solute particles have been studied using MD simulations, showing that MD is, in principle, capable of following growth behavior over large supersaturation and temperature ranges. Using transition state theory, and a nearest-neighbor approximation growth and dissolution rate constants have been extracted from equilibrium MD simulations at a variety of temperatures. The temperature dependence of the rates agrees well with the expected transition state theory behavior. © 2012 American Institute of Physics

A comparison of solute-transport solution techniques based on inverse modelling results

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2000-01-01

Five common numerical techniques (finite difference, predictor-corrector, total-variation-diminishing, method-of-characteristics, and modified-method-of-characteristics) were tested using simulations of a controlled conservative tracer-test experiment through a heterogeneous, two-dimensional sand tank. The experimental facility was constructed using randomly distributed homogeneous blocks of five sand types. This experimental model provides an outstanding opportunity to compare the solution techniques because of the heterogeneous hydraulic conductivity distribution of known structure, and the availability of detailed measurements with which to compare simulated concentrations. The present work uses this opportunity to investigate how three common types of results-simulated breakthrough curves, sensitivity analysis, and calibrated parameter values-change in this heterogeneous situation, given the different methods of simulating solute transport. The results show that simulated peak concentrations, even at very fine grid spacings, varied because of different amounts of numerical dispersion. Sensitivity analysis results were robust in that they were independent of the solution technique. They revealed extreme correlation between hydraulic conductivity and porosity, and that the breakthrough curve data did not provide enough information about the dispersivities to estimate individual values for the five sands. However, estimated hydraulic conductivity values are significantly influenced by both the large possible variations in model dispersion and the amount of numerical dispersion present in the solution technique.Five common numerical techniques (finite difference, predictor-corrector, total-variation-diminishing, method-of-characteristics, and modified-method-of-characteristics) were tested using simulations of a controlled conservative tracer-test experiment through a heterogeneous, two-dimensional sand tank. The experimental facility was constructed using randomly distributed homogeneous blocks of five sand types. This experimental model provides an outstanding opportunity to compare the solution techniques because of the heterogeneous hydraulic conductivity distribution of known structure, and the availability of detailed measurements with which to compare simulated concentrations. The present work uses this opportunity to investigate how three common types of results - simulated breakthrough curves, sensitivity analysis, and calibrated parameter values - change in this heterogeneous situation, given the different methods of simulating solute transport. The results show that simulated peak concentrations, even at very fine grid spacings, varied because of different amounts of numerical dispersion. Sensitivity analysis results were robust in that they were independent of the solution technique. They revealed extreme correlation between hydraulic conductivity and porosity, and that the breakthrough curve data did not provide enough information about the dispersivities to estimate individual values for the five sands. However, estimated hydraulic conductivity values are significantly influenced by both the large possible variations in model dispersion and the amount of numerical dispersion present in the solution technique.

A low-rank control variate for multilevel Monte Carlo simulation of high-dimensional uncertain systems

NASA Astrophysics Data System (ADS)

Fairbanks, Hillary R.; Doostan, Alireza; Ketelsen, Christian; Iaccarino, Gianluca

2017-07-01

Multilevel Monte Carlo (MLMC) is a recently proposed variation of Monte Carlo (MC) simulation that achieves variance reduction by simulating the governing equations on a series of spatial (or temporal) grids with increasing resolution. Instead of directly employing the fine grid solutions, MLMC estimates the expectation of the quantity of interest from the coarsest grid solutions as well as differences between each two consecutive grid solutions. When the differences corresponding to finer grids become smaller, hence less variable, fewer MC realizations of finer grid solutions are needed to compute the difference expectations, thus leading to a reduction in the overall work. This paper presents an extension of MLMC, referred to as multilevel control variates (MLCV), where a low-rank approximation to the solution on each grid, obtained primarily based on coarser grid solutions, is used as a control variate for estimating the expectations involved in MLMC. Cost estimates as well as numerical examples are presented to demonstrate the advantage of this new MLCV approach over the standard MLMC when the solution of interest admits a low-rank approximation and the cost of simulating finer grids grows fast.

Direct Coexistence Methods to Determine the Solubility of Salts in Water from Numerical Simulations. Test Case NaCl.

PubMed

Manzanilla-Granados, Héctor M; Saint-Martín, Humberto; Fuentes-Azcatl, Raúl; Alejandre, José

2015-07-02

The solubility of NaCl, an equilibrium between a saturated solution of ions and a solid with a crystalline structure, was obtained from molecular dynamics simulations using the SPC/E and TIP4P-Ew water models. Four initial setups on supersaturated systems were tested on sodium chloride (NaCl) solutions to determine the equilibrium conditions and computational performance: (1) an ionic solution confined between two crystal plates of periodic NaCl, (2) a solution with all the ions initially distributed randomly, (3) a nanocrystal immersed in pure water, and (4) a nanocrystal immersed in an ionic solution. In some cases, the equilibration of the system can take several microseconds. The results from this work showed that the solubility of NaCl was the same, within simulation error, for the four setups, and in agreement with previously reported values from simulations with the setup (1). The system of a nanocrystal immersed in supersaturated solution was found to equilibrate faster than others. In agreement with laser-Doppler droplet measurements, at equilibrium with the solution the crystals in all the setups had a slight positive charge.

COUPLING OF CORONAL AND HELIOSPHERIC MAGNETOHYDRODYNAMIC MODELS: SOLUTION COMPARISONS AND VERIFICATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merkin, V. G.; Lionello, R.; Linker, J.

2016-11-01

Two well-established magnetohydrodynamic (MHD) codes are coupled to model the solar corona and the inner heliosphere. The corona is simulated using the MHD algorithm outside a sphere (MAS) model. The Lyon–Fedder–Mobarry (LFM) model is used in the heliosphere. The interface between the models is placed in a spherical shell above the critical point and allows both models to work in either a rotating or an inertial frame. Numerical tests are presented examining the coupled model solutions from 20 to 50 solar radii. The heliospheric simulations are run with both LFM and the MAS extension into the heliosphere, and use themore » same polytropic coronal MAS solutions as the inner boundary condition. The coronal simulations are performed for idealized magnetic configurations, with an out-of-equilibrium flux rope inserted into an axisymmetric background, with and without including the solar rotation. The temporal evolution at the inner boundary of the LFM and MAS solutions is shown to be nearly identical, as are the steady-state background solutions, prior to the insertion of the flux rope. However, after the coronal mass ejection has propagated through the significant portion of the simulation domain, the heliospheric solutions diverge. Additional simulations with different resolution are then performed and show that the MAS heliospheric solutions approach those of LFM when run with progressively higher resolution. Following these detailed tests, a more realistic simulation driven by the thermodynamic coronal MAS is presented, which includes solar rotation and an azimuthally asymmetric background and extends to the Earth’s orbit.« less

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.

2016-09-01

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include methods that 1) explicitly model the three-dimensional geometry of pore spaces and 2) those that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of class 1, based on direct numerical simulation using computational fluid dynamics (CFD) codes, against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of class 1 based on the immersed-boundary method (IMB),more » lattice Boltzmann method (LBM), smoothed particle hydrodynamics (SPH), as well as a model of class 2 (a pore-network model or PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results with previously reported experimental observations. Experimental observations are limited to measured pore-scale velocities, so solute transport comparisons are made only among the various models. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations).« less

Brownian dynamics simulation of protein diffusion in crowded environments

NASA Astrophysics Data System (ADS)

Mereghetti, Paolo; Wade, Rebecca C.

2013-02-01

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. We first describe the development of a Brownian dynamics simulation methodology to investigate the dynamic and structural properties of protein solutions using atomic-detail protein structures. We then discuss insights obtained from applying this approach to simulation of solutions of a range of types of proteins.

System Simulation by Recursive Feedback: Coupling a Set of Stand-Alone Subsystem Simulations

NASA Technical Reports Server (NTRS)

Nixon, D. D.

2001-01-01

Conventional construction of digital dynamic system simulations often involves collecting differential equations that model each subsystem, arran g them to a standard form, and obtaining their numerical gin solution as a single coupled, total-system simultaneous set. Simulation by numerical coupling of independent stand-alone subsimulations is a fundamentally different approach that is attractive because, among other things, the architecture naturally facilitates high fidelity, broad scope, and discipline independence. Recursive feedback is defined and discussed as a candidate approach to multidiscipline dynamic system simulation by numerical coupling of self-contained, single-discipline subsystem simulations. A satellite motion example containing three subsystems (orbit dynamics, attitude dynamics, and aerodynamics) has been defined and constructed using this approach. Conventional solution methods are used in the subsystem simulations. Distributed and centralized implementations of coupling have been considered. Numerical results are evaluated by direct comparison with a standard total-system, simultaneous-solution approach.

A new equilibrium torus solution and GRMHD initial conditions

NASA Astrophysics Data System (ADS)

Penna, Robert F.; Kulkarni, Akshay; Narayan, Ramesh

2013-11-01

Context. General relativistic magnetohydrodynamic (GRMHD) simulations are providing influential models for black hole spin measurements, gamma ray bursts, and supermassive black hole feedback. Many of these simulations use the same initial condition: a rotating torus of fluid in hydrostatic equilibrium. A persistent concern is that simulation results sometimes depend on arbitrary features of the initial torus. For example, the Bernoulli parameter (which is related to outflows), appears to be controlled by the Bernoulli parameter of the initial torus. Aims: In this paper, we give a new equilibrium torus solution and describe two applications for the future. First, it can be used as a more physical initial condition for GRMHD simulations than earlier torus solutions. Second, it can be used in conjunction with earlier torus solutions to isolate the simulation results that depend on initial conditions. Methods: We assume axisymmetry, an ideal gas equation of state, constant entropy, and ignore self-gravity. We fix an angular momentum distribution and solve the relativistic Euler equations in the Kerr metric. Results: The Bernoulli parameter, rotation rate, and geometrical thickness of the torus can be adjusted independently. Our torus tends to be more bound and have a larger radial extent than earlier torus solutions. Conclusions: While this paper was in preparation, several GRMHD simulations appeared based on our equilibrium torus. We believe it will continue to provide a more realistic starting point for future simulations.

A texture-based framework for improving CFD data visualization in a virtual environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bivins, Gerrick O'Ron

2005-01-01

In the field of computational fluid dynamics (CFD) accurate representations of fluid phenomena can be simulated hut require large amounts of data to represent the flow domain. Most datasets generated from a CFD simulation can be coarse, ~10,000 nodes or cells, or very fine with node counts on the order of 1,000,000. A typical dataset solution can also contain multiple solutions for each node, pertaining to various properties of the flow at a particular node. Scalar properties such as density, temperature, pressure, and velocity magnitude are properties that are typically calculated and stored in a dataset solution. Solutions are notmore » limited to just scalar properties. Vector quantities, such as velocity, are also often calculated and stored for a CFD simulation. Accessing all of this data efficiently during runtime is a key problem for visualization in an interactive application. Understanding simulation solutions requires a post-processing tool to convert the data into something more meaningful. Ideally, the application would present an interactive visual representation of the numerical data for any dataset that was simulated while maintaining the accuracy of the calculated solution. Most CFD applications currently sacrifice interactivity for accuracy, yielding highly detailed flow descriptions hut limiting interaction for investigating the field.« less

A texture-based frameowrk for improving CFD data visualization in a virtual environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bivins, Gerrick O'Ron

2005-01-01

In the field of computational fluid dynamics (CFD) accurate representations of fluid phenomena can be simulated but require large amounts of data to represent the flow domain. Most datasets generated from a CFD simulation can be coarse, ~ 10,000 nodes or cells, or very fine with node counts on the order of 1,000,000. A typical dataset solution can also contain multiple solutions for each node, pertaining to various properties of the flow at a particular node. Scalar properties such as density, temperature, pressure, and velocity magnitude are properties that are typically calculated and stored in a dataset solution. Solutions aremore » not limited to just scalar properties. Vector quantities, such as velocity, are also often calculated and stored for a CFD simulation. Accessing all of this data efficiently during runtime is a key problem for visualization in an interactive application. Understanding simulation solutions requires a post-processing tool to convert the data into something more meaningful. Ideally, the application would present an interactive visual representation of the numerical data for any dataset that was simulated while maintaining the accuracy of the calculated solution. Most CFD applications currently sacrifice interactivity for accuracy, yielding highly detailed flow descriptions but limiting interaction for investigating the field.« less

Molecular dynamics simulation study of the early stages of nucleation of iron oxyhydroxide nanoparticles in aqueous solutions

DOE PAGES

Zhang, Hengzhong; Waychunas, Glenn A.; Banfield, Jillian F.

2015-07-29

Nucleation is a fundamental step in crystal growth. Of environmental and materials relevance are reactions that lead to nucleation of iron oxyhydroxides in aqueous solutions. These reactions are difficult to study experimentally due to their rapid kinetics. Here, we used classical molecular dynamics simulations to investigate nucleation of iron hydroxide/oxyhydroxide nanoparticles in aqueous solutions. Results show that in a solution containing ferric ions and hydroxyl groups, iron–hydroxyl molecular clusters form by merging ferric monomers, dimers, and other oligomers, driven by strong affinity of ferric ions to hydroxyls. When deprotonation reactions are not considered in the simulations, these clusters aggregate tomore » form small iron hydroxide nanocrystals with a six-membered ring-like layered structure allomeric to gibbsite. By comparison, in a solution containing iron chloride and sodium hydroxide, the presence of chlorine drives cluster assembly along a different direction to form long molecular chains (rather than rings) composed of Fe–O octahedra linked by edge sharing. Further, in chlorine-free solutions, when deprotonation reactions are considered, the simulations predict ultimate formation of amorphous iron oxyhydroxide nanoparticles with local atomic structure similar to that of ferrihydrite nanoparticles. Overall, our simulation results reveal that nucleation of iron oxyhydroxide nanoparticles proceeds via a cluster aggregation-based nonclassical pathway.« less

Structural, thermodynamic, and electrical properties of polar fluids and ionic solutions on a hypersphere: Results of simulations

NASA Astrophysics Data System (ADS)

Caillol, J. M.; Levesque, D.

1992-01-01

The reliability and the efficiency of a new method suitable for the simulations of dielectric fluids and ionic solutions is established by numerical computations. The efficiency depends on the use of a simulation cell which is the surface of a four-dimensional sphere. The reliability originates from a charge-charge potential solution of the Poisson equation in this confining volume. The computation time, for systems of a few hundred molecules, is reduced by a factor of 2 or 3 compared to this of a simulation performed in a cubic volume with periodic boundary conditions and the Ewald charge-charge potential.

Application of Molecular Dynamics Simulations in Molecular Property Prediction II: Diffusion Coefficient

PubMed Central

Wang, Junmei; Hou, Tingjun

2011-01-01

In this work, we have evaluated how well the General AMBER force field (GAFF) performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, 5 organic compounds in aqueous solutions, 4 proteins in aqueous solutions, and 9 organic compounds in non-aqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned error (AUE) and the root-mean-square error (RMSE) are 0.137 and 0.171 ×10−5 cm−2s−1, respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for 8 organic solvents with experimental data (R2 = 0.784), 4 proteins in aqueous solutions (R2 = 0.996) and 9 organic compounds in non-aqueous solutions (R2 = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide (DMSO) and cyclohexane have been studied. The major MD settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement (MSD) collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. PMID:21953689

Simulating the injection of micellar solutions to recover diesel in a sand column.

PubMed

Bernardez, Letícia A; Therrien, René; Lefebvre, René; Martel, Richard

2009-01-26

This paper presents numerical simulations of laboratory experiments where diesel, initially present at 18% residual saturation in a sand column, was recovered by injecting a micellar solution containing the surfactant Hostapur SAS-60 (SAS), and two alcohols, n-butanol (n-BuOH), and n-pentanol (n-PeOH). The micellar solution was developed and optimized for diesel recovery using phase diagrams and soil column experiments. Numerical simulations with the compositional simulator UTCHEM agree with the experimental results and show that the entire residual diesel in the sand column was recovered after the downward injection of 5 pore volumes of the micellar solution. Recovery of diesel occurs by enhanced solubility in the microemulsion phase and by mobilization. An additional series of simulations investigated the effects of phase transfer, alcohol partitioning, and component segregation on diesel recovery. These simulations indicate that diesel can be accurately represented in the model by a single component, but that the pseudo-component approach for active matter and the assumption of local phase equilibrium leads to an underestimation of diesel mobilization.

Simulating the injection of micellar solutions to recover diesel in a sand column

NASA Astrophysics Data System (ADS)

Bernardez, Letícia A.; Therrien, René; Lefebvre, René; Martel, Richard

2009-01-01

This paper presents numerical simulations of laboratory experiments where diesel, initially present at 18% residual saturation in a sand column, was recovered by injecting a micellar solution containing the surfactant Hostapur SAS-60 (SAS), and two alcohols, n-butanol ( n-BuOH), and n-pentanol ( n-PeOH). The micellar solution was developed and optimized for diesel recovery using phase diagrams and soil column experiments. Numerical simulations with the compositional simulator UTCHEM agree with the experimental results and show that the entire residual diesel in the sand column was recovered after the downward injection of 5 pore volumes of the micellar solution. Recovery of diesel occurs by enhanced solubility in the microemulsion phase and by mobilization. An additional series of simulations investigated the effects of phase transfer, alcohol partitioning, and component segregation on diesel recovery. These simulations indicate that diesel can be accurately represented in the model by a single component, but that the pseudo-component approach for active matter and the assumption of local phase equilibrium leads to an underestimation of diesel mobilization.

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2011-01-01

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

3-D simulation of nanopore structure for DNA sequencing.

PubMed

Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho

2012-07-01

In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures.

A simulation study of homogeneous ice nucleation in supercooled salty water

NASA Astrophysics Data System (ADS)

Soria, Guiomar D.; Espinosa, Jorge R.; Ramirez, Jorge; Valeriani, Chantal; Vega, Carlos; Sanz, Eduardo

2018-06-01

We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous calculations of the water chemical potential. Using a seeding approach, in which we simulate ice seeds embedded in a supercooled aqueous solution, we compute the nucleation rate as a function of temperature for a 1.85 NaCl mol per water kilogram solution at 1 bar. To improve the accuracy and reliability of our calculations, we combine seeding with the direct computation of the ice-solution interfacial free energy at coexistence using the Mold Integration method. We compare the results with previous simulation work on pure water to understand the effect caused by the solute. The model captures the experimental trend that the nucleation rate at a given supercooling decreases when adding salt. Despite the fact that the thermodynamic driving force for ice nucleation is higher for salty water for a given supercooling, the nucleation rate slows down with salt due to a significant increase of the ice-fluid interfacial free energy. The salty water model predicts an ice nucleation rate that is in good agreement with experimental measurements, bringing confidence in the predictive ability of the model. We expect that the combination of state-of-the-art simulation methods here employed to study ice nucleation from solution will be of much use in forthcoming numerical investigations of crystallization in mixtures.

A simulation study of homogeneous ice nucleation in supercooled salty water.

PubMed

Soria, Guiomar D; Espinosa, Jorge R; Ramirez, Jorge; Valeriani, Chantal; Vega, Carlos; Sanz, Eduardo

2018-06-14

We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous calculations of the water chemical potential. Using a seeding approach, in which we simulate ice seeds embedded in a supercooled aqueous solution, we compute the nucleation rate as a function of temperature for a 1.85 NaCl mol per water kilogram solution at 1 bar. To improve the accuracy and reliability of our calculations, we combine seeding with the direct computation of the ice-solution interfacial free energy at coexistence using the Mold Integration method. We compare the results with previous simulation work on pure water to understand the effect caused by the solute. The model captures the experimental trend that the nucleation rate at a given supercooling decreases when adding salt. Despite the fact that the thermodynamic driving force for ice nucleation is higher for salty water for a given supercooling, the nucleation rate slows down with salt due to a significant increase of the ice-fluid interfacial free energy. The salty water model predicts an ice nucleation rate that is in good agreement with experimental measurements, bringing confidence in the predictive ability of the model. We expect that the combination of state-of-the-art simulation methods here employed to study ice nucleation from solution will be of much use in forthcoming numerical investigations of crystallization in mixtures.

A comparison of three approaches for simulating fine-scale surface winds in support of wildland fire management. Part II. An exploratory study of the effect of simulated winds on fire growth simulations

Treesearch

Jason M. Forthofer; Bret W. Butler; Charles W. McHugh; Mark A. Finney; Larry S. Bradshaw; Richard D. Stratton; Kyle S. Shannon; Natalie S. Wagenbrenner

2014-01-01

The effect of fine-resolution wind simulations on fire growth simulations is explored. The wind models are (1) a wind field consisting of constant speed and direction applied everywhere over the area of interest; (2) a tool based on the solution of the conservation of mass only (termed mass-conserving model) and (3) a tool based on a solution of conservation of mass...

Simulating contaminant attenuation, double-porosity exchange, and water age in aquifers using MOC3D

USGS Publications Warehouse

Goode, Daniel J.

1999-01-01

MOC3D is a general-purpose computer model developed by the U.S. Geological Survey (USGS) for simulation of three-dimensional solute transport in ground water (Konikow and others, 1996). The model is an update to the widely used USGS two-dimensional solute-transport model (MOC) and is implemented as an optional “package” for the ground-water flow model MODFLOW (Harbaugh and McDonald, 1996). Directly coupling the time-tested MOC transport algorithms with the widely used MODFLOW program makes MOC3D a powerful tool for simulation of solute transport in ground water in many hydrogeologic settings. The model simulates transport processes that include:Advection - Transport of dissolved solutes at the same rate as the average ground-water flow velocity.Diffusion - Spreading of solute from areas of high concentration to areas of low concentration, caused by “random” molecular motionDispersion - Diffusion-like spreading of solute that is caused primarily by spatial variability in aquifer properties, which results in spatial variability in transport velocity.Retardation - Reduction in the apparent solute velocity, compared to the ground-water velocity, caused by linear equilibrium sorption on aquifer materials.Decay - Disappearance of solute caused by reactions such as radioactive decay or biodegradation that are proportional to concentration.Growth - Creation (or disappearance) of solute mass caused by reactions that proceed independent of the solute concentration, such as some cases of biodegradationDouble-porosity exchange - rate-limited exchange of solute mass between mobile and immobile zones; for example, between fractures and the rock matrix.

Modeling mass transfer and reaction of dilute solutes in a ternary phase system by the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Fu, Yu-Hang; Bai, Lin; Luo, Kai-Hong; Jin, Yong; Cheng, Yi

2017-04-01

In this work, we propose a general approach for modeling mass transfer and reaction of dilute solute(s) in incompressible three-phase flows by introducing a collision operator in lattice Boltzmann (LB) method. An LB equation was used to simulate the solute dynamics among three different fluids, in which the newly expanded collision operator was used to depict the interface behavior of dilute solute(s). The multiscale analysis showed that the presented model can recover the macroscopic transport equations derived from the Maxwell-Stefan equation for dilute solutes in three-phase systems. Compared with the analytical equation of state of solute and dynamic behavior, these results are proven to constitute a generalized framework to simulate solute distributions in three-phase flows, including compound soluble in one phase, compound adsorbed on single-interface, compound in two phases, and solute soluble in three phases. Moreover, numerical simulations of benchmark cases, such as phase decomposition, multilayered planar interfaces, and liquid lens, were performed to test the stability and efficiency of the model. Finally, the multiphase mass transfer and reaction in Janus droplet transport in a straight microchannel were well reproduced.

Multi-Conformation Monte Carlo: A Method for Introducing Flexibility in Efficient Simulations of Many-Protein Systems.

PubMed

Prytkova, Vera; Heyden, Matthias; Khago, Domarin; Freites, J Alfredo; Butts, Carter T; Martin, Rachel W; Tobias, Douglas J

2016-08-25

We present a novel multi-conformation Monte Carlo simulation method that enables the modeling of protein-protein interactions and aggregation in crowded protein solutions. This approach is relevant to a molecular-scale description of realistic biological environments, including the cytoplasm and the extracellular matrix, which are characterized by high concentrations of biomolecular solutes (e.g., 300-400 mg/mL for proteins and nucleic acids in the cytoplasm of Escherichia coli). Simulation of such environments necessitates the inclusion of a large number of protein molecules. Therefore, computationally inexpensive methods, such as rigid-body Brownian dynamics (BD) or Monte Carlo simulations, can be particularly useful. However, as we demonstrate herein, the rigid-body representation typically employed in simulations of many-protein systems gives rise to certain artifacts in protein-protein interactions. Our approach allows us to incorporate molecular flexibility in Monte Carlo simulations at low computational cost, thereby eliminating ambiguities arising from structure selection in rigid-body simulations. We benchmark and validate the methodology using simulations of hen egg white lysozyme in solution, a well-studied system for which extensive experimental data, including osmotic second virial coefficients, small-angle scattering structure factors, and multiple structures determined by X-ray and neutron crystallography and solution NMR, as well as rigid-body BD simulation results, are available for comparison.

Aeroacoustic Simulations of a Nose Landing Gear Using FUN3D on Pointwise Unstructured Grids

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Khorrami, Mehdi R.; Rhoads, John; Lockard, David P.

2015-01-01

Numerical simulations have been performed for a partially-dressed, cavity-closed (PDCC) nose landing gear configuration that was tested in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D is used to compute the unsteady flow field for this configuration. Mixed-element grids generated using the Pointwise(TradeMark) grid generation software are used for these simulations. Particular care is taken to ensure quality cells and proper resolution in critical areas of interest in an effort to minimize errors introduced by numerical artifacts. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these simulations. Solutions are also presented for a wall function model coupled to the standard turbulence model. Time-averaged and instantaneous solutions obtained on these Pointwise grids are compared with the measured data and previous numerical solutions. The resulting CFD solutions are used as input to a Ffowcs Williams-Hawkings noise propagation code to compute the farfield noise levels in the flyover and sideline directions. The computed noise levels compare well with previous CFD solutions and experimental data.

Pitting Behavior of L415 Pipeline Steel in Simulated Leaching Liquid Environment

NASA Astrophysics Data System (ADS)

Wan, H. X.; Yang, X. J.; Liu, Z. Y.; Song, D. D.; Du, C. W.; Li, X. G.

2017-02-01

The corrosion behavior and laws of the west-east gas pressure pipeline of L415 steel were studied in simulated leaching liquid. The failure of the L415 steel during the pressure testing process was investigated using electrochemical polarization, electrochemical impedance spectroscopy, and immersion test. The corrosion rate of the L415 steel increased with ion concentration in the leaching liquid. This rate reached about 0.8 mm a-1 and belonged to the severe corrosion grade. Pitting corrosion was observed in various simulated solutions with different aggressive species concentrations. The original ion concentration in the leaching liquid (1×) is the key factor influencing pitting initiation and development. Pitting showed easy nucleation, and its growth rate was relatively slow, in the basic simulating solution of the leach liquid (i.e., the ion content is compactable to the real condition in the rust on the inner steel pipe surface). Pitting was also highly sensitive and easily grew in the solution with doubled ion concentration in the basic simulating solution (2×). A uniform corrosion, instead of pitting, mainly occurred when the ion concentration was up to 10× of the basic solution.

Numerical study of wave effects on groundwater flow and solute transport in a laboratory beach.

PubMed

Geng, Xiaolong; Boufadel, Michel C; Xia, Yuqiang; Li, Hailong; Zhao, Lin; Jackson, Nancy L; Miller, Richard S

2014-09-01

A numerical study was undertaken to investigate the effects of waves on groundwater flow and associated inland-released solute transport based on tracer experiments in a laboratory beach. The MARUN model was used to simulate the density-dependent groundwater flow and subsurface solute transport in the saturated and unsaturated regions of the beach subjected to waves. The Computational Fluid Dynamics (CFD) software, Fluent, was used to simulate waves, which were the seaward boundary condition for MARUN. A no-wave case was also simulated for comparison. Simulation results matched the observed water table and concentration at numerous locations. The results revealed that waves generated seawater-groundwater circulations in the swash and surf zones of the beach, which induced a large seawater-groundwater exchange across the beach face. In comparison to the no-wave case, waves significantly increased the residence time and spreading of inland-applied solutes in the beach. Waves also altered solute pathways and shifted the solute discharge zone further seaward. Residence Time Maps (RTM) revealed that the wave-induced residence time of the inland-applied solutes was largest near the solute exit zone to the sea. Sensitivity analyses suggested that the change in the permeability in the beach altered solute transport properties in a nonlinear way. Due to the slow movement of solutes in the unsaturated zone, the mass of the solute in the unsaturated zone, which reached up to 10% of the total mass in some cases, constituted a continuous slow release of solutes to the saturated zone of the beach. This means of control was not addressed in prior studies. Copyright © 2014 Elsevier B.V. All rights reserved.

Method for treating materials for solidification

DOEpatents

Jantzen, Carol M.; Pickett, John B.; Martin, Hollis L.

1995-01-01

A method for treating materials such as wastes for solidification to form a solid, substantially nonleachable product. Addition of reactive silica rather than ordinary silica to the material when bringing the initial molar ratio of its silica constituent to a desired ratio within a preselected range increases the solubility and retention of the materials in the solidified matrix. Materials include hazardous, radioactive, mixed, and heavy metal species. Amounts of other constituents of the material, in addition to its silica content are also added so that the molar ratio of each of these constituents is within the preselected ranges for the final solidified product. The mixture is then solidified by cement solidification or vitrification. The method can be used to treat a variety of wastes, including but not limited to spent filter aids from waste water treatment, waste sludges, combinations of spent filter aids and waste sludges, combinations of supernate and waste sludges, incinerator ash, incinerator offgas blowdown, combinations of incinerator ash and offgas blowdown, cementitious wastes and contaminated soils.

Analysis of Tank 38H (HTF-38-15-119, 127) Surface, Subsurface and Tank 43H (HTF-43-15-116, 117 and 118) Surface, Feed Pump Suction and Jet Suction Subsurface Supernatant Samples in Support of Enrichment, Corrosion Control and Salt Batch Planning Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oji, L.

Compositional feed limits have been established to ensure that a nuclear criticality event for the 2H and 3H Evaporators is not possible. The Enrichment Control Program (ECP) requires feed sampling to determine the equivalent enriched uranium content prior to transfer of waste other than recycle transfers (requires sampling to determine the equivalent enriched uranium at two locations in Tanks 38H and 43H every 26 weeks) The Corrosion Control Program (CCP) establishes concentration and temperature limits for key constituents and periodic sampling and analysis to confirm that waste supernate is within these limits. This report provides the results of analyses onmore » Tanks 38H and 43H surface and subsurface supernatant liquid samples in support of the ECP, the CCP, and the Salt Batch 10 Planning Program.« less

A new unconditionally stable and consistent quasi-analytical in-stream water quality solution scheme for CSTR-based water quality simulators

NASA Astrophysics Data System (ADS)

Woldegiorgis, Befekadu Taddesse; van Griensven, Ann; Pereira, Fernando; Bauwens, Willy

2017-06-01

Most common numerical solutions used in CSTR-based in-stream water quality simulators are susceptible to instabilities and/or solution inconsistencies. Usually, they cope with instability problems by adopting computationally expensive small time steps. However, some simulators use fixed computation time steps and hence do not have the flexibility to do so. This paper presents a novel quasi-analytical solution for CSTR-based water quality simulators of an unsteady system. The robustness of the new method is compared with the commonly used fourth-order Runge-Kutta methods, the Euler method and three versions of the SWAT model (SWAT2012, SWAT-TCEQ, and ESWAT). The performance of each method is tested for different hypothetical experiments. Besides the hypothetical data, a real case study is used for comparison. The growth factors we derived as stability measures for the different methods and the R-factor—considered as a consistency measure—turned out to be very useful for determining the most robust method. The new method outperformed all the numerical methods used in the hypothetical comparisons. The application for the Zenne River (Belgium) shows that the new method provides stable and consistent BOD simulations whereas the SWAT2012 model is shown to be unstable for the standard daily computation time step. The new method unconditionally simulates robust solutions. Therefore, it is a reliable scheme for CSTR-based water quality simulators that use first-order reaction formulations.

A gold cyano complex in nitromethane: MD simulation and X-ray diffraction.

PubMed

Probst, Michael; Injan, Natcha; Megyes, Tünde; Bako, Imre; Balint, Szabolcz; Limtrakul, Jumras; Nazmutdinov, Renat; Mitev, Pavlin D; Hermansson, Kersti

2012-06-29

The solvation structure around the dicyanoaurate(I) anion (Au(CN) 2 - ) in a dilute nitromethane (CH 3 NO 2 ) solution is presented from X-ray diffraction measurements and molecular dynamics simulation (NVT ensemble, 460 nitromethane molecules at room temperature). The simulations are based on a new solute-solvent force-field fitted to a training set of quantum-chemically derived interaction energies. Radial distribution functions from experiment and simulation are in good agreement. The solvation structure has been further elucidated from MD data. Several shells can be identified. We obtain a solvation number of 13-17 nitromethane molecules with a strong preference to be oriented with their methyl groups towards the solute.

Solutions of conformal Israel-Stewart relativistic viscous fluid dynamics

NASA Astrophysics Data System (ADS)

Marrochio, Hugo; Noronha, Jorge; Denicol, Gabriel S.; Luzum, Matthew; Jeon, Sangyong; Gale, Charles

2015-01-01

We use symmetry arguments developed by Gubser to construct the first radially expanding explicit solutions of the Israel-Stewart formulation of hydrodynamics. Along with a general semi-analytical solution, an exact analytical solution is given which is valid in the cold plasma limit where viscous effects from shear viscosity and the relaxation time coefficient are important. The radially expanding solutions presented in this paper can be used as nontrivial checks of numerical algorithms employed in hydrodynamic simulations of the quark-gluon plasma formed in ultrarelativistic heavy ion collisions. We show this explicitly by comparing such analytic and semi-analytic solutions with the corresponding numerical solutions obtained using the music viscous hydrodynamics simulation code.

Simulation and statistics: Like rhythm and song

NASA Astrophysics Data System (ADS)

Othman, Abdul Rahman

2013-04-01

Simulation has been introduced to solve problems in the form of systems. By using this technique the following two problems can be overcome. First, a problem that has an analytical solution but the cost of running an experiment to solve is high in terms of money and lives. Second, a problem exists but has no analytical solution. In the field of statistical inference the second problem is often encountered. With the advent of high-speed computing devices, a statistician can now use resampling techniques such as the bootstrap and permutations to form pseudo sampling distribution that will lead to the solution of the problem that cannot be solved analytically. This paper discusses how a Monte Carlo simulation was and still being used to verify the analytical solution in inference. This paper also discusses the resampling techniques as simulation techniques. The misunderstandings about these two techniques are examined. The successful usages of both techniques are also explained.

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient.

PubMed

Wang, Junmei; Hou, Tingjun

2011-12-01

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. Copyright © 2011 Wiley Periodicals, Inc.

Existence and numerical simulation of periodic traveling wave solutions to the Casimir equation for the Ito system

NASA Astrophysics Data System (ADS)

Abbasbandy, S.; Van Gorder, R. A.; Hajiketabi, M.; Mesrizadeh, M.

2015-10-01

We consider traveling wave solutions to the Casimir equation for the Ito system (a two-field extension of the KdV equation). These traveling waves are governed by a nonlinear initial value problem with an interesting nonlinearity (which actually amplifies in magnitude as the size of the solution becomes small). The nonlinear problem is parameterized by two initial constant values, and we demonstrate that the existence of solutions is strongly tied to these parameter values. For our interests, we are concerned with positive, bounded, periodic wave solutions. We are able to classify parameter regimes which admit such solutions in full generality, thereby obtaining a nice existence result. Using the existence result, we are then able to numerically simulate the positive, bounded, periodic solutions. We elect to employ a group preserving scheme in order to numerically study these solutions, and an outline of this approach is provided. The numerical simulations serve to illustrate the properties of these solutions predicted analytically through the existence result. Physically, these results demonstrate the existence of a type of space-periodic structure in the Casimir equation for the Ito model, which propagates as a traveling wave.

A computer program for the simulation of heat and moisture flow in soils

NASA Technical Reports Server (NTRS)

Camillo, P.; Schmugge, T. J.

1981-01-01

A computer program that simulates the flow of heat and moisture in soils is described. The space-time dependence of temperature and moisture content is described by a set of diffusion-type partial differential equations. The simulator uses a predictor/corrector to numerically integrate them, giving wetness and temperature profiles as a function of time. The simulator was used to generate solutions to diffusion-type partial differential equations for which analytical solutions are known. These equations include both constant and variable diffusivities, and both flux and constant concentration boundary conditions. In all cases, the simulated and analytic solutions agreed to within the error bounds which were imposed on the integrator. Simulations of heat and moisture flow under actual field conditions were also performed. Ground truth data were used for the boundary conditions and soil transport properties. The qualitative agreement between simulated and measured profiles is an indication that the model equations are reasonably accurate representations of the physical processes involved.

Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics.

PubMed

Alibay, Irfan; Burusco, Kepa K; Bruce, Neil J; Bryce, Richard A

2018-03-08

Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4 C 1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.

Water and Solute Flux Simulation Using Hydropedology Survey Data in South African Catchments

NASA Astrophysics Data System (ADS)

Lorentz, Simon; van Tol, Johan; le Roux, Pieter

2017-04-01

Hydropedology surveys include linking soil profile information in hillslope transects in order to define dominant subsurface flow mechanisms and pathways. This information is useful for deriving hillslope response functions, which aid storage and travel time estimates of water and solute movement in the sub-surface. In this way, the "soft" data of the hydropedological survey can be included in simple hydrological models, where detailed modelling of processes and pathways is prohibitive. Hydropedology surveys were conducted in two catchments and the information used to improve the prediction of water and solute responses. Typical hillslope response functions are then derived using a 2-D finite element model of the hydropedological features. Similar response types are mapped. These mapped response units are invoked in a simple SCS based, hydrological and solute transport model to yield water and solute fluxes at the catchment outlets. The first catchment (1.6 km2) comprises commercial forestry in a sedimentary geology of sandstone and mudstone formation while the second catchment (6.1 km2) includes mine waste impoundments in a granitic geology. In this paper, we demonstrate the method of combining hydropedological interpretation with catchment hydrology and solute transport simulation. The forested catchment, with three dominant hillslope response types, have solute response times in excess of 90 days, whereas the granitic responses occur within 10 days. The use of the hydropedological data improves the solute distribution response and storage simulation, compared to simulations without the hydropedology interpretation. The hydrological responses are similar, with and without the use of the hydropedology data, but the simulated distribution of water in the catchment is improved using the techniques demonstrated.

Numerical Simulation of a Seaway with Breaking

NASA Astrophysics Data System (ADS)

Dommermuth, Douglas; O'Shea, Thomas; Brucker, Kyle; Wyatt, Donald

2012-11-01

The focus of this presentation is to describe the recent efforts to simulate a fully non-linear seaway with breaking by using a high-order spectral (HOS) solution of the free-surface boundary value problem to drive a three-dimensional Volume of Fluid (VOF) solution. Historically, the two main types of simulations to simulate free-surface flows are the boundary integral equations method (BIEM) and high-order spectral (HOS) methods. BIEM calculations fail at the point at which the surface impacts upon itself, if not sooner, and HOS methods can only simulate a single valued free-surface. Both also employ a single-phase approximation in which the effects of the air on the water are neglected. Due to these limitations they are unable to simulate breaking waves and air entrainment. The Volume of Fluid (VOF) method on the other hand is suitable for modeling breaking waves and air entrainment. However it is computationally intractable to generate a realistic non-linear sea-state. Here, we use the HOS solution to quickly drive, or nudge, the VOF solution into a non-linear state. The computational strategies, mathematical formulation, and numerical implementation will be discussed. The results of the VOF simulation of a seaway with breaking will also be presented, and compared to the single phase, single valued HOS results.

Use of simulated evaporation to assess the potential for scale formation during reverse osmosis desalination

USGS Publications Warehouse

Huff, G.F.

2004-01-01

The tendency of solutes in input water to precipitate efficiency lowering scale deposits on the membranes of reverse osmosis (RO) desalination systems is an important factor in determining the suitability of input water for desalination. Simulated input water evaporation can be used as a technique to quantitatively assess the potential for scale formation in RO desalination systems. The technique was demonstrated by simulating the increase in solute concentrations required to form calcite, gypsum, and amorphous silica scales at 25??C and 40??C from 23 desalination input waters taken from the literature. Simulation results could be used to quantitatively assess the potential of a given input water to form scale or to compare the potential of a number of input waters to form scale during RO desalination. Simulated evaporation of input waters cannot accurately predict the conditions under which scale will form owing to the effects of potentially stable supersaturated solutions, solution velocity, and residence time inside RO systems. However, the simulated scale-forming potential of proposed input waters could be compared with the simulated scale-forming potentials and actual scale-forming properties of input waters having documented operational histories in RO systems. This may provide a technique to estimate the actual performance and suitability of proposed input waters during RO.

MODFLOW/MT3DMS-based simulation of variable-density ground water flow and transport

USGS Publications Warehouse

Langevin, C.D.; Guo, W.

2006-01-01

This paper presents an approach for coupling MODFLOW and MT3DMS for the simulation of variable-density ground water flow. MODFLOW routines were modified to solve a variable-density form of the ground water flow equation in which the density terms are calculated using an equation of state and the simulated MT3DMS solute concentrations. Changes to the MODFLOW and MT3DMS input files were kept to a minimum, and thus existing data files and data files created with most pre- and postprocessors can be used directly with the SEAWAT code. The approach was tested by simulating the Henry problem and two of the saltpool laboratory experiments (low- and high-density cases). For the Henry problem, the simulated results compared well with the steady-state semianalytic solution and also the transient isochlor movement as simulated by a finite-element model. For the saltpool problem, the simulated breakthrough curves compared better with the laboratory measurements for the low-density case than for the high-density case but showed good agreement with the measured salinity isosurfaces for both cases. Results from the test cases presented here indicate that the MODFLOW/MT3DMS approach provides accurate solutions for problems involving variable-density ground water flow and solute transport. ?? 2006 National Ground Water Association.

LABORATORY REPORT ON THE REMOVAL OF PERTECHNETATE FROM TANK 241-AN-105 SIMULANT USING PUROLITE A530E

DOE Office of Scientific and Technical Information (OSTI.GOV)

DUNCAN JB; HAGERTY KJ, MOORE WP; JOHNSON JM

2012-04-17

This report documents the laboratory testing and analyses as directed under the test plan, LAB-PLN-11-00010, Evaluation of Technetium Ion Exchange Material against Hanford Double Shell Tank Supernate Simulate with Pertechnetate. Technetium (Tc-99) is a major fission product from nuclear reactors, and because it has few applications outside of scientific research, most of the technetium will ultimately be disposed of as nuclear waste. The radioactive decay of Tc-99 to ruthenium 99 (Ru-99) produces a low energy {beta}{sup -} particle (0.1 MeV max). However, due to its fairly long half-life (t{sub 1/2} = 2.13E05 years), Tc-99 is a major source of radiationmore » in low-level waste (UCRL-JRNL-212334, Current Status of the Thermodynamic Data for Technetium and its Compounds and Aqueous Species). Technetium forms the soluble oxy anion, TcO{sub 4}{sup -} under aerobic conditions. This anion is very mobile in groundwater and poses a health risk (ANL, Radiological and Chemical Fact Sheets to Support Health Risk Analyses for Contaminated Areas). It has been demonstrated that Purolite{reg_sign} A530E is highly effective in removing TcO{sub 4}{sup -} from a water matrix (RPP-RPT-23199, The Removal of Technetium-99 from the Effluent Treatment Facility Basin 44 Waste Using Purolite A-530E, Reillex HPQ, and Sybron IONAC SR-7 Ion Exchange Resins). Purolite{reg_sign} A530E is the commercial product of the Oak Ridge National Laboratory's Biquat{trademark} resin (Gu, B. et. ai, Development of Novel Bifunctional Anion-Exchange Resins with Improved Selectivity for Pertechnetate Sorption from Contaminated Groundwater). Further work has demonstrated that technetium-loaded A530E achieves a leachability index in Cast Stone of 12.5 (ANSI/ASN-16.1-2003, Measurement of the Leachability of Solidified Low-Level Radioactive Wastes by a Short-term Test Procedure) as reported in RPP-RPT-39195, Assessment of Technetium Leachability in Cement-Stabilized Basin 43 Groundwater Brine. This effort falls under the technetium management initiative and will provide data for those who will make decisions on the handling and disposition of technetium. To that end, the objective of this effort was to challenge Purolite{reg_sign} A530E against a double-shell tank (DST) simulant (tank 241-AN-105 or AN-105) spiked with pertechnetate (TcO{sub 4}{sup -}) to determine breakthrough of the lead column.« less

Towards wall functions for the prediction of solute segregation in plane front directional solidification

NASA Astrophysics Data System (ADS)

Chatelain, M.; Rhouzlane, S.; Botton, V.; Albaric, M.; Henry, D.; Millet, S.; Pelletier, D.; Garandet, J. P.

2017-10-01

The present paper focuses on solute segregation occurring in directional solidification processes with sharp solid/liquid interface, like silicon crystal growth. A major difficulty for the simulation of such processes is their inherently multi-scale nature: the impurity segregation problem is controlled at the solute boundary layer scale (micrometers) while the thermal problem is ruled at the crucible scale (meters). The thickness of the solute boundary layer is controlled by the convection regime and requires a specific refinement of the mesh of numerical models. In order to improve numerical simulations, wall functions describing solute boundary layers for convecto-diffusive regimes are derived from a scaling analysis. The aim of these wall functions is to obtain segregation profiles from purely thermo-hydrodynamic simulations, which do not require solute boundary layer refinement at the solid/liquid interface. Regarding industrial applications, various stirring techniques can be used to enhance segregation, leading to fully turbulent flows in the melt. In this context, the scaling analysis is further improved by taking into account the turbulent solute transport. The solute boundary layers predicted by the analytical model are compared to those obtained by transient segregation simulations in a canonical 2D lid driven cavity configuration for validation purposes. Convective regimes ranging from laminar to fully turbulent are considered. Growth rate and molecular diffusivity influences are also investigated. Then, a procedure to predict concentration fields in the solid phase from a hydrodynamic simulation of the solidification process is proposed. This procedure is based on the analytical wall functions and on solute mass conservation. It only uses wall shear-stress profiles at the solidification front as input data. The 2D analytical concentration fields are directly compared to the results of the complete simulation of segregation in the lid driven cavity configuration. Finally, an additional output from the analytical model is also presented. We put in light the correlation between different species convecto-diffusive behaviour; we use it to propose an estimation method for the segregation parameters of various chemical species knowing segregation parameters of one specific species.

Culture of impure human islet fractions in the presence of alpha-1 antitrypsin prevents insulin cleavage and improves islet recovery.

PubMed

Loganathan, G; Dawra, R K; Pugazhenthi, S; Wiseman, A C; Sanders, M A; Saluja, A K; Sutherland, D E R; Hering, B J; Balamurugan, A N

2010-01-01

Exocrine tissue is commonly cotransplanted with islets in autografting and allotransplantation of impure preparations. Proteases and insulin are released by acinar cells and islets, respectively, during pretransplantation culture and also systemically after transplantation. We hypothesized that released proteases could cleave insulin molecules and that addition of alpha-1 antitrypsin (A1AT) to impure islet cultures would block this cleavage, improving islet recovery and function. Trypsin, chymotrypsin, and elastase (TCE) activity and insulin levels were measured in culture supernates of pure (n = 5) and impure (n = 5) islet fractions, which were isolated from deceased donors. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to detect insulin after incubation with proteases. We assessed the effects of A1AT supplementation (0.5 mg/mL; n = 4] on TCE activity, insulin levels, culture recovery, and islet quality. The ultrastructure of islets exposed to TCE versus control medium was examined using electron microscopy (EM). Protease (TCE) activity in culture supernatants was indirectly proportional to the percentage purity of islets: pure, impure, or highly impure. Increasingly lower levels of insulin were detected in culture supernatants when higher protease activity levels were present. Insulin levels measured from supernatants of impure and highly impure islet preparations were 61 +/- 23.7% and 34 +/- 33% of that in pure preparations, respectively. Incubation with commercially available proteases (TCE) or exocrine acinar cell supernatant cleaved insulin molecules as assessed using SDS-PAGE. Addition of A1AT to impure islet preparations reduced protease activity and restored normal insulin levels as detected using enzyme-linked immunosorbent assay (ELISA) and SDS-PAGE of culture supernates. A1AT improved insulin levels to 98% +/- 1.3% in impure and 78% +/- 34.2% in highly impure fractions compared with pure islet fractions. A1AT supplementation improved postculture recovery of islets in impure preparations compared with nontreated controls (72% +/- 9% vs 47% +/- 15%). Islet viability as measured using membrane integrity assays was similar in both the control (98% +/- 2%) and the A1AT-treated groups (99% +/- 1%). EM results revealed a reduction or absence of secretory granules after exposure to proteases (TCE). Culture of impure human islet fractions in the presence of A1AT prevented insulin cleavage and improved islet recovery. A1AT supplementation of islet culture media, therefore, may increase the proportion of human islet products that meet release criteria for transplantation. Copyright 2010 Elsevier Inc. All rights reserved.

Tank 40 Final Sludge Batch 8 Chemical Characterization Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bannochie, Christopher J.

2013-09-19

A sample of Sludge Batch 8 (SB8) was pulled from Tank 40 in order to obtain radionuclide inventory analyses necessary for compliance with the Waste Acceptance Product Specifications (WAPS). The SB8 WAPS sample was also analyzed for chemical composition, including noble metals, and fissile constituents, and these results are reported here. These analyses along with the WAPS radionuclide analyses will help define the composition of the sludge in Tank 40 that is currently being fed to the Defense Waste Processing Facility (DWPF) as SB8. At SRNL, the 3-L Tank 40 SB8 sample was transferred from the shipping container into amore » 4-L high density polyethylene bottle and solids were allowed to settle. Supernate was then siphoned off and circulated through the shipping container to complete the transfer of the sample. Following thorough mixing of the 3-L sample, a 553 g sub-sample was removed. This sub-sample was then utilized for all subsequent slurry sample preparations. Eight separate aliquots of the slurry were digested, four with HNO{sub 3}/HCl (aqua regia) in sealed Teflon(r) vessels and four with NaOH/Na{sub 2}O{sub 2} (alkali or peroxide fusion) using Zr crucibles. Two Analytical Reference Glass - 1 (ARG-1) standards were digested along with a blank for each preparation. Each aqua regia digestion and blank was diluted to 1:100 mL with deionized water and submitted to Analytical Development (AD) for inductively coupled plasma - atomic emission spectroscopy (ICP-AES) analysis, inductively coupled plasma - mass spectrometry (ICP-MS) analysis, atomic absorption spectroscopy (AA) for As and Se, and cold vapor atomic absorption spectroscopy (CV-AA) for Hg. Equivalent dilutions of the alkali fusion digestions and blank were submitted to AD for ICP-AES analysis. Tank 40 SB8 supernate was collected from a mixed slurry sample in the SRNL Shielded Cells and submitted to AD for ICP-AES, ion chromatography (IC), total base/free OH-/other base, total inorganic carbon/total organic carbon (TIC/TOC) analyses. Weighted dilutions of slurry were submitted for IC, TIC/TOC, and total base/free OH-/other base analyses. Activities for U-233, U-235, and Pu-239 were determined from the ICP-MS data for the aqua regia digestions of the Tank 40 WAPS slurry using the specific activity of each isotope. The Pu-241 value was determined from a Pu-238/-241 method developed by SRNL AD and previously described.« less

Tank 40 final sludge batch 9 chemical and fissile radionuclide characterization results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bannochie, C. J.; Kubilius, W. P.; Pareizs, J. M.

A sample of Sludge Batch (SB) 9 was pulled from Tank 40 in order to obtain radionuclide inventory analyses necessary for compliance with the Waste Acceptance Product Specifications (WAPS)i. The SB9 WAPS sample was also analyzed for chemical composition, including noble metals, and fissile constituents, and these results are reported here. These analyses along with the WAPS radionuclide analyses will help define the composition of the sludge in Tank 40 that is fed to the Defense Waste Processing Facility (DWPF) as SB9. At the Savannah River National Laboratory (SRNL), the 3-L Tank 40 SB9 sample was transferred from the shippingmore » container into a 4-L high density polyethylene bottle and solids were allowed to settle. Supernate was then siphoned off and circulated through the shipping container to complete the transfer of the sample. Following thorough mixing of the 3-L sample, a 547 g sub-sample was removed. This sub-sample was then utilized for all subsequent slurry sample preparations. Eight separate aliquots of the slurry were digested, four with HNO3/HCl (aqua regiaii) in sealed Teflon® vessels and four with NaOH/Na2O2 (alkali or peroxide fusioniii) using Zr crucibles. Three Analytical Reference Glass – 1iv (ARG-1) standards were digested along with a blank for each preparation. Each aqua regia digestion and blank was diluted to 1:100 with deionized water and submitted to Analytical Development (AD) for inductively coupled plasma – atomic emission spectroscopy (ICP-AES) analysis, inductively coupled plasma – mass spectrometry (ICP-MS) analysis, atomic absorption spectroscopy (AA) for As and Se, and cold vapor atomic absorption spectroscopy (CV-AA) for Hg. Equivalent dilutions of the alkali fusion digestions and blank were submitted to AD for ICP-AES analysis. Tank 40 SB9 supernate was collected from a mixed slurry sample in the SRNL Shielded Cells and submitted to AD for ICP-AES, ion chromatography (IC), total base/free OH-/other base, total inorganic carbon/total organic carbon (TIC/TOC) analyses. Weighted dilutions of slurry were submitted for IC, TIC/TOC, and total base/free OH-/other base analyses. Activities for U-233, U-235, and Pu-239 were determined from the ICP-MS data for the aqua regia digestions of the SB9 WAPS slurry using the specific activity of each isotope. The Pu-241 value was determined from a Pu-238/-241 method developed by SRNL AD and previously described.v« less

The effect of pH on phosphorus availability and speciation in an aquaponics nutrient solution.

PubMed

Cerozi, Brunno da Silva; Fitzsimmons, Kevin

2016-11-01

The interaction between the main ions in aquaponics nutrient solutions affects chemical composition and availability of nutrients, and nutrient uptake by plant roots. This study determined the effect of pH on phosphorus (P) speciation and availability in an aquaponics nutrient solution and used Visual MINTEQ to simulate P species and P activity. In both experimental and simulated results, P availability decreased with increase in pH of aquaponics nutrient solutions. According to simulations, P binds to several cations leaving less free phosphate ions available in solution. High pH values resulted in the formation of insoluble calcium phosphate species. The study also demonstrated the importance of organic matter and alkalinity in keeping free phosphate ions in solution at high pH ranges. It is recommended though that pH in aquaponics systems is maintained at a 5.5-7.2 range for optimal availability and uptake by plants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Translational and rotational dynamics of monosaccharide solutions.

PubMed

Lelong, Gérald; Howells, W Spencer; Brady, John W; Talón, César; Price, David L; Saboungi, Marie-Louise

2009-10-01

Molecular dynamics computer simulations have been carried out on aqueous solutions of glucose at concentrations bracketing those previously measured with quasi-elastic neutron scattering (QENS), in order to investigate the motions and interactions of the sugar and water molecules. In addition, QENS measurements have been carried out on fructose solutions to determine whether the effects previously observed for glucose apply to monosaccharide solutions. The simulations indicate a dynamical analogy between higher solute concentration and lower temperature that could provide a key explanation of the bioprotective phenomena observed in many living organisms. The experimental results on fructose solutions show qualitatively similar behavior to the glucose solutions. The dynamics of the water molecules are essentially the same, while the translational diffusion of the sugar molecules is slightly faster in the fructose solutions.

Interactions of solutes and streambed sediment: 2. A dynamic analysis of coupled hydrologic and chemical processes that determine solute transport

USGS Publications Warehouse

Bencala, Kenneth E.

1984-01-01

Solute transport in streams is determined by the interaction of physical and chemical processes. Data from an injection experiment for chloride and several cations indicate significant influence of solutestreambed processes on transport in a mountain stream. These data are interpreted in terms of transient storage processes for all tracers and sorption processes for the cations. Process parameter values are estimated with simulations based on coupled quasi-two-dimensional transport and first-order mass transfer sorption. Comparative simulations demonstrate the relative roles of the physical and chemical processes in determining solute transport. During the first 24 hours of the experiment, chloride concentrations were attenuated relative to expected plateau levels. Additional attenuation occurred for the sorbing cation strontium. The simulations account for these storage processes. Parameter values determined by calibration compare favorably with estimates from other studies in mountain streams. Without further calibration, the transport of potassium and lithium is adequately simulated using parameters determined in the chloride-strontium simulation and with measured cation distribution coefficients.

Freezing point depression in model Lennard-Jones solutions

NASA Astrophysics Data System (ADS)

Koschke, Konstantin; Jörg Limbach, Hans; Kremer, Kurt; Donadio, Davide

2015-09-01

Crystallisation of liquid solutions is of uttermost importance in a wide variety of processes in materials, atmospheric and food science. Depending on the type and concentration of solutes the freezing point shifts, thus allowing control on the thermodynamics of complex fluids. Here we investigate the basic principles of solute-induced freezing point depression by computing the melting temperature of a Lennard-Jones fluid with low concentrations of solutes, by means of equilibrium molecular dynamics simulations. The effect of solvophilic and weakly solvophobic solutes at low concentrations is analysed, scanning systematically the size and the concentration. We identify the range of parameters that produce deviations from the linear dependence of the freezing point on the molal concentration of solutes, expected for ideal solutions. Our simulations allow us also to link the shifts in coexistence temperature to the microscopic structure of the solutions.

Atomic-level simulation of ferroelectricity in perovskite solid solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sepliarsky, M.; Instituto de Fisica Rosario, CONICET-UNR, Rosario,; Phillpot, S. R.

2000-06-26

Building on the insights gained from electronic-structure calculations and from experience obtained with an earlier atomic-level method, we developed an atomic-level simulation approach based on the traditional Buckingham potential with shell model which correctly reproduces the ferroelectric phase behavior and dielectric and piezoelectric properties of KNbO{sub 3}. This approach now enables the simulation of solid solutions and defected systems; we illustrate this capability by elucidating the ferroelectric properties of a KTa{sub 0.5}Nb{sub 0.5}O{sub 3} random solid solution. (c) 2000 American Institute of Physics.

Determination of the bioaccessible fraction of metals in urban aerosol using simulated lung fluids

NASA Astrophysics Data System (ADS)

Coufalík, Pavel; Mikuška, Pavel; Matoušek, Tomáš; Večeřa, Zbyněk

2016-09-01

Determination of the bioaccessible fraction of metals in atmospheric aerosol is a significant issue with respect to air pollution in the urban environment. The aim of this work was to compare of metal bioaccessibility determined according to the extraction yields of six simulated lung fluids. Aerosol samples of the PM1 fraction were collected in Brno, Czech Republic. The total contents of Cd, Ce, Cr, Cu, Fe, Mn, Ni, Pb, V, and Zn in the samples were determined and their enrichment factors were calculated. The bioaccessible proportions of elements were determined by means of extraction in Gamble's solution, Gamble's solution with dipalmitoyl phosphatidyl choline (DPPC), artificial lysosomal fluid, saline, water, and in a newly proposed solution based on DPPC, referred to as "Simulated Alveoli Fluid" (SAF). The chemical composition and surface tension of the simulated lung fluids were the main parameters influencing extraction yields. Gamble's solutions and the newly designed solution of SAF exhibited the lowest extraction efficiency, and also had the lowest surface tensions. The bioaccessibility of particulate metals should be assessed by synthetic lung fluids with a low surface tension, which simulate better the behavior and composition of native lung surfactant. The bioaccessibility of metals in aerosol assessed by means of the extraction in water or artificial lysosomal fluid can be overestimated.

Physical compatibility of various drugs with neonatal total parenteral nutrient solution during simulated Y-site administration.

PubMed

Fox, Laura M; Wilder, Alyson G; Foushee, Jaime A

2013-03-15

The physical compatibility of various drugs with neonatal total parenteral nutrient (TPN) solution during simulated Y-site administration was evaluated. Study drugs were selected based on the lack of compatibility data with them and neonatal TPN solution and the frequency of use in a local neonatal unit. These drugs included amiodarone, caffeine citrate, clindamycin, enalaprilat, epinephrine, fluconazole, fosphenytoin sodium, hydrocortisone, metoclopramide, midazolam, pentobarbital, phenobarbital, and rifampin. Equal volumes of neonatal TPN solution or sterile water for injection were combined with study drugs or sterile water for injection at concentrations used clinically in neonates. Each test was performed in triplicate. The samples were examined via turbidimetric analysis and visually against light and dark backgrounds immediately after mixing and at 0.25, 0.5, 1, 2, and 3 hours after mixing. Analysis of variance was used to determine statistically significant differences between the test and control solutions. Many of the drugs studied exhibited no visual or turbidimetric evidence of incompatibility when combined with neonatal TPN solution for up to three hours in a simulated Y-site injection. Pentobarbital, phenobarbital, and rifampin formed visible precipitation immediately after mixing with the neonatal TPN solution. Caffeine citrate, clindamycin, enalaprilat, epinephrine, fluconazole, fosphenytoin sodium, hydrocortisone, metoclopramide, and midazolam exhibited no visual or turbidimetric evidence of incompatibility when combined with a neonatal TPN solution for up to three hours in a simulated Y-site injection. Amiodarone, pentobarbital, phenobarbital, and rifampin were not compatible with the neonatal TPN solution and should not be coadministered via Y-site injection.

Verification assessment of piston boundary conditions for Lagrangian simulation of compressible flow similarity solutions

DOE PAGES

Ramsey, Scott D.; Ivancic, Philip R.; Lilieholm, Jennifer F.

2015-12-10

This work is concerned with the use of similarity solutions of the compressible flow equations as benchmarks or verification test problems for finite-volume compressible flow simulation software. In practice, this effort can be complicated by the infinite spatial/temporal extent of many candidate solutions or “test problems.” Methods can be devised with the intention of ameliorating this inconsistency with the finite nature of computational simulation; the exact strategy will depend on the code and problem archetypes under investigation. For example, self-similar shock wave propagation can be represented in Lagrangian compressible flow simulations as rigid boundary-driven flow, even if no such “piston”more » is present in the counterpart mathematical similarity solution. The purpose of this work is to investigate in detail the methodology of representing self-similar shock wave propagation as a piston-driven flow in the context of various test problems featuring simple closed-form solutions of infinite spatial/temporal extent. The closed-form solutions allow for the derivation of similarly closed-form piston boundary conditions (BCs) for use in Lagrangian compressible flow solvers. Finally, the consequences of utilizing these BCs (as opposed to directly initializing the self-similar solution in a computational spatial grid) are investigated in terms of common code verification analysis metrics (e.g., shock strength/position errors and global convergence rates).« less

Verification assessment of piston boundary conditions for Lagrangian simulation of compressible flow similarity solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramsey, Scott D.; Ivancic, Philip R.; Lilieholm, Jennifer F.

This work is concerned with the use of similarity solutions of the compressible flow equations as benchmarks or verification test problems for finite-volume compressible flow simulation software. In practice, this effort can be complicated by the infinite spatial/temporal extent of many candidate solutions or “test problems.” Methods can be devised with the intention of ameliorating this inconsistency with the finite nature of computational simulation; the exact strategy will depend on the code and problem archetypes under investigation. For example, self-similar shock wave propagation can be represented in Lagrangian compressible flow simulations as rigid boundary-driven flow, even if no such “piston”more » is present in the counterpart mathematical similarity solution. The purpose of this work is to investigate in detail the methodology of representing self-similar shock wave propagation as a piston-driven flow in the context of various test problems featuring simple closed-form solutions of infinite spatial/temporal extent. The closed-form solutions allow for the derivation of similarly closed-form piston boundary conditions (BCs) for use in Lagrangian compressible flow solvers. Finally, the consequences of utilizing these BCs (as opposed to directly initializing the self-similar solution in a computational spatial grid) are investigated in terms of common code verification analysis metrics (e.g., shock strength/position errors and global convergence rates).« less

Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

PubMed Central

Yang, Pei-Kun

2013-01-01

To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD) simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes. PMID:23852018

Using Grand Canonical Monte Carlo Simulations to Understand the Role of Interfacial Fluctuations on Solvation at the Water-Vapor Interface.

PubMed

Rane, Kaustubh; van der Vegt, Nico F A

2016-09-15

The present work investigates the effect of interfacial fluctuations (predominantly capillary wave-like fluctuations) on the solvation free energy (Δμ) of a monatomic solute at the water-vapor interface. We introduce a grand-canonical-ensemble-based simulation approach that quantifies the contribution of interfacial fluctuations to Δμ. This approach is used to understand how the above contribution depends on the strength of dispersive and electrostatic solute-water interactions at the temperature of 400 K. At this temperature, we observe that interfacial fluctuations do play a role in the variation of Δμ with the strength of the electrostatic solute-water interaction. We also use grand canonical simulations to further investigate how interfacial fluctuations affect the propensity of the solute toward the water-vapor interface. To this end, we track a quantity called the interface potential (surface excess free energy) with the number of water molecules. With increasing number of water molecules, the liquid-vapor interface moves across a solute, which is kept at a fixed position in the simulation. Hence, the dependence of the interface potential on the number of waters models the process of moving the solute through the water-vapor interface. We analyze the change of the interface potential with the number of water molecules to explain that solute-induced changes in the interfacial fluctuations, like the pinning of capillary-wave-like undulations, do not play any role in the propensity of solutes toward water-vapor interfaces. The above analysis also shows that the dampening of interfacial fluctuations accompanies the adsorption of any solute at the liquid-vapor interface, irrespective of the chemical nature of the solute and solvent. However, such a correlation does not imply that dampening of fluctuations causes adsorption.

Spatial distribution of solute leaching with snowmelt and irrigation: measurements and simulations

NASA Astrophysics Data System (ADS)

Schotanus, D.; van der Ploeg, M. J.; van der Zee, S. E. A. T. M.

2013-04-01

Transport of a tracer and a degradable solute in a heterogeneous soil was measured in the field, and simulated with several transient and steady state infiltration rates. Leaching surfaces were used to investigate the solute leaching in space and time simultaneously. In the simulations, a random field for the scaling factor in the retention curve was used for the heterogeneous soil, which was based on the spatial distribution of drainage in an experiment with a multi-compartment sampler. As a criterion to compare the results from simulations and observations, the sorted and cumulative total drainage in a cell was used. The effect of the ratio of the infiltration rate over the degradation rate on leaching of degradable solutes was investigated. Furthermore, the spatial distribution of the leaching of degradable and non-degradable solutes was compared. The infiltration rate determines the amount of leaching of the degradable solute. This can be partly explained by a decreasing travel time with an increasing infiltration rate. The spatial distribution of the leaching also depends on the infiltration rate. When the infiltration rate is high compared to the degradation rate, the leaching of the degradable solute is similar as for the tracer. The fraction of the pore space of the soil that contributes to solute leaching increases with an increasing infiltration rate. This fraction is similar for a tracer and a degradable solute. With increasing depth, the leaching becomes more homogeneous, as a result of dispersion. The spatial distribution of the solute leaching is different under different transient infiltration rates, therefore, also the amount of leaching is different. With independent stream tube approaches, this effect would be ignored.

Spatial distribution of solute leaching with snowmelt and irrigation: measurements and simulations

NASA Astrophysics Data System (ADS)

Schotanus, D.; van der Ploeg, M. J.; van der Zee, S. E. A. T. M.

2012-12-01

Transport of a tracer and a degradable solute in a heterogeneous soil was measured in the field, and simulated with several transient and steady state infiltration rates. Leaching surfaces were used to investigate the solute leaching in space and time simultaneously. In the simulations, a random field for the scaling factor in the retention curve was used for the heterogeneous soil, which was based on the spatial distribution of drainage in an experiment with a multi-compartment sampler. As a criterion to compare the results from simulations and observations, the sorted and cumulative total drainage in a cell was used. The effect of the ratio of the infiltration rate over the degradation rate on leaching of degradable solutes was investigated. Furthermore, the spatial distribution of the leaching of degradable and non-degradable solutes was compared. The infiltration rate determines the amount of leaching of the degradable solute. This can be partly explained by a decreasing travel time with an increasing infiltration rate. The spatial distribution of the leaching also depends on the infiltration rate. When the infiltration rate is high compared to the degradation rate, the leaching of the degradable solute is similar as for the tracer. The fraction of the soil that contributes to solute leaching increases with an increasing infiltration rate. This fraction is similar for a tracer and a degradable solute. With increasing depth, the leaching becomes more homogeneous, as a result of dispersion. The spatial distribution of the solute leaching is different under different transient infiltration rates, therefore also the amount of leaching is different. With independent stream tube approaches, this effect would be ignored.

Analytical solutions for a soil vapor extraction model that incorporates gas phase dispersion and molecular diffusion

NASA Astrophysics Data System (ADS)

Huang, Junqi; Goltz, Mark N.

2017-06-01

To greatly simplify their solution, the equations describing radial advective/dispersive transport to an extraction well in a porous medium typically neglect molecular diffusion. While this simplification is appropriate to simulate transport in the saturated zone, it can result in significant errors when modeling gas phase transport in the vadose zone, as might be applied when simulating a soil vapor extraction (SVE) system to remediate vadose zone contamination. A new analytical solution for the equations describing radial gas phase transport of a sorbing contaminant to an extraction well is presented. The equations model advection, dispersion (including both mechanical dispersion and molecular diffusion), and rate-limited mass transfer of dissolved, separate phase, and sorbed contaminants into the gas phase. The model equations are analytically solved by using the Laplace transform with respect to time. The solutions are represented by confluent hypergeometric functions in the Laplace domain. The Laplace domain solutions are then evaluated using a numerical Laplace inversion algorithm. The solutions can be used to simulate the spatial distribution and the temporal evolution of contaminant concentrations during operation of a soil vapor extraction well. Results of model simulations show that the effect of gas phase molecular diffusion upon concentrations at the extraction well is relatively small, although the effect upon the distribution of concentrations in space is significant. This study provides a tool that can be useful in designing SVE remediation strategies, as well as verifying numerical models used to simulate SVE system performance.

Numerical simulations to the nonlinear model of interpersonal relationships with time fractional derivative

NASA Astrophysics Data System (ADS)

Gencoglu, Muharrem Tuncay; Baskonus, Haci Mehmet; Bulut, Hasan

2017-01-01

The main aim of this manuscript is to obtain numerical solutions for the nonlinear model of interpersonal relationships with time fractional derivative. The variational iteration method is theoretically implemented and numerically conducted only to yield the desired solutions. Numerical simulations of desired solutions are plotted by using Wolfram Mathematica 9. The authors would like to thank the reviewers for their comments that help improve the manuscript.

Analysis of Plume Impingement Effects from Orion Crew Service Module Dual Reaction Control System Engine Firings

NASA Technical Reports Server (NTRS)

Prisbell, Andrew; Marichalar, J.; Lumpkin, F.; LeBeau, G.

2010-01-01

Plume impingement effects on the Orion Crew Service Module (CSM) were analyzed for various dual Reaction Control System (RCS) engine firings and various configurations of the solar arrays. The study was performed using a decoupled computational fluid dynamics (CFD) and Direct Simulation Monte Carlo (DSMC) approach. This approach included a single jet plume solution for the R1E RCS engine computed with the General Aerodynamic Simulation Program (GASP) CFD code. The CFD solution was used to create an inflow surface for the DSMC solution based on the Bird continuum breakdown parameter. The DSMC solution was then used to model the dual RCS plume impingement effects on the entire CSM geometry with deployed solar arrays. However, because the continuum breakdown parameter of 0.5 could not be achieved due to geometrical constraints and because high resolution in the plume shock interaction region is desired, a focused DSMC simulation modeling only the plumes and the shock interaction region was performed. This high resolution intermediate solution was then used as the inflow to the larger DSMC solution to obtain plume impingement heating, forces, and moments on the CSM and the solar arrays for a total of 21 cases that were analyzed. The results of these simulations were used to populate the Orion CSM Aerothermal Database.

Biocorrosion properties of antibacterial Ti-10Cu sintered alloy in several simulated biological solutions.

PubMed

Liu, Cong; Zhang, Erlin

2015-03-01

Ti-10Cu sintered alloy has shown strong antibacterial properties against S. aureus and E. coli and good cell biocompatibility, which displays potential application in dental application. The corrosion behaviors of the alloy in five different simulated biological solutions have been investigated by electrochemical technology, surface observation, roughness measurement and immersion test. Five different simulated solutions were chosen to simulate oral condition, oral condition with F(-) ion, human body fluids with different pH values and blood system. It has been shown that Ti-10Cu alloy exhibits high corrosion rate in Saliva pH 3.5 solution and Saliva pH 6.8 + 0.2F solution but low corrosion rate in Hank's, Tyrode's and Saliva pH 6.8 solutions. The corrosion rate of Ti-10Cu alloy was in a order of Hank's, Tyrode's, Saliva pH 6.8, Saliva-pH 3.5 and Saliva pH 6.8 + 0.2F from slow to fast. All results indicated acid and F(-) containing conditions prompt the corrosion reaction of Ti-Cu alloy. It was suggested that the Cu ion release in the biological environments, especially in the acid and F(-) containing condition would lead to high antibacterial properties without any cell toxicity, displaying wide potential application of this alloy.

Accelerating potential of mean force calculations for lipid membrane permeation: System size, reaction coordinate, solute-solute distance, and cutoffs

NASA Astrophysics Data System (ADS)

Nitschke, Naomi; Atkovska, Kalina; Hub, Jochen S.

2016-09-01

Molecular dynamics simulations are capable of predicting the permeability of lipid membranes for drug-like solutes, but the calculations have remained prohibitively expensive for high-throughput studies. Here, we analyze simple measures for accelerating potential of mean force (PMF) calculations of membrane permeation, namely, (i) using smaller simulation systems, (ii) simulating multiple solutes per system, and (iii) using shorter cutoffs for the Lennard-Jones interactions. We find that PMFs for membrane permeation are remarkably robust against alterations of such parameters, suggesting that accurate PMF calculations are possible at strongly reduced computational cost. In addition, we evaluated the influence of the definition of the membrane center of mass (COM), used to define the transmembrane reaction coordinate. Membrane-COM definitions based on all lipid atoms lead to artifacts due to undulations and, consequently, to PMFs dependent on membrane size. In contrast, COM definitions based on a cylinder around the solute lead to size-independent PMFs, down to systems of only 16 lipids per monolayer. In summary, compared to popular setups that simulate a single solute in a membrane of 128 lipids with a Lennard-Jones cutoff of 1.2 nm, the measures applied here yield a speedup in sampling by factor of ˜40, without reducing the accuracy of the calculated PMF.

Modeling variably saturated subsurface solute transport with MODFLOW-UZF and MT3DMS

USGS Publications Warehouse

Morway, Eric D.; Niswonger, Richard G.; Langevin, Christian D.; Bailey, Ryan T.; Healy, Richard W.

2013-01-01

The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated-zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume-averaged approach in which Lagrangian-based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF-MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two- and three-dimensional simulations also were investigated to ensure unsaturated-saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large-scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF-MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three-dimensional variably saturated flow and transport simulations revealed UZF-MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide-spread use of both MODFLOW and MT3DMS, the added capability of unsaturated-zone transport in this familiar modeling framework stands to benefit a broad user-ship.

Modeling variably saturated subsurface solute transport with MODFLOW-UZF and MT3DMS.

PubMed

Morway, Eric D; Niswonger, Richard G; Langevin, Christian D; Bailey, Ryan T; Healy, Richard W

2013-03-01

The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated-zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume-averaged approach in which Lagrangian-based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF-MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two- and three-dimensional simulations also were investigated to ensure unsaturated-saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large-scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF-MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three-dimensional variably saturated flow and transport simulations revealed UZF-MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide-spread use of both MODFLOW and MT3DMS, the added capability of unsaturated-zone transport in this familiar modeling framework stands to benefit a broad user-ship. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions

NASA Astrophysics Data System (ADS)

Olivieri, Giorgia; Parry, Krista M.; Powell, Cedric J.; Tobias, Douglas J.; Brown, Matthew A.

2016-04-01

Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy (XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the vapor (vacuum)-aqueous electrolyte interface. These experiments are often paired with complementary molecular dynamics (MD) simulations in an attempt to provide a complete description of the liquid interface. There is, however, no systematic protocol that permits a straightforward comparison of the two sets of results. XPS is an integrated technique that averages signals from multiple layers in a solution even at the lowest photoelectron kinetic energies routinely employed, whereas MD simulations provide a microscopic layer-by-layer description of the solution composition near the interface. Here, we use the National Institute of Standards and Technology database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to quantitatively interpret atom-density profiles from MD simulations for XPS signal intensities using sodium and potassium iodide solutions as examples. We show that electron inelastic mean free paths calculated from a semi-empirical formula depend strongly on solution composition, varying by up to 30% between pure water and concentrated NaI. The XPS signal thus arises from different information depths in different solutions for a fixed photoelectron kinetic energy. XPS signal intensities are calculated using SESSA as a function of photoelectron kinetic energy (probe depth) and compared with a widely employed ad hoc method. SESSA simulations illustrate the importance of accounting for elastic-scattering events at low photoelectron kinetic energies (<300 eV) where the ad hoc method systematically underestimates the preferential enhancement of anions over cations. Finally, some technical aspects of applying SESSA to liquid interfaces are discussed.

The Space-Time Conservative Schemes for Large-Scale, Time-Accurate Flow Simulations with Tetrahedral Meshes

NASA Technical Reports Server (NTRS)

Venkatachari, Balaji Shankar; Streett, Craig L.; Chang, Chau-Lyan; Friedlander, David J.; Wang, Xiao-Yen; Chang, Sin-Chung

2016-01-01

Despite decades of development of unstructured mesh methods, high-fidelity time-accurate simulations are still predominantly carried out on structured, or unstructured hexahedral meshes by using high-order finite-difference, weighted essentially non-oscillatory (WENO), or hybrid schemes formed by their combinations. In this work, the space-time conservation element solution element (CESE) method is used to simulate several flow problems including supersonic jet/shock interaction and its impact on launch vehicle acoustics, and direct numerical simulations of turbulent flows using tetrahedral meshes. This paper provides a status report for the continuing development of the space-time conservation element solution element (CESE) numerical and software framework under the Revolutionary Computational Aerosciences (RCA) project. Solution accuracy and large-scale parallel performance of the numerical framework is assessed with the goal of providing a viable paradigm for future high-fidelity flow physics simulations.

Simulating 3D deformation using connected polygons

NASA Astrophysics Data System (ADS)

Tarigan, J. T.; Jaya, I.; Hardi, S. M.; Zamzami, E. M.

2018-03-01

In modern 3D application, interaction between user and the virtual world is one of an important factor to increase the realism. This interaction can be visualized in many forms; one of them is object deformation. There are many ways to simulate object deformation in virtual 3D world; each comes with different level of realism and performance. Our objective is to present a new method to simulate object deformation by using a graph-connected polygon. In this solution, each object contains multiple level of polygons in different level of volume. The proposed solution focusses on performance rather while maintaining the acceptable level of realism. In this paper, we present the design and implementation of our solution and show that this solution is usable in performance sensitive 3D application such as games and virtual reality.

Kirkwood–Buff integrals for ideal solutions

PubMed Central

Ploetz, Elizabeth A.; Bentenitis, Nikolaos; Smith, Paul E.

2010-01-01

The Kirkwood–Buff (KB) theory of solutions is a rigorous theory of solution mixtures which relates the molecular distributions between the solution components to the thermodynamic properties of the mixture. Ideal solutions represent a useful reference for understanding the properties of real solutions. Here, we derive expressions for the KB integrals, the central components of KB theory, in ideal solutions of any number of components corresponding to the three main concentration scales. The results are illustrated by use of molecular dynamics simulations for two binary solutions mixtures, benzene with toluene, and methanethiol with dimethylsulfide, which closely approach ideal behavior, and a binary mixture of benzene and methanol which is nonideal. Simulations of a quaternary mixture containing benzene, toluene, methanethiol, and dimethylsulfide suggest this system displays ideal behavior and that ideal behavior is not limited to mixtures containing a small number of components. PMID:20441282

Effect of Solute Diffusion on Dendrite Growth in the Molten Pool of Al-Cu Alloy

NASA Astrophysics Data System (ADS)

Zhan, Xiaohong; Gu, Cheng; Liu, Yun; Wei, Yanhong

2017-10-01

A cellular automaton (CA)-finite difference model is developed to simulate dendrite growth and solute diffusion during solidification process in the molten pool of Al-Cu alloy. In order to explain the interaction between the dendritic growth and solute distribution, a series of CA simulations with different solute diffusion velocity coefficients are carried out. It is concluded that the solute concentration increases with dendrite growing and solute accumulation in the dendrite tip. Converged value of the dendrite tip growth velocity is about 480 μm/s if the mesh size is refined to 2 μm or less. Growth of the primary dendrite and the secondary dendrite is mainly influenced by solute diffusion at the dendrite tips. And growth of secondary and tertiary dendrites is mainly influenced by solute diffusion at interdendrite.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

SEAWAT-based simulation of axisymmetric heat transport.

PubMed

Vandenbohede, Alexander; Louwyck, Andy; Vlamynck, Nele

2014-01-01

Simulation of heat transport has its applications in geothermal exploitation of aquifers and the analysis of temperature dependent chemical reactions. Under homogeneous conditions and in the absence of a regional hydraulic gradient, groundwater flow and heat transport from or to a well exhibit radial symmetry, and governing equations are reduced by one dimension (1D) which increases computational efficiency importantly. Solute transport codes can simulate heat transport and input parameters may be modified such that the Cartesian geometry can handle radial flow. In this article, SEAWAT is evaluated as simulator for heat transport under radial flow conditions. The 1971, 1D analytical solution of Gelhar and Collins is used to compare axisymmetric transport with retardation (i.e., as a result of thermal equilibrium between fluid and solid) and a large diffusion (conduction). It is shown that an axisymmetric simulation compares well with a fully three dimensional (3D) simulation of an aquifer thermal energy storage systems. The influence of grid discretization, solver parameters, and advection solution is illustrated. Because of the high diffusion to simulate conduction, convergence criterion for heat transport must be set much smaller (10(-10) ) than for solute transport (10(-6) ). Grid discretization should be considered carefully, in particular the subdivision of the screen interval. On the other hand, different methods to calculate the pumping or injection rate distribution over different nodes of a multilayer well lead to small differences only. © 2013, National Ground Water Association.

Corrosion protection performance of corrosion inhibitors and epoxy-coated reinforcing steel in a simulated concrete pore water solution.

DOT National Transportation Integrated Search

1998-06-01

We used a simulated concrete pore water solution to evaluate the corrosion protection performance of concrete corrosion-inhibiting admixtures and epoxy-coated reinforcing bars (ECR). We evaluated three commercial corrosion inhibitors, ECR from three ...

Removal of a hazardous heavy metal from aqueous solution using functionalized graphene and boron nitride nanosheets: Insights from simulations.

PubMed

Azamat, Jafar; Sattary, Batoul Shirforush; Khataee, Alireza; Joo, Sang Woo

2015-09-01

A computer simulation was performed to investigate the removal of Zn(2+) as a heavy metal from aqueous solution using the functionalized pore of a graphene nanosheet and boron nitride nanosheet (BNNS). The simulated systems were comprised of a graphene nanosheet or BNNS with a functionalized pore containing an aqueous ionic solution of zinc chloride. In order to remove heavy metal from an aqueous solution using the functionalized pore of a graphene nanosheet and BNNS, an external voltage was applied along the z-axis of the simulated box. For the selective removal of zinc ions, the pores of graphene and BNNS were functionalized by passivating each atom at the pore edge with appropriate atoms. For complete analysis systems, we calculated the potential of the mean force of ions, the radial distribution function of ion-water, the residence time of ions, the hydrogen bond, and the autocorrelation function of the hydrogen bond. Copyright © 2015 Elsevier Inc. All rights reserved.

Simulating the minimum core for hydrophobic collapse in globular proteins.

PubMed Central

Tsai, J.; Gerstein, M.; Levitt, M.

1997-01-01

To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling of the cluster formation observed by simulation indicates that this aggregation is cooperative and that the simulations favor the formation of a single cluster midway through the transition stage. This defines a minimum solute hydrophobic core volume. We compare this with protein hydrophobic core volumes determined from solved crystal structures. Our analysis shows that the solute core volume roughly estimates the minimum core size required for independent hydrophobic stabilization of a protein and defines a limiting concentration of nonpolar residues that can cause hydrophobic collapse. These results suggest that the physical forces driving aggregation of hydrophobic molecules in water is indeed responsible for protein folding. PMID:9416609

Light extraction efficiency analysis of GaN-based light-emitting diodes with nanopatterned sapphire substrates.

PubMed

Pan, Jui-Wen; Tsai, Pei-Jung; Chang, Kao-Der; Chang, Yung-Yuan

2013-03-01

In this paper, we propose a method to analyze the light extraction efficiency (LEE) enhancement of a nanopatterned sapphire substrates (NPSS) light-emitting diode (LED) by comparing wave optics software with ray optics software. Finite-difference time-domain (FDTD) simulations represent the wave optics software and Light Tools (LTs) simulations represent the ray optics software. First, we find the trends of and an optimal solution for the LEE enhancement when the 2D-FDTD simulations are used to save on simulation time and computational memory. The rigorous coupled-wave analysis method is utilized to explain the trend we get from the 2D-FDTD algorithm. The optimal solution is then applied in 3D-FDTD and LTs simulations. The results are similar and the difference in LEE enhancement between the two simulations does not exceed 8.5% in the small LED chip area. More than 10(4) times computational memory is saved during the LTs simulation in comparison to the 3D-FDTD simulation. Moreover, LEE enhancement from the side of the LED can be obtained in the LTs simulation. An actual-size NPSS LED is simulated using the LTs. The results show a more than 307% improvement in the total LEE enhancement of the NPSS LED with the optimal solution compared to the conventional LED.

A computational microscopy study of nanostructural evolution in irradiated pressure vessel steels

NASA Astrophysics Data System (ADS)

Odette, G. R.; Wirth, B. D.

1997-11-01

Nanostructural features that form in reactor pressure vessel steels under neutron irradiation at around 300°C lead to significant hardening and embrittlement. Continuum thermodynamic-kinetic based rate theories have been very successful in modeling the general characteristics of the copper and manganese nickel rich precipitate evolution, often the dominant source of embrittlement. However, a more detailed atomic scale understanding of these features is needed to interpret experimental measurements and better underpin predictive embrittlement models. Further, other embrittling features, believed to be subnanometer defect (vacancy)-solute complexes and small regions of modest enrichment of solutes are not well understood. A general approach to modeling embrittlement nanostructures, based on the concept of a computational microscope, is described. The objective of the computational microscope is to self-consistently integrate atomic scale simulations with other sources of information, including a wide range of experiments. In this work, lattice Monte Carlo (LMC) simulations are used to resolve the chemically and structurally complex nature of CuMnNiSi precipitates. The LMC simulations unify various nanoscale analytical characterization methods and basic thermodynamics. The LMC simulations also reveal that significant coupled vacancy and solute clustering takes place during cascade aging. The cascade clustering produces the metastable vacancy-cluster solute complexes that mediate flux effects. Cascade solute clustering may also play a role in the formation of dilute atmospheres of solute enrichment and enhance the nucleation of manganese-nickel rich precipitates at low Cu levels. Further, the simulations suggest that complex, highly correlated processes (e.g. cluster diffusion, formation of favored vacancy diffusion paths and solute scavenging vacancy cluster complexes) may lead to anomalous fast thermal aging kinetics at temperatures below about 450°C. The potential technical significance of these phenomena is described.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

NASA Astrophysics Data System (ADS)

Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

2009-10-01

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Hybrid Solution-Adaptive Unstructured Cartesian Method for Large-Eddy Simulation of Detonation in Multi-Phase Turbulent Reactive Mixtures

DTIC Science & Technology

2012-03-27

pulse- detonation engines ( PDE ), stage separation, supersonic cav- ity oscillations, hypersonic aerodynamics, detonation induced structural...ADAPTIVE UNSTRUCTURED CARTESIAN METHOD FOR LARGE-EDDY SIMULATION OF DETONATION IN MULTI-PHASE TURBULENT REACTIVE MIXTURES 5b. GRANT NUMBER FA9550...CCL Report TR-2012-03-03 Hybrid Solution-Adaptive Unstructured Cartesian Method for Large-Eddy Simulation of Detonation in Multi-Phase Turbulent

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE PAGES

Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; ...

2015-09-28

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This paper provides support for confidence in a variety of pore-scale modeling methods and motivates further development and application of pore-scale simulation methods.« less

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.

2016-09-01

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence in a variety of pore-scale modeling methods and motivates further development and application of pore-scale simulation methods.« less

Unsteady adjoint for large eddy simulation of a coupled turbine stator-rotor system

NASA Astrophysics Data System (ADS)

Talnikar, Chaitanya; Wang, Qiqi; Laskowski, Gregory

2016-11-01

Unsteady fluid flow simulations like large eddy simulation are crucial in capturing key physics in turbomachinery applications like separation and wake formation in flow over a turbine vane with a downstream blade. To determine how sensitive the design objectives of the coupled system are to control parameters, an unsteady adjoint is needed. It enables the computation of the gradient of an objective with respect to a large number of inputs in a computationally efficient manner. In this paper we present unsteady adjoint solutions for a coupled turbine stator-rotor system. As the transonic fluid flows over the stator vane, the boundary layer transitions to turbulence. The turbulent wake then impinges on the rotor blades, causing early separation. This coupled system exhibits chaotic dynamics which causes conventional adjoint solutions to diverge exponentially, resulting in the corruption of the sensitivities obtained from the adjoint solutions for long-time simulations. In this presentation, adjoint solutions for aerothermal objectives are obtained through a localized adjoint viscosity injection method which aims to stabilize the adjoint solution and maintain accurate sensitivities. Preliminary results obtained from the supercomputer Mira will be shown in the presentation.

Interactions of S-peptide analogue in aqueous urea and trimethylamine-N-oxide solutions: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Sarma, Rahul; Paul, Sandip

2013-07-01

The ability of the osmolyte, trimethylamine-N-oxide (TMAO), to protect proteins from deleterious effect of urea, another commonly available osmolyte, is well-established. However, the molecular mechanism of this counteraction is not understood yet. To provide a molecular level understanding of how TMAO protects proteins in highly concentrated urea solution, we report here molecular dynamics simulation results of a 15-residue model peptide in two different conformations: helix and extended. For both conformations, simulations are carried out in pure water as well as in binary and ternary aqueous solutions of urea and TMAO. Analysis of solvation characteristics reveals direct interactions of urea and TMAO with peptide residues. However, the number of TMAO molecules that enter in the first solvation shell of the peptide is significantly lower than that of urea, and, unlike water and urea, TMAO shows its inability to form hydrogen bond with backbone oxygen and negatively charged sidechains. Preferential accumulation of urea near the peptide surface and preferential exclusion of TMAO from the peptide surface are observed. Inclusion of osmolytes in the peptide solvation shell leads to dehydration of the peptide in binary and ternary solutions of urea and TMAO. Solvation of peptide residues are investigated more closely by calculating the number of hydrogen bonds between the peptide and solution species. It is found that number of hydrogen bonds formed by the peptide with solution species increases in binary urea solution (relative to pure water) and this relative enhancement in hydrogen bond number reduces upon addition of TMAO. Our simulation results also suggest that, in the ternary solution, the peptide solvation layer is better mixed in terms of water and urea as compared to binary urea solution. Implications of the results for counteraction mechanism of TMAO are discussed.

Potentials of mean force for biomolecular simulations: Theory and test on alanine dipeptide

NASA Astrophysics Data System (ADS)

Pellegrini, Matteo; Grønbech-Jensen, Niels; Doniach, Sebastian

1996-06-01

We describe a technique for generating potentials of mean force (PMF) between solutes in an aqueous solution. We first generate solute-solvent correlation functions (CF) using Monte Carlo (MC) simulations in which we place a single atom solute in a periodic boundary box containing a few hundred water molecules. We then make use of the Kirkwood superposition approximation, where the 3-body correlation function is approximated as the product of 2-body CFs, to describe the mean water density around two solutes. Computing the force generated on the solutes by this average water density allows us to compute potentials of mean force between the two solutes. For charged solutes an additional approximation involving dielectric screening is made, by setting the dielectric constant of water to ɛ=80. These potentials account, in an approximate manner, for the average effect of water on the atoms. Following the work of Pettitt and Karplus [Chem. Phys. Lett. 121, 194 (1985)], we approximate the n-body potential of mean force as a sum of the pairwise potentials of mean force. This allows us to run simulations of biomolecules without introducing explicit water, hence gaining several orders of magnitude in efficiency with respect to standard molecular dynamics techniques. We demonstrate the validity of this technique by first comparing the PMFs for methane-methane and sodium-chloride generated with this procedure, with those calculated with a standard Monte Carlo simulation with explicit water. We then compare the results of the free energy profiles between the equilibria of alanine dipeptide generated by the two methods.

Coupling MD Simulations and X-ray Absorption Spectroscopy to Study Ions in Solution

NASA Astrophysics Data System (ADS)

Marcos, E. Sánchez; Beret, E. C.; Martínez, J. M.; Pappalardo, R. R.; Ayala, R.; Muñoz-Páez, A.

2007-12-01

The structure of ionic solutions is a key-point in understanding physicochemical properties of electrolyte solutions. Among the reduced number of experimental techniques which can supply direct information on the ion environment, X-ray Absorption techniques (XAS) have gained importance during the last decades although they are not free of difficulties associated to the data analysis leading to provide reliable structures. Computer simulations of ions in solution is a theoretical alternative to provide information on the solvation structure. Thus, the use of computational chemistry can increase the understanding of these systems although an accurate description of ionic solvation phenomena represents nowadays a significant challenge to theoretical chemistry. We present: (a) the assignment of features in the XANES spectrum to well defined structural motif in the ion environment, (b) MD-based evaluation of EXAFS parameters used in the fitting procedure to make easier the structural resolution, and (c) the use of the agreement between experimental and simulated XANES spectra to help in the choice of a given intermolecular potential for Computer Simulations. Chemical problems examined are: (a) the identification of the second hydration shell in dilute aqueous solutions of highly-charged cations, such as Cr3+, Rh3+, Ir3+, (b) the invisibility by XAS of certain structures characterized by Computer Simulations but exhibiting high dynamical behavior and (c) the solvation of Br- in acetonitrile.

Coupling MD Simulations and X-ray Absorption Spectroscopy to Study Ions in Solution

NASA Astrophysics Data System (ADS)

Marcos, E. Sánchez; Beret, E. C.; Martínez, J. M.; Pappalardo, R. R.; Ayala, R.; Muñoz-Páez, A.

2007-11-01

The structure of ionic solutions is a key-point in understanding physicochemical properties of electrolyte solutions. Among the reduced number of experimental techniques which can supply direct information on the ion environment, X-ray Absorption techniques (XAS) have gained importance during the last decades although they are not free of difficulties associated to the data analysis leading to provide reliable structures. Computer simulations of ions in solution is a theoretical alternative to provide information on the solvation structure. Thus, the use of computational chemistry can increase the understanding of these systems although an accurate description of ionic solvation phenomena represents nowadays a significant challenge to theoretical chemistry. We present: (a) the assignment of features in the XANES spectrum to well defined structural motif in the ion environment, (b) MD-based evaluation of EXAFS parameters used in the fitting procedure to make easier the structural resolution, and (c) the use of the agreement between experimental and simulated XANES spectra to help in the choice of a given intermolecular potential for Computer Simulations. Chemical problems examined are: (a) the identification of the second hydration shell in dilute aqueous solutions of highly-charged cations, such as Cr3+, Rh3+, Ir3+, (b) the invisibility by XAS of certain structures characterized by Computer Simulations but exhibiting high dynamical behavior and (c) the solvation of Br- in acetonitrile.

A web-based rapid assessment tool for production publishing solutions

NASA Astrophysics Data System (ADS)

Sun, Tong

2010-02-01

Solution assessment is a critical first-step in understanding and measuring the business process efficiency enabled by an integrated solution package. However, assessing the effectiveness of any solution is usually a very expensive and timeconsuming task which involves lots of domain knowledge, collecting and understanding the specific customer operational context, defining validation scenarios and estimating the expected performance and operational cost. This paper presents an intelligent web-based tool that can rapidly assess any given solution package for production publishing workflows via a simulation engine and create a report for various estimated performance metrics (e.g. throughput, turnaround time, resource utilization) and operational cost. By integrating the digital publishing workflow ontology and an activity based costing model with a Petri-net based workflow simulation engine, this web-based tool allows users to quickly evaluate any potential digital publishing solutions side-by-side within their desired operational contexts, and provides a low-cost and rapid assessment for organizations before committing any purchase. This tool also benefits the solution providers to shorten the sales cycles, establishing a trustworthy customer relationship and supplement the professional assessment services with a proven quantitative simulation and estimation technology.

Simulations of reactive transport and precipitation with smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Tartakovsky, Alexandre M.; Meakin, Paul; Scheibe, Timothy D.; Eichler West, Rogene M.

2007-03-01

A numerical model based on smoothed particle hydrodynamics (SPH) was developed for reactive transport and mineral precipitation in fractured and porous materials. Because of its Lagrangian particle nature, SPH has several advantages for modeling Navier-Stokes flow and reactive transport including: (1) in a Lagrangian framework there is no non-linear term in the momentum conservation equation, so that accurate solutions can be obtained for momentum dominated flows and; (2) complicated physical and chemical processes such as surface growth due to precipitation/dissolution and chemical reactions are easy to implement. In addition, SPH simulations explicitly conserve mass and linear momentum. The SPH solution of the diffusion equation with fixed and moving reactive solid-fluid boundaries was compared with analytical solutions, Lattice Boltzmann [Q. Kang, D. Zhang, P. Lichtner, I. Tsimpanogiannis, Lattice Boltzmann model for crystal growth from supersaturated solution, Geophysical Research Letters, 31 (2004) L21604] simulations and diffusion limited aggregation (DLA) [P. Meakin, Fractals, scaling and far from equilibrium. Cambridge University Press, Cambridge, UK, 1998] model simulations. To illustrate the capabilities of the model, coupled three-dimensional flow, reactive transport and precipitation in a fracture aperture with a complex geometry were simulated.

Force field dependent solution properties of glycine oligomers

PubMed Central

Drake, Justin A.

2015-01-01

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

PubMed

Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

2011-03-01

The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

Monte Carlo simulation and equation of state for flexible charged hard-sphere chain fluids: polyampholyte and polyelectrolyte solutions.

PubMed

Jiang, Hao; Adidharma, Hertanto

2014-11-07

The thermodynamic modeling of flexible charged hard-sphere chains representing polyampholyte or polyelectrolyte molecules in solution is considered. The excess Helmholtz energy and osmotic coefficients of solutions containing short polyampholyte and the osmotic coefficients of solutions containing short polyelectrolytes are determined by performing canonical and isobaric-isothermal Monte Carlo simulations. A new equation of state based on the thermodynamic perturbation theory is also proposed for flexible charged hard-sphere chains. For the modeling of such chains, the use of solely the structure information of monomer fluid for calculating the chain contribution is found to be insufficient and more detailed structure information must therefore be considered. Two approaches, i.e., the dimer and dimer-monomer approaches, are explored to obtain the contribution of the chain formation to the Helmholtz energy. By comparing with the simulation results, the equation of state with either the dimer or dimer-monomer approach accurately predicts the excess Helmholtz energy and osmotic coefficients of polyampholyte and polyelectrolyte solutions except at very low density. It also well captures the effect of temperature on the thermodynamic properties of these solutions.

A multi-scale Lattice Boltzmann model for simulating solute transport in 3D X-ray micro-tomography images of aggregated porous materials

NASA Astrophysics Data System (ADS)

Zhang, Xiaoxian; Crawford, John W.; Flavel, Richard J.; Young, Iain M.

2016-10-01

The Lattice Boltzmann (LB) model and X-ray computed tomography (CT) have been increasingly used in combination over the past decade to simulate water flow and chemical transport at pore scale in porous materials. Because of its limitation in resolution and the hierarchical structure of most natural soils, the X-ray CT tomography can only identify pores that are greater than its resolution and treats other pores as solid. As a result, the so-called solid phase in X-ray images may in reality be a grey phase, containing substantial connected pores capable of conducing fluids and solute. Although modified LB models have been developed to simulate fluid flow in such media, models for solute transport are relatively limited. In this paper, we propose a LB model for simulating solute transport in binary soil images containing permeable solid phase. The model is based on the single-relaxation time approach and uses a modified partial bounce-back method to describe the resistance caused by the permeable solid phase to chemical transport. We derive the relationship between the diffusion coefficient and the parameter introduced in the partial bounce-back method, and test the model against analytical solution for movement of a pulse of tracer. We also validate it against classical finite volume method for solute diffusion in a simple 2D image, and then apply the model to a soil image acquired using X-ray tomography at resolution of 30 μm in attempts to analyse how the ability of the solid phase to diffuse solute at micron-scale affects the behaviour of the solute at macro-scale after a volumetric average. Based on the simulated results, we discuss briefly the danger in interpreting experimental results using the continuum model without fully understanding the pore-scale processes, as well as the potential of using pore-scale modelling and tomography to help improve the continuum models.

Simulators for training in ultrasound guided procedures.

PubMed

Farjad Sultan, Syed; Shorten, George; Iohom, Gabrielle

2013-06-01

The four major categories of skill sets associated with proficiency in ultrasound guided regional anaesthesia are 1) understanding device operations, 2) image optimization, 3) image interpretation and 4) visualization of needle insertion and injection of the local anesthetic solution. Of these, visualization of needle insertion and injection of local anaesthetic solution can be practiced using simulators and phantoms. This survey of existing simulators summarizes advantages and disadvantages of each. Current deficits pertain to the validation process.

Investigation of Mechanical Properties and Fracture Simulation of Solution-Treated AA 5754

NASA Astrophysics Data System (ADS)

Kumar, Pankaj; Singh, Akhilendra

2017-10-01

In this work, mechanical properties and fracture toughness of as-received and solution-treated aluminum alloy 5754 (AA 5754) are experimentally evaluated. Solution heat treatment of the alloy is performed at 530 °C for 2 h, and then, quenching is done in water. Yield strength, ultimate tensile strength, impact toughness, hardness, fatigue life, brittle fracture toughness (K_{Ic} ) and ductile fracture toughness (J_{Ic} ) are evaluated for as-received and solution-treated alloy. Extended finite element method has been used for the simulation of tensile and fracture behavior of material. Heaviside function and asymptotic crack tip enrichment functions are used for modelling of the crack in the geometry. Ramberg-Osgood material model coupled with fracture energy is used to simulate the crack propagation. Fracture surfaces obtained from various mechanical tests are characterized by scanning electron microscopy.

A new modification in the exponential rational function method for nonlinear fractional differential equations

NASA Astrophysics Data System (ADS)

Ahmed, Naveed; Bibi, Sadaf; Khan, Umar; Mohyud-Din, Syed Tauseef

2018-02-01

We have modified the traditional exponential rational function method (ERFM) and have used it to find the exact solutions of two different fractional partial differential equations, one is the time fractional Boussinesq equation and the other is the (2+1)-dimensional time fractional Zoomeron equation. In both the cases it is observed that the modified scheme provides more types of solutions than the traditional one. Moreover, a comparison of the recent solutions is made with some already existing solutions. We can confidently conclude that the modified scheme works better and provides more types of solutions with almost similar computational cost. Our generalized solutions include periodic, soliton-like, singular soliton and kink solutions. A graphical simulation of all types of solutions is provided and the correctness of the solution is verified by direct substitution. The extended version of the solutions is expected to provide more flexibility to scientists working in the relevant field to test their simulation data.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

Salt weathering in Egyptian limestone after laboratory simulations with continuous flow of salt solutions at different temperatures

NASA Astrophysics Data System (ADS)

Aly, Nevin; Gomez-Heras, Miguel; Hamed, Ayman; Alvarez de Buergo, Monica

2013-04-01

weathering in Egyptian limestone after laboratory simulations with continuous flow of salt solutions at different temperatures Nevin Aly Mohamed (1), Miguel Gomez - Heras(2), Ayman Hamed Ahmed (1), and Monica Alvarez de Buergo(2). (1) Faculty of Pet. & Min. Engineering- Suez Canal University, Suez, Egypt, (2) Instituto de Geociencias (CSIC-UCM) Madrid. Spain. Limestone is one of the most frequent building stones in Egypt and is used since the time of ancient Egyptians and salt weathering is one of the main threats to its conservation. Most of the limestone used in historical monuments in Cairo is a biomicrite extracted from the Mid-Eocene Mokattam Group. During this work, cylindrical samples (2.4 cm diameter and approx. 4.8 cm length) were subjected, in a purpose-made simulation chamber, to simulated laboratory weathering tests with fixed salt concentration (10% weight NaCl solution), at different temperatures, which were kept constant throughout each test (10, 20, 30, 40 oC). During each test, salt solutions flowed continuously imbibing samples by capilarity. Humidity within the simulation chamber was reduced using silica gel to keep it low and constant to increase evaporation rate. Temperature, humidity inside the simulation chamber and samples weight were digitally monitored during each test. Results show the advantages of the proposed experimental methodology using a continuous flow of salt solutions and shed light on the effect of temperature on the dynamics of salt crystallization on and within samples. Research funded by mission sector of high education ministry, Egypt and Geomateriales S2009/MAT-1629.

Numerical simulation of crevice corrosion of titanium: Effect of the bold surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evitts, R.W.; Postlethwaite, J.; Watson, M.K.

1996-12-01

A rigorous crevice corrosion model has been developed that accounts for the bold metal surfaces exterior to the crevice. The model predicts the time change in concentration of all specified chemical species in the crevice and bulk solution, and has the ability to predict active corrosion. It is applied to the crevice corrosion of a small titanium crevice in both oxygenated and anaerobic sodium chloride solutions. The numerical predictions confirm that oxygen is the driving force for crevice corrosion. During the simulations where oxygen is initially present in both the crevice and bulk solution an acidic chloride solution is developed;more » this is the precursor required for crevice corrosion. The anaerobic case displays no tendency to form such a solution. It is also confirmed that those areas in the crevice that are deoxygenated become anodic and the bold metal surface becomes cathodic. As expected, active corrosion is not attained as the simulations are based on electrochemical and chemical parameters at 25 C.« less

Computer model of hydroponics nutrient solution pH control using ammonium.

PubMed

Pitts, M; Stutte, G

1999-01-01

A computer simulation of a hydroponics-based plant growth chamber using ammonium to control pH was constructed to determine the feasibility of such a system. In nitrate-based recirculating hydroponics systems, the pH will increase as plants release hydroxide ions into the nutrient solution to maintain plant charge balance. Ammonium is an attractive alternative to traditional pH controls in an ALSS, but requires careful monitoring and control to avoid overdosing the plants with ammonium. The primary advantage of using NH4+ for pH control is that it exploits the existing plant nutrient uptake charge balance mechanisms to maintain solution pH. The simulation models growth, nitrogen uptake, and pH of a l-m2 stand of wheat. Simulation results indicated that ammonium-based control of nutrient solution pH is feasible using a proportional integral controller. Use of a 1 mmol/L buffer (Ka = 1.6 x 10(-6)) in the nutrient solution is required.

Molecular dynamics study of salt-solution interface: solubility and surface charge of salt in water.

PubMed

Kobayashi, Kazuya; Liang, Yunfeng; Sakka, Tetsuo; Matsuoka, Toshifumi

2014-04-14

The NaCl salt-solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt-solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt-solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules.

Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobayashi, Kazuya; Liang, Yunfeng, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp; Matsuoka, Toshifumi, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp

2014-04-14

The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemicalmore » potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules.« less

Development of solute transport models in YMPYRÄ framework to simulate solute migration in military shooting and training areas

NASA Astrophysics Data System (ADS)

Warsta, L.; Karvonen, T.

2017-12-01

There are currently 25 shooting and training areas in Finland managed by The Finnish Defence Forces (FDF), where military activities can cause contamination of open waters and groundwater reservoirs. In the YMPYRÄ project, a computer software framework is being developed that combines existing open environmental data and proprietary information collected by FDF with computational models to investigate current and prevent future environmental problems. A data centric philosophy is followed in the development of the system, i.e. the models are updated and extended to handle available data from different areas. The results generated by the models are summarized as easily understandable flow and risk maps that can be opened in GIS programs and used in environmental assessments by experts. Substances investigated with the system include explosives and metals such as lead, and both surface and groundwater dominated areas can be simulated. The YMPYRÄ framework is composed of a three dimensional soil and groundwater flow model, several solute transport models and an uncertainty assessment system. Solute transport models in the framework include particle based, stream tube and finite volume based approaches. The models can be used to simulate solute dissolution from source area, transport in the unsaturated layers to groundwater and finally migration in groundwater to water extraction wells and springs. The models can be used to simulate advection, dispersion, equilibrium adsorption on soil particles, solubility and dissolution from solute phase and dendritic solute decay chains. Correct numerical solutions were confirmed by comparing results to analytical 1D and 2D solutions and by comparing the numerical solutions to each other. The particle based and stream tube type solute transport models were useful as they could complement the traditional finite volume based approach which in certain circumstances produced numerical dispersion due to piecewise solution of the governing equations in computational grids and included computationally intensive and in some cases unstable iterative solutions. The YMPYRÄ framework is being developed by WaterHope, Gain Oy, and SITO Oy consulting companies and funded by FDF.

Assessment of a hybrid finite element and finite volume code for turbulent incompressible flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Yidong, E-mail: yidong.xia@inl.gov; Wang, Chuanjin; Luo, Hong

Hydra-TH is a hybrid finite-element/finite-volume incompressible/low-Mach flow simulation code based on the Hydra multiphysics toolkit being developed and used for thermal-hydraulics applications. In the present work, a suite of verification and validation (V&V) test problems for Hydra-TH was defined to meet the design requirements of the Consortium for Advanced Simulation of Light Water Reactors (CASL). The intent for this test problem suite is to provide baseline comparison data that demonstrates the performance of the Hydra-TH solution methods. The simulation problems vary in complexity from laminar to turbulent flows. A set of RANS and LES turbulence models were used in themore » simulation of four classical test problems. Numerical results obtained by Hydra-TH agreed well with either the available analytical solution or experimental data, indicating the verified and validated implementation of these turbulence models in Hydra-TH. Where possible, some form of solution verification has been attempted to identify sensitivities in the solution methods, and suggest best practices when using the Hydra-TH code. -- Highlights: •We performed a comprehensive study to verify and validate the turbulence models in Hydra-TH. •Hydra-TH delivers 2nd-order grid convergence for the incompressible Navier–Stokes equations. •Hydra-TH can accurately simulate the laminar boundary layers. •Hydra-TH can accurately simulate the turbulent boundary layers with RANS turbulence models. •Hydra-TH delivers high-fidelity LES capability for simulating turbulent flows in confined space.« less

A new variable parallel holes collimator for scintigraphic device with validation method based on Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Trinci, G.; Massari, R.; Scandellari, M.; Boccalini, S.; Costantini, S.; Di Sero, R.; Basso, A.; Sala, R.; Scopinaro, F.; Soluri, A.

2010-09-01

The aim of this work is to show a new scintigraphic device able to change automatically the length of its collimator in order to adapt the spatial resolution value to gamma source distance. This patented technique replaces the need for collimator change that standard gamma cameras still feature. Monte Carlo simulations represent the best tool in searching new technological solutions for such an innovative collimation structure. They also provide a valid analysis on response of gamma cameras performances as well as on advantages and limits of this new solution. Specifically, Monte Carlo simulations are realized with GEANT4 (GEometry ANd Tracking) framework and the specific simulation object is a collimation method based on separate blocks that can be brought closer and farther, in order to reach and maintain specific spatial resolution values for all source-detector distances. To verify the accuracy and the faithfulness of these simulations, we have realized experimental measurements with identical setup and conditions. This confirms the power of the simulation as an extremely useful tool, especially where new technological solutions need to be studied, tested and analyzed before their practical realization. The final aim of this new collimation system is the improvement of the SPECT techniques, with the real control of the spatial resolution value during tomographic acquisitions. This principle did allow us to simulate a tomographic acquisition of two capillaries of radioactive solution, in order to verify the possibility to clearly distinguish them.

Optimal Spatial Design of Capacity and Quantity of Rainwater Catchment Systems for Urban Flood Mitigation

NASA Astrophysics Data System (ADS)

Huang, C.; Hsu, N.

2013-12-01

This study imports Low-Impact Development (LID) technology of rainwater catchment systems into a Storm-Water runoff Management Model (SWMM) to design the spatial capacity and quantity of rain barrel for urban flood mitigation. This study proposes a simulation-optimization model for effectively searching the optimal design. In simulation method, we design a series of regular spatial distributions of capacity and quantity of rainwater catchment facilities, and thus the reduced flooding circumstances using a variety of design forms could be simulated by SWMM. Moreover, we further calculate the net benefit that is equal to subtract facility cost from decreasing inundation loss and the best solution of simulation method would be the initial searching solution of the optimization model. In optimizing method, first we apply the outcome of simulation method and Back-Propagation Neural Network (BPNN) for developing a water level simulation model of urban drainage system in order to replace SWMM which the operating is based on a graphical user interface and is hard to combine with optimization model and method. After that we embed the BPNN-based simulation model into the developed optimization model which the objective function is minimizing the negative net benefit. Finally, we establish a tabu search-based algorithm to optimize the planning solution. This study applies the developed method in Zhonghe Dist., Taiwan. Results showed that application of tabu search and BPNN-based simulation model into the optimization model not only can find better solutions than simulation method in 12.75%, but also can resolve the limitations of previous studies. Furthermore, the optimized spatial rain barrel design can reduce 72% of inundation loss according to historical flood events.

Dielectric spectroscopy in aqueous solutions of oligosaccharides: Experiment meets simulation

NASA Astrophysics Data System (ADS)

Weingärtner, Hermann; Knocks, Andrea; Boresch, Stefan; Höchtl, Peter; Steinhauser, Othmar

2001-07-01

We report the frequency-dependent complex dielectric permittivity of aqueous solutions of the homologous saccharides D(+)-glucose, maltose, and maltotriose in the frequency range 200 MHz⩽ν⩽20 GHz. For each solute, solutions having concentrations between 0.01 and 1 mol dm-3 were studied. In all measured spectra two dispersion/loss regions could be discerned. With the exception of the two most concentrated maltotriose solutions, a good description of the spectra by the superposition of two Debye processes was possible. The amplitudes and correlation times of the glucose and maltose solutions determined from fits of the experimental data were compared to those obtained in an earlier molecular dynamics study of such systems; the overall agreement between experiment and simulation is quite satisfactory. A dielectric component analysis of the simulation results permitted a more detailed assignment of the relaxation processes occurring on the molecular level. The physical picture emerging from this analysis is compared with traditional hydration models used in the interpretation of measured dielectric data. It is shown that the usual standard models do not capture an important contribution arising from cross terms due to dipolar interactions between solute and water, as well as between hydration water and bulk water. This finding suggests that conventional approaches to determine molecular dipole moments of the solutes may be problematic. This is certainly the case for solutes with small molecular dipole moments, but strong solute-solvent interactions, such as the saccharides studied here.

Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jakobtorweihen, S., E-mail: jakobtorweihen@tuhh.de; Ingram, T.; Gerlach, T.

2014-07-28

Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realisticmore » solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.« less

Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

2015-03-01

We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

VS2DI: Model use, calibration, and validation

USGS Publications Warehouse

Healy, Richard W.; Essaid, Hedeff I.

2012-01-01

VS2DI is a software package for simulating water, solute, and heat transport through soils or other porous media under conditions of variable saturation. The package contains a graphical preprocessor for constructing simulations, a postprocessor for displaying simulation results, and numerical models that solve for flow and solute transport (VS2DT) and flow and heat transport (VS2DH). Flow is described by the Richards equation, and solute and heat transport are described by advection-dispersion equations; the finite-difference method is used to solve these equations. Problems can be simulated in one, two, or three (assuming radial symmetry) dimensions. This article provides an overview of calibration techniques that have been used with VS2DI; included is a detailed description of calibration procedures used in simulating the interaction between groundwater and a stream fed by drainage from agricultural fields in central Indiana. Brief descriptions of VS2DI and the various types of problems that have been addressed with the software package are also presented.

A regularized vortex-particle mesh method for large eddy simulation

NASA Astrophysics Data System (ADS)

Spietz, H. J.; Walther, J. H.; Hejlesen, M. M.

2017-11-01

We present recent developments of the remeshed vortex particle-mesh method for simulating incompressible fluid flow. The presented method relies on a parallel higher-order FFT based solver for the Poisson equation. Arbitrary high order is achieved through regularization of singular Green's function solutions to the Poisson equation and recently we have derived novel high order solutions for a mixture of open and periodic domains. With this approach the simulated variables may formally be viewed as the approximate solution to the filtered Navier Stokes equations, hence we use the method for Large Eddy Simulation by including a dynamic subfilter-scale model based on test-filters compatible with the aforementioned regularization functions. Further the subfilter-scale model uses Lagrangian averaging, which is a natural candidate in light of the Lagrangian nature of vortex particle methods. A multiresolution variation of the method is applied to simulate the benchmark problem of the flow past a square cylinder at Re = 22000 and the obtained results are compared to results from the literature.

LES-ODT Simulations of Turbulent Reacting Shear Layers

NASA Astrophysics Data System (ADS)

Hoffie, Andreas; Echekki, Tarek

2012-11-01

Large-eddy simulations (LES) combined with the one-dimensional turbulence (ODT) simulations of a spatially developing turbulent reacting shear layer with heat release and high Reynolds numbers were conducted and compared to results from direct numerical simulations (DNS) of the same configuration. The LES-ODT approach is based on LES solutions for momentum on a coarse grid and solutions for momentum and reactive scalars on a fine ODT grid, which is embedded in the LES computational domain. The shear layer is simulated with a single-step, second-order reaction with an Arrhenius reaction rate. The transport equations are solved using a low Mach number approximation. The LES-ODT simulations yield reasonably accurate predictions of turbulence and passive/reactive scalars' statistics compared to DNS results.

Modeling of multi-band drift in nanowires using a full band Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Hathwar, Raghuraj; Saraniti, Marco; Goodnick, Stephen M.

2016-07-01

We report on a new numerical approach for multi-band drift within the context of full band Monte Carlo (FBMC) simulation and apply this to Si and InAs nanowires. The approach is based on the solution of the Krieger and Iafrate (KI) equations [J. B. Krieger and G. J. Iafrate, Phys. Rev. B 33, 5494 (1986)], which gives the probability of carriers undergoing interband transitions subject to an applied electric field. The KI equations are based on the solution of the time-dependent Schrödinger equation, and previous solutions of these equations have used Runge-Kutta (RK) methods to numerically solve the KI equations. This approach made the solution of the KI equations numerically expensive and was therefore only applied to a small part of the Brillouin zone (BZ). Here we discuss an alternate approach to the solution of the KI equations using the Magnus expansion (also known as "exponential perturbation theory"). This method is more accurate than the RK method as the solution lies on the exponential map and shares important qualitative properties with the exact solution such as the preservation of the unitary character of the time evolution operator. The solution of the KI equations is then incorporated through a modified FBMC free-flight drift routine and applied throughout the nanowire BZ. The importance of the multi-band drift model is then demonstrated for the case of Si and InAs nanowires by simulating a uniform field FBMC and analyzing the average carrier energies and carrier populations under high electric fields. Numerical simulations show that the average energy of the carriers under high electric field is significantly higher when multi-band drift is taken into consideration, due to the interband transitions allowing carriers to achieve higher energies.

Prediction of Solution Properties of Flexible-Chain Polymers: A Computer Simulation Undergraduate Experiment

ERIC Educational Resources Information Center

de la Torre, Jose Garcia; Cifre, Jose G. Hernandez; Martinez, M. Carmen Lopez

2008-01-01

This paper describes a computational exercise at undergraduate level that demonstrates the employment of Monte Carlo simulation to study the conformational statistics of flexible polymer chains, and to predict solution properties. Three simple chain models, including excluded volume interactions, have been implemented in a public-domain computer…

Chemistry of through-fall and stem-flow leachate following rainfall simulation over pinyon and juniper

USDA-ARS?s Scientific Manuscript database

We hypothesized that leachate from pinyon and juniper canopies, following rainfall events, may contribute sizable levels of solutes and C to the soil surface. We quantified solutes and dissolved carbon in stem-flow (SF) and through-fall (TF) following replicated rainfall simulation events in a pinyo...

Molecular dynamics simulations of the dielectric properties of fructose aqueous solutions

NASA Astrophysics Data System (ADS)

Sonoda, Milton T.; Elola, M. Dolores; Skaf, Munir S.

2016-10-01

The static dielectric permittivity and dielectric relaxation properties of fructose aqueous solutions of different concentrations ranging from 1.0 to 4.0 mol l-1 are investigated by means of molecular dynamics simulations. The contributions from intra- and interspecies molecular correlations were computed individually for both the static and frequency-dependent dielectric properties, and the results were compared with the available experimental data. Simulation results in the time- and frequency-domains were analyzed and indicate that the presence of fructose has little effect on the position of the fast, high-frequency (>500 cm-1) components of the dielectric response spectrum. The low-frequency (<0.1 cm-1) components, however, are markedly influenced by sugar concentration. Our analysis indicates that fructose-fructose and fructose-water interactions strongly affect the rotational-diffusion regime of molecular motions in the solutions. Increasing fructose concentration not only enhances sugar-sugar and sugar-water low frequency contributions to the dielectric loss spectrum but also slows down the reorientational dynamics of water molecules. These results are consistent with previous computer simulations carried out for other disaccharide aqueous solutions.

Assessment of a Hybrid Continuous/Discontinuous Galerkin Finite Element Code for Geothermal Reservoir Simulations

DOE PAGES

Xia, Yidong; Podgorney, Robert; Huang, Hai

2016-03-17

FALCON (“Fracturing And Liquid CONvection”) is a hybrid continuous / discontinuous Galerkin finite element geothermal reservoir simulation code based on the MOOSE (“Multiphysics Object-Oriented Simulation Environment”) framework being developed and used for multiphysics applications. In the present work, a suite of verification and validation (“V&V”) test problems for FALCON was defined to meet the design requirements, and solved to the interests of enhanced geothermal system (“EGS”) design. Furthermore, the intent for this test problem suite is to provide baseline comparison data that demonstrates the performance of the FALCON solution methods. The simulation problems vary in complexity from singly mechanical ormore » thermo process, to coupled thermo-hydro-mechanical processes in geological porous media. Numerical results obtained by FALCON agreed well with either the available analytical solution or experimental data, indicating the verified and validated implementation of these capabilities in FALCON. Some form of solution verification has been attempted to identify sensitivities in the solution methods, where possible, and suggest best practices when using the FALCON code.« less

Assessment of a hybrid finite element and finite volume code for turbulent incompressible flows

DOE PAGES

Xia, Yidong; Wang, Chuanjin; Luo, Hong; ...

2015-12-15

Hydra-TH is a hybrid finite-element/finite-volume incompressible/low-Mach flow simulation code based on the Hydra multiphysics toolkit being developed and used for thermal-hydraulics applications. In the present work, a suite of verification and validation (V&V) test problems for Hydra-TH was defined to meet the design requirements of the Consortium for Advanced Simulation of Light Water Reactors (CASL). The intent for this test problem suite is to provide baseline comparison data that demonstrates the performance of the Hydra-TH solution methods. The simulation problems vary in complexity from laminar to turbulent flows. A set of RANS and LES turbulence models were used in themore » simulation of four classical test problems. Numerical results obtained by Hydra-TH agreed well with either the available analytical solution or experimental data, indicating the verified and validated implementation of these turbulence models in Hydra-TH. Where possible, we have attempted some form of solution verification to identify sensitivities in the solution methods, and to suggest best practices when using the Hydra-TH code.« less

Assessment of a hybrid finite element and finite volume code for turbulent incompressible flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Yidong; Wang, Chuanjin; Luo, Hong

Hydra-TH is a hybrid finite-element/finite-volume incompressible/low-Mach flow simulation code based on the Hydra multiphysics toolkit being developed and used for thermal-hydraulics applications. In the present work, a suite of verification and validation (V&V) test problems for Hydra-TH was defined to meet the design requirements of the Consortium for Advanced Simulation of Light Water Reactors (CASL). The intent for this test problem suite is to provide baseline comparison data that demonstrates the performance of the Hydra-TH solution methods. The simulation problems vary in complexity from laminar to turbulent flows. A set of RANS and LES turbulence models were used in themore » simulation of four classical test problems. Numerical results obtained by Hydra-TH agreed well with either the available analytical solution or experimental data, indicating the verified and validated implementation of these turbulence models in Hydra-TH. Where possible, we have attempted some form of solution verification to identify sensitivities in the solution methods, and to suggest best practices when using the Hydra-TH code.« less

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour.

PubMed

Land, Sander; Gurev, Viatcheslav; Arens, Sander; Augustin, Christoph M; Baron, Lukas; Blake, Robert; Bradley, Chris; Castro, Sebastian; Crozier, Andrew; Favino, Marco; Fastl, Thomas E; Fritz, Thomas; Gao, Hao; Gizzi, Alessio; Griffith, Boyce E; Hurtado, Daniel E; Krause, Rolf; Luo, Xiaoyu; Nash, Martyn P; Pezzuto, Simone; Plank, Gernot; Rossi, Simone; Ruprecht, Daniel; Seemann, Gunnar; Smith, Nicolas P; Sundnes, Joakim; Rice, J Jeremy; Trayanova, Natalia; Wang, Dafang; Jenny Wang, Zhinuo; Niederer, Steven A

2015-12-08

Models of cardiac mechanics are increasingly used to investigate cardiac physiology. These models are characterized by a high level of complexity, including the particular anisotropic material properties of biological tissue and the actively contracting material. A large number of independent simulation codes have been developed, but a consistent way of verifying the accuracy and replicability of simulations is lacking. To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces. The benchmark was solved by 11 different groups to generate consensus solutions, with typical differences in higher-resolution solutions at approximately 0.5%, and consistent results between linear, quadratic and cubic finite elements as well as different approaches to simulating incompressible materials. Online tools and solutions are made available to allow these tests to be effectively used in verification of future cardiac mechanics software.

The scaling of oblique plasma double layers

NASA Technical Reports Server (NTRS)

Borovsky, J. E.

1983-01-01

Strong oblique plasma double layers are investigated using three methods, i.e., electrostatic particle-in-cell simulations, numerical solutions to the Poisson-Vlasov equations, and analytical approximations to the Poisson-Vlasov equations. The solutions to the Poisson-Vlasov equations and numerical simulations show that strong oblique double layers scale in terms of Debye lengths. For very large potential jumps, theory and numerical solutions indicate that all effects of the magnetic field vanish and the oblique double layers follow the same scaling relation as the field-aligned double layers.

Monte Carlo Simulation of the Rapid Crystallization of Bismuth-Doped Silicon

NASA Technical Reports Server (NTRS)

Jackson, Kenneth A.; Gilmer, George H.; Temkin, Dmitri E.

1995-01-01

In this Letter we report Ising model simulations of the growth of alloys which predict quite different behavior near and far from equilibrium. Our simulations reproduce the phenomenon which has been termed 'solute trapping,' where concentrations of solute, which are far in excess of the equilibrium concentrations, are observed in the crystal after rapid crystallization. This phenomenon plays an important role in many processes which involve first order phase changes which take place under conditions far from equilibrium. The underlying physical basis for it has not been understood, but these Monte Carlo simulations provide a powerful means for investigating it.

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Molecular dynamics simulations of the surface tension and structure of salt solutions and clusters.

PubMed

Sun, Lu; Li, Xin; Hede, Thomas; Tu, Yaoquan; Leck, Caroline; Ågren, Hans

2012-03-15

Sodium halides, which are abundant in sea salt aerosols, affect the optical properties of aerosols and are active in heterogeneous reactions that cause ozone depletion and acid rain problems. Interfacial properties, including surface tension and halide anion distributions, are crucial issues in the study of the aerosols. We present results from molecular dynamics simulations of water solutions and clusters containing sodium halides with the interatomic interactions described by a conventional force field. The simulations reproduce experimental observations that sodium halides increase the surface tension with respect to pure water and that iodide anions reach the outermost layer of water clusters or solutions. It is found that the van der Waals interactions have an impact on the distribution of the halide anions and that a conventional force field with optimized parameters can model the surface tension of the salt solutions with reasonable accuracy. © 2012 American Chemical Society

A comparison of solute-transport solution techniques and their effect on sensitivity analysis and inverse modeling results

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2001-01-01

Five common numerical techniques for solving the advection-dispersion equation (finite difference, predictor corrector, total variation diminishing, method of characteristics, and modified method of characteristics) were tested using simulations of a controlled conservative tracer-test experiment through a heterogeneous, two-dimensional sand tank. The experimental facility was constructed using discrete, randomly distributed, homogeneous blocks of five sand types. This experimental model provides an opportunity to compare the solution techniques: the heterogeneous hydraulic-conductivity distribution of known structure can be accurately represented by a numerical model, and detailed measurements can be compared with simulated concentrations and total flow through the tank. The present work uses this opportunity to investigate how three common types of results - simulated breakthrough curves, sensitivity analysis, and calibrated parameter values - change in this heterogeneous situation given the different methods of simulating solute transport. The breakthrough curves show that simulated peak concentrations, even at very fine grid spacings, varied between the techniques because of different amounts of numerical dispersion. Sensitivity-analysis results revealed: (1) a high correlation between hydraulic conductivity and porosity given the concentration and flow observations used, so that both could not be estimated; and (2) that the breakthrough curve data did not provide enough information to estimate individual values of dispersivity for the five sands. This study demonstrates that the choice of assigned dispersivity and the amount of numerical dispersion present in the solution technique influence estimated hydraulic conductivity values to a surprising degree.

Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

PubMed

Lee, Cheng-Kuang; Pao, Chun-Wei

2016-08-17

Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies.

SUTRA: A model for 2D or 3D saturated-unsaturated, variable-density ground-water flow with solute or energy transport

USGS Publications Warehouse

Voss, Clifford I.; Provost, A.M.

2002-01-01

SUTRA (Saturated-Unsaturated Transport) is a computer program that simulates fluid movement and the transport of either energy or dissolved substances in a subsurface environment. This upgraded version of SUTRA adds the capability for three-dimensional simulation to the former code (Voss, 1984), which allowed only two-dimensional simulation. The code employs a two- or three-dimensional finite-element and finite-difference method to approximate the governing equations that describe the two interdependent processes that are simulated: 1) fluid density-dependent saturated or unsaturated ground-water flow; and 2) either (a) transport of a solute in the ground water, in which the solute may be subject to: equilibrium adsorption on the porous matrix, and both first-order and zero-order production or decay; or (b) transport of thermal energy in the ground water and solid matrix of the aquifer. SUTRA may also be used to simulate simpler subsets of the above processes. A flow-direction-dependent dispersion process for anisotropic media is also provided by the code and is introduced in this report. As the primary calculated result, SUTRA provides fluid pressures and either solute concentrations or temperatures, as they vary with time, everywhere in the simulated subsurface system. SUTRA flow simulation may be employed for two-dimensional (2D) areal, cross sectional and three-dimensional (3D) modeling of saturated ground-water flow systems, and for cross sectional and 3D modeling of unsaturated zone flow. Solute-transport simulation using SUTRA may be employed to model natural or man-induced chemical-species transport including processes of solute sorption, production, and decay. For example, it may be applied to analyze ground-water contaminant transport problems and aquifer restoration designs. In addition, solute-transport simulation with SUTRA may be used for modeling of variable-density leachate movement, and for cross sectional modeling of saltwater intrusion in aquifers at near-well or regional scales, with either dispersed or relatively sharp transition zones between freshwater and saltwater. SUTRA energy-transport simulation may be employed to model thermal regimes in aquifers, subsurface heat conduction, aquifer thermal-energy storage systems, geothermal reservoirs, thermal pollution of aquifers, and natural hydrogeologic convection systems. Mesh construction, which is quite flexible for arbitrary geometries, employs quadrilateral finite elements in 2D Cartesian or radial-cylindrical coordinate systems, and hexahedral finite elements in 3D systems. 3D meshes are currently restricted to be logically rectangular; in other words, they are similar to deformable finite-difference-style grids. Permeabilities may be anisotropic and may vary in both direction and magnitude throughout the system, as may most other aquifer and fluid properties. Boundary conditions, sources and sinks may be time dependent. A number of input data checks are made to verify the input data set. An option is available for storing intermediate results and restarting a simulation at the intermediate time. Output options include fluid velocities, fluid mass and solute mass or energy budgets, and time-varying observations at points in the system. Both the mathematical basis for SUTRA and the program structure are highly general, and are modularized to allow for straightforward addition of new methods or processes to the simulation. The FORTRAN-90 coding stresses clarity and modularity rather than efficiency, providing easy access for later modifications.

Evolutionary online behaviour learning and adaptation in real robots.

PubMed

Silva, Fernando; Correia, Luís; Christensen, Anders Lyhne

2017-07-01

Online evolution of behavioural control on real robots is an open-ended approach to autonomous learning and adaptation: robots have the potential to automatically learn new tasks and to adapt to changes in environmental conditions, or to failures in sensors and/or actuators. However, studies have so far almost exclusively been carried out in simulation because evolution in real hardware has required several days or weeks to produce capable robots. In this article, we successfully evolve neural network-based controllers in real robotic hardware to solve two single-robot tasks and one collective robotics task. Controllers are evolved either from random solutions or from solutions pre-evolved in simulation. In all cases, capable solutions are found in a timely manner (1 h or less). Results show that more accurate simulations may lead to higher-performing controllers, and that completing the optimization process in real robots is meaningful, even if solutions found in simulation differ from solutions in reality. We furthermore demonstrate for the first time the adaptive capabilities of online evolution in real robotic hardware, including robots able to overcome faults injected in the motors of multiple units simultaneously, and to modify their behaviour in response to changes in the task requirements. We conclude by assessing the contribution of each algorithmic component on the performance of the underlying evolutionary algorithm.

Simulation of macromolecule self-assembly in solution: A multiscale approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lavino, Alessio D., E-mail: alessiodomenico.lavino@studenti.polito.it; Barresi, Antonello A., E-mail: antonello.barresi@polito.it; Marchisio, Daniele L., E-mail: daniele.marchisio@polito.it

2015-12-17

One of the most common processes to produce polymer nanoparticles is to induce self-assembly by using the solvent-displacement method, in which the polymer is dissolved in a “good” solvent and the solution is then mixed with an “anti-solvent”. The polymer ability to self-assemble in solution is therefore determined by its structural and transport properties in solutions of the pure solvents and at the intermediate compositions. In this work, we focus on poly-ε-caprolactone (PCL) which is a biocompatible polymer that finds widespread application in the pharmaceutical and biomedical fields, performing simulation at three different scales using three different computational tools: fullmore » atomistic molecular dynamics (MD), population balance modeling (PBM) and computational fluid dynamics (CFD). Simulations consider PCL chains of different molecular weight in solution of pure acetone (good solvent), of pure water (anti-solvent) and their mixtures, and mixing at different rates and initial concentrations in a confined impinging jets mixer (CIJM). Our MD simulations reveal that the nano-structuring of one of the solvents in the mixture leads to an unexpected identical polymer structure irrespectively of the concentration of the two solvents. In particular, although in pure solvents the behavior of the polymer is, as expected, very different, at intermediate compositions, the PCL chain shows properties very similar to those found in pure acetone as a result of the clustering of the acetone molecules in the vicinity of the polymer chain. We derive an analytical expression to predict the polymer structural properties in solution at different solvent compositions and use it to formulate an aggregation kernel to describe the self-assembly in the CIJM via PBM and CFD. Simulations are eventually validated against experiments.« less

Thermal Analysis System

NASA Technical Reports Server (NTRS)

DiStefano, III, Frank James (Inventor); Wobick, Craig A. (Inventor); Chapman, Kirt Auldwin (Inventor); McCloud, Peter L. (Inventor)

2014-01-01

A thermal fluid system modeler including a plurality of individual components. A solution vector is configured and ordered as a function of one or more inlet dependencies of the plurality of individual components. A fluid flow simulator simulates thermal energy being communicated with the flowing fluid and between first and second components of the plurality of individual components. The simulation extends from an initial time to a later time step and bounds heat transfer to be substantially between the flowing fluid, walls of tubes formed in each of the individual components of the plurality, and between adjacent tubes. Component parameters of the solution vector are updated with simulation results for each of the plurality of individual components of the simulation.

TH-CD-202-05: DECT Based Tissue Segmentation as Input to Monte Carlo Simulations for Proton Treatment Verification Using PET Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berndt, B; Wuerl, M; Dedes, G

Purpose: To improve agreement of predicted and measured positron emitter yields in patients, after proton irradiation for PET-based treatment verification, using a novel dual energy CT (DECT) tissue segmentation approach, overcoming known deficiencies from single energy CT (SECT). Methods: DECT head scans of 5 trauma patients were segmented and compared to existing decomposition methods with a first focus on the brain. For validation purposes, three brain equivalent solutions [water, white matter (WM) and grey matter (GM) – equivalent with respect to their reference carbon and oxygen contents and CT numbers at 90kVp and 150kVp] were prepared from water, ethanol, sucrosemore » and salt. The activities of all brain solutions, measured during a PET scan after uniform proton irradiation, were compared to Monte Carlo simulations. Simulation inputs were various solution compositions obtained from different segmentation approaches from DECT, SECT scans, and known reference composition. Virtual GM solution salt concentration corrections were applied based on DECT measurements of solutions with varying salt concentration. Results: The novel tissue segmentation showed qualitative improvements in %C for patient brain scans (ground truth unavailable). The activity simulations based on reference solution compositions agree with the measurement within 3–5% (4–8Bq/ml). These reference simulations showed an absolute activity difference between WM (20%C) and GM (10%C) to H2O (0%C) of 43 Bq/ml and 22 Bq/ml, respectively. Activity differences between reference simulations and segmented ones varied from −6 to 1 Bq/ml for DECT and −79 to 8 Bq/ml for SECT. Conclusion: Compared to the conventionally used SECT segmentation, the DECT based segmentation indicates a qualitative and quantitative improvement. In controlled solutions, a MC input based on DECT segmentation leads to better agreement with the reference. Future work will address the anticipated improvement of quantification accuracy in patients, comparing different tissue decomposition methods with an MR brain segmentation. Acknowledgement: DFG-MAP and HIT-Heidelberg Deutsche Forschungsgemeinschaft (MAP); Bundesministerium fur Bildung und Forschung (01IB13001)« less

A computer simulation study of the temperature dependence of the hydrophobic hydration

NASA Astrophysics Data System (ADS)

Guillot, B.; Guissani, Y.

1993-11-01

The test particle method is used to evaluate by molecular dynamics calculations the solubility of rare gases and of methane in water between the freezing point and the critical point. A quantitative agreement is obtained between solubility data and simulation results when the simulated water is modeled by the extended simple point charge model (SPCE). From a thermodynamical point of view, it is shown that the hierarchy of rare gases solubilities in water is governed by the solute-water interaction energy while an entropic term of cavity formation is found to be responsible for the peculiar temperature dependence of the solubility along the coexistence curve, and more precisely, of the solubility minimum exhibited by all the investigated solutes. Near the water critical point, the asymptotic behaviors of the Henry's constant and of the vapor-liquid partition coefficient, respectively, as deduced from the simulation data follow with a good accuracy the critical laws recently proposed in the literature for these quantities. Moreover, the calculated partial molar volume of the solute shows a steep increase above 473 K and becomes proportional to the isothermal compressibility of the pure solvent in the vicinity of the critical point as it is observed experimentally. From a microscopic point of view, the evaluation of the solute-solvent pair distribution functions permits to establish a relationship between the increase of the solubility with the decrease of the temperature in cold water on the one hand, and the formation of cages of the clathrate-type around the solute on the other hand. Nevertheless, as soon as the boiling point of water is reached the computer simulation shows that the water molecules of the first hydration shell are no longer oriented tangentially to the solute and tend to reorientate towards the bulk. At higher temperatures a deficit of water molecules progressively appears around the solute, a deficit which is directly associated with an increase of the partial molar volume. Although this phenomenon could be related to what is observed in supercritical mixtures it is emphasized that no long range critical fluctuation is present in the simulated sample.

A chemiluminescence biosensor for the detection of thrombin based on the aptamer composites

NASA Astrophysics Data System (ADS)

Lin, Yanna; Li, Jianbo; Wang, Yanhui; Sun, Yuanling; Ding, Chaofan; Sun, Weiyan; Luo, Chuannan

2018-03-01

An efficient, rapid, simple and ultrasensitive chemiluminescence (CL) approach was proposed for thrombin detection based on the aptamer-thrombin recognition. The aptamer composites were synthesized in this work using graphene oxide (GO) as the backing material. The thrombin was adsorbed on the aptamer composites based on the aptamer-thrombin recognition. Thus, thrombin could be quantified by the difference value of the CL intensity between supernate of the sample and the mixture which composed of thrombin and coexisted substances. The CL intensity exhibits a stable response to thrombin over a concentration range from 2.5 × 10- 10 to 1 × 10- 9 mol·L- 1 with a detection limit as low as 8.3 × 10- 11 mol·L- 1, the relative standard deviation (RSD) was found to be 4.9% for 11 determinations of 1.25 × 10- 9 mol·L- 1 thrombin. Finally, the applicability of the method was verified by applying to serum samples. The recoveries were in the range of 90.3-101.0% with RSD of 2.6-3.2%.

Distribution of thiobarbituric acid-reactive substances in lipoproteins and proteins in serum.

PubMed

Bonnefont, D; Legrand, A; Peynet, J; Emerit, J; Delattre, J; Galli, A

1989-10-01

We assessed the distribution of malondialdehyde (MDA) in lipoproteins and proteins in serum after using two procedures to separate the lipoproteins: sequential ultracentrifugation or selective precipitation with a sodium phosphotungstate and magnesium chloride reagent followed by ultracentrifugation of the supernate. MDA concentrations were determined by the thiobarbituric acid reaction and quantified by fluorometry. We found that 43% of the thiobarbituric acid-reactive substances (TBARS) was bound to the lipoproteins--27% to very-low- and low-density lipoproteins (VLDL-LDL) and 16% to high-density lipoproteins (HDL)--and from 11.5% to 15.8% to proteins, depending on the separation procedure. Residual unbound TBARS were located in the ultracentrifugation layers that contained no lipoproteins or proteins. The TBARS concentration in serum lipoproteins containing apolipoprotein B (i.e., VLDL-LDL) was the same after ultracentrifugation or selective precipitation. We therefore consider the precipitation method more suitable for routine TBARS determination in these lipoproteins, because it is easier to handle and faster. However, for determination of TBARS in HDL, selective precipitation requires subsequent ultracentrifugation at a density of 1.21 kg/L.

Spectrometric Analysis for Pulse Jet Mixer Testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

ZEIGLER, KRISTINE

2004-07-12

The Analytical Development Section (ADS) was tasked with providing support for a Hanford River Protection Program-Waste Treatment Program (RPP-WTP) project test involving absorption analysis for non-Newtonian pulse jet mixer testing for small scale (PJM) and prototype (CRV) tanks with sparging. Tanks filled with clay were mixed with various amounts of powdered dye as a tracer. The objective of the entire project was to determine the best mixing protocol (nozzle velocity, number of spargers used, total air flow, etc.) by determining the percent mixed volume through the use of an ultraviolet-visible (UV-Vis) spectrometer. The dye concentration within the sample could bemore » correlated to the volume fraction mixed in the tank. Samples were received in vials, a series of dilutions were generated from the clay, allowed to equilibrate, then centrifuged and siphoned for the supernate liquid to analyze by absorption spectroscopy. Equilibration of the samples and thorough mixing of the samples were a continuous issue with dilution curves being difficult to obtain. Despite these technical issues, useful data was obtained for evaluation of various mix conditions.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ingebretsen, O.C.; Borgen, J.; Farstad, M.

A reversed-phase liquid-chromatographic procedure is presented for quantitation or uric acid in human serum, with absorbance measured at 292 nm. The mobile phase was sodium acetate (35 mmol/L, pH 5.0)/acetonitrile (9/1 by vol). Complete precipitation of serum proteins was obtained by mixing serum (50-500 microL) with an equal volume of acetonitrile, and the precipitate was removed by centrifugation. Aliquots (20 microL) of the supernate were injected directly into the liquid chromatograph, which was adjusted so that the absorbance reading of the uric acid peak was as high as possible. Routinely, a full-scale deflection of 1.28 absorbance units was used. Themore » within-run precision (CV) was 0.6% for a serum uric acid concentration of 227 mumol/L and day-to-day precision over a 15-day period was 0.8% for uric acid of 345 mumol/L. No interferences from related compounds were observed. Researchers compared results by this method with those by kinetic and equilibrium adaptations of uricase methods. The method reported is simple, and can be used in a fully automatic liquid-chromatographic system.« less

Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

NASA Technical Reports Server (NTRS)

Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

1999-01-01

We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results.

PubMed

Bellich, Barbara; Gamini, Amelia; Brady, John W; Cesàro, Attilio

2018-04-05

The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules. Copyright © 2018. Published by Elsevier B.V.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

First-principles molecular dynamics simulation study on electrolytes for use in redox flow battery

NASA Astrophysics Data System (ADS)

Choe, Yoong-Kee; Tsuchida, Eiji; Tokuda, Kazuya; Ootsuka, Jun; Saito, Yoshihiro; Masuno, Atsunobu; Inoue, Hiroyuki

2017-11-01

Results of first-principles molecular dynamics simulations carried out to investigate structural aspects of electrolytes for use in a redox flow battery are reported. The electrolytes studied here are aqueous sulfuric acid solutions where its property is of importance for dissolving redox couples in redox flow battery. The simulation results indicate that structural features of the acid solutions depend on the concentration of sulfuric acid. Such dependency arises from increase of proton dissociation from sulfuric acid.

Prediction of the glass transition in aqueous solutions of simple amides by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kreck, Cara A.; Mandumpal, Jestin B.; Mancera, Ricardo L.

2011-01-01

Some simple amides in aqueous solution are used in the cryopreservation of biological tissues as they are believed to promote the vitrification of water, inhibiting its crystallisation and the ensuing damage from ice formation. Molecular dynamics annealing simulations reveal a broadening in the glass transition of aqueous acetamide and N-methylacetamide solutions, suggesting a thermodynamic stabilisation of the glassy state, which may be responsible for their increased tendency of vitrification and their cryoprotective ability. By contrast, aqueous formamide solutions do not exhibit broadening of the glass transition; instead, it is shifted to lower temperatures, which explains their lack of vitrification properties.

Check-Cases for Verification of 6-Degree-of-Freedom Flight Vehicle Simulations

NASA Technical Reports Server (NTRS)

Murri, Daniel G.; Jackson, E. Bruce; Shelton, Robert O.

2015-01-01

The rise of innovative unmanned aeronautical systems and the emergence of commercial space activities have resulted in a number of relatively new aerospace organizations that are designing innovative systems and solutions. These organizations use a variety of commercial off-the-shelf and in-house-developed simulation and analysis tools including 6-degree-of-freedom (6-DOF) flight simulation tools. The increased affordability of computing capability has made highfidelity flight simulation practical for all participants. Verification of the tools' equations-of-motion and environment models (e.g., atmosphere, gravitation, and geodesy) is desirable to assure accuracy of results. However, aside from simple textbook examples, minimal verification data exists in open literature for 6-DOF flight simulation problems. This assessment compared multiple solution trajectories to a set of verification check-cases that covered atmospheric and exo-atmospheric (i.e., orbital) flight. Each scenario consisted of predefined flight vehicles, initial conditions, and maneuvers. These scenarios were implemented and executed in a variety of analytical and real-time simulation tools. This tool-set included simulation tools in a variety of programming languages based on modified flat-Earth, round- Earth, and rotating oblate spheroidal Earth geodesy and gravitation models, and independently derived equations-of-motion and propagation techniques. The resulting simulated parameter trajectories were compared by over-plotting and difference-plotting to yield a family of solutions. In total, seven simulation tools were exercised.

A Green's function method for simulation of time-dependent solute transport and reaction in realistic microvascular geometries

PubMed Central

Secomb, Timothy W.

2016-01-01

A novel theoretical method is presented for simulating the spatially resolved convective and diffusive transport of reacting solutes between microvascular networks and the surrounding tissues. The method allows for efficient computational solution of problems involving convection and non-linear binding of solutes in blood flowing through microvascular networks with realistic 3D geometries, coupled with transvascular exchange and diffusion and reaction in the surrounding tissue space. The method is based on a Green's function approach, in which the solute concentration distribution in the tissue is expressed as a sum of fields generated by time-varying distributions of discrete sources and sinks. As an example of the application of the method, the washout of an inert diffusible tracer substance from a tissue region perfused by a network of microvessels is simulated, showing its dependence on the solute's transvascular permeability and tissue diffusivity. Exponential decay of the washout concentration is predicted, with rate constants that are about 10–30% lower than the rate constants for a tissue cylinder model with the same vessel length, vessel surface area and blood flow rate per tissue volume. PMID:26443811

Monte Carlo simulation and equation of state for flexible charged hard-sphere chain fluids: Polyampholyte and polyelectrolyte solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Hao; Adidharma, Hertanto, E-mail: adidharm@uwyo.edu

The thermodynamic modeling of flexible charged hard-sphere chains representing polyampholyte or polyelectrolyte molecules in solution is considered. The excess Helmholtz energy and osmotic coefficients of solutions containing short polyampholyte and the osmotic coefficients of solutions containing short polyelectrolytes are determined by performing canonical and isobaric-isothermal Monte Carlo simulations. A new equation of state based on the thermodynamic perturbation theory is also proposed for flexible charged hard-sphere chains. For the modeling of such chains, the use of solely the structure information of monomer fluid for calculating the chain contribution is found to be insufficient and more detailed structure information must thereforemore » be considered. Two approaches, i.e., the dimer and dimer-monomer approaches, are explored to obtain the contribution of the chain formation to the Helmholtz energy. By comparing with the simulation results, the equation of state with either the dimer or dimer-monomer approach accurately predicts the excess Helmholtz energy and osmotic coefficients of polyampholyte and polyelectrolyte solutions except at very low density. It also well captures the effect of temperature on the thermodynamic properties of these solutions.« less

Kidney-inspired algorithm for optimization problems

NASA Astrophysics Data System (ADS)

Jaddi, Najmeh Sadat; Alvankarian, Jafar; Abdullah, Salwani

2017-01-01

In this paper, a population-based algorithm inspired by the kidney process in the human body is proposed. In this algorithm the solutions are filtered in a rate that is calculated based on the mean of objective functions of all solutions in the current population of each iteration. The filtered solutions as the better solutions are moved to filtered blood and the rest are transferred to waste representing the worse solutions. This is a simulation of the glomerular filtration process in the kidney. The waste solutions are reconsidered in the iterations if after applying a defined movement operator they satisfy the filtration rate, otherwise it is expelled from the waste solutions, simulating the reabsorption and excretion functions of the kidney. In addition, a solution assigned as better solution is secreted if it is not better than the worst solutions simulating the secreting process of blood in the kidney. After placement of all the solutions in the population, the best of them is ranked, the waste and filtered blood are merged to become a new population and the filtration rate is updated. Filtration provides the required exploitation while generating a new solution and reabsorption gives the necessary exploration for the algorithm. The algorithm is assessed by applying it on eight well-known benchmark test functions and compares the results with other algorithms in the literature. The performance of the proposed algorithm is better on seven out of eight test functions when it is compared with the most recent researches in literature. The proposed kidney-inspired algorithm is able to find the global optimum with less function evaluations on six out of eight test functions. A statistical analysis further confirms the ability of this algorithm to produce good-quality results.

SINERGIA laparoscopic virtual reality simulator: didactic design and technical development.

PubMed

Lamata, Pablo; Gómez, Enrique J; Sánchez-Margallo, Francisco M; López, Oscar; Monserrat, Carlos; García, Verónica; Alberola, Carlos; Florido, Miguel Angel Rodríguez; Ruiz, Juan; Usón, Jesús

2007-03-01

VR laparoscopic simulators have demonstrated its validity in recent studies, and research should be directed towards a high training effectiveness and efficacy. In this direction, an insight into simulators' didactic design and technical development is provided, by describing the methodology followed in the building of the SINERGIA simulator. It departs from a clear analysis of training needs driven by a surgical training curriculum. Existing solutions and validation studies are an important reference for the definition of specifications, which are described with a suitable use of simulation technologies. Five new didactic exercises are proposed to train some of the basic laparoscopic skills. Simulator construction has required existing algorithms and the development of a particle-based biomechanical model, called PARSYS, and a collision handling solution based in a multi-point strategy. The resulting VR laparoscopic simulator includes new exercises and enhanced simulation technologies, and is finding a very good acceptance among surgeons.

Technetium and Iodine Getters to Improve Cast Stone Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qafoku, Nikolla; Neeway, James J.; Lawter, Amanda R.

2014-07-01

To determine the effectiveness of the various getter materials prior to their solidification in Cast Stone, a series of batch sorption experiments was performed at Pacific Northwest National Laboratory. To quantify the effectiveness of the removal of Tc(VII) and I(I) from solution by getters, the distribution coefficient, Kd (mL/g), was calculated. Testing involved placing getter material in contact with spiked waste solutions at a 1:100 solid-to-solution ratio for periods up to 45 days with periodic solution sampling. One Tc getter was also tested at a 1:10 solid-to-solution ratio. Two different solution media, 18.2 MΩ deionized water (DI H2O) and amore » 7.8 M Na LAW simulant, were used in the batch sorption tests. Each test was conducted at room temperature in an anoxic chamber containing N2 with a small amount of H2 (0.7%) to maintain anoxic conditions. Each getter-solution combination was run in duplicate. Three Tc- and I-doping concentrations were used separately in aliquots of both the 18.2 MΩ DI H2O and a 7.8 M Na LAW waste simulant. The 1× concentration was developed based on Hanford Tank Waste Operations Simulator (HTWOS) model runs to support the River Protection Project System Plan Revision 6. The other two concentrations were 5× and 10× of the HTWOS values. The Tc and I tests were run separately (i.e., the solutions did not contain both solutes). Sampling of the solid-solution mixtures occurred nominally after 0.2, 1, 3, 6, 9, 12, 15 days and ~35 to 45 days. Seven getter materials were tested for Tc and five materials were tested for I. The seven Tc getters were blast furnace slag 1 (BFS1) (northwest source), BFS2 (southeast source), Sn(II)-treated apatite, Sn(II) chloride, nano tin phosphate, KMS (a potassium-metal-sulfide), and tin hydroxapatite. The five iodine getters were layered bismuth hydroxide (LBH), argentite mineral, synthetic argentite, silver-treated carbon, and silver-treated zeolite. The Tc Kd values measured from experiments conducted using the 7.8 M Na LAW simulant (the simulant selected to represent LAW) for the first 15 days for four Tc getters (BFS1, BFS2, Sn(II)-treated apatite, and Sn(II) chloride) show no, to a very small, capacity to remove Tc from the LAW simulant. For the Tc-getter experiments in the 7.8 M LAW simulant, the majority of the effluent samples show very small drops in Tc concentrations for the 35-day compared to the 15-day samplings. However, the Tc concentration in the simulant blanks also dropped slightly during this period, so the effect of the getter contacting LAW simulant at 35 days compared to 15 days is minimal; except that the BFS1 1:10 test shows a slow but steady decrease in Tc concentration in the LAW simulant supernatant from the beginning to the 35 day contact at which point about 20% of the original Tc has been removed from solution. Lastly, the KMS getter gives the highest Kd value for Tc at 35 days where Kd values have increased to 104 mL/g. When considering the different I getters reacting with the 7.8 M LAW simulant, two getters are much more effective than the others: Ag zeolite and Syn Arg. The other getters have calculated iodide distribution coefficients that show very limited effectiveness in the caustic conditions created by the LAW simulant. These are preliminary results that will need more detailed analyses including both pre- and post-batch sorption getter solid-phase characterization using state-of-the-art instrumentation such as synchrotron X ray absorption spectroscopy, which can delineate the oxidation state of the Tc and likely iodine species as well as some of the getters key major components, sulfur and iron in the BFS, and tin and sulfur in the tin-bearing and sulfur-bearing getters. This report also describes future experimental studies to be performed to better elucidate the mechanisms controlling the Tc and I sequestration processes in the various getters and leach tests of getter-bearing Cast Stone monoliths.« less

Technetium and Iodine Getters to Improve Cast Stone Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qafoku, Nikolla; Neeway, James J.; Lawter, Amanda R.

2015-02-19

To determine the effectiveness of the various getter materials prior to their solidification in Cast Stone, a series of batch sorption experiments was performed at Pacific Northwest National Laboratory. To quantify the effectiveness of the removal of Tc(VII) and I(I) from solution by getters, the distribution coefficient, K d (mL/g), was calculated. Testing involved placing getter material in contact with spiked waste solutions at a 1:100 solid-to-solution ratio for periods up to 45 days with periodic solution sampling. One Tc getter was also tested at a 1:10 solid-to-solution ratio. Two different solution media, 18.2 MΩ deionized water (DI H 2O)more » and a 7.8 M Na LAW simulant, were used in the batch sorption tests. Each test was conducted at room temperature in an anoxic chamber containing N2 with a small amount of H 2 (0.7%) to maintain anoxic conditions. Each getter-solution combination was run in duplicate. Three Tc- and I-doping concentrations were used separately in aliquots of both the 18.2 MΩ DI H2O and a 7.8 M Na LAW waste simulant. The 1× concentration was developed based on Hanford Tank Waste Operations Simulator (HTWOS) model runs to support the River Protection Project System Plan Revision 6. The other two concentrations were 5× and 10× of the HTWOS values. The Tc and I tests were run separately (i.e., the solutions did not contain both solutes). Sampling of the solid-solution mixtures occurred nominally after 0.2, 1, 3, 6, 9, 12, 15 days and ~35 to 45 days. Seven getter materials were tested for Tc and five materials were tested for I. The seven Tc getters were blast furnace slag 1 (BFS1) (northwest source), BFS2 (southeast source), Sn(II)-treated apatite, Sn(II) chloride, nano tin phosphate, KMS (a potassium-metal-sulfide), and tin hydroxapatite. The five iodine getters were layered bismuth hydroxide (LBH), argentite mineral, synthetic argentite, silver-treated carbon, and silver-treated zeolite. The Tc Kd values measured from experiments conducted using the 7.8 M Na LAW simulant (the simulant selected to represent LAW) for the first 15 days for four Tc getters (BFS1, BFS2, Sn(II)-treated apatite, and Sn(II) chloride) show no, to a very small, capacity to remove Tc from the LAW simulant. For the Tc-getter experiments in the 7.8 M LAW simulant, the majority of the effluent samples show very small drops in Tc concentrations for the 35-day compared to the 15-day samplings. However, the Tc concentration in the simulant blanks also dropped slightly during this period, so the effect of the getter contacting LAW simulant at 35 days compared to 15 days is minimal; except that the BFS1 1:10 test shows a slow but steady decrease in Tc concentration in the LAW simulant supernatant from the beginning to the 35 day contact at which point about 20% of the original Tc has been removed from solution. Lastly, the KMS getter gives the highest K d value for Tc at 35 days where K d values have increased to 104 mL/g. When considering the different I getters reacting with the 7.8 M LAW simulant, two getters are much more effective than the others: Ag zeolite and Syn Arg. The other getters have calculated iodide distribution coefficients that show very limited effectiveness in the caustic conditions created by the LAW simulant. These are preliminary results that will need more detailed analyses including both pre- and post-batch sorption getter solid-phase characterization using state-of-the-art instrumentation such as synchrotron X-ray absorption spectroscopy, which can delineate the oxidation state of the Tc and likely iodine species as well as some of the getters key major components, sulfur and iron in the BFS, and tin and sulfur in the tin-bearing and sulfur-bearing getters. This report also describes future experimental studies to be performed to better elucidate the mechanisms controlling the Tc and I sequestration processes in the various getters and leach tests of getter-bearing Cast Stone monoliths.« less

Medical Simulation in the Community College Health Science Curriculum: A Matrix for Future Implementation

ERIC Educational Resources Information Center

McLaughlin, Michael P.; Starobin, Soko S.; Laanan, Frankie Santos

2010-01-01

As the nation's healthcare education system struggles to keep pace with the demand for its services, educators are seeking creative and innovative solutions to meet the needs of a growing number of students. The integration of medical simulation technology into the community college health science curriculum is a creative solution that can meet…

Simulated effects of reduced sulfur, nitrogen, and base cation deposition on soils and solutions in Southern Appalachian forests

Treesearch

D.W. Johnson; R.B. Susfalk; P.F. Brewer; W.T. Swank

1999-01-01

Effects of reduced deposition of N, S, and CB on nutrient pools, fluxes, soil, and soil solution chemistry were simulated for two Appalachian forest ecosystems using the nutrient cycling model. In the extremely acidic, N- and S-saturated red spruce (Picea rubens (Sarg.)) forest (Nolan Divide), reducing

Extending atomistic simulation timescale in solid/liquid systems: crystal growth from solution by a parallel-replica dynamics and continuum hybrid method.

PubMed

Lu, Chun-Yaung; Voter, Arthur F; Perez, Danny

2014-01-28

Deposition of solid material from solution is ubiquitous in nature. However, due to the inherent complexity of such systems, this process is comparatively much less understood than deposition from a gas or vacuum. Further, the accurate atomistic modeling of such systems is computationally expensive, therefore leaving many intriguing long-timescale phenomena out of reach. We present an atomistic/continuum hybrid method for extending the simulation timescales of dynamics at solid/liquid interfaces. We demonstrate the method by simulating the deposition of Ag on Ag (001) from solution with a significant speedup over standard MD. The results reveal specific features of diffusive deposition dynamics, such as a dramatic increase in the roughness of the film.

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

DOE PAGES

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.; ...

2016-11-07

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abhyankar, Shrirang; Constantinescu, Emil M.; Smith, Barry F.

Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including amore » real utility network, show good scalability on different computing architectures.« less

Global Properties of Fully Convective Accretion Disks from Local Simulations

NASA Astrophysics Data System (ADS)

Bodo, G.; Cattaneo, F.; Mignone, A.; Ponzo, F.; Rossi, P.

2015-08-01

We present an approach to deriving global properties of accretion disks from the knowledge of local solutions derived from numerical simulations based on the shearing box approximation. The approach consists of a two-step procedure. First, a local solution valid for all values of the disk height is constructed by piecing together an interior solution obtained numerically with an analytical exterior radiative solution. The matching is obtained by assuming hydrostatic balance and radiative equilibrium. Although in principle the procedure can be carried out in general, it simplifies considerably when the interior solution is fully convective. In these cases, the construction is analogous to the derivation of the Hayashi tracks for protostars. The second step consists of piecing together the local solutions at different radii to obtain a global solution. Here we use the symmetry of the solutions with respect to the defining dimensionless numbers—in a way similar to the use of homology relations in stellar structure theory—to obtain the scaling properties of the various disk quantities with radius.

Enhanced nonlinearity interval mapping scheme for high-performance simulation-optimization of watershed-scale BMP placement

NASA Astrophysics Data System (ADS)

Zou, Rui; Riverson, John; Liu, Yong; Murphy, Ryan; Sim, Youn

2015-03-01

Integrated continuous simulation-optimization models can be effective predictors of a process-based responses for cost-benefit optimization of best management practices (BMPs) selection and placement. However, practical application of simulation-optimization model is computationally prohibitive for large-scale systems. This study proposes an enhanced Nonlinearity Interval Mapping Scheme (NIMS) to solve large-scale watershed simulation-optimization problems several orders of magnitude faster than other commonly used algorithms. An efficient interval response coefficient (IRC) derivation method was incorporated into the NIMS framework to overcome a computational bottleneck. The proposed algorithm was evaluated using a case study watershed in the Los Angeles County Flood Control District. Using a continuous simulation watershed/stream-transport model, Loading Simulation Program in C++ (LSPC), three nested in-stream compliance points (CP)—each with multiple Total Maximum Daily Loads (TMDL) targets—were selected to derive optimal treatment levels for each of the 28 subwatersheds, so that the TMDL targets at all the CP were met with the lowest possible BMP implementation cost. Genetic Algorithm (GA) and NIMS were both applied and compared. The results showed that the NIMS took 11 iterations (about 11 min) to complete with the resulting optimal solution having a total cost of 67.2 million, while each of the multiple GA executions took 21-38 days to reach near optimal solutions. The best solution obtained among all the GA executions compared had a minimized cost of 67.7 million—marginally higher, but approximately equal to that of the NIMS solution. The results highlight the utility for decision making in large-scale watershed simulation-optimization formulations.

Predict the glass transition temperature of glycerol-water binary cryoprotectant by molecular dynamic simulation.

PubMed

Li, Dai-Xi; Liu, Bao-Lin; Liu, Yi-shu; Chen, Cheng-lung

2008-04-01

Vitrification is proposed to be the best way for the cryopreservation of organs. The glass transition temperature (T(g)) of vitrification solutions is a critical parameter of fundamental importance for cryopreservation by vitrification. The instruments that can detect the thermodynamic, mechanical and dielectric changes of a substance may be used to determine the glass transition temperature. T(g) is usually measured by using differential scanning calorimetry (DSC). In this study, the T(g) of the glycerol-aqueous solution (60%, wt/%) was determined by isothermal-isobaric molecular dynamic simulation (NPT-MD). The software package Discover in Material Studio with the Polymer Consortium Force Field (PCFF) was used for the simulation. The state parameters of heat capacity at constant pressure (C(p)), density (rho), amorphous cell volume (V(cell)) and specific volume (V(specific)) and radial distribution function (rdf) were obtained by NPT-MD in the temperature range of 90-270K. These parameters showed a discontinuity at a specific temperature in the plot of state parameter versus temperature. The temperature at the discontinuity is taken as the simulated T(g) value for glycerol-water binary solution. The T(g) values determined by simulation method were compared with the values in the literatures. The simulation values of T(g) (160.06-167.51K) agree well with the DSC results (163.60-167.10K) and the DMA results (159.00K). We drew the conclusion that molecular dynamic simulation (MDS) is a potential method for investigating the glass transition temperature (T(g)) of glycerol-water binary cryoprotectants and may be used for other vitrification solutions.

Program Code Generator for Cardiac Electrophysiology Simulation with Automatic PDE Boundary Condition Handling

PubMed Central

Punzalan, Florencio Rusty; Kunieda, Yoshitoshi; Amano, Akira

2015-01-01

Clinical and experimental studies involving human hearts can have certain limitations. Methods such as computer simulations can be an important alternative or supplemental tool. Physiological simulation at the tissue or organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and distributed parameters, such as those used in pharmacokinetics simulation, add to the complexity of the PDE solution. These factors can tailor PDE solutions and their corresponding program code to specific problems. Boundary condition and parameter changes in the customized code are usually prone to errors and time-consuming. We propose a general approach for handling PDEs and boundary conditions in computational models using a replacement scheme for discretization. This study is an extension of a program generator that we introduced in a previous publication. The program generator can generate code for multi-cell simulations of cardiac electrophysiology. Improvements to the system allow it to handle simultaneous equations in the biological function model as well as implicit PDE numerical schemes. The replacement scheme involves substituting all partial differential terms with numerical solution equations. Once the model and boundary equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to generate the program code. The resulting program code are in Java or C programming language. To validate the automatic handling of boundary conditions in the program code generator, we generated simulation code using the FHN, Luo-Rudy 1, and Hund-Rudy cell models and run cell-to-cell coupling and action potential propagation simulations. One of the simulations is based on a published experiment and simulation results are compared with the experimental data. We conclude that the proposed program code generator can be used to generate code for physiological simulations and provides a tool for studying cardiac electrophysiology. PMID:26356082

HST3D; a computer code for simulation of heat and solute transport in three-dimensional ground-water flow systems

USGS Publications Warehouse

Kipp, K.L.

1987-01-01

The Heat- and Soil-Transport Program (HST3D) simulates groundwater flow and associated heat and solute transport in three dimensions. The three governing equations are coupled through the interstitial pore velocity, the dependence of the fluid density on pressure, temperature, the solute-mass fraction , and the dependence of the fluid viscosity on temperature and solute-mass fraction. The solute transport equation is for only a single, solute species with possible linear equilibrium sorption and linear decay. Finite difference techniques are used to discretize the governing equations using a point-distributed grid. The flow-, heat- and solute-transport equations are solved , in turn, after a particle Gauss-reduction scheme is used to modify them. The modified equations are more tightly coupled and have better stability for the numerical solutions. The basic source-sink term represents wells. A complex well flow model may be used to simulate specified flow rate and pressure conditions at the land surface or within the aquifer, with or without pressure and flow rate constraints. Boundary condition types offered include specified value, specified flux, leakage, heat conduction, and approximate free surface, and two types of aquifer influence functions. All boundary conditions can be functions of time. Two techniques are available for solution of the finite difference matrix equations. One technique is a direct-elimination solver, using equations reordered by alternating diagonal planes. The other technique is an iterative solver, using two-line successive over-relaxation. A restart option is available for storing intermediate results and restarting the simulation at an intermediate time with modified boundary conditions. This feature also can be used as protection against computer system failure. Data input and output may be in metric (SI) units or inch-pound units. Output may include tables of dependent variables and parameters, zoned-contour maps, and plots of the dependent variables versus time. (Lantz-PTT)

Quantification of mixing in vesicle suspensions using numerical simulations in two dimensions.

PubMed

Kabacaoğlu, G; Quaife, B; Biros, G

2017-02-01

We study mixing in Stokesian vesicle suspensions in two dimensions on a cylindrical Couette apparatus using numerical simulations. The vesicle flow simulation is done using a boundary integral method, and the advection-diffusion equation for the mixing of the solute is solved using a pseudo-spectral scheme. We study the effect of the area fraction, the viscosity contrast between the inside (the vesicles) and the outside (the bulk) fluid, the initial condition of the solute, and the mixing metric. We compare mixing in the suspension with mixing in the Couette apparatus without vesicles. On the one hand, the presence of vesicles in most cases slightly suppresses mixing. This is because the solute can be only diffused across the vesicle interface and not advected. On the other hand, there exist spatial distributions of the solute for which the unperturbed Couette flow completely fails to mix whereas the presence of vesicles enables mixing. We derive a simple condition that relates the velocity and solute and can be used to characterize the cases in which the presence of vesicles promotes mixing.

Quantification of mixing in vesicle suspensions using numerical simulations in two dimensions

PubMed Central

Quaife, B.; Biros, G.

2017-01-01

We study mixing in Stokesian vesicle suspensions in two dimensions on a cylindrical Couette apparatus using numerical simulations. The vesicle flow simulation is done using a boundary integral method, and the advection-diffusion equation for the mixing of the solute is solved using a pseudo-spectral scheme. We study the effect of the area fraction, the viscosity contrast between the inside (the vesicles) and the outside (the bulk) fluid, the initial condition of the solute, and the mixing metric. We compare mixing in the suspension with mixing in the Couette apparatus without vesicles. On the one hand, the presence of vesicles in most cases slightly suppresses mixing. This is because the solute can be only diffused across the vesicle interface and not advected. On the other hand, there exist spatial distributions of the solute for which the unperturbed Couette flow completely fails to mix whereas the presence of vesicles enables mixing. We derive a simple condition that relates the velocity and solute and can be used to characterize the cases in which the presence of vesicles promotes mixing. PMID:28344432

Using MD simulations to calculate how solvents modulate solubility

PubMed Central

Liu, Shuai; Cao, Shannon; Hoang, Kevin; Young, Kayla L.; Paluch, Andrew S.; Mobley, David L.

2016-01-01

Here, our interest is in predicting solubility in general, and we focus particularly on predicting how the solubility of particular solutes is modulated by the solvent environment. Solubility in general is extremely important, both for theoretical reasons – it provides an important probe of the balance between solute-solute and solute-solvent interactions – and for more practical reasons, such as how to control the solubility of a given solute via modulation of its environment, as in process chemistry and separations. Here, we study how the change of solvent affects the solubility of a given compound. That is, we calculate relative solubilities. We use MD simulations to calculate relative solubility and compare our calculated values with experiment as well as with results from several other methods, SMD and UNIFAC, the latter of which is commonly used in chemical engineering design. We find that straightforward solubility calculations based on molecular simulations using a general small-molecule force field outperform SMD and UNIFAC both in terms of accuracy and coverage of the relevant chemical space. PMID:26878198

Capacitive Deionization of High-Salinity Solutions

DOE PAGES

Sharma, Ketki; Gabitto, Jorge; Mayes, Richard T.; ...

2014-12-22

Desalination of high salinity solutions has been studied using a novel experimental technique and a theoretical model. Neutron imaging has been employed to visualize lithium ions in mesoporous carbon materials, which are used as electrodes in capacitive deionization for water desalination. Experiments were conducted with a flow-through capacitive deionization cell designed for neutron imaging and with lithium chloride ( 6LiCl) as the electrolyte. Sequences of neutron images have been obtained at a relatively high concentration of lithium chloride ( 6LiCl) solution to provide information on the transport of ions within the electrodes. A new model that computes the individual ionicmore » concentration profiles inside mesoporous carbon electrodes has been used to simulate the capacitive deionization process. Modifications have also been introduced into the simulation model to calculate results at high electrolyte concentrations. Experimental data and simulation results provide insight into why capacitive deionization is not effective for desalination of high ionic-strength solutions. The combination of experimental information, obtained through neutron imaging, with the theoretical model will help in the design of capacitive deionization devices, which can improve the process for high ionic-strength solutions.« less

The combined effect of food-simulating solutions, brushing and staining on color stability of composite resins

PubMed Central

Silva, Tânia Mara Da; Sales, Ana Luísa Leme Simões; Pucci, Cesar Rogerio; Borges, Alessandra Bühler; Torres, Carlos Rocha Gomes

2017-01-01

Abstract Objective: This study evaluated the effect of food-simulating media associated with brushing and coffee staining on color stability of different composite resins. Materials and methods: Eighty specimens were prepared for each composite: Grandio SO (Voco), Amaris (Voco), Filtek Z350XT (3M/ESPE), Filtek P90 (3M/ESPE). They were divided into four groups according to food-simulating media for 7 days: artificial saliva (control), heptane, citric acid and ethanol. The composite surface was submitted to 10,950 brushing cycles (200 g load) in an automatic toothbrushing machine. The specimens were darkened with coffee solution at 37 °C for 24 h. After each treatment, color measurements were assessed by spectrophotometry, using CIE L*a*b* system. The overall color change (ΔE) was determined for each specimen at baseline (C1) and after the treatments (food-simulating media immersion/C2, brushing/C3 and dye solution/C4). Data were analyzed by two-way repeated measures ANOVA and Tukey’s tests (p < .05). Results: The results of RM-ANOVA showed significant differences for composites (p = .001), time (p = .001) and chemical degradation (p = .002). The mean of ΔE for composites were: Z350XT (5.39)a, Amaris (3.89)b, Grandio (3.75)bc, P90 (3.36)c. According to food-simulating media: heptane (4.41)a, citric acid (4.24)a, ethanol (4.02)ab, artificial saliva (3.76)b. For the treatments: dye solution (4.53)a, brushing (4.26)a, after food-simulating media (3.52)b. Conclusions: The composite resin Filtek Z350XT showed significantly higher staining than all other composite resin tested. The immersion in heptane and citric acid produced the highest color alteration than other food-simulating media. The exposure of samples to brushing protocols and darkening in coffee solution resulted in significant color alteration of the composite resins. PMID:28642926

Organics Characterization Of DWPF Alternative Reductant Simulants, Glycolic Acid, And Antifoam 747

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, T. L.; Wiedenman, B. J.; Lambert, D. P.

The present study examines the fate of glycolic acid and other organics added in the Chemical Processing Cell (CPC) of the Defense Waste Processing Facility (DWPF) as part of the glycolic alternate flowsheet. Adoption of this flowsheet is expected to provide certain benefits in terms of a reduction in the processing time, a decrease in hydrogen generation, simplification of chemical storage and handling issues, and an improvement in the processing characteristics of the waste stream including an increase in the amount of nitrate allowed in the CPC process. Understanding the fate of organics in this flowsheet is imperative because tankmore » farm waste processed in the CPC is eventually immobilized by vitrification; thus, the type and amount of organics present in the melter feed may affect optimal melt processing and the quality of the final glass product as well as alter flammability calculations on the DWPF melter off gas. To evaluate the fate of the organic compounds added as the part of the glycolic flowsheet, mainly glycolic acid and antifoam 747, samples of simulated waste that was processed using the DWPF CPC protocol for tank farm sludge feed were generated and analyzed for organic compounds using a variety of analytical techniques at the Savannah River National Laboratory (SRNL). These techniques included Ion Chromatography (IC), Gas Chromatography-Mass Spectrometry (GC-MS), Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES), and Nuclear Magnetic Resonance (NMR) Spectroscopy. A set of samples were also sent to the Catholic University of America Vitreous State Laboratory (VSL) for analysis by NMR Spectroscopy at the University of Maryland, College Park. Analytical methods developed and executed at SRNL collectively showed that glycolic acid was the most prevalent organic compound in the supernatants of Slurry Mix Evaporator (SME) products examined. Furthermore, the studies suggested that commercially available glycolic acid contained minor amounts of impurities such as formic and diglycolic acid that were then carried over in the SME products. Oxalic acid present in the simulated tank farm waste was also detected. Finally, numerous other compounds, at low concentrations, were observed present in etheric extracts of aqueous supernate solutions of the SME samples and are thought to be breakdown products of antifoam 747. The data collectively suggest that although addition of glycolic acid and antifoam 747 will introduce a number of impurities and breakdown products into the melter feed, the concentrations of these organics is expected to remain low and may not significantly impact REDOX or off-gas flammability predictions. In the SME products examined presently, which contained variant amounts of glycolic acid and antifoam 747, no unexpected organic degradation product was found at concentrations above 500 mg/kg, a reasonable threshold concentration for an organic compound to be taken into account in the REDOX modeling. This statement does not include oxalic or formic acid that were sometimes observed above 500 mg/kg and acetic acid that has an analytical detection limit of 1250 mg/kg due to high glycolate concentration in the SME products tested. Once a finalized REDOX equation has been developed and implemented, REDOX properties of known organic species will be determined and their impact assessed. Although no immediate concerns arose during the study in terms of a negative impact of organics present in SME products of the glycolic flowsheet, evidence of antifoam degradation suggest that an alternative antifoam to antifoam 747 is worth considering. The determination and implementation of an antifoam that is more hydrolysis resistant would have benefits such as increasing its effectiveness over time and reducing the generation of degradation products.« less

Numerical Modeling of Solidification in Space With MEPHISTO-4. Part 2

NASA Technical Reports Server (NTRS)

Simpson, James E.; Yoa, Minwu; deGroh, Henry C., III; Garimella, V. Suresh

1998-01-01

A pre-flight analysis of the directional solidification of BiSn with MEPHISTO-4 is presented. Simplified Bridgman growth under microgravity conditions is simulated using a two dimensional finite element model. This numerical model is a single domain, pseudo-steady state model, and includes the effects of both thermal and solutal convection. The results show that for all orientations of the applied steady state gravity vector, of magnitude 1 micro-g, the directional solidification process remains diffusion controlled. The maximum convective velocity was found to be 4.424 x 10(exp -5) cm/s for the horizontal Bridgman growth configuration. This value is an order of magnitude lower than the growth velocity. The maximum and minimum values or solute concentration in the liquid at the crystal-melt interface were 13.867 at.% and 13.722 at.%, respectively. This gives a radial segregation value of xi = 1.046% at the interface. A secondary objective of this work was to compare the results obtained to those that consider thermal convection only (no solutal convection). It was found that the convective flow patterns in simulations which included solutal convection were significantly different from those which ignored solutal convection. The level of radial segregation predicted by the current simulations is an order of magnitude lower than that found in simulations which ignore solutal convection. The final aim was to investigate the effect of g-jitter on the crystal growth process. A simulation was performed to calculate the system response to a 1 second, 100 micro-g gravity impulse acting normal to the direction of growth. This pulse is consistent with that induced by Orbiter thruster firings. The results obtained indicate that such a gravity pulse causes an increase in the level of radial solute segregation at the interface from the steady state values. The maximum value of solute concentration in the liquid was found to be 13.888 at.%, the minimum value calculated was 13.706 at.%, yielding a radial segregation value of xi = 1.31% at the interface. These values occurred 126 seconds after the pulse terminated. Thus it is anticipated that the process will remain diffusion controlled even when subjected to such g-jitter.

VS2DRTI: Simulating Heat and Reactive Solute Transport in Variably Saturated Porous Media.

PubMed

Healy, Richard W; Haile, Sosina S; Parkhurst, David L; Charlton, Scott R

2018-01-29

Variably saturated groundwater flow, heat transport, and solute transport are important processes in environmental phenomena, such as the natural evolution of water chemistry of aquifers and streams, the storage of radioactive waste in a geologic repository, the contamination of water resources from acid-rock drainage, and the geologic sequestration of carbon dioxide. Up to now, our ability to simulate these processes simultaneously with fully coupled reactive transport models has been limited to complex and often difficult-to-use models. To address the need for a simple and easy-to-use model, the VS2DRTI software package has been developed for simulating water flow, heat transport, and reactive solute transport through variably saturated porous media. The underlying numerical model, VS2DRT, was created by coupling the flow and transport capabilities of the VS2DT and VS2DH models with the equilibrium and kinetic reaction capabilities of PhreeqcRM. Flow capabilities include two-dimensional, constant-density, variably saturated flow; transport capabilities include both heat and multicomponent solute transport; and the reaction capabilities are a complete implementation of geochemical reactions of PHREEQC. The graphical user interface includes a preprocessor for building simulations and a postprocessor for visual display of simulation results. To demonstrate the simulation of multiple processes, the model is applied to a hypothetical example of injection of heated waste water to an aquifer with temperature-dependent cation exchange. VS2DRTI is freely available public domain software. © 2018, National Ground Water Association.

Modeling flow and solute transport in irrigation furrows

USDA-ARS?s Scientific Manuscript database

This paper presents an internally coupled flow and solute transport model for free-draining irrigation furrows. Furrow hydraulics is simulated with a numerical zero-inertia model and solute transport is computed with a model based on a numerical solution of the cross-section averaged advection-dispe...

Numerical System Solver Developed for the National Cycle Program

NASA Technical Reports Server (NTRS)

Binder, Michael P.

1999-01-01

As part of the National Cycle Program (NCP), a powerful new numerical solver has been developed to support the simulation of aeropropulsion systems. This software uses a hierarchical object-oriented design. It can provide steady-state and time-dependent solutions to nonlinear and even discontinuous problems typically encountered when aircraft and spacecraft propulsion systems are simulated. It also can handle constrained solutions, in which one or more factors may limit the behavior of the engine system. Timedependent simulation capabilities include adaptive time-stepping and synchronization with digital control elements. The NCP solver is playing an important role in making the NCP a flexible, powerful, and reliable simulation package.

First Molecular Dynamics simulation insight into the mechanism of organics adsorption from aqueous solutions on microporous carbons

NASA Astrophysics Data System (ADS)

Terzyk, Artur P.; Gauden, Piotr A.; Zieliński, Wojciech; Furmaniak, Sylwester; Wesołowski, Radosław P.; Klimek, Kamil K.

2011-10-01

The results of 84 MD simulations showing the influence of porosity and carbon surface oxidation on adsorption of three organic compounds from aqueous solutions on carbons are reported. Based on a model of 'soft' activated carbon, three carbon structures with gradually changed microporosity were created. Next, different number of surface oxygen groups was introduced. We observe quantitative agreement between simulation and experiment i.e. the decrease in adsorption from benzene down to paracetamol. Simulation results clearly demonstrate that the balance between porosity and carbon surface chemical composition in organics adsorption on carbons, and the pore blocking determine adsorption properties of carbons.

Some VTOL head-up display drive-law problems and solutions

NASA Technical Reports Server (NTRS)

Merrick, Vernon K.

1993-01-01

A piloted simulation test was conducted on the Ames Research Center's vertical motion simulator (VMS) in support of the Phase 2A flight test of NASA's V/STOL systems research aircraft (VSRA). During the simulation several problems were found with the head-up display (HUD) symbol drive laws and the flightpath synthesis. These problems and the solutions devised to solve them are described. Most of the resulting HUD drive-law changes were implemented during the simulation and their effectiveness was verified. Subsequently both the HUD symbol drive-law and flightpath-synthesis changes were implemented in the VSRA and tested successfully in the Phase 2A flight tests.

Computer simulation of solutions of polyharmonic equations in plane domain

NASA Astrophysics Data System (ADS)

Kazakova, A. O.

2018-05-01

A systematic study of plane problems of the theory of polyharmonic functions is presented. A method of reducing boundary problems for polyharmonic functions to the system of integral equations on the boundary of the domain is given and a numerical algorithm for simulation of solutions of this system is suggested. Particular attention is paid to the numerical solution of the main tasks when the values of the function and its derivatives are given. Test examples are considered that confirm the effectiveness and accuracy of the suggested algorithm.

Kinetics of the electric double layer formation modelled by the finite difference method

NASA Astrophysics Data System (ADS)

Valent, Ivan

2017-11-01

Dynamics of the elctric double layer formation in 100 mM NaCl solution for sudden potentail steps of 10 and 20 mV was simulated using the Poisson-Nernst-Planck theory and VLUGR2 solver for partial differential equations. The used approach was verified by comparing the obtained steady-state solution with the available exact solution. The simulations allowed for detailed analysis of the relaxation processes of the individual ions and the electric potential. Some computational aspects of the problem were discussed.

Molecular dynamics simulation study of hydrogen bonding in aqueous poly(ethylene oxide) solutions.

PubMed

Smith, G D; Bedrov, D; Borodin, O

2000-12-25

A molecular dynamics simulation study of hydrogen bonding in poly(ethylene oxide) (PEO)/water solutions was performed. PEO-water and water-water hydrogen bonding manifested complex dependence on both composition and temperature. Strong water clustering in concentrated solutions was seen. Saturation of hydrogen bonding at w(p) approximately equal to 0.5 and a dramatic decrease in PEO-water hydrogen bonding with increasing temperature, consistent with experimentally observed closed-loop phase behavior, were observed. Little tendency toward intermolecular bridging of PEO chains by water molecules was seen.

Numerical Modeling Tools for the Prediction of Solution Migration Applicable to Mining Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martell, M.; Vaughn, P.

1999-01-06

Mining has always had an important influence on cultures and traditions of communities around the globe and throughout history. Today, because mining legislation places heavy emphasis on environmental protection, there is great interest in having a comprehensive understanding of ancient mining and mining sites. Multi-disciplinary approaches (i.e., Pb isotopes as tracers) are being used to explore the distribution of metals in natural environments. Another successful approach is to model solution migration numerically. A proven method to simulate solution migration in natural rock salt has been applied to project through time for 10,000 years the system performance and solution concentrations surroundingmore » a proposed nuclear waste repository. This capability is readily adaptable to simulate solution migration around mining.« less

Diffusion, Viscosity and Crystal Growth in Microgravity

NASA Technical Reports Server (NTRS)

Myerson, Allan S.

1996-01-01

The diffusivity of TriGlycine Sulfate (TGS), Potassium Dihydrogen Phosphate (KDP), Ammonium Dihydrogen Phosphate (ADF) and other compounds of interest to microgravity crystal growth, in supersaturated solutions as a function of solution concentration, 'age' and 'history was studied experimentally. The factors that affect the growth of crystals from water solutions in microgravity have been examined. Three non-linear optical materials have been studied, potassium dihydrogen phosphate (KDP), ammonium dihydrogen phosphate (ADP) and triglycine sulfate (TGC). The diffusion coefficient and viscosity of supersaturated water solutions were measured. Also theoretical model of diffusivity and viscosity in a metastable state, model of crystal growth from solution including non-linear time dependent diffusivity and viscosity effect and computer simulation of the crystal growth process which allows simulation of the microgravity crystal growth were developed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olivieri, Giorgia; Brown, Matthew A., E-mail: matthew.brown@mat.ethz.ch; Parry, Krista M.

Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy (XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the vapor (vacuum)-aqueous electrolyte interface. These experiments are often paired with complementary molecular dynamics (MD) simulations in an attempt to provide a complete description of the liquid interface. There is, however, no systematic protocol that permits a straightforward comparison of the two sets of results. XPS is an integrated technique that averages signals from multiple layers in a solution even at the lowest photoelectron kinetic energies routinely employed, whereas MD simulations provide a microscopic layer-by-layer descriptionmore » of the solution composition near the interface. Here, we use the National Institute of Standards and Technology database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to quantitatively interpret atom-density profiles from MD simulations for XPS signal intensities using sodium and potassium iodide solutions as examples. We show that electron inelastic mean free paths calculated from a semi-empirical formula depend strongly on solution composition, varying by up to 30% between pure water and concentrated NaI. The XPS signal thus arises from different information depths in different solutions for a fixed photoelectron kinetic energy. XPS signal intensities are calculated using SESSA as a function of photoelectron kinetic energy (probe depth) and compared with a widely employed ad hoc method. SESSA simulations illustrate the importance of accounting for elastic-scattering events at low photoelectron kinetic energies (<300 eV) where the ad hoc method systematically underestimates the preferential enhancement of anions over cations. Finally, some technical aspects of applying SESSA to liquid interfaces are discussed.« less

Evaluation of a Pair-Wise Conflict Detection and Resolution Algorithm in a Multiple Aircraft Scenario

NASA Technical Reports Server (NTRS)

Carreno, Victor A.

2002-01-01

The KB3D algorithm is a pairwise conflict detection and resolution (CD&R) algorithm. It detects and generates trajectory vectoring for an aircraft which has been predicted to be in an airspace minima violation within a given look-ahead time. It has been proven, using mechanized theorem proving techniques, that for a pair of aircraft, KB3D produces at least one vectoring solution and that all solutions produced are correct. Although solutions produced by the algorithm are mathematically correct, they might not be physically executable by an aircraft or might not solve multiple aircraft conflicts. This paper describes a simple solution selection method which assesses all solutions generated by KB3D and determines the solution to be executed. The solution selection method and KB3D are evaluated using a simulation in which N aircraft fly in a free-flight environment and each aircraft in the simulation uses KB3D to maintain separation. Specifically, the solution selection method filters KB3D solutions which are procedurally undesirable or physically not executable and uses a predetermined criteria for selection.

Difference of carboxybetaine and oligo(ethylene glycol) moieties in altering hydrophobic interactions: a molecular simulation study.

PubMed

Shao, Qing; White, Andrew D; Jiang, Shaoyi

2014-01-09

Polycarboxybetaine and poly(ethylene glycol) materials resist nonspecific protein adsorption but differ in influencing biological functions such as enzymatic activity. To investigate this difference, we studied the influence of carboxybetaine and oligo(ethylene glycol) moieties on hydrophobic interactions using molecular simulations. We employed a model system composed of two non-polar plates and studied the potential of mean force of plate-plate association in carboxybetaine, (ethylene glycol)4, and (ethylene glycol)2 solutions using well-tempered metadynamics simulations. Water, trimethylamine N-oxide, and urea solutions were used as reference systems. We analyzed the variation of the potential of mean force in various solutions to study how carboxybetaine and oligo(ethylene glycol) moieties influence the hydrophobic interactions. To study the origin of their influence, we analyzed the normalized distributions of moieties and water molecules using molecular dynamics simulations. The simulation results showed that oligo(ethylene glycol) moieties repel water molecules away from the non-polar plates and weaken the hydrophobic interactions. Carboxybetaine moieties do not repel water molecules away from the plates and therefore do not influence the hydrophobic interactions.

Wall interference and boundary simulation in a transonic wind tunnel with a discretely slotted test section

NASA Technical Reports Server (NTRS)

Al-Saadi, Jassim A.

1993-01-01

A computational simulation of a transonic wind tunnel test section with longitudinally slotted walls is developed and described herein. The nonlinear slot model includes dynamic pressure effects and a plenum pressure constraint, and each slot is treated individually. The solution is performed using a finite-difference method that solves an extended transonic small disturbance equation. The walls serve as the outer boundary conditions in the relaxation technique, and an interaction procedure is used at the slotted walls. Measured boundary pressures are not required to establish the wall conditions but are currently used to assess the accuracy of the simulation. This method can also calculate a free-air solution as well as solutions that employ the classical homogeneous wall conditions. The simulation is used to examine two commercial transport aircraft models at a supercritical Mach number for zero-lift and cruise conditions. Good agreement between measured and calculated wall pressures is obtained for the model geometries and flow conditions examined herein. Some localized disagreement is noted, which is attributed to improper simulation of viscous effects in the slots.

Application of Hybrid Real-Time Power System Simulator for Designing and Researching of Relay Protection and Automation

NASA Astrophysics Data System (ADS)

Borovikov, Yu S.; Sulaymanov, A. O.; Andreev, M. V.

2015-10-01

Development, research and operation of smart grids (SG) with active-adaptive networks (AAS) are actual tasks for today. Planned integration of high-speed FACTS devices greatly complicates complex dynamic properties of power systems. As a result the operating conditions of equipment of power systems are significantly changing. Such situation creates the new actual problem of development and research of relay protection and automation (RPA) which will be able to adequately operate in the SGs and adapt to its regimes. Effectiveness of solution of the problem depends on using tools - different simulators of electric power systems. Analysis of the most famous and widely exploited simulators led to the conclusion about the impossibility of using them for solution of the mentioned problem. In Tomsk Polytechnic University developed the prototype of hybrid multiprocessor software and hardware system - Hybrid Real-Time Power System Simulator (HRTSim). Because of its unique features this simulator can be used for solution of mentioned tasks. This article introduces the concept of development and research of relay protection and automation with usage of HRTSim.

Integrated dynamic analysis simulation of space stations with controllable solar array

NASA Technical Reports Server (NTRS)

Heinrichs, J. A.; Fee, J. J.

1972-01-01

A methodology is formulated and presented for the integrated structural dynamic analysis of space stations with controllable solar arrays and non-controllable appendages. The structural system flexibility characteristics are considered in the dynamic analysis by a synthesis technique whereby free-free space station modal coordinates and cantilever appendage coordinates are inertially coupled. A digital simulation of this analysis method is described and verified by comparison of interaction load solutions with other methods of solution. Motion equations are simulated for both the zero gravity and artificial gravity (spinning) orbital conditions. Closed loop controlling dynamics for both orientation control of the arrays and attitude control of the space station are provided in the simulation by various generic types of controlling systems. The capability of the simulation as a design tool is demonstrated by utilizing typical space station and solar array structural representations and a specific structural perturbing force. Response and interaction load solutions are presented for this structural configuration and indicate the importance of using an integrated type analysis for the predictions of structural interactions.

Simulation and analysis of airborne antenna radiation patterns

NASA Technical Reports Server (NTRS)

Kim, J. J.; Burnside, Walter D.

1984-01-01

The objective is to develop an accurate and efficient analytic solution for predicting high frequency radiation patterns of fuselage-mounted airborne antennas. This is an analytic study of airborne antenna patterns using the Uniform Geometrical Theory of Diffraction (UTD). The aircraft is modeled in its most basic form so that the solution is applicable to general-type aircraft. The fuselage is modeled as a perfectly conducting composite ellipsoid; whereas, the wings, stabilizers, nose, fuel tanks, and engines, are simulated as perfectly conducting flat plates that can be attached to the fuselage and/or to each other. The composite-ellipsoid fuselage model is necessary to successfully simulate the wide variety of real world fuselage shapes. Since the antenna is mounted on the fuselage, it has a dominant effect on the resulting radiation pattern so it must be simulated accurately, especially near the antenna. Various radiation patterns are calculated for commercial, private, and military aircraft, and the Space Shuttle Orbiter. The application of this solution to numerous practical airborne antenna problems illustrates its versatility and design capability. In most cases, the solution accuracy is verified by the comparisons between the calculated and measured data.

Evolutionary online behaviour learning and adaptation in real robots

PubMed Central

Correia, Luís; Christensen, Anders Lyhne

2017-01-01

Online evolution of behavioural control on real robots is an open-ended approach to autonomous learning and adaptation: robots have the potential to automatically learn new tasks and to adapt to changes in environmental conditions, or to failures in sensors and/or actuators. However, studies have so far almost exclusively been carried out in simulation because evolution in real hardware has required several days or weeks to produce capable robots. In this article, we successfully evolve neural network-based controllers in real robotic hardware to solve two single-robot tasks and one collective robotics task. Controllers are evolved either from random solutions or from solutions pre-evolved in simulation. In all cases, capable solutions are found in a timely manner (1 h or less). Results show that more accurate simulations may lead to higher-performing controllers, and that completing the optimization process in real robots is meaningful, even if solutions found in simulation differ from solutions in reality. We furthermore demonstrate for the first time the adaptive capabilities of online evolution in real robotic hardware, including robots able to overcome faults injected in the motors of multiple units simultaneously, and to modify their behaviour in response to changes in the task requirements. We conclude by assessing the contribution of each algorithmic component on the performance of the underlying evolutionary algorithm. PMID:28791130

A simple and effective solution to the constrained QM/MM simulations

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki; Kambe, Hiroyuki; Morita, Akihiro

2018-04-01

It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential. The point of the BCC method is to compensate the error in a statistical property due to the bias potential by adding a correction term obtained through a set of QM/MM simulations. The BCC method is designed so that the effect of the bias potential completely vanishes when the QM solvent is identical with the MM solvent. Furthermore, the desirable conditions, that is, the continuities of energy and force and the conservations of energy and momentum, are fulfilled in principle. We applied the QM/MM-BCC method to a hydronium ion(H3O+) in aqueous solution to construct the radial distribution function (RDF) of the solvent around the solute. It was demonstrated that the correction term fairly compensated the error and led the RDF in good agreement with the result given by an ab initio molecular dynamics simulation.

Insights into water-mediated ion clustering in aqueous CaSO4 solutions: pre-nucleation cluster characteristics studied by ab initio calculations and molecular dynamics simulations.

PubMed

Li, Hui-Ji; Yan, Dan; Cai, Hou-Qin; Yi, Hai-Bo; Min, Xiao-Bo; Xia, Fei-Fei

2017-05-10

The molecular structure of growth units building crystals is a fundamental issue in the crystallization processes from aqueous solutions. In this work, a systematic investigation of pre-nucleation clusters and their hydration characteristics in aqueous CaSO 4 solutions was performed using ab initio calculations and molecular dynamics (MD) simulations. The results of ab initio calculations and MD simulations indicate that the dominant species in aqueous CaSO 4 solutions are monodentate ion-associated structures. Compared with charged ion clusters, neutral clusters are more likely to be present in an aqueous CaSO 4 solution. Neutral (CaSO 4 ) m clusters are probably the growth units involved in the pre-nucleation or crystallization processes. Meanwhile, hydration behavior around ion associated species in aqueous CaSO 4 solutions plays an important role in related phase/polymorphism selections. Upon ion clustering, the residence of some water molecules around Ca 2+ in ion-associated species is weakened while that of some bridging waters is enhanced due to dual interaction by Ca 2+ and SO 4 2- . Some phase/polymorphism selections can be achieved in aqueous CaSO 4 solutions by controlling the hydration around pre-nucleation clusters. Moreover, the association trend between calcium and sulfate is found to be relatively strong, which hints at the low solubility of calcium sulfate in water.

A smart grid simulation testbed using Matlab/Simulink

NASA Astrophysics Data System (ADS)

Mallapuram, Sriharsha; Moulema, Paul; Yu, Wei

2014-06-01

The smart grid is the integration of computing and communication technologies into a power grid with a goal of enabling real time control, and a reliable, secure, and efficient energy system [1]. With the increased interest of the research community and stakeholders towards the smart grid, a number of solutions and algorithms have been developed and proposed to address issues related to smart grid operations and functions. Those technologies and solutions need to be tested and validated before implementation using software simulators. In this paper, we developed a general smart grid simulation model in the MATLAB/Simulink environment, which integrates renewable energy resources, energy storage technology, load monitoring and control capability. To demonstrate and validate the effectiveness of our simulation model, we created simulation scenarios and performed simulations using a real-world data set provided by the Pecan Street Research Institute.

The scaling of relativistic double-year widths - Poisson-Vlasov solutions and particle-in-cell simulations

NASA Technical Reports Server (NTRS)

Sulkanen, Martin E.; Borovsky, Joseph E.

1992-01-01

The study of relativistic plasma double layers is described through the solution of the one-dimensional, unmagnetized, steady-state Poisson-Vlasov equations and by means of one-dimensional, unmagnetized, particle-in-cell simulations. The thickness vs potential-drop scaling law is extended to relativistic potential drops and relativistic plasma temperatures. The transition in the scaling law for 'strong' double layers suggested by analytical two-beam models by Carlqvist (1982) is confirmed, and causality problems of standard double-layer simulation techniques applied to relativistic plasma systems are discussed.

Reparameterization of Solute—Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

PubMed Central

Lay, Wesley K.; Miller, Mark S.

2018-01-01

AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental osmotic pressures of mixed aqueous solutions of diglycine and sucrose. The modified parameters also improve the ΔGtrans of diglycine from water to aqueous sucrose and, with AMBERff99SB/GLYCAM06, eliminate a caging effect seen in previous simulations of the protein ubiquitin with glucose. PMID:28437100

3D Modeling of Transport Phenomena and the Injection of the Solution Droplets in the Solution Precursor Plasma Spraying

NASA Astrophysics Data System (ADS)

Shan, Yanguang; Coyle, Thomas W.; Mostaghimi, Javad

2007-12-01

Solution precursor plasma spraying has been used to produce finely structured ceramic coatings with nano- and sub-micrometric features. This process involves the injection of a solution spray of ceramic salts into a DC plasma jet under atmospheric condition. During the process, the solvent vaporizes as the droplet travel downstream. Solid particles are finally formed due to the precipitation of the solute, and the particle are heated up and accelerated to the substrate to generate the coating. This article describes a 3D model to simulate the transport phenomena and the trajectory and heating of the solution spray in the process. The jet-spray two-way interactions are considered. A simplified model is employed to simulate the evolution process and the formation of the solid particle from the solution droplet in the plasma jet. The temperature and velocity fields of the jet are obtained and validated. The particle size, velocity, temperature, and position distribution on the substrate are predicted.

Analyst-to-Analyst Variability in Simulation-Based Prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glickman, Matthew R.; Romero, Vicente J.

This report describes findings from the culminating experiment of the LDRD project entitled, "Analyst-to-Analyst Variability in Simulation-Based Prediction". For this experiment, volunteer participants solving a given test problem in engineering and statistics were interviewed at different points in their solution process. These interviews are used to trace differing solutions to differing solution processes, and differing processes to differences in reasoning, assumptions, and judgments. The issue that the experiment was designed to illuminate -- our paucity of understanding of the ways in which humans themselves have an impact on predictions derived from complex computational simulations -- is a challenging and openmore » one. Although solution of the test problem by analyst participants in this experiment has taken much more time than originally anticipated, and is continuing past the end of this LDRD, this project has provided a rare opportunity to explore analyst-to-analyst variability in significant depth, from which we derive evidence-based insights to guide further explorations in this important area.« less

A Green's function method for simulation of time-dependent solute transport and reaction in realistic microvascular geometries.

PubMed

Secomb, Timothy W

2016-12-01

A novel theoretical method is presented for simulating the spatially resolved convective and diffusive transport of reacting solutes between microvascular networks and the surrounding tissues. The method allows for efficient computational solution of problems involving convection and non-linear binding of solutes in blood flowing through microvascular networks with realistic 3D geometries, coupled with transvascular exchange and diffusion and reaction in the surrounding tissue space. The method is based on a Green's function approach, in which the solute concentration distribution in the tissue is expressed as a sum of fields generated by time-varying distributions of discrete sources and sinks. As an example of the application of the method, the washout of an inert diffusible tracer substance from a tissue region perfused by a network of microvessels is simulated, showing its dependence on the solute's transvascular permeability and tissue diffusivity. Exponential decay of the washout concentration is predicted, with rate constants that are about 10-30% lower than the rate constants for a tissue cylinder model with the same vessel length, vessel surface area and blood flow rate per tissue volume. © The authors 2015. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

One-Dimensional Transport with Inflow and Storage (OTIS): A Solute Transport Model for Streams and Rivers

USGS Publications Warehouse

Runkel, Robert L.

1998-01-01

OTIS is a mathematical simulation model used to characterize the fate and transport of water-borne solutes in streams and rivers. The governing equation underlying the model is the advection-dispersion equation with additional terms to account for transient storage, lateral inflow, first-order decay, and sorption. This equation and the associated equations describing transient storage and sorption are solved using a Crank-Nicolson finite-difference solution. OTIS may be used in conjunction with data from field-scale tracer experiments to quantify the hydrologic parameters affecting solute transport. This application typically involves a trial-and-error approach wherein parameter estimates are adjusted to obtain an acceptable match between simulated and observed tracer concentrations. Additional applications include analyses of nonconservative solutes that are subject to sorption processes or first-order decay. OTIS-P, a modified version of OTIS, couples the solution of the governing equation with a nonlinear regression package. OTIS-P determines an optimal set of parameter estimates that minimize the squared differences between the simulated and observed concentrations, thereby automating the parameter estimation process. This report details the development and application of OTIS and OTIS-P. Sections of the report describe model theory, input/output specifications, sample applications, and installation instructions.

Solute transport with equilibrium aqueous complexation and either sorption or ion exchange: Simulation methodology and applications

USGS Publications Warehouse

Lewis, F.M.; Voss, C.I.; Rubin, J.

1987-01-01

Methodologies that account for specific types of chemical reactions in the simulation of solute transport can be developed so they are compatible with solution algorithms employed in existing transport codes. This enables the simulation of reactive transport in complex multidimensional flow regimes, and provides a means for existing codes to account for some of the fundamental chemical processes that occur among transported solutes. Two equilibrium-controlled reaction systems demonstrate a methodology for accommodating chemical interaction into models of solute transport. One system involves the sorption of a given chemical species, as well as two aqueous complexations in which the sorbing species is a participant. The other reaction set involves binary ion exchange coupled with aqueous complexation involving one of the exchanging species. The methodology accommodates these reaction systems through the addition of nonlinear terms to the transport equations for the sorbing species. Example simulation results show (1) the effect equilibrium chemical parameters have on the spatial distributions of concentration for complexing solutes; (2) that an interrelationship exists between mechanical dispersion and the various reaction processes; (3) that dispersive parameters of the porous media cannot be determined from reactive concentration distributions unless the reaction is accounted for or the influence of the reaction is negligible; (4) how the concentration of a chemical species may be significantly affected by its participation in an aqueous complex with a second species which also sorbs; and (5) that these coupled chemical processes influencing reactive transport can be demonstrated in two-dimensional flow regimes. ?? 1987.

Influences of passivating elements on the corrosion and biocompatibility of super stainless steels.

PubMed

Yoo, Young-Ran; Jang, Soon-Geun; Oh, Keun-Taek; Kim, Jung-Gu; Kim, Young-Sik

2008-08-01

Biometals need high corrosion resistance since metallic implants in the body should be biocompatible and metal ion release should be minimized. In this work, we designed three kinds of super stainless steel and adjusted the alloying elements to obtain different microstructures. Super stainless steels contain larger amounts of Cr, Mo, W, and N than commercial alloys. These elements play a very important role in localized corrosion and, thus, their effects can be represented by the "pitting resistance equivalent number (PREN)." This work focused on the behavior which can arise when the bare surface of an implant in the body is exposed during walking, heavy exercise, and so on. Among the experimental alloys examined herein, Alloy Al and 316L stainless steels were mildly cytotoxic, whereas the other super austenitic, duplex, and ferritic stainless steels were noncytotoxic. This behavior is primarily related to the passive current and pitting resistance of the alloys. When the PREN value was increased, the passivation behavior in simulated body solution was totally different from that in acidic chloride solution and, thus, the Cr(2)O(3)/Cr(OH)(3) and [Metal oxide]/[Metal + Metal oxide] ratios of the passive film in the simulated body solution were larger than those in acidic chloride solution. Also, the critical current density in simulated body solution increased and, thus, active dissolution may induce metal ion release into the body when the PREN value and Ni content are increased. This behavior was closely related to the presence of EDTA in the simulated body solution. (c) 2007 Wiley Periodicals, Inc.

Multiple Solutions of Real-time Tsunami Forecasting Using Short-term Inundation Forecasting for Tsunamis Tool

NASA Astrophysics Data System (ADS)

Gica, E.

2016-12-01

The Short-term Inundation Forecasting for Tsunamis (SIFT) tool, developed by NOAA Center for Tsunami Research (NCTR) at the Pacific Marine Environmental Laboratory (PMEL), is used in forecast operations at the Tsunami Warning Centers in Alaska and Hawaii. The SIFT tool relies on a pre-computed tsunami propagation database, real-time DART buoy data, and an inversion algorithm to define the tsunami source. The tsunami propagation database is composed of 50×100km unit sources, simulated basin-wide for at least 24 hours. Different combinations of unit sources, DART buoys, and length of real-time DART buoy data can generate a wide range of results within the defined tsunami source. For an inexperienced SIFT user, the primary challenge is to determine which solution, among multiple solutions for a single tsunami event, would provide the best forecast in real time. This study investigates how the use of different tsunami sources affects simulated tsunamis at tide gauge locations. Using the tide gauge at Hilo, Hawaii, a total of 50 possible solutions for the 2011 Tohoku tsunami are considered. Maximum tsunami wave amplitude and root mean square error results are used to compare tide gauge data and the simulated tsunami time series. Results of this study will facilitate SIFT users' efforts to determine if the simulated tide gauge tsunami time series from a specific tsunami source solution would be within the range of possible solutions. This study will serve as the basis for investigating more historical tsunami events and tide gauge locations.

Simulation of saltwater movement in the Upper Floridan aquifer in the Savannah, Georgia-Hilton Head Island, South Carolina, area, predevelopment-2004, and projected movement for 2000 pumping conditions

USGS Publications Warehouse

Provost, Alden M.; Payne, Dorothy F.; Voss, Clifford I.

2006-01-01

A digital model was developed to simulate ground-water flow and solute transport for the Upper Floridan aquifer in the Savannah, Georgia-Hilton Head Island, South Carolina, area. The model was used to (1) simulate trends of saltwater intrusion from predevelopment to the present day (1885-2004), (2) project these trends from the present day into the future, and (3) evaluate the relative influence of different assumptions regarding initial and boundary conditions and physical properties. The model is based on a regional, single-density ground-water flow model of coastal Georgia and adjacent parts of South Carolina and Florida. Variable-density ground-water flow and solute transport were simulated using the U.S. Geological Survey finite-element, variable-density solute-transport simulator SUTRA, 1885-2004. The model comprises seven layers: the surficial aquifer system, the Brunswick aquifer system, the Upper Floridan aquifer, the Lower Floridan aquifer, and the intervening confining units. The model was calibrated to September 1998 water levels, for single-density freshwater conditions, then refined using variable density and chloride concentration to give a reasonable match to the trend in the chloride distribution in the Upper Floridan aquifer inferred from field measurements of specific conductance made during 2000, 2002, 2003, and 2004. The model was modified to simulate solute transport by allowing saltwater to enter the system through localized areas near the northern end of Hilton Head Island, at Pinckney Island, and near the Colleton River, and was calibrated to match chloride concentrations inferred from field measurements of specific conductance. This simulation is called the 'Base Case.'

Advanced in Visualization of 3D Time-Dependent CFD Solutions

NASA Technical Reports Server (NTRS)

Lane, David A.; Lasinski, T. A. (Technical Monitor)

1995-01-01

Numerical simulations of complex 3D time-dependent (unsteady) flows are becoming increasingly feasible because of the progress in computing systems. Unfortunately, many existing flow visualization systems were developed for time-independent (steady) solutions and do not adequately depict solutions from unsteady flow simulations. Furthermore, most systems only handle one time step of the solutions individually and do not consider the time-dependent nature of the solutions. For example, instantaneous streamlines are computed by tracking the particles using one time step of the solution. However, for streaklines and timelines, particles need to be tracked through all time steps. Streaklines can reveal quite different information about the flow than those revealed by instantaneous streamlines. Comparisons of instantaneous streamlines with dynamic streaklines are shown. For a complex 3D flow simulation, it is common to generate a grid system with several millions of grid points and to have tens of thousands of time steps. The disk requirement for storing the flow data can easily be tens of gigabytes. Visualizing solutions of this magnitude is a challenging problem with today's computer hardware technology. Even interactive visualization of one time step of the flow data can be a problem for some existing flow visualization systems because of the size of the grid. Current approaches for visualizing complex 3D time-dependent CFD solutions are described. The flow visualization system developed at NASA Ames Research Center to compute time-dependent particle traces from unsteady CFD solutions is described. The system computes particle traces (streaklines) by integrating through the time steps. This system has been used by several NASA scientists to visualize their CFD time-dependent solutions. The flow visualization capabilities of this system are described, and visualization results are shown.

Extended Magnetohydrodynamics with Embedded Particle-in-Cell Simulation of Ganymede's Magnetosphere

NASA Technical Reports Server (NTRS)

Toth, Gabor; Jia, Xianzhe; Markidis, Stefano; Peng, Ivy Bo; Chen, Yuxi; Daldorff, Lars K. S.; Tenishev, Valeriy M.; Borovikov, Dmitry; Haiducek, John D.; Gombosi, Tamas I.;

Comparison of DSMC and CFD Solutions of Fire II Including Radiative Heating

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Johnston, Christopher O.; Lewis, Mark J.

2011-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. These flows may also contain significant radiative heating. To prepare for these missions, NASA is developing the capability to simulate rarefied, ionized flows and to then calculate the resulting radiative heating to the vehicle's surface. In this study, the DSMC codes DAC and DS2V are used to obtain charge-neutral ionization solutions. NASA s direct simulation Monte Carlo code DAC is currently being updated to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced Quantum-Kinetic chemistry model, and to include electronic energy levels as an additional internal energy mode. The Fire II flight test is used in this study to assess these new capabilities. The 1634 second data point was chosen for comparisons to be made in order to include comparisons to computational fluid dynamics solutions. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid. It is shown that there can be quite a bit of variability in the vibrational temperature inferred from DSMC solutions and that, from how radiative heating is computed, the electronic temperature is much better suited for radiative calculations. To include the radiative portion of heating, the flow-field solutions are post-processed by the non-equilibrium radiation code HARA. Acceptable agreement between CFD and DSMC flow field solutions is demonstrated and the progress of the updates to DAC, along with an appropriate radiative heating solution, are discussed. In addition, future plans to generate more high fidelity radiative heat transfer solutions are discussed.

A compartmentalized solute transport model for redox zones in contaminated aquifers: 1. Theory and development

USGS Publications Warehouse

Abrams , Robert H.; Loague, Keith

2000-01-01

This paper, the first of two parts [see Abrams and Loague, this issue], takes the compartmentalized approach for the geochemical evolution of redox zones presented by Abrams et al. [1998] and embeds it within a solute transport framework. In this paper the compartmentalized approach is generalized to facilitate the description of its incorporation into a solute transport simulator. An equivalent formulation is developed which removes any discontinuities that may occur when switching compartments. Rate‐limited redox reactions are modeled with a modified Monod relationship that allows either the organic substrate or the electron acceptor to be the rate‐limiting reactant. Thermodynamic constraints are used to inhibit lower‐energy redox reactions from occurring under infeasible geochemical conditions without imposing equilibrium on the lower‐energy reactions. The procedure used allows any redox reaction to be simulated as being kinetically limited or thermodynamically limited, depending on local geochemical conditions. Empirical reaction inhibition methods are not needed. The sequential iteration approach (SIA), a technique which allows the number of solute transport equations to be reduced, is adopted to solve the coupled geochemical/solute transport problem. When the compartmentalized approach is embedded within the SIA, with the total analytical concentration of each component as the dependent variable in the transport equation, it is possible to reduce the number of transport equations even further than with the unmodified SIA. A one‐dimensional, coupled geochemical/solute transport simulation is presented in which redox zones evolve dynamically in time and space. The compartmentalized solute transport (COMPTRAN) model described in this paper enables the development of redox zones to be simulated under both kinetic and thermodynamic constraints. The modular design of COMPTRAN facilitates the use of many different, preexisting solute transport and geochemical codes. The companion paper [Abrams and Loague, this issue] presents examples of the application of COMPTRAN to field‐scale problems.

Next Generation Vehicle Positioning and Simulation Solutions : Using GPS and Advanced Simulation Tools to Improve Highway Safety

DOT National Transportation Integrated Search

2013-06-03

"Integrated Global Positioning System and Inertial Navigation Unit (GPS/INU) Simulator for Enhanced Traffic Safety," is a project awarded to Ohio State University to integrate different simulation models to accurately study the relationship between v...

What Makes a Simulation Useful

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eubank, S.G.

1999-10-12

Modern computers make possible a new blending of systems, man, and cybernetics in the detailed simulation of large sociotechnical systems. Several such simulations are currently under development at Los Alamos National Laboratory and elsewhere. When deployed, they will affect the daily lives of hundreds of millions of people and the allocation of billions of dollars. Whether they are deployed depends entirely on their perceived usefulness, which in turn depends on answers to the following: What kinds of questions does the simulation address and what kinds of solutions does it provide? How can the solutions be validated? Is simulation more cost-effectivemore » than other methods? Answers to these questions lead us to define a useful simulation as one which efficiently provides correct, robust estimates required by decision-making needs, together with well understood variability for the outcomes in hypothetical situations. This paper examines the implications of this criterion for the design o f TRANSIMS, a regional transportation network simulation, and by extension, for simulations of other sociotechnical systems.« less

Molecular Dynamic Simulation of Diffusion Coefficients for Alkanols in Supercritical CO2 1

NASA Astrophysics Data System (ADS)

Li, Zhiwei; Lai, Shuhui; Gao, Wei; Chen, Liuping

2018-07-01

The infinite dilution diffusion coefficients ( D 12) of methanol, ethanol, 1-propanol, 1-butanol and 1-pentanol in supercritical CO2 (scCO2) at 313.2 K and 10-16 MPa were simulated by molecular dynamics (MD) simulation. The microscopic structure was also analyzed by calculation of the radial distribution function, coordination number (CN) between the center mass of solute and solvent molecules, and the average number of hydrogen bonding of this system. In infinite dilute solution, the probability of forming hydrogen bond between alkanol molecules is greatly reduced relative to pure alkanol fluid, and the weak hydrogen bonds formed between alkanol and CO2 molecules. In general, this work provides a reliable simulation method for transfer properties of solutes in scCO2. The prediction data were provides for the design and development of chemical processing. The results are helpful for one to deeper understand the relationship between microscopic structures of fluid and its transfer properties.

Variability simulations with a steady, linearized primitive equations model

NASA Technical Reports Server (NTRS)

Kinter, J. L., III; Nigam, S.

1985-01-01

Solutions of the steady, primitive equations on a sphere, linearized about a zonally symmetric basic state are computed for the purpose of simulating monthly mean variability in the troposphere. The basic states are observed, winter monthly mean, zonal means of zontal and meridional velocities, temperatures and surface pressures computed from the 15 year NMC time series. A least squares fit to a series of Legendre polynomials is used to compute the basic states between 20 H and the equator, and the hemispheres are assumed symmetric. The model is spectral in the zonal direction, and centered differences are employed in the meridional and vertical directions. Since the model is steady and linear, the solution is obtained by inversion of a block, pente-diagonal matrix. The model simulates the climatology of the GFDL nine level, spectral general circulation model quite closely, particularly in middle latitudes above the boundary layer. This experiment is an extension of that simulation to examine variability of the steady, linear solution.

Making On-line Science Course Materials Easily Translatable and Accessible Worldwide: Challenges and Solutions

NASA Astrophysics Data System (ADS)

Adams, Wendy K.; Alhadlaq, Hisham; Malley, Christopher V.; Perkins, Katherine K.; Olson, Jonathan; Alshaya, Fahad; Alabdulkareem, Saleh; Wieman, Carl E.

2012-02-01

The PhET Interactive Simulations Project partnered with the Excellence Research Center of Science and Mathematics Education at King Saud University with the joint goal of making simulations useable worldwide. One of the main challenges of this partnership is to make PhET simulations and the website easily translatable into any language. The PhET project team overcame this challenge by creating the Translation Utility. This tool allows a person fluent in both English and another language to easily translate any of the PhET simulations and requires minimal computer expertise. In this paper we discuss the technical issues involved in this software solution, as well as the issues involved in obtaining accurate translations. We share our solutions to many of the unexpected problems we encountered that would apply generally to making on-line scientific course materials available in many different languages, including working with: languages written right-to-left, different character sets, and different conventions for expressing equations, variables, units and scientific notation.

Experiences with serial and parallel algorithms for channel routing using simulated annealing

NASA Technical Reports Server (NTRS)

Brouwer, Randall Jay

1988-01-01

Two algorithms for channel routing using simulated annealing are presented. Simulated annealing is an optimization methodology which allows the solution process to back up out of local minima that may be encountered by inappropriate selections. By properly controlling the annealing process, it is very likely that the optimal solution to an NP-complete problem such as channel routing may be found. The algorithm presented proposes very relaxed restrictions on the types of allowable transformations, including overlapping nets. By freeing that restriction and controlling overlap situations with an appropriate cost function, the algorithm becomes very flexible and can be applied to many extensions of channel routing. The selection of the transformation utilizes a number of heuristics, still retaining the pseudorandom nature of simulated annealing. The algorithm was implemented as a serial program for a workstation, and a parallel program designed for a hypercube computer. The details of the serial implementation are presented, including many of the heuristics used and some of the resulting solutions.

Large eddy simulation of shock train in a convergent-divergent nozzle

NASA Astrophysics Data System (ADS)

Mousavi, Seyed Mahmood; Roohi, Ehsan

2014-12-01

This paper discusses the suitability of the Large Eddy Simulation (LES) turbulence modeling for the accurate simulation of the shock train phenomena in a convergent-divergent nozzle. To this aim, we selected an experimentally tested geometry and performed LES simulation for the same geometry. The structure and pressure recovery inside the shock train in the nozzle captured by LES model are compared with the experimental data, analytical expressions and numerical solutions obtained using various alternative turbulence models, including k-ɛ RNG, k-ω SST, and Reynolds stress model (RSM). Comparing with the experimental data, we observed that the LES solution not only predicts the "locations of the first shock" precisely, but also its results are quite accurate before and after the shock train. After validating the LES solution, we investigate the effects of the inlet total pressure on the shock train starting point and length. The effects of changes in the back pressure, nozzle inlet angle (NIA) and wall temperature on the behavior of the shock train are investigated by details.

Developing a Problem-Based Learning Simulation: An Economics Unit on Trade

ERIC Educational Resources Information Center

Maxwell, Nan L.; Mergendoller, John R.; Bellisimo, Yolanda

2004-01-01

This article argues that the merger of simulations and problem-based learning (PBL) can enhance both active-learning strategies. Simulations benefit by using a PBL framework to promote student-directed learning and problem-solving skills to explain a simulated dilemma with multiple solutions. PBL benefits because simulations structure the…

Analysis of an Air Conditioning Coolant Solution for Metal Contamination Using Atomic Absorption Spectroscopy: An Undergraduate Instrumental Analysis Exercise Simulating an Industrial Assignment

ERIC Educational Resources Information Center

Baird, Michael J.

2004-01-01

A real-life analytical assignment is presented to students, who had to examine an air conditioning coolant solution for metal contamination using an atomic absorption spectroscopy (AAS). This hands-on access to a real problem exposed the undergraduate students to the mechanism of AAS, and promoted participation in a simulated industrial activity.

Exploration of DGVM Parameter Solution Space Using Simulated Annealing: Implications for Forecast Uncertainties

NASA Astrophysics Data System (ADS)

Wells, J. R.; Kim, J. B.

2011-12-01

Parameters in dynamic global vegetation models (DGVMs) are thought to be weakly constrained and can be a significant source of errors and uncertainties. DGVMs use between 5 and 26 plant functional types (PFTs) to represent the average plant life form in each simulated plot, and each PFT typically has a dozen or more parameters that define the way it uses resource and responds to the simulated growing environment. Sensitivity analysis explores how varying parameters affects the output, but does not do a full exploration of the parameter solution space. The solution space for DGVM parameter values are thought to be complex and non-linear; and multiple sets of acceptable parameters may exist. In published studies, PFT parameters are estimated from published literature, and often a parameter value is estimated from a single published value. Further, the parameters are "tuned" using somewhat arbitrary, "trial-and-error" methods. BIOMAP is a new DGVM created by fusing MAPSS biogeography model with Biome-BGC. It represents the vegetation of North America using 26 PFTs. We are using simulated annealing, a global search method, to systematically and objectively explore the solution space for the BIOMAP PFTs and system parameters important for plant water use. We defined the boundaries of the solution space by obtaining maximum and minimum values from published literature, and where those were not available, using +/-20% of current values. We used stratified random sampling to select a set of grid cells representing the vegetation of the conterminous USA. Simulated annealing algorithm is applied to the parameters for spin-up and a transient run during the historical period 1961-1990. A set of parameter values is considered acceptable if the associated simulation run produces a modern potential vegetation distribution map that is as accurate as one produced by trial-and-error calibration. We expect to confirm that the solution space is non-linear and complex, and that multiple acceptable parameter sets exist. Further we expect to demonstrate that the multiple parameter sets produce significantly divergent future forecasts in NEP, C storage, and ET and runoff; and thereby identify a highly important source of DGVM uncertainty

Addition of simultaneous heat and solute transport and variable fluid viscosity to SEAWAT

USGS Publications Warehouse

Thorne, D.; Langevin, C.D.; Sukop, M.C.

2006-01-01

SEAWAT is a finite-difference computer code designed to simulate coupled variable-density ground water flow and solute transport. This paper describes a new version of SEAWAT that adds the ability to simultaneously model energy and solute transport. This is necessary for simulating the transport of heat and salinity in coastal aquifers for example. This work extends the equation of state for fluid density to vary as a function of temperature and/or solute concentration. The program has also been modified to represent the effects of variable fluid viscosity as a function of temperature and/or concentration. The viscosity mechanism is verified against an analytical solution, and a test of temperature-dependent viscosity is provided. Finally, the classic Henry-Hilleke problem is solved with the new code. ?? 2006 Elsevier Ltd. All rights reserved.

Numerical Simulations of STOVL Hot Gas Ingestion in Ground Proximity Using a Multigrid Solution Procedure

NASA Technical Reports Server (NTRS)

Wang, Gang

2003-01-01

A multi grid solution procedure for the numerical simulation of turbulent flows in complex geometries has been developed. A Full Multigrid-Full Approximation Scheme (FMG-FAS) is incorporated into the continuity and momentum equations, while the scalars are decoupled from the multi grid V-cycle. A standard kappa-Epsilon turbulence model with wall functions has been used to close the governing equations. The numerical solution is accomplished by solving for the Cartesian velocity components either with a traditional grid staggering arrangement or with a multiple velocity grid staggering arrangement. The two solution methodologies are evaluated for relative computational efficiency. The solution procedure with traditional staggering arrangement is subsequently applied to calculate the flow and temperature fields around a model Short Take-off and Vertical Landing (STOVL) aircraft hovering in ground proximity.

SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation.

PubMed

Schmit, Jeremy D; Kariyawasam, Nilusha L; Needham, Vince; Smith, Paul E

2018-04-10

An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number of ions in the simulation box to capture screening effects. However, the number of ions that should be added to the box is seldom given by the bulk salt concentration because a charged biomolecule solute will perturb the local solvent environment. We present a simple method for calculating the number of ions that requires only the total solute charge, solvent volume, and bulk salt concentration as inputs. We show that the most commonly used method for adding salt to a simulation results in an effective salt concentration that is too high. These findings are confirmed using simulations of lysozyme. We have established a web server where these calculations can be readily performed to aid simulation setup.

Simulation of Benchmark Cases with the Terminal Area Simulation System (TASS)

NASA Technical Reports Server (NTRS)

Ahmad, Nash'at; Proctor, Fred

2011-01-01

The hydrodynamic core of the Terminal Area Simulation System (TASS) is evaluated against different benchmark cases. In the absence of closed form solutions for the equations governing atmospheric flows, the models are usually evaluated against idealized test cases. Over the years, various authors have suggested a suite of these idealized cases which have become standards for testing and evaluating the dynamics and thermodynamics of atmospheric flow models. In this paper, simulations of three such cases are described. In addition, the TASS model is evaluated against a test case that uses an exact solution of the Navier-Stokes equations. The TASS results are compared against previously reported simulations of these banchmark cases in the literature. It is demonstrated that the TASS model is highly accurate, stable and robust.

Simulation of Benchmark Cases with the Terminal Area Simulation System (TASS)

NASA Technical Reports Server (NTRS)

Ahmad, Nashat N.; Proctor, Fred H.

2011-01-01

The hydrodynamic core of the Terminal Area Simulation System (TASS) is evaluated against different benchmark cases. In the absence of closed form solutions for the equations governing atmospheric flows, the models are usually evaluated against idealized test cases. Over the years, various authors have suggested a suite of these idealized cases which have become standards for testing and evaluating the dynamics and thermodynamics of atmospheric flow models. In this paper, simulations of three such cases are described. In addition, the TASS model is evaluated against a test case that uses an exact solution of the Navier-Stokes equations. The TASS results are compared against previously reported simulations of these benchmark cases in the literature. It is demonstrated that the TASS model is highly accurate, stable and robust.

A gold cyano complex in nitromethane: MD simulation and X-ray diffraction

PubMed Central

Probst, Michael; Injan, Natcha; Megyes, Tünde; Bako, Imre; Balint, Szabolcz; Limtrakul, Jumras; Nazmutdinov, Renat; Mitev, Pavlin D.; Hermansson, Kersti

2012-01-01

The solvation structure around the dicyanoaurate(I) anion (Au(CN)2−) in a dilute nitromethane (CH3NO2) solution is presented from X-ray diffraction measurements and molecular dynamics simulation (NVT ensemble, 460 nitromethane molecules at room temperature). The simulations are based on a new solute–solvent force-field fitted to a training set of quantum-chemically derived interaction energies. Radial distribution functions from experiment and simulation are in good agreement. The solvation structure has been further elucidated from MD data. Several shells can be identified. We obtain a solvation number of 13–17 nitromethane molecules with a strong preference to be oriented with their methyl groups towards the solute. PMID:25540462

Applying Parallel Adaptive Methods with GeoFEST/PYRAMID to Simulate Earth Surface Crustal Dynamics

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Glasscoe, Margaret; Donnellan, Andrea; Li, Peggy

2006-01-01

This viewgraph presentation reviews the use Adaptive Mesh Refinement (AMR) in simulating the Crustal Dynamics of Earth's Surface. AMR simultaneously improves solution quality, time to solution, and computer memory requirements when compared to generating/running on a globally fine mesh. The use of AMR in simulating the dynamics of the Earth's Surface is spurred by future proposed NASA missions, such as InSAR for Earth surface deformation and other measurements. These missions will require support for large-scale adaptive numerical methods using AMR to model observations. AMR was chosen because it has been successful in computation fluid dynamics for predictive simulation of complex flows around complex structures.

GLOBAL PROPERTIES OF FULLY CONVECTIVE ACCRETION DISKS FROM LOCAL SIMULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodo, G.; Ponzo, F.; Rossi, P.

2015-08-01

We present an approach to deriving global properties of accretion disks from the knowledge of local solutions derived from numerical simulations based on the shearing box approximation. The approach consists of a two-step procedure. First, a local solution valid for all values of the disk height is constructed by piecing together an interior solution obtained numerically with an analytical exterior radiative solution. The matching is obtained by assuming hydrostatic balance and radiative equilibrium. Although in principle the procedure can be carried out in general, it simplifies considerably when the interior solution is fully convective. In these cases, the construction ismore » analogous to the derivation of the Hayashi tracks for protostars. The second step consists of piecing together the local solutions at different radii to obtain a global solution. Here we use the symmetry of the solutions with respect to the defining dimensionless numbers—in a way similar to the use of homology relations in stellar structure theory—to obtain the scaling properties of the various disk quantities with radius.« less

Engineering workstation: Sensor modeling

NASA Technical Reports Server (NTRS)

Pavel, M; Sweet, B.

1993-01-01

The purpose of the engineering workstation is to provide an environment for rapid prototyping and evaluation of fusion and image processing algorithms. Ideally, the algorithms are designed to optimize the extraction of information that is useful to a pilot for all phases of flight operations. Successful design of effective fusion algorithms depends on the ability to characterize both the information available from the sensors and the information useful to a pilot. The workstation is comprised of subsystems for simulation of sensor-generated images, image processing, image enhancement, and fusion algorithms. As such, the workstation can be used to implement and evaluate both short-term solutions and long-term solutions. The short-term solutions are being developed to enhance a pilot's situational awareness by providing information in addition to his direct vision. The long term solutions are aimed at the development of complete synthetic vision systems. One of the important functions of the engineering workstation is to simulate the images that would be generated by the sensors. The simulation system is designed to use the graphics modeling and rendering capabilities of various workstations manufactured by Silicon Graphics Inc. The workstation simulates various aspects of the sensor-generated images arising from phenomenology of the sensors. In addition, the workstation can be used to simulate a variety of impairments due to mechanical limitations of the sensor placement and due to the motion of the airplane. Although the simulation is currently not performed in real-time, sequences of individual frames can be processed, stored, and recorded in a video format. In that way, it is possible to examine the appearance of different dynamic sensor-generated and fused images.

Verification of fluid-structure-interaction algorithms through the method of manufactured solutions for actuator-line applications

NASA Astrophysics Data System (ADS)

Vijayakumar, Ganesh; Sprague, Michael

2017-11-01

Demonstrating expected convergence rates with spatial- and temporal-grid refinement is the ``gold standard'' of code and algorithm verification. However, the lack of analytical solutions and generating manufactured solutions presents challenges for verifying codes for complex systems. The application of the method of manufactured solutions (MMS) for verification for coupled multi-physics phenomena like fluid-structure interaction (FSI) has only seen recent investigation. While many FSI algorithms for aeroelastic phenomena have focused on boundary-resolved CFD simulations, the actuator-line representation of the structure is widely used for FSI simulations in wind-energy research. In this work, we demonstrate the verification of an FSI algorithm using MMS for actuator-line CFD simulations with a simplified structural model. We use a manufactured solution for the fluid velocity field and the displacement of the SMD system. We demonstrate the convergence of both the fluid and structural solver to second-order accuracy with grid and time-step refinement. This work was funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Wind Energy Technologies Office, under Contract No. DE-AC36-08-GO28308 with the National Renewable Energy Laboratory.

Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study

PubMed Central

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W.

2012-01-01

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 molal solution of α-D-glucopyranose, at a caffeine concentration of 0.083 molal; a single caffeine in a 3 molal solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 molal solution of sucrose (table sugar). Parallel Nuclear Magnetic Resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and that the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration, and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol. PMID:22897449

Caffeine and sugars interact in aqueous solutions: a simulation and NMR study.

PubMed

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W

2012-09-27

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 m solution of α-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 m solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

A new and inexpensive non-bit-for-bit solution reproducibility test based on time step convergence (TSC1.0)

NASA Astrophysics Data System (ADS)

Wan, Hui; Zhang, Kai; Rasch, Philip J.; Singh, Balwinder; Chen, Xingyuan; Edwards, Jim

2017-02-01

A test procedure is proposed for identifying numerically significant solution changes in evolution equations used in atmospheric models. The test issues a fail signal when any code modifications or computing environment changes lead to solution differences that exceed the known time step sensitivity of the reference model. Initial evidence is provided using the Community Atmosphere Model (CAM) version 5.3 that the proposed procedure can be used to distinguish rounding-level solution changes from impacts of compiler optimization or parameter perturbation, which are known to cause substantial differences in the simulated climate. The test is not exhaustive since it does not detect issues associated with diagnostic calculations that do not feedback to the model state variables. Nevertheless, it provides a practical and objective way to assess the significance of solution changes. The short simulation length implies low computational cost. The independence between ensemble members allows for parallel execution of all simulations, thus facilitating fast turnaround. The new method is simple to implement since it does not require any code modifications. We expect that the same methodology can be used for any geophysical model to which the concept of time step convergence is applicable.

Guidelines for Computing Longitudinal Dynamic Stability Characteristics of a Subsonic Transport

NASA Technical Reports Server (NTRS)

Thompson, Joseph R.; Frank, Neal T.; Murphy, Patrick C.

2010-01-01

A systematic study is presented to guide the selection of a numerical solution strategy for URANS computation of a subsonic transport configuration undergoing simulated forced oscillation about its pitch axis. Forced oscillation is central to the prevalent wind tunnel methodology for quantifying aircraft dynamic stability derivatives from force and moment coefficients, which is the ultimate goal for the computational simulations. Extensive computations are performed that lead in key insights of the critical numerical parameters affecting solution convergence. A preliminary linear harmonic analysis is included to demonstrate the potential of extracting dynamic stability derivatives from computational solutions.

The improvement of the energy resolution in epi-thermal neutron region of Bonner sphere using boric acid water solution moderator.

PubMed

Ueda, H; Tanaka, H; Sakurai, Y

2015-10-01

Bonner sphere is useful to evaluate the neutron spectrum in detail. We are improving the energy resolution in epi-thermal neutron region of Bonner sphere, using boric acid water solution as a moderator. Its response function peak is narrower than that for polyethylene moderator and the improvement of the resolution is expected. The resolutions between polyethylene moderator and boric acid water solution moderator were compared by simulation calculation. Also the influence in the uncertainty of Bonner sphere configuration to spectrum estimation was simulated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantum Chemical Simulation of the Interaction of Functional Groups in Polyurethanes with 3 d-Metal Ions During Their Extraction from Aqueous Solutions

NASA Astrophysics Data System (ADS)

Ksenofontov, M. A.; Bobkova, E. Yu.; Shundalau, M. B.; Ostrovskaya, L. E.; Vasil'eva, V. S.

2017-11-01

The interaction of the functional groups in the polyurethane foam adsorbent Penopurm® with the cations of some 3d-metals upon their extraction from aqueous solutions has been studied by atomic emission spectroscopy, UV/Vis and vibrational IR spectroscopy, and quantum chemical simulation using density functional theory. Penopurm® absorbs 3d-metal cations from aqueous solutions in the pH range 5-7. Some spectral criteria have been found indicating a predominant interaction of Ni2+ ions with various fragments of the polyurethane foam structure.

Genipin-crosslinked O-carboxymethyl chitosan-gum Arabic coacervate as a pH-sensitive delivery system and microstructure characterization.

PubMed

Huang, Guo-Qing; Cheng, Ling-Yun; Xiao, Jun-Xia; Wang, Shi-Qing; Han, Xiao-Na

2016-08-01

The possibility of genipin-crosslinked O-carboxymethyl chitosan-gum Arabic coacervate as a pH-sensitive delivery vehicle was investigated. O-carboxymethyl chitosan-gum Arabic coacervates separated in pH 3.0, 4.5, and 6.0 were crosslinked by genipin for different durations and the crosslinked products were subjected to crosslinking degree, swelling behavior, bovine serum albumin release profile, and microstructure characterization. Genipin-crosslinking greatly improved the stability of the coacervates against the simulated gastric solution and created certain pH-sensitivity. The coacervates displayed higher swelling ratios in the simulated gastric solution than in the simulated intestine and colon solutions; meanwhile, the coacervates prepared in pH 4.5 and 6.0 swelled more severely than the complex separated in pH 3.0. Nevertheless, the bovine serum albumin release in the simulated gastric solution from the microcapsules prepared in pH 6.0 was much lower than those prepared in pH 4.5 and 3.0, whose cumulative release percentages in the three simulated solutions were 17.14%, 55.23%, and 79.79%, respectively, in crosslinking duration 2 h. X-ray diffraction, scanning electron microscopy, and transmission electron microscopy analysis revealed that genipin-crosslinking improved the regularity and compactness of coacervate structure, whereas confocal laser scanning microscopy observation indicated that O-carboxymethyl chitosan content was possibly the major reason for the different swelling and bovine serum albumin release behavior of the coacervates. It was concluded that the genipin-crosslinked O-carboxymethyl chitosan-gum Arabic coacervate was a potential intestine-targeted delivery system and its delivery performance could be tailored by varying the crosslinking degree and coacervation acidity. © The Author(s) 2016.

[Comparison between colorimetry and HPLC on the stability test of roxithromycin].

PubMed

Wei, Z P; Mao, S R; Bi, D Z

2000-11-01

To compare the stability of roxithromycin in solutions of different pH. Roxithromycin solutions of different pH were prepared with water, simulate intestinal fluid (SIF) and simulate gastric fluid (SGF) shown to be the stability of these solutions were tested by colorimetry and HPLC. Roxithromycin was stable in water, SGF and SIF determined by colorimetry. However, it was found to be stable only in water and SIF but unstable in SGF as determined by HPLC. Roxithromycin is unstable in acidic medium like SGF. The metabolite of roxithromycin showed unfavorable interference on the assay of roxithromycin when colorimetry was used. Colorimetry can not be used for the determination and assay of roxithromycin in acidic solution like SGF.

A Cloud-Based Simulation Architecture for Pandemic Influenza Simulation

PubMed Central

Eriksson, Henrik; Raciti, Massimiliano; Basile, Maurizio; Cunsolo, Alessandro; Fröberg, Anders; Leifler, Ola; Ekberg, Joakim; Timpka, Toomas

2011-01-01

High-fidelity simulations of pandemic outbreaks are resource consuming. Cluster-based solutions have been suggested for executing such complex computations. We present a cloud-based simulation architecture that utilizes computing resources both locally available and dynamically rented online. The approach uses the Condor framework for job distribution and management of the Amazon Elastic Computing Cloud (EC2) as well as local resources. The architecture has a web-based user interface that allows users to monitor and control simulation execution. In a benchmark test, the best cost-adjusted performance was recorded for the EC2 H-CPU Medium instance, while a field trial showed that the job configuration had significant influence on the execution time and that the network capacity of the master node could become a bottleneck. We conclude that it is possible to develop a scalable simulation environment that uses cloud-based solutions, while providing an easy-to-use graphical user interface. PMID:22195089

Three-dimensional variable-density flow simulation of a coastal aquifer in southern Oahu, Hawaii, USA

USGS Publications Warehouse

Gingerich, S.B.; Voss, C.I.

2005-01-01

Three-dimensional modeling of groundwater flow and solute transport in the Pearl Harbor aquifer, southern Oahu, Hawaii, shows that the readjustment of the freshwater-saltwater transition zone takes a long time following changes in pumping, irrigation, or recharge in the aquifer system. It takes about 50-years for the transition zone to move 90% of the distance to its new steady position. Further, the Ghyben-Herzberg estimate of the freshwater/saltwater interface depth occurred between the 10 and 50% simulated seawater concentration contours in a complex manner during 100-years of the pumping history of the aquifer. Thus, it is not a good predictor of the depth of potable water. Pre-development recharge was used to simulate the 1880 freshwater-lens configuration. Historical pumpage and recharge distributions were used and the resulting freshwater-lens size and position were simulated through 1980. Simulations show that the transition zone moved upward and landward during the period simulated. Previous groundwater flow models for Oahu have been limited to areal models that simulate a sharp interface between freshwater and saltwater or solute-transport models that simulate a vertical aquifer section. The present model is based on the US Geological Survey's three-dimensional solute transport (3D SUTRA) computer code. Using several new tools for pre- and post-processing of model input and results have allowed easy model construction and unprecedented visualization of the freshwater lens and underlying transition zone in Hawaii's most developed aquifer. ?? Springer-Verlag 2005.

Agent-based model for the h-index - exact solution

NASA Astrophysics Data System (ADS)

Żogała-Siudem, Barbara; Siudem, Grzegorz; Cena, Anna; Gagolewski, Marek

2016-01-01

Hirsch's h-index is perhaps the most popular citation-based measure of scientific excellence. In 2013, Ionescu and Chopard proposed an agent-based model describing a process for generating publications and citations in an abstract scientific community [G. Ionescu, B. Chopard, Eur. Phys. J. B 86, 426 (2013)]. Within such a framework, one may simulate a scientist's activity, and - by extension - investigate the whole community of researchers. Even though the Ionescu and Chopard model predicts the h-index quite well, the authors provided a solution based solely on simulations. In this paper, we complete their results with exact, analytic formulas. What is more, by considering a simplified version of the Ionescu-Chopard model, we obtained a compact, easy to compute formula for the h-index. The derived approximate and exact solutions are investigated on a simulated and real-world data sets.

Structural, thermodynamic, and electrical properties of polar fluids and ionic solutions on a hypersphere: Theoretical aspects

NASA Astrophysics Data System (ADS)

Caillol, J. M.

1992-01-01

We generalize previous work [J. Chem. Phys. 94, 597 (1991)] on an alternative to the Ewald method for the numerical simulations of Coulomb fluids. This new method consists in using as a simulation cell the three-dimensional surface of a four-dimensional sphere, or hypersphere. Here, we consider the case of polar fluids and electrolyte solutions. We derive all the formal expressions which are needed for numerical simulations of such systems. It includes a derivation of the multipolar interactions on a hypersphere, the expansion of the pair-correlation functions on rotational invariants, the expression of the static dielectric constant of a polar liquid, the expressions of the frequency-dependent conductivity and dielectric constant of an ionic solution, and the derivation of the Stillinger-Lovett sum rules for conductive systems.

Efficient solution of ordinary differential equations modeling electrical activity in cardiac cells.

PubMed

Sundnes, J; Lines, G T; Tveito, A

2001-08-01

The contraction of the heart is preceded and caused by a cellular electro-chemical reaction, causing an electrical field to be generated. Performing realistic computer simulations of this process involves solving a set of partial differential equations, as well as a large number of ordinary differential equations (ODEs) characterizing the reactive behavior of the cardiac tissue. Experiments have shown that the solution of the ODEs contribute significantly to the total work of a simulation, and there is thus a strong need to utilize efficient solution methods for this part of the problem. This paper presents how an efficient implicit Runge-Kutta method may be adapted to solve a complicated cardiac cell model consisting of 31 ODEs, and how this solver may be coupled to a set of PDE solvers to provide complete simulations of the electrical activity.

Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mester, Zoltan; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu

The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictionsmore » also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development.« less

MOOSE: A parallel computational framework for coupled systems of nonlinear equations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Derek Gaston; Chris Newman; Glen Hansen

Systems of coupled, nonlinear partial differential equations (PDEs) often arise in simulation of nuclear processes. MOOSE: Multiphysics Object Oriented Simulation Environment, a parallel computational framework targeted at the solution of such systems, is presented. As opposed to traditional data-flow oriented computational frameworks, MOOSE is instead founded on the mathematical principle of Jacobian-free Newton-Krylov (JFNK) solution methods. Utilizing the mathematical structure present in JFNK, physics expressions are modularized into `Kernels,'' allowing for rapid production of new simulation tools. In addition, systems are solved implicitly and fully coupled, employing physics based preconditioning, which provides great flexibility even with large variance in timemore » scales. A summary of the mathematics, an overview of the structure of MOOSE, and several representative solutions from applications built on the framework are presented.« less

Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other

PubMed Central

Andrews, Casey T.

2013-01-01

Although it is now commonly accepted that the highly crowded conditions encountered inside biological cells have the potential to significantly alter the thermodynamic properties of biomolecules, it is not known to what extent the thermodynamics of fundamental types of interactions such as salt bridges and hydrophobic interactions are strengthened or weakened by high biomolecular concentrations. As one way of addressing this question we have performed a series of all-atom explicit solvent molecular dynamics (MD) simulations to investigate the effect of increasing solute concentration on the behavior of four types of zwitterionic amino acids in aqueous solution. We have simulated systems containing glycine, valine, phenylalanine or asparagine at concentrations of 50, 100, 200 and 300 mg/ml. Each molecular system has been simulated for 1 μs in order to obtain statistically converged estimates of thermodynamic parameters, and each has been conducted with 8 different force fields and water models; the combined simulation time is 128 μs. The density, viscosity, and dielectric increments of the four amino acids calculated from the simulations have been compared to corresponding experimental measurements. While all of the force fields perform well at reproducing the density increments, discrepancies for the viscosity and dielectric increments raise questions both about the accuracy of the simulation force fields and, in certain cases, the experimental data. We also observe large differences between the various force fields' descriptions of the interaction thermodynamics of salt bridges and, surprisingly, these differences also lead to qualitatively different predictions of their dependences on solute concentration. For the aliphatic interactions of valine sidechains, fewer differences are observed between the force fields, but significant differences are again observed for aromatic interactions of phenylalanine sidechains. Taken together, the results highlight the potential power of using explicit-solvent simulation methods to understand behavior in concentrated systems but also hint at potential difficulties in using these methods to obtain consistent views of behavior in intracellular environments. PMID:24409104

Numerical Simulations of Crystal Growth of an Alloy Under Microgravity Conditions

NASA Technical Reports Server (NTRS)

Simpson, James E.; deGroh, Henry C., III; Garimella, Suresh V.; Abbaschian, Reza

1999-01-01

The directional solidification of a dilute binary alloy (Bi-1.0 at.%Sn)is investigated. Results are obtained at a gravity level of I pg. Computations are performed in two dimensions with a fixed, non-uniform grid. The simulation involves a solution of the species concentration equation (modified to account for solute rejection at the interface) and energy equation (modified to account for phase-change) for both the solid and liquid phases, in addition to the constitutive equations for describing convective flow in the melt. The effects of conductive heat transfer in the ampoule and in a capillary tube in the sample are included. To gauge the effects of including this growth capillary tube in the apparatus, simulations both with and without the capillary tube are presented and compared. Fully transient simulations have been performed; no simplifying steady-state approximations are used, however, the influence of solute on the melting temperature at the interface is not included. Both thermal and solutal convective cells are seen to form. Convective velocities are significantly damped inside the capillary, causing less segregation due to convection. As solidification proceeds beyond the capillary tube, longitudinal segregation arises as a result of the change in cross-sectional area of solidifying material. The magnitudes of the velocities in this cell increase significantly once the solid/liquid front passes beyond the end of the capillary tube; this causes a corresponding increase in the level of radial solute segregation in the solidified material.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozgur, Utku; Tonyali, Samet; Akkaya, Kemal

Although smart meters are deployed in a lot of countries as a result of aiming to make the power grid more resilient and efficient, the data collection process from smart meters in Smart Grid (SG) has still challenges that relate to consumer privacy. Referred to as Advanced Metering Infrastructure (AMI), the data collected and transmitted through this AMI can leak sensitive information about the consumers if it is sent as plaintext. While a number of solutions have been proposed in the past, the deployment of these solutions in real-life was not possible since the actual AMIs were not accessible tomore » researchers. Therefore, a lot of solutions relied on simulations which may not be able to capture the performance of these solutions. In this paper, we pick a widely used homomorphic-based aggregation and implement it in a realistic testbed so that it can be compared with a simulation-based solution. Specifically, we develop a system that provides privacy with the Paillier cryptosystem and twofactor authentication with ECDSA and OpenSSL certificates. In order to test the system, an IEEE 802.11s-based SG AMI network testbed is constructed with Beaglebone Black boards that imitate the behavior of smart meters. The same network is also simulated in widely used ns-3. The results showed that ns-3 simulation and testbed results are parallel in most cases and the proposed system can perform effectively. However, there are still many differences that need to be taken into account in deploying real systems.« less

Solvation and Aggregation of Meta-Aminobenzoic Acid in Water: Density Functional Theory and Molecular Dynamics Study

PubMed Central

Gaines, Etienne

2018-01-01

Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA) and zwitterionic (mABA±) forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and to compute the Gibbs free energies in water of nonionic, (mABA)2, zwitterionic, (mABA±)2, and nonionic-zwitterionic, (mABA)(mABA±), species. Classical molecular dynamics simulations of mixed mABA–mABA± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations, the selective crystallization of the polymorphs whose constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA)2 and (mABA)(mABA±) pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution. PMID:29360788

Experimental testing and modeling analysis of solute mixing at water distribution pipe junctions.

PubMed

Shao, Yu; Jeffrey Yang, Y; Jiang, Lijie; Yu, Tingchao; Shen, Cheng

2014-06-01

Flow dynamics at a pipe junction controls particle trajectories, solute mixing and concentrations in downstream pipes. The effect can lead to different outcomes of water quality modeling and, hence, drinking water management in a distribution network. Here we have investigated solute mixing behavior in pipe junctions of five hydraulic types, for which flow distribution factors and analytical equations for network modeling are proposed. First, based on experiments, the degree of mixing at a cross is found to be a function of flow momentum ratio that defines a junction flow distribution pattern and the degree of departure from complete mixing. Corresponding analytical solutions are also validated using computational-fluid-dynamics (CFD) simulations. Second, the analytical mixing model is further extended to double-Tee junctions. Correspondingly the flow distribution factor is modified to account for hydraulic departure from a cross configuration. For a double-Tee(A) junction, CFD simulations show that the solute mixing depends on flow momentum ratio and connection pipe length, whereas the mixing at double-Tee(B) is well represented by two independent single-Tee junctions with a potential water stagnation zone in between. Notably, double-Tee junctions differ significantly from a cross in solute mixing and transport. However, it is noted that these pipe connections are widely, but incorrectly, simplified as cross junctions of assumed complete solute mixing in network skeletonization and water quality modeling. For the studied pipe junction types, analytical solutions are proposed to characterize the incomplete mixing and hence may allow better water quality simulation in a distribution network. Published by Elsevier Ltd.

One-dimensional potential of mean force underestimates activation barrier for transport across flexible lipid membranes

NASA Astrophysics Data System (ADS)

Kopelevich, Dmitry I.

2013-10-01

Transport of a fullerene-like nanoparticle across a lipid bilayer is investigated by coarse-grained molecular dynamics (MD) simulations. Potentials of mean force (PMF) acting on the nanoparticle in a flexible bilayer suspended in water and a bilayer restrained to a flat surface are computed by constrained MD simulations. The rate of the nanoparticle transport into the bilayer interior is predicted using one-dimensional Langevin models based on these PMFs. The predictions are compared with the transport rates obtained from a series of direct (unconstrained) MD simulations of the solute transport into the flexible bilayer. It is observed that the PMF acting on the solute in the flexible membrane underestimates the transport rate by more than an order of magnitude while the PMF acting on the solute in the restrained membrane yields an accurate estimate of the activation energy for transport into the flexible membrane. This paradox is explained by a coexistence of metastable membrane configurations for a range of the solute positions inside and near the flexible membrane. This leads to a significant reduction of the contribution of the transition state to the mean force acting on the solute. Restraining the membrane shape ensures that there is only one stable membrane configuration corresponding to each solute position and thus the transition state is adequately represented in the PMF. This mechanism is quite general and thus this phenomenon is expected to occur in a wide range of interfacial systems. A simple model for the free energy landscape of the coupled solute-membrane system is proposed and validated. This model explicitly accounts for effects of the membrane deformations on the solute transport and yields an accurate prediction of the activation energy for the solute transport.

A conservative approach to parallelizing the Sharks World simulation

NASA Technical Reports Server (NTRS)

Nicol, David M.; Riffe, Scott E.

1990-01-01

Parallelizing a benchmark problem for parallel simulation, the Sharks World, is described. The described solution is conservative, in the sense that no state information is saved, and no 'rollbacks' occur. The used approach illustrates both the principal advantage and principal disadvantage of conservative parallel simulation. The advantage is that by exploiting lookahead an approach was found that dramatically improves the serial execution time, and also achieves excellent speedups. The disadvantage is that if the model rules are changed in such a way that the lookahead is destroyed, it is difficult to modify the solution to accommodate the changes.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

2017-05-01

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

Stability of nitrate-ion concentrations in simulated deposition samples used for quality-assurance activities by the U.S. Geological Survey

USGS Publications Warehouse

Willoughby, T.C.; See, R.B.; Schroder, L.J.

1989-01-01

Three experiments were conducted to determine the stability of nitrate-ion concentrations in simulated deposition samples. In the four experiment-A solutions, nitric acid provided nitrate-ion concentrations ranging from 0.6 to 10.0 mg/L and that had pH values ranging from 3.8 to 5.0. In the five experiment-B solutions, sodium nitrate provided nitrate-ion concentrations ranging from 0.5 to 3.0 mg/L. The pH was adjusted to about 4.5 for each of the solutions by addition of sulfuric acid. In the four experiment-C solutions, nitric acid provided nitrate-ion concentrations ranging from 0.5 to 3.0 mg/L. Major cation and anion concentrations were added to each solution to simulate natural deposition. Aliquots were removed from the 13 original solutions and analyzed by ion chromatography about once a week for 100 days to determine if any changes occurred in nitrate-ion concentrations throughout the study period. No substantial changes were observed in the nitrate-ion concentrations in solutions that had initial concentrations below 4.0 mg/L in experiments A and B, although most of the measured nitrate-ion concentrations for the 100-day study were below the initial concentrations. In experiment C, changes in nitrate-ion concentrations were much more pronounced; the measured nitrate-ion concentrations for the study period were less than the initial concentrations for 62 of the 67 analyses. (USGS)

Reply to ``Comment on `Free surface Hele-Shaw flows around an obstacle: A random walk simulation' ''

NASA Astrophysics Data System (ADS)

Bogoyavlenskiy, Vladislav A.; Cotts, Eric J.

2007-09-01

As pointed out by Vasconcelos in his Comment, our computer simulations of Hele-Shaw flows around series of wedges differ from analytical solutions existing for this problem. We attribute the discrepancy to the notion that these analytical solutions correspond to ideal, steady-state flow regimes which are hardly applicable when a rigid obstacle interacts with a moving liquid-gas interface.

War-gaming application for future space systems acquisition part 1: program and technical baseline war-gaming modeling and simulation approaches

NASA Astrophysics Data System (ADS)

Nguyen, Tien M.; Guillen, Andy T.

2017-05-01

This paper describes static Bayesian game models with "Pure" and "Mixed" games for the development of an optimum Program and Technical Baseline (PTB) solution for affordable acquisition of future space systems. The paper discusses System Engineering (SE) frameworks and analytical and simulation modeling approaches for developing the optimum PTB solutions from both the government and contractor perspectives.

A Fourier analysis for a fast simulation algorithm. [for switching converters

NASA Technical Reports Server (NTRS)

King, Roger J.

1988-01-01

This paper presents a derivation of compact expressions for the Fourier series analysis of the steady-state solution of a typical switching converter. The modeling procedure for the simulation and the steady-state solution is described, and some desirable traits for its matrix exponential subroutine are discussed. The Fourier analysis algorithm was tested on a phase-controlled parallel-loaded resonant converter, providing an experimental confirmation.

On the Use of Linearized Euler Equations in the Prediction of Jet Noise

NASA Technical Reports Server (NTRS)

Mankbadi, Reda R.; Hixon, R.; Shih, S.-H.; Povinelli, L. A.

1995-01-01

Linearized Euler equations are used to simulate supersonic jet noise generation and propagation. Special attention is given to boundary treatment. The resulting solution is stable and nearly free from boundary reflections without the need for artificial dissipation, filtering, or a sponge layer. The computed solution is in good agreement with theory and observation and is much less CPU-intensive as compared to large-eddy simulations.

WATSFAR: numerical simulation of soil WATer and Solute fluxes using a FAst and Robust method

NASA Astrophysics Data System (ADS)

Crevoisier, David; Voltz, Marc

2013-04-01

To simulate the evolution of hydro- and agro-systems, numerous spatialised models are based on a multi-local approach and improvement of simulation accuracy by data-assimilation techniques are now used in many application field. The latest acquisition techniques provide a large amount of experimental data, which increase the efficiency of parameters estimation and inverse modelling approaches. In turn simulations are often run on large temporal and spatial domains which requires a large number of model runs. Eventually, despite the regular increase in computing capacities, the development of fast and robust methods describing the evolution of saturated-unsaturated soil water and solute fluxes is still a challenge. Ross (2003, Agron J; 95:1352-1361) proposed a method, solving 1D Richards' and convection-diffusion equation, that fulfil these characteristics. The method is based on a non iterative approach which reduces the numerical divergence risks and allows the use of coarser spatial and temporal discretisations, while assuring a satisfying accuracy of the results. Crevoisier et al. (2009, Adv Wat Res; 32:936-947) proposed some technical improvements and validated this method on a wider range of agro- pedo- climatic situations. In this poster, we present the simulation code WATSFAR which generalises the Ross method to other mathematical representations of soil water retention curve (i.e. standard and modified van Genuchten model) and includes a dual permeability context (preferential fluxes) for both water and solute transfers. The situations tested are those known to be the less favourable when using standard numerical methods: fine textured and extremely dry soils, intense rainfall and solute fluxes, soils near saturation, ... The results of WATSFAR have been compared with the standard finite element model Hydrus. The analysis of these comparisons highlights two main advantages for WATSFAR, i) robustness: even on fine textured soil or high water and solute fluxes - where Hydrus simulations may fail to converge - no numerical problem appears, and ii) accuracy of simulations even for loose spatial domain discretisations, which can only be obtained by Hydrus with fine discretisations.

The effect of material heterogeneities in long term multiscale seismic cycle simulations

NASA Astrophysics Data System (ADS)

Kyriakopoulos, C.; Richards-Dinger, K. B.; Dieterich, J. H.

2016-12-01

A fundamental part of the simulation of the earthquake cycles in large-scale multicycle earthquake simulators is the pre-computation of elastostatic Greens functions collected into the stiffness matrix (K). The stiffness matrices are typically based on the elastostatic solutions of Okada (1992), Gimbutas et al. (2012), or similar. While these analytic solutions are computationally very fast, they are limited to modeling a homogeneous isotropic half-space. It is thus unknown how such simulations may be affected by material heterogeneity characterizing the earth medium. We are currently working on the estimation of the effects of heterogeneous material properties in the earthquake simulator RSQSim (Richards-Dinger and Dieterich, 2012). In order to do that we are calculating elastostatic solutions in a heterogeneous medium using the Finite Element (FE) method instead of any of the analytical solutions. The investigated region is a 400 x 400 km area centered on the Anza zone in southern California. The fault system geometry is based on that of the UCERF3 deformation models in the area of interest, which we then implement in a finite element mesh using Trelis 15. The heterogeneous elastic structure is based on available tomographic data (seismic wavespeeds and density) for the region (SCEC CVM and Allam et al., 2014). For computation of the Greens functions we are using the open source FE code Defmod (https://bitbucket.org/stali/defmod/wiki/Home) to calculate the elastostatic solutions due to unit slip on each patch. Earthquake slip on the fault plane is implemented through linear constraint equations (Ali et al., 2014, Kyriakopoulos et al., 2013, Aagard et al, 2015) and more specifically with the use of Lagrange multipliers adjunction. The elementary responses are collected into the "heterogeneous" stiffness matrix Khet and used in RSQSim instead of the ones generated with Okada. Finally, we compare the RSQSim results based on the "heterogeneous" Khet with results from Khom (stiffness matrix generated from the same mesh as Khet but using homogeneous material properties). The estimation of the effect of heterogeneous material properties in the seismic cycles simulated by RSQSim is a needed experiment that will allow us to evaluate the impact of heterogeneities in earthquake simulators.

Aeroacoustic Simulation of Nose Landing Gear on Adaptive Unstructured Grids With FUN3D

NASA Technical Reports Server (NTRS)

Vatsa, Veer N.; Khorrami, Mehdi R.; Park, Michael A.; Lockard, David P.

2013-01-01

Numerical simulations have been performed for a partially-dressed, cavity-closed nose landing gear configuration that was tested in NASA Langley s closed-wall Basic Aerodynamic Research Tunnel (BART) and in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D, developed at NASA Langley Research center, is used to compute the unsteady flow field for this configuration. Starting with a coarse grid, a series of successively finer grids were generated using the adaptive gridding methodology available in the FUN3D code. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these computations. Time-averaged and instantaneous solutions obtained on these grids are compared with the measured data. In general, the correlation with the experimental data improves with grid refinement. A similar trend is observed for sound pressure levels obtained by using these CFD solutions as input to a FfowcsWilliams-Hawkings noise propagation code to compute the farfield noise levels. In general, the numerical solutions obtained on adapted grids compare well with the hand-tuned enriched fine grid solutions and experimental data. In addition, the grid adaption strategy discussed here simplifies the grid generation process, and results in improved computational efficiency of CFD simulations.

Authigenic molybdenum formation in marine sediments: A link to pore water sulfide in the Santa Barbara Basin

USGS Publications Warehouse

Zheng, Yen; Anderson, Robert F.; VanGeen, A.; Kuwabara, J.

2000-01-01

Pore water and sediment Mo concentrations were measured in a suite of multicores collected at four sites along the northeastern flank of the Santa Barbara Basin to examine the connection between authigenic Mo formation and pore water sulfide concentration. Only at the deepest site (580 m), where pore water sulfide concentrations rise to >0.1 ??M right below the sediment water interface, was there active authigenic Mo formation. At shallower sites (550,430, and 340 m), where pore water sulfide concentrations were consistently <0.05 ??M, Mo precipitation was not occuring at the time of sampling. A sulfide concentration of ???0.1 ??M appears to be a threshold for the onset of Mo-Fe-S co-precipitation. A second threshold sulfide concentration of ???100 ??M is required for Mo precipitation without Fe, possibly as Mo-S or as particle-bound Mo. Mass budgets for Mo were constructed by combining pore water and sediment results for Mo with analyses of sediment trap material from Santa Barbara Basin as well as sediment accumulation rates derived from 210Pb. The calculations show that most of the authigenic Mo in the sediment at the deepest site is supplied by diffusion from overlying bottom waters. There is, however, a non-lithogenic particulate Mo associated with sinking particles that contributes ???15% to the total authigenic Mo accumulation. Analysis of sediment trap samples and supernant brine solutions indicates the presence of non-lithogenic particulate Mo, a large fraction of which is easily remobilized and, perhaps, associated with Mn-oxides. Our observations show that even with the very high flux of organic carbon reaching the sediment of Santa Barbara Basin, active formation of sedimentary authigenic Mo requires a bottom water oxygen concentration below 3 ??M. However, small but measurable rates of authigenic Mo accumulation were observed at sites where bottom water oxygen ranged between 5 and 23 ??M, indicating that the formation of authigenic Mo occured in the recent past, but not at the time of sampling. Copyright ?? 2000 Elsevier Science Ltd.

Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations.

PubMed

Zhao, Jing; Wang, Mei; Fu, Aiyun; Yang, Hongfang; Bu, Yuxiang

2015-08-03

We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of transient stream flow on water exchange and reactions in the hyporheic zone of an in-stream gravel bar

NASA Astrophysics Data System (ADS)

Trauth, Nico; Schmidt, Christian; Fleckenstein, Jan H.

2015-04-01

Groundwater-surface water exchange is an important process that can facilitate the degradation of critical substances like nitrogen-species and contaminants, supporting a healthy status of the aquatic ecosystem. In our study, we simulate water exchange, solute transport and reactions within a natural in-stream gravel bar using a coupled surface and subsurface numerical model. Stream water flow is simulated by computational fluid dynamics software that provides hydraulic head distributions at the streambed, which are used as an upper boundary condition for a groundwater model. In the groundwater model water exchange, solute transport, aerobic respiration and denitrification in the subsurface are simulated. Ambient groundwater flow is introduced by lateral upstream and downstream hydraulic head boundaries that generate neutral, losing or gaining stream conditions. Stream water transports dissolved oxygen, organic carbon (as the dominant electron donor) and nitrate into the subsurface, whereas an additional nitrate source exists in the ambient groundwater. Scenarios of stream flow events varying in duration and stream stage are simulated and compared with steady state scenarios with respect to water fluxes, residence times and the solute turn-over rates. Results show, that water exchange and solute turn-over rates highly depend on the interplay between event characteristics and ambient groundwater levels. For scenarios, where the stream flow event shifts the hydraulic system to a net-neutral hydraulic gradient between the average stream stage and the ambient groundwater level (minimal exchange between ground- and surface water), solute consumption is higher, compared to the steady losing or gaining case. In contrast, events that induce strong losing conditions lead to a lower potential of solute consumption.

Effects of Heat Treatment on Corrosion and Wear Behaviors of Mg-6Gd-2Zn-0.4Zr Alloy in Simulated Body Fluid

NASA Astrophysics Data System (ADS)

Zhao, Li; Chen, Wei; Dai, Jianwei; Wang, Zhangzhong; Zhang, Xiaobo

2017-11-01

Mg-6Gd-2Zn-0.4Zr (wt.%, GZ62K) alloy was processed by solution treatment under different temperatures. The microstructure, hardness, corrosion and wear behaviors in simulated body fluid (SBF) have been studied. The results indicate that the (Mg, Zn)3Gd phase decreases, the precipitated phases gradually increase, and the long-period stacking ordered structure disappears with the increase of solution temperature. The alloy has better corrosion resistance after solution treatment, and that solution treated at 490 °C for 12 h shows the best corrosion resistance. The friction coefficient of the alloy under dry sliding condition decreases slightly, but the mass loss increases with increasing the solution temperature. The alloy solution treated at 460 °C for 12 h exhibits the lowest friction coefficient and mass loss in SBF, and it also has the best wear resistance under dry sliding condition.

Sedimentary Geothermal Feasibility Study: October 2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Augustine, Chad; Zerpa, Luis

The objective of this project is to analyze the feasibility of commercial geothermal projects using numerical reservoir simulation, considering a sedimentary reservoir with low permeability that requires productivity enhancement. A commercial thermal reservoir simulator (STARS, from Computer Modeling Group, CMG) is used in this work for numerical modeling. In the first stage of this project (FY14), a hypothetical numerical reservoir model was developed, and validated against an analytical solution. The following model parameters were considered to obtain an acceptable match between the numerical and analytical solutions: grid block size, time step and reservoir areal dimensions; the latter related to boundarymore » effects on the numerical solution. Systematic model runs showed that insufficient grid sizing generates numerical dispersion that causes the numerical model to underestimate the thermal breakthrough time compared to the analytic model. As grid sizing is decreased, the model results converge on a solution. Likewise, insufficient reservoir model area introduces boundary effects in the numerical solution that cause the model results to differ from the analytical solution.« less

Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2016-06-01

The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein-protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density Nbulk; and relative solvent molecular density g. For a molecular solute, 4πr2p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss's law of Maxwell's equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

Magnetic Field in a Screw Flow with Fluctuations

NASA Astrophysics Data System (ADS)

Titov, V. V.; Stepanov, R. A.; Sokoloff, D. D.

2018-04-01

We consider the influence of fluctuations in a screw flow of a conducting liquid on the effect of magnetic field self-excitation; the solution of this problem is important for experimental realization of a turbulent dynamo. We propose a theoretical approach based on the solution of averaged equations obtained in the limit of a short correlation time. The applicability of this approach is confirmed by direct numerical simulation of the initial equations. We demonstrate the influence of the correlation of fluctuations on the dynamo effect threshold. It is shown that the solution of the mean-field equations differs from the solution based on direct numerical simulation for a finite correlation time. The advantages and disadvantages of the two approaches are estimates, as well as the importance of the discovered difference in the context of problems of magnetic field self-excitation. The influence of helicity and intermittency on the type of the solution is considered.

Calculation of open and closed system elastic coefficients for multicomponent solids

NASA Astrophysics Data System (ADS)

Mishin, Y.

2015-06-01

Thermodynamic equilibrium in multicomponent solids subject to mechanical stresses is a complex nonlinear problem whose exact solution requires extensive computations. A few decades ago, Larché and Cahn proposed a linearized solution of the mechanochemical equilibrium problem by introducing the concept of open system elastic coefficients [Acta Metall. 21, 1051 (1973), 10.1016/0001-6160(73)90021-7]. Using the Ni-Al solid solution as a model system, we demonstrate that open system elastic coefficients can be readily computed by semigrand canonical Monte Carlo simulations in conjunction with the shape fluctuation approach. Such coefficients can be derived from a single simulation run, together with other thermodynamic properties needed for prediction of compositional fields in solid solutions containing defects. The proposed calculation approach enables streamlined solutions of mechanochemical equilibrium problems in complex alloys. Second order corrections to the linear theory are extended to multicomponent systems.

Limit Theorems and Their Relation to Solute Transport in Simulated Fractured Media

NASA Astrophysics Data System (ADS)

Reeves, D. M.; Benson, D. A.; Meerschaert, M. M.

2003-12-01

Solute particles that travel through fracture networks are subject to wide velocity variations along a restricted set of directions. This may result in super-Fickian dispersion along a few primary scaling directions. The fractional advection-dispersion equation (FADE), a modification of the original advection-dispersion equation in which a fractional derivative replaces the integer-order dispersion term, has the ability to model rapid, non-Gaussian solute transport. The FADE assumes that solute particle motions converge to either α -stable or operator stable densities, which are modeled by spatial fractional derivatives. In multiple dimensions, the multi-fractional dispersion derivative dictates the order and weight of differentiation in all directions, which correspond to the statistics of large particle motions in all directions. This study numerically investigates the presence of super- Fickian solute transport through simulated two-dimensional fracture networks. An ensemble of networks is gen

Intrinsic Viscosity of Dendrimers via Equilibrium Molecular Dynamics

NASA Astrophysics Data System (ADS)

Drew, Phil; Adolf, David

2004-03-01

Equilibrium molecular dynamics simulations of dendrimers in dilute solution have been performed using dl-poly. Analysis of the system stress tensor via the Green-Kubo formula produces the viscosity of the dendrimer solution which, when coupled with that of a solvent only system leads to the intrinsic viscosity of the dendrimer solute. Particular attention has been paid to error analysis as the auto-correlation of the stress tensor exhibits a long time tail, potentially leading to large uncertainties in the solution, and hence intrinsic, viscosities. In order to counter this effect and provide reliable statistical averaging, simulations have been run spanning very many times the longest system relaxation. Comparison is made to previous studies, using different techniques, which suggest a peak in the intrinsic viscosity of dendrimers at around generation four. Results are also presented from investigations in to the individual contributions to the system stress tensor from the solvent and the solute.

Recovery of metals from simulant spent lithium-ion battery as organophosphonate coordination polymers in aqueous media.

PubMed

Perez, Emilie; Andre, Marie-Laure; Navarro Amador, Ricardo; Hyvrard, François; Borrini, Julien; Carboni, Michaël; Meyer, Daniel

2016-11-05

An innovative approach is proposed for the recycling of metals from a simulant lithium-ion battery (LIBs) waste aqueous solution. Phosphonate organic linkers are introduced as precipitating agents to selectively react with the metals to form coordination polymers from an aqueous solution containing Ni, Mn and Co in a hydrothermal process. The supernatant is analyzed by ICP-AES to quantify the efficiency and the selectivity of the precipitation and the materials are characterized by Scanning Electron Microscopy (SEM), Powder X-Ray Diffraction (PXRD), Thermogravimetric Analyses (TGA) and nitrogen gas sorption (BET). Conditions have been achieved to selectively precipitate Manganese or Manganese/Cobalt from this solution with a high efficiency. This work describes a novel method to obtain potentially valuable coordination polymers from a waste metal solution that can be generalized on any waste solution. Copyright © 2016 Elsevier B.V. All rights reserved.

Dispersion Analysis Using Particle Tracking Simulations Through Heterogeneity Based on Outcrop Lidar Imagery

NASA Astrophysics Data System (ADS)

Klise, K. A.; Weissmann, G. S.; McKenna, S. A.; Tidwell, V. C.; Frechette, J. D.; Wawrzyniec, T. F.

2007-12-01

Solute plumes are believed to disperse in a non-Fickian manner due to small-scale heterogeneity and variable velocities that create preferential pathways. In order to accurately predict dispersion in naturally complex geologic media, the connection between heterogeneity and dispersion must be better understood. Since aquifer properties can not be measured at every location, it is common to simulate small-scale heterogeneity with random field generators based on a two-point covariance (e.g., through use of sequential simulation algorithms). While these random fields can produce preferential flow pathways, it is unknown how well the results simulate solute dispersion through natural heterogeneous media. To evaluate the influence that complex heterogeneity has on dispersion, we utilize high-resolution terrestrial lidar to identify and model lithofacies from outcrop for application in particle tracking solute transport simulations using RWHet. The lidar scan data are used to produce a lab (meter) scale two-dimensional model that captures 2-8 mm scale natural heterogeneity. Numerical simulations utilize various methods to populate the outcrop structure captured by the lidar-based image with reasonable hydraulic conductivity values. The particle tracking simulations result in residence time distributions used to evaluate the nature of dispersion through complex media. Particle tracking simulations through conductivity fields produced from the lidar images are then compared to particle tracking simulations through hydraulic conductivity fields produced from sequential simulation algorithms. Based on this comparison, the study aims to quantify the difference in dispersion when using realistic and simplified representations of aquifer heterogeneity. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

The efficiency of different irrigation solutions and techniques for the removal of triple antibiotic paste from simulated immature root canals.

PubMed

Ustun, Y; Düzgün, S; Aslan, T; Aktı, A

2018-03-01

The purpose of this study was to evaluate the efficiencies of different irrigation protocols in the removal of triple antibiotic paste (TAP) from root canals. A total of 127 extracted human maxillary incisor teeth were prepared. Then, root-end resection of 3 mm was accomplished to simulate immature apex model. The root canals were filled with TAP, after 21 days, randomly divided into nine groups according to irrigation systems and solutions (n = 13). Conventional irrigation (CI) groups - Group 1: Root canal irrigation was performed with CI by Peracetic acid (PAA) solution, Group 2: Root canal irrigation was performed with CI by etidronic acid 1-hydroxyethylidene-1, 1-bisphosphonate (HEBP) + sodium hypochlorite (NaOCl) solution, Group 3: Root canal irrigation was performed with CI by ethylenediaminetetraacetic acid (EDTA)/NaOCl solutions. Vibringe system groups - Group 4: Root canal irrigation was performed with Vibringe system by PAA solution, Group 5: Root canal irrigation was performed with Vibringe system by HEBP + NaOCl solution, Group 6: Root canal irrigation was performed with Vibringe system by EDTA/NaOCl solution. EndoVac system groups - Group 7: Root canal irrigation was performed with EndoVac system by PAA solution, Group 8: Root canal irrigation was performed with EndoVac system by HEBP + NaOCl solution, Group 9: Root canal irrigation was performed with EndoVac system by EDTA/NaOCl solution. Control Group: (n = 0). Samples were sectioned vertically, and the amount of remaining medicament was scored for each root half and data were statistically analyzed. Among the irrigation systems, CI groups showed the highest scores at both apical and coronal parts (P < 0.05). In comparisons among the solutions, at the apical part, PAA groups showed the highest scores (P < 0.05). At the coronal part, EDTA + NaOCl groups showed the lowest score values (P < 0.05). The use of irrigation systems improved the removal of TAP from the simulated immature root canals. Also, as an irrigation solution EDTA gives more promising results than PAA and HEBP solutions.

Protonation-modulated localization of excess electrons in histidine aqueous solutions revealed by ab initio molecular dynamics simulations: anion-centered versus cation-centered localization.

PubMed

Gao, Liang; Bu, Yuxiang

2017-05-31

In this work, we present an ab initio molecular dynamics simulation study on the interaction of an excess electron (EE) with histidine in its aqueous solution. Two different configurations of histidine (imidazole group protonated or not) are considered to reflect its different existing forms in neutral or slightly acidic surroundings. The simulation results indicate that localizations of EEs in different aqueous histidine solutions are quite different and are strongly affected by protonation of the side chain imidazole group and are thus pH-controlled. In neutral aqueous histidine solution, an EE localizes onto the carboxyl anionic group of the amino acid backbone after a relatively lengthy diffuse state, performing just like in an aliphatic amino acid solution. But in weakly acidic solution in which the side chain imidazole group is protonated, an EE undergoes a short lifetime diffuse state and finally localizes on the protonated imidazole group. We carefully examine these two different localization dynamics processes and analyze the competition between different dominating groups in their corresponding electron localization mechanisms. To explain the difference, we investigate the frontier molecular orbitals of these two systems and find that their energy levels and compositions are important to determine these differences. These findings can provide helpful information to understand the interaction mechanisms of low energy EEs with amino acids and even oligopeptides, especially with aromatic rings.

Macroion solutions in the cell model studied by field theory and Monte Carlo simulations.

PubMed

Lue, Leo; Linse, Per

2011-12-14

Aqueous solutions of charged spherical macroions with variable dielectric permittivity and their associated counterions are examined within the cell model using a field theory and Monte Carlo simulations. The field theory is based on separation of fields into short- and long-wavelength terms, which are subjected to different statistical-mechanical treatments. The simulations were performed by using a new, accurate, and fast algorithm for numerical evaluation of the electrostatic polarization interaction. The field theory provides counterion distributions outside a macroion in good agreement with the simulation results over the full range from weak to strong electrostatic coupling. A low-dielectric macroion leads to a displacement of the counterions away from the macroion. © 2011 American Institute of Physics

Numerical simulations of Kadomtsev-Petviashvili soliton interactions

NASA Astrophysics Data System (ADS)

Infeld, E.; Senatorski, A.; Skorupski, A. A.

1995-04-01

The Kadomtsev-Petviashvili equation generalizes that of Korteweg and de Vries to two space dimensions and arises in various weakly dispersive media. Two very different species of soliton solutions are known for one variant, KPI. The first species to be discovered are line solitons, the second are two dimensional lumps. This paper describes numerical simulations, consistent with all constraints of the equation, in which very distorted line solitons break up into smaller line solitons and arrays of lumps. The arrays can interact with one another. In some cases, aspects of the results of the simulations can be understood in the light of specially constructed exact solutions. Simulations in which initial conditions fail to satisfy the constraints of the equation are also described.

MO-D-PinS Room/Hall E-00: MR Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

2016-06-15

MRI, with its excellent soft tissue contrast and its ability to provide physiological as well as anatomical information, is becoming increasingly used in radiation therapy for treatment planning, image-guided radiation therapy, and treatment evaluation. This session will explore solutions to integrating MRI into the simulation process. Obstacles for using MRI for simulation include distortions and artifacts, image acquisition speed, complexity of imaging techniques, and lack of electron density information. Partners in Solutions presents vendor representatives who will present their approaches to meeting these challenges and others. An increased awareness of how MRI simulation works will allow physicists to better understandmore » and use this powerful technique. The speakers are all employees who are presenting information about their company’s products.« less

Reflectivity of the atmosphere-inhomogeneous surfaces system Laboratory simulation

NASA Technical Reports Server (NTRS)

Mekler, Y.; Kaufman, Y. J.; Fraser, R. S.

1984-01-01

Theoretical two- and three-dimensional solutions of the radiative transfer equation have been applied to the earth-atmosphere system. Such solutions have not been verified experimentally. A laboratory experiment simulates such a system to test the theory. The atmosphere was simulated by latex spheres suspended in water and the ground by a nonuniform surface, half white and half black. A stable radiation source provided uniform illumination over the hydrosol. The upward radiance along a line orthogonal to the boundary of the two-halves field was recorded for different amounts of the hydrosol. The simulation is a well-defined radiative transfer experiment to test radiative transfer models involving nonuniform surfaces. Good agreement is obtained between the measured and theoretical results.

The SCEC/USGS dynamic earthquake rupture code verification exercise

USGS Publications Warehouse

Harris, R.A.; Barall, M.; Archuleta, R.; Dunham, E.; Aagaard, Brad T.; Ampuero, J.-P.; Bhat, H.; Cruz-Atienza, Victor M.; Dalguer, L.; Dawson, P.; Day, S.; Duan, B.; Ely, G.; Kaneko, Y.; Kase, Y.; Lapusta, N.; Liu, Yajing; Ma, S.; Oglesby, D.; Olsen, K.; Pitarka, A.; Song, S.; Templeton, E.

2009-01-01

Numerical simulations of earthquake rupture dynamics are now common, yet it has been difficult to test the validity of these simulations because there have been few field observations and no analytic solutions with which to compare the results. This paper describes the Southern California Earthquake Center/U.S. Geological Survey (SCEC/USGS) Dynamic Earthquake Rupture Code Verification Exercise, where codes that simulate spontaneous rupture dynamics in three dimensions are evaluated and the results produced by these codes are compared using Web-based tools. This is the first time that a broad and rigorous examination of numerous spontaneous rupture codes has been performed—a significant advance in this science. The automated process developed to attain this achievement provides for a future where testing of codes is easily accomplished.Scientists who use computer simulations to understand earthquakes utilize a range of techniques. Most of these assume that earthquakes are caused by slip at depth on faults in the Earth, but hereafter the strategies vary. Among the methods used in earthquake mechanics studies are kinematic approaches and dynamic approaches.The kinematic approach uses a computer code that prescribes the spatial and temporal evolution of slip on the causative fault (or faults). These types of simulations are very helpful, especially since they can be used in seismic data inversions to relate the ground motions recorded in the field to slip on the fault(s) at depth. However, these kinematic solutions generally provide no insight into the physics driving the fault slip or information about why the involved fault(s) slipped that much (or that little). In other words, these kinematic solutions may lack information about the physical dynamics of earthquake rupture that will be most helpful in forecasting future events.To help address this issue, some researchers use computer codes to numerically simulate earthquakes and construct dynamic, spontaneous rupture (hereafter called “spontaneous rupture”) solutions. For these types of numerical simulations, rather than prescribing the slip function at each location on the fault(s), just the friction constitutive properties and initial stress conditions are prescribed. The subsequent stresses and fault slip spontaneously evolve over time as part of the elasto-dynamic solution. Therefore, spontaneous rupture computer simulations of earthquakes allow us to include everything that we know, or think that we know, about earthquake dynamics and to test these ideas against earthquake observations.

The estimation of lower refractivity uncertainty from radar sea clutter using the Bayesian—MCMC method

NASA Astrophysics Data System (ADS)

Sheng, Zheng

2013-02-01

The estimation of lower atmospheric refractivity from radar sea clutter (RFC) is a complicated nonlinear optimization problem. This paper deals with the RFC problem in a Bayesian framework. It uses the unbiased Markov Chain Monte Carlo (MCMC) sampling technique, which can provide accurate posterior probability distributions of the estimated refractivity parameters by using an electromagnetic split-step fast Fourier transform terrain parabolic equation propagation model within a Bayesian inversion framework. In contrast to the global optimization algorithm, the Bayesian—MCMC can obtain not only the approximate solutions, but also the probability distributions of the solutions, that is, uncertainty analyses of solutions. The Bayesian—MCMC algorithm is implemented on the simulation radar sea-clutter data and the real radar sea-clutter data. Reference data are assumed to be simulation data and refractivity profiles are obtained using a helicopter. The inversion algorithm is assessed (i) by comparing the estimated refractivity profiles from the assumed simulation and the helicopter sounding data; (ii) the one-dimensional (1D) and two-dimensional (2D) posterior probability distribution of solutions.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

CO2 capture in amine solutions: modelling and simulations with non-empirical methods

NASA Astrophysics Data System (ADS)

Andreoni, Wanda; Pietrucci, Fabio

2016-12-01

Absorption in aqueous amine solutions is the most advanced technology for the capture of CO2, although suffering from drawbacks that do not allow exploitation on large scale. The search for optimum solvents has been pursued with empirical methods and has also motivated a number of computational approaches over the last decade. However, a deeper level of understanding of the relevant chemical reactions in solution is required so as to contribute to this effort. We present here a brief critical overview of the most recent applications of computer simulations using ab initio methods. Comparison of their outcome shows a strong dependence on the structural models employed to represent the molecular systems in solution and on the strategy used to simulate the reactions. In particular, the results of very recent ab initio molecular dynamics augmented with metadynamics are summarized, showing the crucial role of water, which has been so far strongly underestimated both in the calculations and in the interpretation of experimental data. Indications are given for advances in computational approaches that are necessary if meant to contribute to the rational design of new solvents.

Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.

PubMed

Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W

2011-09-22

Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.

Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes.

PubMed Central

Ashbaugh, H S; Garde, S; Hummer, G; Kaler, E W; Paulaitis, M E

1999-01-01

Conformational free energies of butane, pentane, and hexane in water are calculated from molecular simulations with explicit waters and from a simple molecular theory in which the local hydration structure is estimated based on a proximity approximation. This proximity approximation uses only the two nearest carbon atoms on the alkane to predict the local water density at a given point in space. Conformational free energies of hydration are subsequently calculated using a free energy perturbation method. Quantitative agreement is found between the free energies obtained from simulations and theory. Moreover, free energy calculations using this proximity approximation are approximately four orders of magnitude faster than those based on explicit water simulations. Our results demonstrate the accuracy and utility of the proximity approximation for predicting water structure as the basis for a quantitative description of n-alkane conformational equilibria in water. In addition, the proximity approximation provides a molecular foundation for extending predictions of water structure and hydration thermodynamic properties of simple hydrophobic solutes to larger clusters or assemblies of hydrophobic solutes. PMID:10423414

Molecular dynamics simulation studies of the interactions between ionic liquids and amino acids in aqueous solution.

PubMed

Tomé, Luciana I N; Jorge, Miguel; Gomes, José R B; Coutinho, João A P

2012-02-16

Although the understanding of the influence of ionic liquids (ILs) on the solubility behavior of biomolecules in aqueous solutions is relevant for the design and optimization of novel biotechnological processes, the underlying molecular-level mechanisms are not yet consensual or clearly elucidated. In order to contribute to the understanding of the molecular interactions established between amino acids and ILs in aqueous media, classical molecular dynamics (MD) simulations were performed for aqueous solutions of five amino acids with different structural characteristics (glycine, alanine, valine, isoleucine, and glutamic acid) in the presence of 1-butyl-3-methylimidazolium bis(trifluoromethyl)sulfonyl imide. The results from MD simulations enable to relate the properties of the amino acids, namely their hydrophobicity, to the type and strength of their interactions with ILs in aqueous solutions and provide an explanation for the direction and magnitude of the solubility phenomena observed in [IL + amino acid + water] systems by a mechanism governed by a balance between competitive interactions of the IL cation, IL anion, and water with the amino acids.

A scaled-ionic-charge simulation model that reproduces enhanced and suppressed water diffusion in aqueous salt solutions.

PubMed

Kann, Z R; Skinner, J L

2014-09-14

Non-polarizable models for ions and water quantitatively and qualitatively misrepresent the salt concentration dependence of water diffusion in electrolyte solutions. In particular, experiment shows that the water diffusion coefficient increases in the presence of salts of low charge density (e.g., CsI), whereas the results of simulations with non-polarizable models show a decrease of the water diffusion coefficient in all alkali halide solutions. We present a simple charge-scaling method based on the ratio of the solvent dielectric constants from simulation and experiment. Using an ion model that was developed independently of a solvent, i.e., in the crystalline solid, this method improves the water diffusion trends across a range of water models. When used with a good-quality water model, e.g., TIP4P/2005 or E3B, this method recovers the qualitative behaviour of the water diffusion trends. The model and method used were also shown to give good results for other structural and dynamic properties including solution density, radial distribution functions, and ion diffusion coefficients.

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations.

PubMed

Duboué-Dijon, Elise; Mason, Philip E; Fischer, Henry E; Jungwirth, Pavel

2018-04-05

Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.

Towards real-time photon Monte Carlo dose calculation in the cloud

NASA Astrophysics Data System (ADS)

Ziegenhein, Peter; Kozin, Igor N.; Kamerling, Cornelis Ph; Oelfke, Uwe

2017-06-01

Near real-time application of Monte Carlo (MC) dose calculation in clinic and research is hindered by the long computational runtimes of established software. Currently, fast MC software solutions are available utilising accelerators such as graphical processing units (GPUs) or clusters based on central processing units (CPUs). Both platforms are expensive in terms of purchase costs and maintenance and, in case of the GPU, provide only limited scalability. In this work we propose a cloud-based MC solution, which offers high scalability of accurate photon dose calculations. The MC simulations run on a private virtual supercomputer that is formed in the cloud. Computational resources can be provisioned dynamically at low cost without upfront investment in expensive hardware. A client-server software solution has been developed which controls the simulations and transports data to and from the cloud efficiently and securely. The client application integrates seamlessly into a treatment planning system. It runs the MC simulation workflow automatically and securely exchanges simulation data with the server side application that controls the virtual supercomputer. Advanced encryption standards were used to add an additional security layer, which encrypts and decrypts patient data on-the-fly at the processor register level. We could show that our cloud-based MC framework enables near real-time dose computation. It delivers excellent linear scaling for high-resolution datasets with absolute runtimes of 1.1 seconds to 10.9 seconds for simulating a clinical prostate and liver case up to 1% statistical uncertainty. The computation runtimes include the transportation of data to and from the cloud as well as process scheduling and synchronisation overhead. Cloud-based MC simulations offer a fast, affordable and easily accessible alternative for near real-time accurate dose calculations to currently used GPU or cluster solutions.

Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

NASA Astrophysics Data System (ADS)

Dednam, W.; Botha, A. E.

2015-01-01

Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution function method.

Equiaxed and columnar dendrite growth simulation in Al-7Si- Mg ternary alloys using cellular automaton method

NASA Astrophysics Data System (ADS)

Chen, Rui; Xu, Qingyan; Liu, Baicheng

2015-06-01

In this paper, a modified cellular automaton (MCA) model allowing for the prediction of dendrite growth of Al-Si-Mg ternary alloys in two and three dimensions is presented. The growth kinetic of S/L interface is calculated based on the solute equilibrium approach. In order to describe the dendrite growth with arbitrarily crystallographic orientations, this model introduces a modified decentered octahedron algorithm for neighborhood tracking to eliminate the effect of mesh dependency on dendrite growth. The thermody namic and kinetic data needed for dendrite growth is obtained through coupling with Pandat software package in combination with thermodynamic/kinetic/equilibrium phase diagram calculation databases. The effect of interactions between various alloying elements on solute diffusion coefficient is considered in the model. This model has first been used to simulate Al-7Si (weight percent) binary dendrite growth followed by a validation using theoretical predictions. For ternary alloy, Al-7Si-0.5Mg dendrite simulation has been carried out and the effects of solute interactions on diffusion matrix as well as the differences of Si and Mg in solute distribution have been analyzed. For actual application, this model has been applied to simulate the equiaxed dendrite growth with various crystallographic orientations of Al-7Si-0.36Mg ternary alloy, and the predicted secondary dendrite arm spacing (SDAS) shows a reasonable agreement with the experimental ones. Furthermore, the columnar dendrite growth in directional solidification has also been simulated and the predicted primary dendrite arm spacing (PDAS) is in good agreement with experiments. The simulated results effectively demonstrate the abilities of the model in prediction of dendritic microstructure of Al-Si-Mg ternary alloy.

Towards real-time photon Monte Carlo dose calculation in the cloud.

PubMed

Ziegenhein, Peter; Kozin, Igor N; Kamerling, Cornelis Ph; Oelfke, Uwe

2017-06-07

Near real-time application of Monte Carlo (MC) dose calculation in clinic and research is hindered by the long computational runtimes of established software. Currently, fast MC software solutions are available utilising accelerators such as graphical processing units (GPUs) or clusters based on central processing units (CPUs). Both platforms are expensive in terms of purchase costs and maintenance and, in case of the GPU, provide only limited scalability. In this work we propose a cloud-based MC solution, which offers high scalability of accurate photon dose calculations. The MC simulations run on a private virtual supercomputer that is formed in the cloud. Computational resources can be provisioned dynamically at low cost without upfront investment in expensive hardware. A client-server software solution has been developed which controls the simulations and transports data to and from the cloud efficiently and securely. The client application integrates seamlessly into a treatment planning system. It runs the MC simulation workflow automatically and securely exchanges simulation data with the server side application that controls the virtual supercomputer. Advanced encryption standards were used to add an additional security layer, which encrypts and decrypts patient data on-the-fly at the processor register level. We could show that our cloud-based MC framework enables near real-time dose computation. It delivers excellent linear scaling for high-resolution datasets with absolute runtimes of 1.1 seconds to 10.9 seconds for simulating a clinical prostate and liver case up to 1% statistical uncertainty. The computation runtimes include the transportation of data to and from the cloud as well as process scheduling and synchronisation overhead. Cloud-based MC simulations offer a fast, affordable and easily accessible alternative for near real-time accurate dose calculations to currently used GPU or cluster solutions.

Synthetic Seismograms of Explosive Sources Calculated by the Earth Simulator

NASA Astrophysics Data System (ADS)

Tsuboi, S.; Matsumoto, H.; Rozhkov, M.; Stachnik, J.

2017-12-01

We calculate broadband synthetic seismograms using the spectral-element method (Komatitsch & Tromp, 2001) for recent explosive events in northern Korean peninsula. We use supercomputer Earth Simulator system in JAMSTEC to compute synthetic seismograms using the spectral-element method. The simulations are performed on 8,100 processors, which require 2,025 nodes of the Earth Simulator. We use one chunk with the angular distance 40 degrees to compute synthetic seismograms. On this number of nodes, a simulation of 5 minutes of wave propagation accurate at periods of 1.5 seconds and longer requires about 10 hours of CPU time. We use CMT solution of Rozhkov et al (2016) as a source model for this event. One example of CMT solution for this source model has 28% double couple component and 51% isotropic component. The hypocenter depth of this solution is 1.4 km. Comparisons of the synthetic waveforms with the observation show that the arrival time of Pn and Pg waves matches well with the observation. Comparison also shows that the agreement of amplitude of other phases is not necessarily well, which demonstrates that the crustal structure should be improved to include in the simulation. The surface waves observed are also modeled well in the synthetics, which shows that the CMT solution we have used for this computation correctly grasps the source characteristics of this event. Because of characteristics of artificial explosive sources of which hypocenter location is already known, we may evaluate crustal structure along the propagation path from the waveform modeling for these sources. We may discuss the limitation of one dimensional crustal structure model by comparing the synthetic waveform of 3D crustal structure and the observed seismograms.

Specific Anion Effects on Na+ Adsorption at the Aqueous Solution-Air Interface: MD Simulations, SESSA Calculations, and Photoelectron Spectroscopy Experiments.

PubMed

Olivieri, Giorgia; Parry, Krista M; D'Auria, Raffaella; Tobias, Douglas J; Brown, Matthew A

2018-01-18

Specific ion effects of the large halide anions have been shown to moderate anion adsorption to the air-water interface (AWI), but little quantitative attention has been paid to the behavior of alkali cations. Here we investigate the concentration and local distribution of sodium (Na + ) at the AWI in dilute (<1 M) aqueous solutions of NaCl, NaBr, and NaI using a combination of molecular dynamics (MD) and SESSA simulations, and liquid jet ambient pressure photoelectron spectroscopy measurements. We use SESSA to simulate Na 2p photoelectron intensities on the basis of the atom density profiles obtained from MD simulations, and we compare the simulation results with photoelectron spectroscopy experiments to evaluate the performance of a nonpolarizable force field model versus that of an induced dipole polarizable one. Our results show that the nonpolarizable force model developed by Horinek and co-workers (Chem. Phys. Lett. 2009, 479, 173-183) accurately predicts the local concentration and distribution of Na + near the AWI for all three electrolytes, whereas the polarizable model does not. To our knowledge, this is the first interface-specific spectroscopic validation of a MD force field. The molecular origins of the unique Na + distributions for the three electrolytes are analyzed on the basis of electrostatic arguments, and shown to arise from an indirect anion effect wherein the identity of the anion affects the strength of the attractive Na + -H 2 O electrostatic interaction. Finally, we use the photoelectron spectroscopy results to constrain the range of inelastic mean free paths (IMFPs) for the three electrolyte solutions used in the SESSA simulations that are able to reproduce the experimental intensities. Our results suggest that earlier estimates of IMFPs for aqueous solutions are likely too high.

Simulating nonlinear steady-state traveling waves on the falling liquid film entrained by a gas flow

NASA Astrophysics Data System (ADS)

Tsvelodub, O. Yu; Bocharov, A. A.

2017-09-01

The article is devoted to the simulation of nonlinear waves on a liquid film flowing under gravity in the known stress field at the interface. The paper studies nonlinear waves on a liquid film, flowing under the action of gravity in a known stress field at the interface. In the case of small Reynolds numbers the problem is reduced to the consideration of solutions of the nonlinear integral-differential equation for film thickness deviation from the undisturbed level. The periodic and soliton steady-state traveling solutions of this equation have been numerically found. The analysis of branching of new families of steady-state traveling solutions has been performed. In particular, it is shown that this model equation has solutions in the form of solitons-humps.

Numerical simulation of air hypersonic flows with equilibrium chemical reactions

NASA Astrophysics Data System (ADS)

Emelyanov, Vladislav; Karpenko, Anton; Volkov, Konstantin

2018-05-01

The finite volume method is applied to solve unsteady three-dimensional compressible Navier-Stokes equations on unstructured meshes. High-temperature gas effects altering the aerodynamics of vehicles are taken into account. Possibilities of the use of graphics processor units (GPUs) for the simulation of hypersonic flows are demonstrated. Solutions of some test cases on GPUs are reported, and a comparison between computational results of equilibrium chemically reacting and perfect air flowfields is performed. Speedup of solution on GPUs with respect to the solution on central processor units (CPUs) is compared. The results obtained provide promising perspective for designing a GPU-based software framework for practical applications.

Note: Nonpolar solute partial molar volume response to attractive interactions with water.

PubMed

Williams, Steven M; Ashbaugh, Henry S

2014-01-07

The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.

Ab initio molecular dynamics simulation of aqueous solution of nitric oxide in different formal oxidation states

NASA Astrophysics Data System (ADS)

Venâncio, Mateus F.; Rocha, Willian R.

2015-10-01

Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NOrad), nitrosonium cation (NO+) and nitroxide anion (NO-) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4 × 10-13 s, which is shorter than the value of 3 × 10-10 s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2- ion as the final product. The dynamics of NOrad revealed the reversibly formation of a transient anion radical species HONOrad -.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Note: Nonpolar solute partial molar volume response to attractive interactions with water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Steven M.; Ashbaugh, Henry S., E-mail: hanka@tulane.edu

2014-01-07

The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.

Time-partitioning simulation models for calculation on parallel computers

NASA Technical Reports Server (NTRS)

Milner, Edward J.; Blech, Richard A.; Chima, Rodrick V.

1987-01-01

A technique allowing time-staggered solution of partial differential equations is presented in this report. Using this technique, called time-partitioning, simulation execution speedup is proportional to the number of processors used because all processors operate simultaneously, with each updating of the solution grid at a different time point. The technique is limited by neither the number of processors available nor by the dimension of the solution grid. Time-partitioning was used to obtain the flow pattern through a cascade of airfoils, modeled by the Euler partial differential equations. An execution speedup factor of 1.77 was achieved using a two processor Cray X-MP/24 computer.

Simulators' validation study: Problem solution logic

NASA Technical Reports Server (NTRS)

Schoultz, M. B.

1974-01-01

A study was conducted to validate the ground based simulators used for aircraft environment in ride-quality research. The logic to the approach for solving this problem is developed. The overall problem solution flow chart is presented. The factors which could influence the human response to the environment on board the aircraft are analyzed. The mathematical models used in the study are explained. The steps which were followed in conducting the validation tests are outlined.

Numerical simulations of an elastica pendulum

NASA Astrophysics Data System (ADS)

Sinclair, R.

Folklore would have it that a massless clamped-free elastica undergoing planar motion with a point end mass possesses periodic solutions corresponding to a single mode of oscillation. We present a battery of numerical simulations leading to the single conclusion that these supposed periodic solutions do not exist, due to a strong nonlinear coupling of two modes, the frequency of one of which is apparently inversely proportional to the magnitude of the force acting on the elastica.

Modeling ultrasonic compression wave absorption during the seeded crystallization of copper (II) sulphate pentahydrate from aqueous solution.

PubMed

Marshall, Thomas; Challis, Richard E; Holmes, Andrew K; Tebbutt, John S

2002-11-01

Ultrasonic compression wave absorption is investigated as a means to monitor the seeded crystallization of copper (II) sulphate pentahydrate from aqueous solution. Simple models are applied to predict crystal yield, crystal size distribution, and the changing nature of the continuous phase. The Allegra-Hawley scattering formulation is used to simulate ultrasonic absorption as crystallization proceeds. Experiments confirm that simulated attenuation is in agreement with measured results.

Semi-analytical solution for the generalized absorbing boundary condition in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Lee, Chung-Shuo; Chen, Yan-Yu; Yu, Chi-Hua; Hsu, Yu-Chuan; Chen, Chuin-Shan

2017-07-01

We present a semi-analytical solution of a time-history kernel for the generalized absorbing boundary condition in molecular dynamics (MD) simulations. To facilitate the kernel derivation, the concept of virtual atoms in real space that can conform with an arbitrary boundary in an arbitrary lattice is adopted. The generalized Langevin equation is regularized using eigenvalue decomposition and, consequently, an analytical expression of an inverse Laplace transform is obtained. With construction of dynamical matrices in the virtual domain, a semi-analytical form of the time-history kernel functions for an arbitrary boundary in an arbitrary lattice can be found. The time-history kernel functions for different crystal lattices are derived to show the generality of the proposed method. Non-equilibrium MD simulations in a triangular lattice with and without the absorbing boundary condition are conducted to demonstrate the validity of the solution.

Molecular-dynamics simulations of urea nucleation from aqueous solution

PubMed Central

Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

2015-01-01

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete. PMID:25492932

Molecular-dynamics simulations of urea nucleation from aqueous solution.

PubMed

Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

2015-01-06

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

Multiphysics Simulation of Welding-Arc and Nozzle-Arc System: Mathematical-Model, Solution-Methodology and Validation

NASA Astrophysics Data System (ADS)

Pawar, Sumedh; Sharma, Atul

2018-01-01

This work presents mathematical model and solution methodology for a multiphysics engineering problem on arc formation during welding and inside a nozzle. A general-purpose commercial CFD solver ANSYS FLUENT 13.0.0 is used in this work. Arc formation involves strongly coupled gas dynamics and electro-dynamics, simulated by solution of coupled Navier-Stoke equations, Maxwell's equations and radiation heat-transfer equation. Validation of the present numerical methodology is demonstrated with an excellent agreement with the published results. The developed mathematical model and the user defined functions (UDFs) are independent of the geometry and are applicable to any system that involves arc-formation, in 2D axisymmetric coordinates system. The high-pressure flow of SF6 gas in the nozzle-arc system resembles arc chamber of SF6 gas circuit breaker; thus, this methodology can be extended to simulate arcing phenomenon during current interruption.

Monte Carlo simulation of a near-continuum shock-shock interaction problem

NASA Technical Reports Server (NTRS)

Carlson, Ann B.; Wilmoth, Richard G.

1992-01-01

A complex shock interaction is calculated with direct simulation Monte Carlo (DSMC). The calculation is performed for the near-continuum flow produced when an incident shock impinges on the bow shock of a 0.1 in. radius cowl lip for freestream conditions of approximately Mach 15 and 35 km altitude. Solutions are presented both for a full finite-rate chemistry calculation and for a case with chemical reactions suppressed. In each case, both the undisturbed flow about the cowl lip and the full shock interaction flowfields are calculated. Good agreement has been obtained between the no-chemistry simulation of the undisturbed flow and a perfect gas solution obtained with the viscous shock-layer method. Large differences in calculated surface properties when different chemical models are used demonstrate the necessity of adequately representing the chemistry when making surface property predictions. Preliminary grid refinement studies make it possible to estimate the accuracy of the solutions.

Passivation and electrochemical behavior of 316L stainless steel in chlorinated simulated concrete pore solution

NASA Astrophysics Data System (ADS)

Luo, Hong; Su, Huaizhi; Dong, Chaofang; Li, Xiaogang

2017-04-01

In this paper, the passivation and electrochemical behavior of 316L stainless steel in chlorinated simulated concrete pore solutions at different pH was evaluated by potentiodynamic measurements, electrochemical impedance spectroscopy. The composition of the passive film and surface morphology were investigated by X-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), and scanning electron microscopy, respectively. The results reveal that metastable pitting susceptibility, stable pitting corrosion, and composition of the passive film are influenced by pH value. After long time immersion, a bilayer structure passive film can be formed in this environment. The appearance of molybdates on the outermost surface layer, further enhancing the stability of the passive film. Moreover, the good pitting corrosion resistance of 316L stainless steel in simulated concrete pore solution without carbonated is mainly due to the presence of high Cr/Fe ratio and molybdates ions within the passive film.

Simplified Predictive Models for CO 2 Sequestration Performance Assessment: Research Topical Report on Task #4 - Reduced-Order Method (ROM) Based Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Srikanta; Jin, Larry; He, Jincong

2015-06-30

Reduced-order models provide a means for greatly accelerating the detailed simulations that will be required to manage CO 2 storage operations. In this work, we investigate the use of one such method, POD-TPWL, which has previously been shown to be effective in oil reservoir simulation problems. This method combines trajectory piecewise linearization (TPWL), in which the solution to a new (test) problem is represented through a linearization around the solution to a previously-simulated (training) problem, with proper orthogonal decomposition (POD), which enables solution states to be expressed in terms of a relatively small number of parameters. We describe the applicationmore » of POD-TPWL for CO 2-water systems simulated using a compositional procedure. Stanford’s Automatic Differentiation-based General Purpose Research Simulator (AD-GPRS) performs the full-order training simulations and provides the output (derivative matrices and system states) required by the POD-TPWL method. A new POD-TPWL capability introduced in this work is the use of horizontal injection wells that operate under rate (rather than bottom-hole pressure) control. Simulation results are presented for CO 2 injection into a synthetic aquifer and into a simplified model of the Mount Simon formation. Test cases involve the use of time-varying well controls that differ from those used in training runs. Results of reasonable accuracy are consistently achieved for relevant well quantities. Runtime speedups of around a factor of 370 relative to full- order AD-GPRS simulations are achieved, though the preprocessing needed for POD-TPWL model construction corresponds to the computational requirements for about 2.3 full-order simulation runs. A preliminary treatment for POD-TPWL modeling in which test cases differ from training runs in terms of geological parameters (rather than well controls) is also presented. Results in this case involve only small differences between training and test runs, though they do demonstrate that the approach is able to capture basic solution trends. The impact of some of the detailed numerical treatments within the POD-TPWL formulation is considered in an Appendix.« less

Exact traveling soliton solutions for the generalized Benjamin-Bona-Mahony equation

NASA Astrophysics Data System (ADS)

Boudoue Hubert, Malwe; Kudryashov, Nikolai A.; Justin, Mibaile; Abbagari, Souleymanou; Betchewe, Gambo; Doka, Serge Y.

2018-03-01

In this paper, we investigate the generalized Benjamin-Bona-Mahony equation which better describes long waves with arbitrary power-law nonlinearity. As a result, we obtain exact travelling wave soliton solutions, such as anti-kink soliton solution, bright soliton solution, dark soliton solution and periodic solution. These solutions have many free parameters such that they may be used to simulate many experimental situations. The main contribution, in this work, is to not apply the computer codes for construction of exact solutions and not consider the integration constants as zero, because they give all variants for solutions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiedenman, B. J.; White, T. L.; Mahannah, R. N.

Ion Chromatography (IC) is the principal analytical method used to support studies of Sludge Reciept and Adjustment Tank (SRAT) chemistry at DWPF. A series of prior analytical ''Round Robin'' (RR) studies included both supernate and sludge samples from SRAT simulant, previously reported as memos, are tabulated in this report.2,3 From these studies it was determined to standardize IC column size to 4 mm diameter, eliminating the capillary column from use. As a follow on test, the DWPF laboratory, the PSAL laboratory, and the AD laboratory participated in the current analytical RR to determine a suite of anions in SRAT simulantmore » by IC, results also are tabulated in this report. The particular goal was to confirm the laboratories ability to measure and quantitate glycolate ion. The target was + or - 20% inter-lab agreement of the analyte averages for the RR. Each of the three laboratories analyzed a batch of 12 samples. For each laboratory, the percent relative standard deviation (%RSD) of the averages on nitrate, glycolate, and oxalate, was 10% or less. The three laboratories all met the goal of 20% relative agreement for nitrate and glycolate. For oxalate, the PSAL laboratory reported an average value that was 20% higher than the average values reported by the DWPF laboratory and the AD laboratory. Because of this wider window of agreement, it was concluded to continue the practice of an additional acid digestion for total oxalate measurement. It should also be noted that large amounts of glycolate in the SRAT samples will have an impact on detection limits of near eluting peaks, namely Fluoride and Formate. A suite of scoping experiments are presented in the report to identify and isolate other potential interlaboratory disceprancies. Specific ion chromatography inter-laboratory method conditions and differences are tabulated. Most differences were minor but there are some temperature control equipment differences that are significant leading to a recommendation of a heated jacket for analytical columns that are remoted for use in radiohoods. A suggested method improvement would be to implement column temperture control at a temperature slightly above ambient to avoid peak shifting due to temperature fluctuations. Temperature control in this manner would improve short and longer term peak retention time stability. An unknown peak was observed during the analysis of glycolic acid and SRAT simulant. The unknown peak was determined to best match diglycolic acid. The development of a method for acetate is summaraized, and no significant amount of acetate was observed in the SRAT products tested. In addition, an alternative Gas Chromatograph (GC) method for glycolate is summarized.« less

MoleculaRnetworks: an integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation.

PubMed

Mooney, Barbara Logan; Corrales, L René; Clark, Aurora E

2012-03-30

This work discusses scripts for processing molecular simulations data written using the software package R: A Language and Environment for Statistical Computing. These scripts, named moleculaRnetworks, are intended for the geometric and solvent network analysis of aqueous solutes and can be extended to other H-bonded solvents. New algorithms, several of which are based on graph theory, that interrogate the solvent environment about a solute are presented and described. This includes a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute and an exploratory approach for describing H-bonding, both based on the PageRank algorithm of Google search fame. The moleculaRnetworks codes include a preprocessor, which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, and correlation analysis, and other data mining. The goal of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations. Copyright © 2012 Wiley Periodicals, Inc.

Structural dynamic model obtained from flight use with piloted simulation and handling qualities analysis

NASA Technical Reports Server (NTRS)

Powers, Bruce G.

1996-01-01

The ability to use flight data to determine an aircraft model with structural dynamic effects suitable for piloted simulation. and handling qualities analysis has been developed. This technique was demonstrated using SR-71 flight test data. For the SR-71 aircraft, the most significant structural response is the longitudinal first-bending mode. This mode was modeled as a second-order system, and the other higher order modes were modeled as a time delay. The distribution of the modal response at various fuselage locations was developed using a uniform beam solution, which can be calibrated using flight data. This approach was compared to the mode shape obtained from the ground vibration test, and the general form of the uniform beam solution was found to be a good representation of the mode shape in the areas of interest. To calibrate the solution, pitch-rate and normal-acceleration instrumentation is required for at least two locations. With the resulting structural model incorporated into the simulation, a good representation of the flight characteristics was provided for handling qualities analysis and piloted simulation.

Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

PubMed

Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao

2013-09-10

Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

Removal and recovery of acetic acid and two furans during sugar purification of simulated phenols-free biomass hydrolysates.

PubMed

Lee, Sang Cheol

2017-12-01

A cost-effective five-step sugar purification process involving simultaneous removal and recovery of fermentation inhibitors from biomass hydrolysates was first proposed here. Only the three separation steps (PB, PC and PD) in the process were investigated here. Furfural was selectively removed up to 98.4% from a simulated five-component hydrolysate in a cross-current three-stage extraction system with n-hexane. Most of acetic acid in a simulated four-component hydrolysate was selectively removed by emulsion liquid membrane, and it could be concentrated in the stripping solution up to 4.5 times its initial concentration in the feed solution. 5-Hydroxymethylfurfural was selectively removed from a simulated three-component hydrolysate in batch and continuous fixed-bed column adsorption systems with L-493 adsorbent. Also, 5-hydroxymethylfurfural could be concentrated to about 9 times its feed concentration in the continuous adsorption system through a fixed-bed column desorption experiment with aqueous ethanol solution. These results have shown that the proposed purification process was valid. Copyright © 2017 Elsevier Ltd. All rights reserved.

The influence of ion hydration on nucleation and growth of LiF crystals in aqueous solution.

PubMed

Lanaro, G; Patey, G N

2018-01-14

Molecular dynamics (MD) simulations are employed to investigate crystal nucleation and growth in oversaturated aqueous LiF solutions. Results obtained for a range of temperatures provide evidence that the rate of crystal growth is determined by a substantial energy barrier (∼49 kJ mol -1 ) related to the loss of water from the ion hydration shells. Employing direct MD simulations, we do not observe spontaneous nucleation of LiF crystals at 300 K, but nucleation is easily observable in NVT simulations at 500 K. This contrasts with the NaCl case, where crystal nucleation is directly observed in similar simulations at 300 K. Based on these observations, together with a detailed analysis of ion clustering in metastable LiF solutions, we argue that the ion dehydration barrier also plays a key role in crystal nucleation. The hydration of the relatively small Li + and F - ions strongly influences the probability of forming large, crystal-like ion clusters, which are a necessary precursor to nucleation. This important factor is not accounted for in classical nucleation theory.

Cosmic Reionization On Computers: Numerical and Physical Convergence

DOE PAGES

Gnedin, Nickolay Y.

2016-04-01

In this paper I show that simulations of reionization performed under the Cosmic Reionization On Computers (CROC) project do converge in space and mass, albeit rather slowly. A fully converged solution (for a given star formation and feedback model) can be determined at a level of precision of about 20%, but such a solution is useless in practice, since achieving it in production-grade simulations would require a large set of runs at various mass and spatial resolutions, and computational resources for such an undertaking are not yet readily available. In order to make progress in the interim, I introduce amore » weak convergence correction factor in the star formation recipe, which allows one to approximate the fully converged solution with finite resolution simulations. The accuracy of weakly converged simulations approaches a comparable, ~20% level of precision for star formation histories of individual galactic halos and other galactic properties that are directly related to star formation rates, like stellar masses and metallicities. Yet other properties of model galaxies, for example, their HI masses, are recovered in the weakly converged runs only within a factor of two.« less

Using sequential self-calibration method to identify conductivity distribution: Conditioning on tracer test data

USGS Publications Warehouse

Hu, B.X.; He, C.

2008-01-01

An iterative inverse method, the sequential self-calibration method, is developed for mapping spatial distribution of a hydraulic conductivity field by conditioning on nonreactive tracer breakthrough curves. A streamline-based, semi-analytical simulator is adopted to simulate solute transport in a heterogeneous aquifer. The simulation is used as the forward modeling step. In this study, the hydraulic conductivity is assumed to be a deterministic or random variable. Within the framework of the streamline-based simulator, the efficient semi-analytical method is used to calculate sensitivity coefficients of the solute concentration with respect to the hydraulic conductivity variation. The calculated sensitivities account for spatial correlations between the solute concentration and parameters. The performance of the inverse method is assessed by two synthetic tracer tests conducted in an aquifer with a distinct spatial pattern of heterogeneity. The study results indicate that the developed iterative inverse method is able to identify and reproduce the large-scale heterogeneity pattern of the aquifer given appropriate observation wells in these synthetic cases. ?? International Association for Mathematical Geology 2008.

Cosmic Reionization On Computers: Numerical and Physical Convergence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gnedin, Nickolay Y.

In this paper I show that simulations of reionization performed under the Cosmic Reionization On Computers (CROC) project do converge in space and mass, albeit rather slowly. A fully converged solution (for a given star formation and feedback model) can be determined at a level of precision of about 20%, but such a solution is useless in practice, since achieving it in production-grade simulations would require a large set of runs at various mass and spatial resolutions, and computational resources for such an undertaking are not yet readily available. In order to make progress in the interim, I introduce amore » weak convergence correction factor in the star formation recipe, which allows one to approximate the fully converged solution with finite resolution simulations. The accuracy of weakly converged simulations approaches a comparable, ~20% level of precision for star formation histories of individual galactic halos and other galactic properties that are directly related to star formation rates, like stellar masses and metallicities. Yet other properties of model galaxies, for example, their HI masses, are recovered in the weakly converged runs only within a factor of two.« less

Solar Assisted Ground Source Heat Pump Performance in Nearly Zero Energy Building in Baltic Countries

NASA Astrophysics Data System (ADS)

Januševičius, Karolis; Streckienė, Giedrė

2013-12-01

In near zero energy buildings (NZEB) built in Baltic countries, heat production systems meet the challenge of large share domestic hot water demand and high required heating capacity. Due to passive solar design, cooling demand in residential buildings also needs an assessment and solution. Heat pump systems are a widespread solution to reduce energy use. A combination of heat pump and solar thermal collectors helps to meet standard requirements and increases the share of renewable energy use in total energy balance of country. The presented paper describes a simulation study of solar assisted heat pump systems carried out in TRNSYS. The purpose of this simulation was to investigate how the performance of a solar assisted heat pump combination varies in near zero energy building. Results of three systems were compared to autonomous (independent) systems simulated performance. Different solar assisted heat pump design solutions with serial and parallel solar thermal collector connections to the heat pump loop were modelled and a passive cooling possibility was assessed. Simulations were performed for three Baltic countries: Lithuania, Latvia and Estonia.

The influence of ion hydration on nucleation and growth of LiF crystals in aqueous solution

NASA Astrophysics Data System (ADS)

Lanaro, G.; Patey, G. N.

2018-01-01

Molecular dynamics (MD) simulations are employed to investigate crystal nucleation and growth in oversaturated aqueous LiF solutions. Results obtained for a range of temperatures provide evidence that the rate of crystal growth is determined by a substantial energy barrier (˜49 kJ mol-1) related to the loss of water from the ion hydration shells. Employing direct MD simulations, we do not observe spontaneous nucleation of LiF crystals at 300 K, but nucleation is easily observable in NVT simulations at 500 K. This contrasts with the NaCl case, where crystal nucleation is directly observed in similar simulations at 300 K. Based on these observations, together with a detailed analysis of ion clustering in metastable LiF solutions, we argue that the ion dehydration barrier also plays a key role in crystal nucleation. The hydration of the relatively small Li+ and F- ions strongly influences the probability of forming large, crystal-like ion clusters, which are a necessary precursor to nucleation. This important factor is not accounted for in classical nucleation theory.

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, W. D.; Restivo, M. L.; Martino, C. J.

Radioactive waste samples retrieved from Savannah River Site (SRS) Tanks 38H and 43H (concentrate receipt and feed tanks, respectively, for the 2H Evaporator system) were evaluated with regard to their tendency to form foams during air sparging. This work was conducted due to recent processing issues and outages in the evaporator that were believed to have resulted from sample foaming. The samples evaluated for foam formation included supernate collected in April of 2014 (near the time of the evaporator outage) as well as historical samples available within the SRNL shielded cells facility. The April samples included one Tank 43H surfacemore » sample (HTF-43-14-42), one Tank 43H sub-surface sample (HTF-43-14-43), and one Tank 38H (HTF-38-14-41) surface sample. In addition, two Tank 43H samples (HTF-43-14-8 and HTF-43-14-9) and one Tank 38H sample (HTF-38-14-6) were also evaluated along with a blended sample of various historical Tank 38H and 43H samples. Characterization results for the April samples are also provided. The composition of the samples was similar to historical evaporator system samples received at SRNL.« less

Generation and partial characterization of an eosinophil chemotactic cytokine produced by sensitized equine mononuclear cells stimulated with Strongylus vulgaris antigen.

PubMed

Dennis, V A; Klei, T R; Chapman, M R

1993-07-01

Supernatants generated by stimulation of peripheral blood mononuclear cells (PBMC) from Strongylus vulgaris sensitized or immunized ponies were assayed in vitro for eosinophil chemotactic activity (ECA) using the filter system in blind well chambers. The supernatants from these cultures were chemotactic for eosinophils, but not for neutrophils. Supernates from cultures of unsensitized PBMC stimulated with S. vulgaris antigen were not chemotactic for eosinophils. ECA was first detected in culture supernatants after 1.5 h of incubation and was dependent on both antigen and PBMC concentrations, but independent of serum concentrations. Both female and male S. vulgaris worm antigens stimulated ECA production from sensitized PBMC. ECA was not induced by in vitro stimulation of sensitized S. vulgaris PBMC by female Strongylus edentatus worm antigen. Partial characterization of the eosinophil chemotactic cytokine showed it to be nondialyzable, greater than 8000 molecular weight (MW), and sensitive to heating (56 and 95 degrees C), trypsin, and sodium metaperiodate treatments, suggesting that the cytokine is a protein containing some essential carbohydrate moieties. The cytokine described in this paper could partially contribute to the in vivo blood and tissue eosinophilia in experimental S. vulgaris infection.

Effect of purified fractions from cell culture supernate of high-density pre-B acute lymphoblastic leukemia cells (ALL3) on the growth of ALL3 cells at low density.

PubMed

Patel, Sapan J; Darie, Costel C; Clarkson, Bayard D

2017-02-01

The mechanisms underlying the aberrant growth and interactions between cells are not understood very well. The pre-B acute lymphoblastic leukemia cells directly obtained from an adult patient grow very poorly or do not grow at all at low density (LD), but grow better at high starting cell density (HD). We found that the LD ALL3 cells can be stimulated to grow in the presence of diffusible, soluble factors secreted by ALL3 cells themselves growing at high starting cell density. We then developed a biochemical purification procedure that allowed us to purify the factor(s) with stimulatory activity and analyzed them by nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS). Using nanoLC-MS/MS we have identified several proteins which were further processed using various bioinformatics tools. This resulted in eight protein candidates which might be responsible for the growth activity on non-growing LD ALL3 cells and their involvement in the stimulatory activity are discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A compartmentalized solute transport model for redox zones in contaminated aquifers: 2. Field‐scale simulations

USGS Publications Warehouse

Abrams , Robert H.; Loague, Keith

2000-01-01

This paper, the second of two parts [see Abrams and Loague, this issue], reports the field‐scale application of COMPTRAN (compartmentalized solute transport model) for simulating the development of redox zones. COMPTRAN is fully developed and described in the companion paper. Redox zones, which are often delineated by the relative concentrations of dissolved oxygen, have been observed around the globe. The distribution of other redox‐sensitive species is affected by redox zonation. At the U.S. Geological Survey's Cape Cod research site, an anoxic zone containing high concentrations of dissolved iron has been observed. Field data were abstracted from the Cape Cod site for the one‐dimensional and two‐dimensional COMPTRAN simulations reported in this paper. The purpose of the concept‐development simulations was to demonstrate that the compartmentalized approach reported by Abrams et al. [1998] can be linked with a solute transport model to simulate field‐scale phenomena. The results presented in this paper show that COMPTRAN successfully simulated the development of redox zones at the field scale, including trends in pH and alkalinity. Thermodynamic constraints were used to prevent lower‐energy redox reactions from occurring under infeasible geochemical conditions without imposing equilibrium among all redox species. Empirical methods of reaction inhibition were not needed for the simulations conducted for this study. COMPTRAN can be extended easily to include additional compartments and reactions and is capable of handling complex velocity fields in more than one dimension.

Dynamic Simulation over Long Time Periods with 100% Solar Generation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Concepcion, Ricky James; Elliott, Ryan Thomas

2015-12-01

This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.

Simulating Osmotic Equilibria: A New Tool for Calculating Activity Coefficients in Concentrated Aqueous Salt Solutions.

PubMed

Bley, Michael; Duvail, Magali; Guilbaud, Philippe; Dufrêche, Jean-François

2017-10-19

Herein, a new theoretical method is presented for predicting osmotic equilibria and activities, where a bulk liquid and its corresponding vapor phase are simulated by means of molecular dynamics using explicit polarization. Calculated time-averaged number density profiles provide the amount of evaporated molecules present in the vapor phase and consequently the vapor-phase density. The activity of the solvent and the corresponding osmotic coefficient are determined by the vapor density at different solute concentrations with respect to the reference vapor density of the pure solvent. With the extended Debye-Hückel equation for the activity coefficient along with the corresponding Gibbs-Duhem relation, the activity coefficients of the solutes are calculated by fitting the osmotic coefficients. A simple model based on the combination of Poisson processes and Maxwell-Boltzmann velocity distributions is introduced to interpret statistical phenomena observed during the simulations, which are related to evaporation and recondensation. This method is applied to aqueous dysprosium nitrate [Dy(NO 3 ) 3 ] solutions at different concentrations. The obtained densities of the liquid bulk and the osmotic and activity coefficients are in good agreement with the experimental results for concentrated and saturated solutions. Density profiles of the liquid-vapor interface at different concentrations provide detailed insight into the spatial distributions of all compounds.

CHARACTERIZATION OF ACTINIDES IN SIMULATED ALKALINE TANK WASTE SLUDGES AND LEACHATES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nash, Kenneth L.

In this project, both the fundamental chemistry of actinides in alkaline solutions (relevant to those present in Hanford-style waste storage tanks), and their dissolution from sludge simulants (and interactions with supernatants) have been investigated under representative sludge leaching procedures. The leaching protocols were designed to go beyond conventional alkaline sludge leaching limits, including the application of acidic leachants, oxidants and complexing agents. The simulant leaching studies confirm in most cases the basic premise that actinides will remain in the sludge during leaching with 2-3 M NaOH caustic leach solutions. However, they also confirm significant chances for increased mobility of actinidesmore » under oxidative leaching conditions. Thermodynamic data generated improves the general level of experiemental information available to predict actinide speciation in leach solutions. Additional information indicates that improved Al removal can be achieved with even dilute acid leaching and that acidic Al(NO3)3 solutions can be decontaminated of co-mobilized actinides using conventional separations methods. Both complexing agents and acidic leaching solutions have significant potential to improve the effectiveness of conventional alkaline leaching protocols. The prime objective of this program was to provide adequate insight into actinide behavior under these conditions to enable prudent decision making as tank waste treatment protocols develop.« less

High-Order Ca(II)-Chloro Complexes in Mixed CaCl2-LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations.

PubMed

Wang, Yu-Lin; Wang, Ying; Yi, Hai-Bo

2016-07-21

In this study, the structural characteristics of high-coordinated Ca-Cl complexes present in mixed CaCl2-LiCl aqueous solution were investigated using density functional theory (DFT) and molecular dynamics (MD) simulations. The DFT results show that [CaClx](2-x) (x = 4-6) clusters are quite unstable in the gas phase, but these clusters become metastable when hydration is considered. The MD simulations show that high-coordinated Ca-chloro complexes are possible transient species that exist for up to nanoseconds in concentrated (11.10 mol·kg(-1)) Cl(-) solution at 273 and 298 K. As the temperature increases to 423 K, these high-coordinated structures tend to disassociate and convert into smaller clusters and single free ions. The presence of high-order Ca-Cl species in concentrated LiCl solution can be attributed to their enhanced hydration shell and the inadequate hydration of ions. The probability of the [CaClx](2-x)aq (x = 4-6) species being present in concentrated LiCl solution decreases greatly with increasing temperature, which also indicates that the formation of the high-coordinated Ca-Cl structure is related to its hydration characteristics.

Effects of the Canopy and Flux Tube Anchoring on Evaporation Flow of a Solar Flare

NASA Astrophysics Data System (ADS)

Unverferth, John; Longcope, Dana

2018-06-01

Spectroscopic observations of flare ribbons typically show chromospheric evaporation flows, which are subsonic for their high temperatures. This contrasts with many numerical simulations where evaporation is typically supersonic. These simulations typically assume flow along a flux tube with a uniform cross-sectional area. A simple model of the magnetic canopy, however, includes many regions of low magnetic field strength, where flux tubes achieve local maxima in their cross-sectional area. These are analgous to a chamber in a flow tube. We find that one-third of all field lines in a model have some form of chamber through which evaporation flow must pass. Using a one-dimensional isothermal hydrodynamic code, we simulated supersonic flow through an assortment of chambers and found that a subset of solutions exhibit a stationary standing shock within the chamber. These shocked solutions have slower and denser upflows than a flow through a uniform tube would. We use our solution to construct synthetic spectral lines and find that the shocked solutions show higher emission and lower Doppler shifts. When these synthetic lines are combined into an ensemble representing a single canopy cell, the composite line appears slower, even subsonic, than expected due to the outsized contribution from shocked solutions.

Numerical simulation of the interaction of biological cells with an ice front during freezing

NASA Astrophysics Data System (ADS)

Carin, M.; Jaeger, M.

2001-12-01

The goal of this study is a better understanding of the interaction between cells and a solidification front during a cryopreservation process. This technique of freezing is commonly used to conserve biological material for long periods at low temperatures. However the biophysical mechanisms of cell injuries during freezing are difficult to understand because a cell is a very sophisticated microstructure interacting with its environment. We have developed a finite element model to simulate the response of cells to an advancing solidification front. A special front-tracking technique is used to compute the motion of the cell membrane and the ice front during freezing. The model solves the conductive heat transfer equation and the diffusion equation of a solute on a domain containing three phases: one or more cells, the extra-cellular solution and the growing ice. This solid phase growing from a binary salt solution rejects the solute in the liquid phase and increases the solute gradient around the cell. This induces the shrinkage of the cell. The model is used to simulate the engulfment of one cell modelling a red blood cell by an advancing solidification front initially planar or not is computed. We compare the incorporation of a cell with that of a solid particle.

A new and inexpensive non-bit-for-bit solution reproducibility test based on time step convergence (TSC1.0)

DOE PAGES

Wan, Hui; Zhang, Kai; Rasch, Philip J.; ...

2017-02-03

A test procedure is proposed for identifying numerically significant solution changes in evolution equations used in atmospheric models. The test issues a fail signal when any code modifications or computing environment changes lead to solution differences that exceed the known time step sensitivity of the reference model. Initial evidence is provided using the Community Atmosphere Model (CAM) version 5.3 that the proposed procedure can be used to distinguish rounding-level solution changes from impacts of compiler optimization or parameter perturbation, which are known to cause substantial differences in the simulated climate. The test is not exhaustive since it does not detect issues associatedmore » with diagnostic calculations that do not feedback to the model state variables. Nevertheless, it provides a practical and objective way to assess the significance of solution changes. The short simulation length implies low computational cost. The independence between ensemble members allows for parallel execution of all simulations, thus facilitating fast turnaround. The new method is simple to implement since it does not require any code modifications. We expect that the same methodology can be used for any geophysical model to which the concept of time step  convergence is applicable.« less

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

PubMed Central

Raschke, Tanya M.; Tsai, Jerry; Levitt, Michael

2001-01-01

The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 ± 6 cal/mol⋅Å2. The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol⋅Å2. Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology. PMID:11353861

Simulation of ground-water flow and solute transport in the Glen Canyon aquifer, East-Central Utah

USGS Publications Warehouse

Freethey, Geoffrey W.; Stolp, Bernard J.

2010-01-01

The extraction of methane from coal beds in the Ferron coal trend in central Utah started in the mid-1980s. Beginning in 1994, water from the extraction process was pressure injected into the Glen Canyon aquifer. The lateral extent of the aquifer that could be affected by injection is about 7,600 square miles. To address regional-scale effects of injection over a decadal time frame, a conceptual model of ground-water movement and transport of dissolved solids was formulated. A numerical model that incorporates aquifer concepts was then constructed and used to simulate injection.The Glen Canyon aquifer within the study area is conceptualized in two parts—an active area of ground-water flow and solute transport that exists between recharge areas in the San Rafael Swell and Desert, Waterpocket Fold, and Henry Mountains and discharge locations along the Muddy, Dirty Devil, San Rafael, and Green Rivers. An area of little or negligible ground-water flow exists north of Price, Utah, and beneath the Wasatch Plateau. Pressurized injection of coal-bed methane production water occurs in this area where dissolved-solids concentrations can be more than 100,000 milligrams per liter. Injection has the potential to increase hydrologic interaction with the active flow area, where dissolved-solids concentrations are generally less than 3,000 milligrams per liter.Pressurized injection of coal-bed methane production water in 1994 initiated a net addition of flow and mass of solutes into the Glen Canyon aquifer. To better understand the regional scale hydrologic interaction between the two areas of the Glen Canyon aquifer, pressurized injection was numerically simulated. Data constraints precluded development of a fully calibrated simulation; instead, an uncalibrated model was constructed that is a plausible representation of the conceptual flow and solute-transport processes. The amount of injected water over the 36-year simulation period is about 25,000 acre-feet. As a result, simulated water levels in the injection areas increased by 50 feet and dissolved-solids concentrations increased by 100 milligrams per liter or more. These increases are accrued into aquifer storage and do not extend to the rivers during the 36-year simulation period. The amount of change in simulated discharge and solute load to the rivers is less than the resolution accuracy of the numerical simulation and is interpreted as no significant change over the considered time period.

Rheology and hydrodynamic properties of Tolypocladium inflatum fermentation broth and its simulation.

PubMed

Benchapattarapong, N; Anderson, W A; Bai, F; Moo-Young, M

2005-07-01

A physico-chemical, two phase simulated pseudoplastic fermentation (SPF) broth was investigated in which Solka Floc cellulose fibre was used to simulate the filamentous biomass, and a mixture of 0.1% (w/v) carboxymethyl cellulose (CMC) and 0.15 M aqueous sodium chloride was used to simulate the liquid fraction of the fermentation broth. An investigation of the rheological behaviour and hydrodynamic properties of the SPF broth was carried out, and compared to both a fungal Tolypocladium inflatum fermentation broth and a CMC solution in a 50 L stirred tank bioreactor equipped with conventional Rushton turbines. The experimental data confirmed the ability of the two phase SPF broth to mimic both the T. inflatum broth bulk rheology as well as the mixing and mass transfer behaviour. In contrast, using a homogeneous CMC solution with a similar bulk rheology to simulate the fermentation resulted in a significant underestimation of the mass transfer and mixing times. The presence of the solid phase and its microstructure in the SPF broth appear to play a significant role in gas holdup and bubble size, thus leading to the different behaviours. The SPF broth seems to be a more accurate simulation fluid that can be used to predict the bioreactor mixing and mass transfer performance in filamentous fermentations, in comparison with CMC solutions used in some previous studies.

Simulation of cooperating robot manipulators on a mobile platform

NASA Technical Reports Server (NTRS)

Murphy, Steve H.; Wen, John T.; Saridis, George N.

1990-01-01

The dynamic equations of motion for two manipulators holding a common object on a freely moving mobile platform are developed. The full dynamic interactions from arms to platform and arm-tip to arm-tip are included in the formulation. The development of the closed chain dynamics allows for the use of any solution for the open topological tree of base and manipulator links. In particular, because the system has 18 degrees of freedom, recursive solutions for the dynamic simulation become more promising for efficient calculations of the motion. Simulation of the system is accomplished through a MATLAB program, and the response is visualized graphically using the SILMA Cimstation.

Molecular dynamics simulation study of the role of evenly spaced poly(ethylene oxide) tethers on the aggregation of C60 fullerenes in water.

PubMed

Bedrov, Dmitry; Smith, Grant D; Li, Liwei

2005-06-07

The aggregation behavior of C60 fullerenes and C60 fullerenes with six symmetrically tethered poly(ethylene oxide) oligomers [(PEO)-6-C60] in aqueous solutions has been studied using implicit solvent molecular dynamics simulations. Our simulations reveal that while the attraction between two (PEO)-6-C60 fullerenes in aqueous solution is stronger and longer range than that between two bare C60 fullerenes, the (PEO)-6-C60 fullerenes do not phase-separate in water but rather aggregate in chain-like clusters at concentrations where unmodified fullerenes completely phase-separate.

Numerical Simulation of the Flow over a Segment-Conical Body on the Basis of Reynolds Equations

NASA Astrophysics Data System (ADS)

Egorov, I. V.; Novikov, A. V.; Palchekovskaya, N. V.

2018-01-01

Numerical simulation was used to study the 3D supersonic flow over a segment-conical body similar in shape to the ExoMars space vehicle. The nonmonotone behavior of the normal force acting on the body placed in a supersonic gas flow was analyzed depending on the angle of attack. The simulation was based on the numerical solution of the unsteady Reynolds-averaged Navier-Stokes equations with a two-parameter differential turbulence model. The solution of the problem was obtained using the in-house solver HSFlow with an efficient parallel algorithm intended for multiprocessor super computers.

Toward Rigorous Parameterization of Underconstrained Neural Network Models Through Interactive Visualization and Steering of Connectivity Generation

PubMed Central

Nowke, Christian; Diaz-Pier, Sandra; Weyers, Benjamin; Hentschel, Bernd; Morrison, Abigail; Kuhlen, Torsten W.; Peyser, Alexander

2018-01-01

Simulation models in many scientific fields can have non-unique solutions or unique solutions which can be difficult to find. Moreover, in evolving systems, unique final state solutions can be reached by multiple different trajectories. Neuroscience is no exception. Often, neural network models are subject to parameter fitting to obtain desirable output comparable to experimental data. Parameter fitting without sufficient constraints and a systematic exploration of the possible solution space can lead to conclusions valid only around local minima or around non-minima. To address this issue, we have developed an interactive tool for visualizing and steering parameters in neural network simulation models. In this work, we focus particularly on connectivity generation, since finding suitable connectivity configurations for neural network models constitutes a complex parameter search scenario. The development of the tool has been guided by several use cases—the tool allows researchers to steer the parameters of the connectivity generation during the simulation, thus quickly growing networks composed of multiple populations with a targeted mean activity. The flexibility of the software allows scientists to explore other connectivity and neuron variables apart from the ones presented as use cases. With this tool, we enable an interactive exploration of parameter spaces and a better understanding of neural network models and grapple with the crucial problem of non-unique network solutions and trajectories. In addition, we observe a reduction in turn around times for the assessment of these models, due to interactive visualization while the simulation is computed. PMID:29937723

Thermodynamics of mixtures of patchy and spherical colloids of different sizes: A multi-body association theory with complete reference fluid information.

PubMed

Bansal, Artee; Valiya Parambathu, Arjun; Asthagiri, D; Cox, Kenneth R; Chapman, Walter G

2017-04-28

We present a theory to predict the structure and thermodynamics of mixtures of colloids of different diameters, building on our earlier work [A. Bansal et al., J. Chem. Phys. 145, 074904 (2016)] that considered mixtures with all particles constrained to have the same size. The patchy, solvent particles have short-range directional interactions, while the solute particles have short-range isotropic interactions. The hard-sphere mixture without any association site forms the reference fluid. An important ingredient within the multi-body association theory is the description of clustering of the reference solvent around the reference solute. Here we account for the physical, multi-body clusters of the reference solvent around the reference solute in terms of occupancy statistics in a defined observation volume. These occupancy probabilities are obtained from enhanced sampling simulations, but we also present statistical mechanical models to estimate these probabilities with limited simulation data. Relative to an approach that describes only up to three-body correlations in the reference, incorporating the complete reference information better predicts the bonding state and thermodynamics of the physical solute for a wide range of system conditions. Importantly, analysis of the residual chemical potential of the infinitely dilute solute from molecular simulation and theory shows that whereas the chemical potential is somewhat insensitive to the description of the structure of the reference fluid, the energetic and entropic contributions are not, with the results from the complete reference approach being in better agreement with particle simulations.

Thermodynamics of mixtures of patchy and spherical colloids of different sizes: A multi-body association theory with complete reference fluid information

NASA Astrophysics Data System (ADS)

Bansal, Artee; Valiya Parambathu, Arjun; Asthagiri, D.; Cox, Kenneth R.; Chapman, Walter G.

2017-04-01

We present a theory to predict the structure and thermodynamics of mixtures of colloids of different diameters, building on our earlier work [A. Bansal et al., J. Chem. Phys. 145, 074904 (2016)] that considered mixtures with all particles constrained to have the same size. The patchy, solvent particles have short-range directional interactions, while the solute particles have short-range isotropic interactions. The hard-sphere mixture without any association site forms the reference fluid. An important ingredient within the multi-body association theory is the description of clustering of the reference solvent around the reference solute. Here we account for the physical, multi-body clusters of the reference solvent around the reference solute in terms of occupancy statistics in a defined observation volume. These occupancy probabilities are obtained from enhanced sampling simulations, but we also present statistical mechanical models to estimate these probabilities with limited simulation data. Relative to an approach that describes only up to three-body correlations in the reference, incorporating the complete reference information better predicts the bonding state and thermodynamics of the physical solute for a wide range of system conditions. Importantly, analysis of the residual chemical potential of the infinitely dilute solute from molecular simulation and theory shows that whereas the chemical potential is somewhat insensitive to the description of the structure of the reference fluid, the energetic and entropic contributions are not, with the results from the complete reference approach being in better agreement with particle simulations.

Stochastic resource allocation in emergency departments with a multi-objective simulation optimization algorithm.

PubMed

Feng, Yen-Yi; Wu, I-Chin; Chen, Tzu-Li

2017-03-01

The number of emergency cases or emergency room visits rapidly increases annually, thus leading to an imbalance in supply and demand and to the long-term overcrowding of hospital emergency departments (EDs). However, current solutions to increase medical resources and improve the handling of patient needs are either impractical or infeasible in the Taiwanese environment. Therefore, EDs must optimize resource allocation given limited medical resources to minimize the average length of stay of patients and medical resource waste costs. This study constructs a multi-objective mathematical model for medical resource allocation in EDs in accordance with emergency flow or procedure. The proposed mathematical model is complex and difficult to solve because its performance value is stochastic; furthermore, the model considers both objectives simultaneously. Thus, this study develops a multi-objective simulation optimization algorithm by integrating a non-dominated sorting genetic algorithm II (NSGA II) with multi-objective computing budget allocation (MOCBA) to address the challenges of multi-objective medical resource allocation. NSGA II is used to investigate plausible solutions for medical resource allocation, and MOCBA identifies effective sets of feasible Pareto (non-dominated) medical resource allocation solutions in addition to effectively allocating simulation or computation budgets. The discrete event simulation model of ED flow is inspired by a Taiwan hospital case and is constructed to estimate the expected performance values of each medical allocation solution as obtained through NSGA II. Finally, computational experiments are performed to verify the effectiveness and performance of the integrated NSGA II and MOCBA method, as well as to derive non-dominated medical resource allocation solutions from the algorithms.

Exploring the feasibility of focusing CW light through a scattering medium into closely spaced twin peaks via numerical solutions of Maxwell’s equations

NASA Astrophysics Data System (ADS)

Tseng, Snow H.; Chang, Shih-Hui

2018-04-01

Here we present a numerical simulation to analyze the effect of scattering on focusing light into closely-spaced twin peaks. The pseudospectral time-domain (PSTD) is implemented to model continuous-wave (CW) light propagation through a scattering medium. Simulations show that CW light can propagate through a scattering medium and focus into closely-spaced twin peaks. CW light of various wavelengths focusing into twin peaks with sub-diffraction spacing is simulated. In advance, light propagation through scattering media of various number densities is simulated to decipher the dependence of CW light focusing phenomenon on the scattering medium. The reported simulations demonstrate the feasibility of focusing CW light into twin peaks with sub-diffraction dimensions. More importantly, based upon numerical solutions of Maxwell’s equations, research findings show that the sub-diffraction focusing phenomenon can be achieved with scarce or densely-packed scattering media.

Implementing Parquet equations using HPX

NASA Astrophysics Data System (ADS)

Kellar, Samuel; Wagle, Bibek; Yang, Shuxiang; Tam, Ka-Ming; Kaiser, Hartmut; Moreno, Juana; Jarrell, Mark

A new C++ runtime system (HPX) enables simulations of complex systems to run more efficiently on parallel and heterogeneous systems. This increased efficiency allows for solutions to larger simulations of the parquet approximation for a system with impurities. The relevancy of the parquet equations depends upon the ability to solve systems which require long runs and large amounts of memory. These limitations, in addition to numerical complications arising from stability of the solutions, necessitate running on large distributed systems. As the computational resources trend towards the exascale and the limitations arising from computational resources vanish efficiency of large scale simulations becomes a focus. HPX facilitates efficient simulations through intelligent overlapping of computation and communication. Simulations such as the parquet equations which require the transfer of large amounts of data should benefit from HPX implementations. Supported by the the NSF EPSCoR Cooperative Agreement No. EPS-1003897 with additional support from the Louisiana Board of Regents.

Simulating Porous Magnetite Layer Deposited on Alloy 690TT Steam Generator Tubes

PubMed Central

Jeon, Soon-Hyeok; Son, Yeong-Ho; Choi, Won-Ik; Song, Geun Dong; Hur, Do Haeng

2018-01-01

In nuclear power plants, the main corrosion product that is deposited on the outside of steam generator tubes is porous magnetite. The objective of this study was to simulate porous magnetite that is deposited on thermally treated (TT) Alloy 690 steam generator tubes. A magnetite layer was electrodeposited on an Alloy 690TT substrate in an Fe(III)-triethanolamine solution. After electrodeposition, the dense magnetite layer was immersed to simulate porous magnetite deposits in alkaline solution for 50 days at room temperature. The dense morphology of the magnetite layer was changed to a porous structure by reductive dissolution reaction. The simulated porous magnetite layer was compared with flakes of steam generator tubes, which were collected from the secondary water system of a real nuclear power plant during sludge lancing. Possible nuclear research applications using simulated porous magnetite specimens are also proposed. PMID:29301316

Efficient field-theoretic simulation of polymer solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villet, Michael C.; Fredrickson, Glenn H., E-mail: ghf@mrl.ucsb.edu; Department of Materials, University of California, Santa Barbara, California 93106

2014-12-14

We present several developments that facilitate the efficient field-theoretic simulation of polymers by complex Langevin sampling. A regularization scheme using finite Gaussian excluded volume interactions is used to derive a polymer solution model that appears free of ultraviolet divergences and hence is well-suited for lattice-discretized field theoretic simulation. We show that such models can exhibit ultraviolet sensitivity, a numerical pathology that dramatically increases sampling error in the continuum lattice limit, and further show that this pathology can be eliminated by appropriate model reformulation by variable transformation. We present an exponential time differencing algorithm for integrating complex Langevin equations for fieldmore » theoretic simulation, and show that the algorithm exhibits excellent accuracy and stability properties for our regularized polymer model. These developments collectively enable substantially more efficient field-theoretic simulation of polymers, and illustrate the importance of simultaneously addressing analytical and numerical pathologies when implementing such computations.« less

Size effects of pore density and solute size on water osmosis through nanoporous membrane.

PubMed

Zhao, Kuiwen; Wu, Huiying

2012-11-15

Understanding the behavior of osmotic transport across nanoporous membranes at molecular level is critical to their design and applications, and it is also beneficial to the comprehension of the mechanism of biological transmembrane transport processes. Pore density is an important parameter for nanoporous membranes. To better understand the influence of pore density on osmotic transport, we have performed systematic molecular dynamics simulations on water osmosis across nanoporous membranes with different pore densities (i.e., number of pores per unit area of membrane). The simulation results reveal that significant size effects occur when the pore density is so high that the center-to-center distance between neighboring nanopores is comparable to the solute size. The size effects are independent of the pore diameter and solute concentration. A simple quantitative correlation between pore density, solute size, and osmotic flux has been established. The results are excellently consistent with the theoretical predictions. It is also shown that solute hydration plays an important role in real osmotic processes. Solute hydration strengthens the size effects of pore density on osmotic processes due to the enlarged effective solute size induced by hydration. The influence of pore density, solute size, and solute hydration on water osmosis through nanoporous membranes can be introduced to eliminate the deviations of real osmotic processes from ideal behavior.

An analytic, approximate method for modeling steady, three-dimensional flow to partially penetrating wells

NASA Astrophysics Data System (ADS)

Bakker, Mark

2001-05-01

An analytic, approximate solution is derived for the modeling of three-dimensional flow to partially penetrating wells. The solution is written in terms of a correction on the solution for a fully penetrating well and is obtained by dividing the aquifer up, locally, in a number of aquifer layers. The resulting system of differential equations is solved by application of the theory for multiaquifer flow. The presented approach has three major benefits. First, the solution may be applied to any groundwater model that can simulate flow to a fully penetrating well; the solution may be superimposed onto the solution for the fully penetrating well to simulate the local three-dimensional drawdown and flow field. Second, the approach is applicable to isotropic, anisotropic, and stratified aquifers and to both confined and unconfined flow. Third, the solution extends over a small area around the well only; outside this area the three-dimensional effect of the partially penetrating well is negligible, and no correction to the fully penetrating well is needed. A number of comparisons are made to existing three-dimensional, analytic solutions, including radial confined and unconfined flow and a well in a uniform flow field. It is shown that a subdivision in three layers is accurate for many practical cases; very accurate solutions are obtained with more layers.

Three-dimensional benchmark for variable-density flow and transport simulation: matching semi-analytic stability modes for steady unstable convection in an inclined porous box

USGS Publications Warehouse

Voss, Clifford I.; Simmons, Craig T.; Robinson, Neville I.

2010-01-01

This benchmark for three-dimensional (3D) numerical simulators of variable-density groundwater flow and solute or energy transport consists of matching simulation results with the semi-analytical solution for the transition from one steady-state convective mode to another in a porous box. Previous experimental and analytical studies of natural convective flow in an inclined porous layer have shown that there are a variety of convective modes possible depending on system parameters, geometry and inclination. In particular, there is a well-defined transition from the helicoidal mode consisting of downslope longitudinal rolls superimposed upon an upslope unicellular roll to a mode consisting of purely an upslope unicellular roll. Three-dimensional benchmarks for variable-density simulators are currently (2009) lacking and comparison of simulation results with this transition locus provides an unambiguous means to test the ability of such simulators to represent steady-state unstable 3D variable-density physics.

Numerical investigation of coupled density-driven flow and hydrogeochemical processes below playas

NASA Astrophysics Data System (ADS)

Hamann, Enrico; Post, Vincent; Kohfahl, Claus; Prommer, Henning; Simmons, Craig T.

2015-11-01

Numerical modeling approaches with varying complexity were explored to investigate coupled groundwater flow and geochemical processes in saline basins. Long-term model simulations of a playa system gain insights into the complex feedback mechanisms between density-driven flow and the spatiotemporal patterns of precipitating evaporites and evolving brines. Using a reactive multicomponent transport model approach, the simulations reproduced, for the first time in a numerical study, the evaporite precipitation sequences frequently observed in saline basins ("bull's eyes"). Playa-specific flow, evapoconcentration, and chemical divides were found to be the primary controls for the location of evaporites formed, and the resulting brine chemistry. Comparative simulations with the computationally far less demanding surrogate single-species transport models showed that these were still able to replicate the major flow patterns obtained by the more complex reactive transport simulations. However, the simulated degree of salinization was clearly lower than in reactive multicomponent transport simulations. For example, in the late stages of the simulations, when the brine becomes halite-saturated, the nonreactive simulation overestimated the solute mass by almost 20%. The simulations highlight the importance of the consideration of reactive transport processes for understanding and quantifying geochemical patterns, concentrations of individual dissolved solutes, and evaporite evolution.

Algebraic Turbulence-Chemistry Interaction Model

NASA Technical Reports Server (NTRS)

Norris, Andrew T.

2012-01-01

The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

Permeability Sensitivity Functions and Rapid Simulation of Hydraulic-Testing Measurements Using Perturbation Theory

NASA Astrophysics Data System (ADS)

Escobar Gómez, J. D.; Torres-Verdín, C.

2018-03-01

Single-well pressure-diffusion simulators enable improved quantitative understanding of hydraulic-testing measurements in the presence of arbitrary spatial variations of rock properties. Simulators of this type implement robust numerical algorithms which are often computationally expensive, thereby making the solution of the forward modeling problem onerous and inefficient. We introduce a time-domain perturbation theory for anisotropic permeable media to efficiently and accurately approximate the transient pressure response of spatially complex aquifers. Although theoretically valid for any spatially dependent rock/fluid property, our single-phase flow study emphasizes arbitrary spatial variations of permeability and anisotropy, which constitute key objectives of hydraulic-testing operations. Contrary to time-honored techniques, the perturbation method invokes pressure-flow deconvolution to compute the background medium's permeability sensitivity function (PSF) with a single numerical simulation run. Subsequently, the first-order term of the perturbed solution is obtained by solving an integral equation that weighs the spatial variations of permeability with the spatial-dependent and time-dependent PSF. Finally, discrete convolution transforms the constant-flow approximation to arbitrary multirate conditions. Multidimensional numerical simulation studies for a wide range of single-well field conditions indicate that perturbed solutions can be computed in less than a few CPU seconds with relative errors in pressure of <5%, corresponding to perturbations in background permeability of up to two orders of magnitude. Our work confirms that the proposed joint perturbation-convolution (JPC) method is an efficient alternative to analytical and numerical solutions for accurate modeling of pressure-diffusion phenomena induced by Neumann or Dirichlet boundary conditions.

Real-Time Wing-Vortex and Pressure Distribution Estimation on Wings Via Displacements and Strains in Unsteady and Transitional Flight Conditions

DTIC Science & Technology

2016-09-07

approach in co simulation with fluid-dynamics solvers is used. An original variational formulation is developed for the inverse problem of...by the inverse solution meshing. The same approach is used to map the structural and fluid interface kinematics and loads during the fluid structure...co-simulation. The inverse analysis is verified by reconstructing the deformed solution obtained with a corresponding direct formulation, based on

A review of recent advances in the spherical harmonics expansion method for semiconductor device simulation.

PubMed

Rupp, K; Jungemann, C; Hong, S-M; Bina, M; Grasser, T; Jüngel, A

The Boltzmann transport equation is commonly considered to be the best semi-classical description of carrier transport in semiconductors, providing precise information about the distribution of carriers with respect to time (one dimension), location (three dimensions), and momentum (three dimensions). However, numerical solutions for the seven-dimensional carrier distribution functions are very demanding. The most common solution approach is the stochastic Monte Carlo method, because the gigabytes of memory requirements of deterministic direct solution approaches has not been available until recently. As a remedy, the higher accuracy provided by solutions of the Boltzmann transport equation is often exchanged for lower computational expense by using simpler models based on macroscopic quantities such as carrier density and mean carrier velocity. Recent developments for the deterministic spherical harmonics expansion method have reduced the computational cost for solving the Boltzmann transport equation, enabling the computation of carrier distribution functions even for spatially three-dimensional device simulations within minutes to hours. We summarize recent progress for the spherical harmonics expansion method and show that small currents, reasonable execution times, and rare events such as low-frequency noise, which are all hard or even impossible to simulate with the established Monte Carlo method, can be handled in a straight-forward manner. The applicability of the method for important practical applications is demonstrated for noise simulation, small-signal analysis, hot-carrier degradation, and avalanche breakdown.

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field

PubMed Central

Stark, Austin C.; Andrews, Casey T.

2013-01-01

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods – especially with regard to using them to model, for example, intracellular environments – is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields. PMID:24223529

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

PubMed

Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

2013-09-10

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

Parsing partial molar volumes of small molecules: a molecular dynamics study.

PubMed

Patel, Nisha; Dubins, David N; Pomès, Régis; Chalikian, Tigran V

2011-04-28

We used molecular dynamics (MD) simulations in conjunction with the Kirkwood-Buff theory to compute the partial molar volumes for a number of small solutes of various chemical natures. We repeated our computations using modified pair potentials, first, in the absence of the Coulombic term and, second, in the absence of the Coulombic and the attractive Lennard-Jones terms. Comparison of our results with experimental data and the volumetric results of Monte Carlo simulation with hard sphere potentials and scaled particle theory-based computations led us to conclude that, for small solutes, the partial molar volume computed with the Lennard-Jones potential in the absence of the Coulombic term nearly coincides with the cavity volume. On the other hand, MD simulations carried out with the pair interaction potentials containing only the repulsive Lennard-Jones term produce unrealistically large partial molar volumes of solutes that are close to their excluded volumes. Our simulation results are in good agreement with the reported schemes for parsing partial molar volume data on small solutes. In particular, our determined interaction volumes() and the thickness of the thermal volume for individual compounds are in good agreement with empirical estimates. This work is the first computational study that supports and lends credence to the practical algorithms of parsing partial molar volume data that are currently in use for molecular interpretations of volumetric data.

Validation a solid-phase extraction-HPLC method for determining the migration behaviour of five aromatic amines from packaging bags into seafood simulants.

PubMed

OuYang, Xiao-Kun; Luo, Yu-Yang; Wang, Yang-Guang; Yang, Li-Ye

2014-01-01

The simultaneous determination of five aromatic amines and their potential migration from packaging bags into seafood simulants were investigated. A validated HPLC method was developed for the separation and qualification of five aromatic amines in seafood simulants. By combining solid-phase extraction (SPE), these amines were efficiently separated on a Halo C18 column (150 × 4.6 mm i.d., 2.7 μm, particle size) using a mobile phase of methanol/phosphate buffer solution (5 mmol l(-1), pH 6.9) with gradient elution. The linear range was 0.1-10.0 mg l(-1); the absolute recoveries ranged from 85.3% to 98.4%; and the limits of detection of the five aromatic amines were between 0.015 and 0.08 mg l(-1). In this work the migration profile of aromatic amines from black plastic bags was investigated at temperatures of 4°C with water, 3% acetic acid solution, 10% ethanol solution and 50% ethanol solution as seafood simulants, respectively. The migration of the five aromatic amines under different conditions showed that residual o-methoxyaniline, p-chloroaniline, aniline and 2,6-dimethylaniline leaching from black plastic bags increased with incubation time. No detectable 3,3´-dimethylbenzidine was found to leach from the bags.

Simulated water-level and water-quality changes in the bolson-fill aquifer, Post Headquarters area, White Sands Missile Range, New Mexico

USGS Publications Warehouse

Risser, D.W.

1988-01-01

The quantity of freshwater available in the Post Headquarters well field, White Sand Missile Range, New Mexico, is limited and its quality is threatened by saltwater enroachment. A three-dimensional, finite-difference, groundwater flow model and a cross-sectional, density-dependent solute-transport model were constructed to simulate possible future water level declines and water quality changes in the Post Headquarters well field. A six-layer flow model was constructed using hydraulic-conductivity values in the upper 600 ft of saturated aquifer ranging from 0.1 to 10 ft/day, specific yield of 0.15, and average recharge of about 1,590 acre-ft/yr. Water levels simulated by the model closely matched measured water levels for 1948-82. Possible future water level changes for 1983-2017 were simulated using rates of groundwater withdrawal of 1,033 and 2 ,066 acre-ft/year and wastewater return flow of 0 or 30% of the groundwater withdrawal rate. The cross-sectional solute-transport model indicated that the freshwater zone is about 1,500 to 2,000 ft thick beneath the well field. Transient simulations show that solutes probably will move laterally toward the well field rather than from beneath the well field. (USGS)

Temperature and solute-transport simulation in streamflow using a Lagrangian reference frame

USGS Publications Warehouse

Jobson, Harvey E.

1980-01-01

A computer program for simulating one-dimensional, unsteady temperature and solute transport in a river has been developed and documented for general use. The solution approach to the convective-diffusion equation uses a moving reference frame (Lagrangian) which greatly simplifies the mathematics of the solution procedure and dramatically reduces errors caused by numerical dispersion. The model documentation is presented as a series of four programs of increasing complexity. The conservative transport model can be used to route a single conservative substance. The simplified temperature model is used to predict water temperature in rivers when only temperature and windspeed data are available. The complete temperature model is highly accurate but requires rather complete meteorological data. Finally, the 10-parameter model can be used to route as many as 10 interacting constituents through a river reach. (USGS)

CFD study of mixing miscible liquid with high viscosity difference in a stirred tank

NASA Astrophysics Data System (ADS)

Madhania, S.; Cahyani, A. B.; Nurtono, T.; Muharam, Y.; Winardi, S.; Purwanto, W. W.

2018-03-01

The mixing process of miscible liquids with high viscosity difference is crucial role even though the solution mutually dissolved. This paper describes the mixing behaviour of the water-molasses system in a conical-bottomed cylindrical stirred tank (D = 0.28 m and H = 0.395 m) equipped with a side-entry Marine propeller (d = 0.036 m) under the turbulence regime using a three-dimensional and transient CFD-simulation. The objective of this work is to compare the solution strategies was applied in the computational analysis to capture the detail phenomena of mixing two miscible liquid with high viscosity difference. Four solution strategies that have been used are the RANS Standards k-ε (SKE) model as the turbulence model coupled with the Multiple Reference Frame (MRF) method for impeller motion, the RANS Realizable k-ε (RKE) combine with the MRF, the Large Eddy Simulation (LES) coupled with the Sliding Mesh (SM) method and the LES-MRF combination. The transient calculations were conducted with Ansys Fluent 17.1 version. The mixing behaviour and the propeller characteristic are to be compared and discussed in this work. The simulation results show the differences of flow pattern and the molasses distribution profile for every solution strategy. The variation of the flow pattern which happened in each solution strategy showing an instability of the mixing process in stirred tank. The LES-SM strategy shows the realistic direction of flow than another solution strategies.

Synchrony, waves and ripple in spatially coupled Kuramoto oscillators with Mexican hat connectivity.

PubMed

Heitmann, Stewart; Ermentrout, G Bard

2015-06-01

Spatiotemporal waves of synchronized activity are known to arise in oscillatory neural networks with lateral inhibitory coupling. How such patterns respond to dynamic changes in coupling strength is largely unexplored. The present study uses analysis and simulation to investigate the evolution of wave patterns when the strength of lateral inhibition is varied dynamically. Neural synchronization was modeled by a spatial ring of Kuramoto oscillators with Mexican hat lateral coupling. Broad bands of coexisting stable wave solutions were observed at all levels of inhibition. The stability of these waves was formally analyzed in both the infinite ring and the finite ring. The broad range of multi-stability predicted hysteresis in transitions between neighboring wave solutions when inhibition is slowly varied. Numerical simulation confirmed the predicted transitions when inhibition was ramped down from a high initial value. However, non-wave solutions emerged from the uniform solution when inhibition was ramped upward from zero. These solutions correspond to spatially periodic deviations of phase that we call ripple states. Numerical continuation showed that stable ripple states emerge from synchrony via a supercritical pitchfork bifurcation. The normal form of this bifurcation was derived analytically, and its predictions compared against the numerical results. Ripple states were also found to bifurcate from wave solutions, but these were locally unstable. Simulation also confirmed the existence of hysteresis and ripple states in two spatial dimensions. Our findings show that spatial synchronization patterns can remain structurally stable despite substantial changes in network connectivity.

Terahertz absorption of lysozyme in solution

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2017-08-01

Absorption of radiation by solution is described by its frequency-dependent dielectric function and can be viewed as a specific application of the dielectric theory of solutions. For ideal solutions, the dielectric boundary-value problem separates the polar response into the polarization of the void in the liquid, created by the solute, and the response of the solute dipole. In the case of a protein as a solute, protein nuclear dynamics do not project on significant fluctuations of the dipole moment in the terahertz domain of frequencies and the protein dipole can be viewed as dynamically frozen. Absorption of radiation then reflects the interfacial polarization. Here we apply an analytical theory and computer simulations to absorption of radiation by an ideal solution of lysozyme. Comparison with the experiment shows that Maxwell electrostatics fails to describe the polarization of the protein-water interface and the "Lorentz void," which does not anticipate polarization of the interface by the external field (no surface charges), better represents the data. An analytical theory for the slope of the solution absorption against the volume fraction of the solute is formulated in terms of the cavity field response function. It is calculated from molecular dynamics simulations in good agreement with the experiment. The protein hydration shell emerges as a separate sub-ensemble, which, collectively, is not described by the standard electrostatics of dielectrics.

Simulation of a Wall-Bounded Flow using a Hybrid LES/RAS Approach with Turbulence Recycling

NASA Technical Reports Server (NTRS)

Quinlan, Jesse R.; Mcdaniel, James; Baurle, Robert A.

2012-01-01

Simulations of a supersonic recessed-cavity flow are performed using a hybrid large-eddy/ Reynolds-averaged simulation approach utilizing an inflow turbulence recycling procedure and hybridized inviscid flux scheme. Calorically perfect air enters the three-dimensional domain at a free stream Mach number of 2.92. Simulations are performed to assess grid sensitivity of the solution, efficacy of the turbulence recycling, and effect of the shock sensor used with the hybridized inviscid flux scheme. Analysis of the turbulent boundary layer upstream of the rearward-facing step for each case indicates excellent agreement with theoretical predictions. Mean velocity and pressure results are compared to Reynolds-averaged simulations and experimental data for each case, and these comparisons indicate good agreement on the finest grid. Simulations are repeated on a coarsened grid, and results indicate strong grid density sensitivity. The effect of turbulence recycling on the solution is illustrated by performing coarse grid simulations with and without inflow turbulence recycling. Two shock sensors, one of Ducros and one of Larsson, are assessed for use with the hybridized inviscid flux reconstruction scheme.

Assessment of Flood Mitigation Solutions Using a Hydrological Model and Refined 2D Hydrodynamic Simulations

NASA Astrophysics Data System (ADS)

Khuat Duy, B.; Archambeau, P.; Dewals, B. J.; Erpicum, S.; Pirotton, M.

2009-04-01

Following recurrent inundation problems on the Berwinne catchment, in Belgium, a combined hydrologic and hydrodynamic study has been carried out in order to find adequate solutions for the floods mitigation. Thanks to detailed 2D simulations, the effectiveness of the solutions can be assessed not only in terms of discharge and height reductions in the river, but also with other aspects such as the inundated surfaces reduction and the decrease of inundated buildings and roads. The study is carried out in successive phases. First, the hydrological runoffs are generated using a physically based and spatially distributed multi-layer model solving depth-integrated equations for overland flow, subsurface flow and baseflow. Real floods events are simulated using rainfall series collected at 8 stations (over 20 years of available data). The hydrological inputs are routed through the river network (and through the sewage network if relevant) with the 1D component of the modelling system, which solves the Saint-Venant equations for both free-surface and pressurized flows in a unified way. On the main part of the river, the measured river cross-sections are included in the modelling, and existing structures along the river (such as bridges, sluices or pipes) are modelled explicitely with specific cross sections. Two gauging stations with over 15 years of continuous measurements allow the calibration of both the hydrologic and hydrodynamic models. Second, the flood mitigation solutions are tested in the simulations in the case of an extreme flooding event, and their effects are assessed using detailed 2D simulations on a few selected sensitive areas. The digital elevation model comes from an airborne laser survey with a spatial resolution of 1 point per square metre and is completed in the river bed with a bathymetry interpolated from cross-section data. The upstream discharge is extracted from the 1D simulation for the selected rainfall event. The study carried out with this methodology allowed to assess the suggested solutions with multiple effectiveness criteria and therefore constitutes a very useful support for decision makers.

Quantification of solute entry into cochlear perilymph through the round window membrane.

PubMed

Salt, A N; Ma, Y

2001-04-01

The administration of drugs to the inner ear via the round window membrane is becoming more widely used for both clinical and experimental purposes. The actual drug levels achieved in different regions of the inner ear by this method have not been established. The present study has made use of simulations of solute movements in the cochlear fluids to describe the distribution of a marker solute in the guinea pig cochlear fluid spaces. Simulation parameters were derived from experimental measurements using a marker ion, trimethylphenylammonium (TMPA). The distribution of this ion in the cochlea was monitored without volume disturbance using TMPA-selective microelectrodes sealed into the first and second turns of scala tympani (ST). TMPA was applied to perilymph by irrigation of the intact round window membrane with 2 mM solution. At the end of a 90 min application period, TMPA in the first turn, 1.4 mm from the base of ST, reached an average concentration of 330 microM (standard deviation (S.D.) 147 microM, n = 8). TMPA in the second turn, 7.5 mm from the base of ST reached a concentration of 15 microM (S.D. 33 microM, n = 5). The measured time courses of TMPA concentration change were interpreted using the Washington University Cochlear Fluids Simulator (V 1.4), a public-domain program available on the internet at http ://oto.wustl.edu/cochlea/. Simulations with parameters producing concentration time courses comparable to those measured were: (1) round window permeability: 1.9 x 10(-80 cm/s; (2) ST clearance half-time: 60 min; (3) longitudinal perilymph flow rate: 4.4 nl/min, directed from base to apex. Solute concentrations in apical regions of the cochlea were found to be determined primarily by the rate at which the solute diffuses, balanced by the rate of clearance of the solute from perilymph. Longitudinal perilymph flow was not an important factor in solute distribution unless the bony otic capsule was perforated, which rapidly caused substantial changes to solute distribution. This study demonstrates the basic processes by which substances are distributed in the cochlea and provides a foundation to understand how other applied substances will be distributed in the ear.

CFD Code Validation of Wall Heat Fluxes for a G02/GH2 Single Element Combustor

NASA Technical Reports Server (NTRS)

Lin, Jeff; West, Jeff S.; Williams, Robert W.; Tucker, P. Kevin

2005-01-01

This paper puts forth the case for the need for improved injector design tools to meet NASA s Vision for Space Exploration goals. Requirements for this improved tool are outlined and discussed. The potential for Computational Fluid Dynamics (CFD) to meet these requirements is noted along with its current shortcomings, especially relative to demonstrated solution accuracy. The concept of verification and validation is introduced as the primary process for building and quantifying the confidence necessary for CFD to be useful as an injector design tool. The verification and validation process is considered in the context of the Marshall Space Flight Center (MSFC) Combustion Devices CFD Simulation Capability Roadmap via the Simulation Readiness Level (SRL) concept. The portion of the validation process which demonstrates the ability of a CFD code to simulate heat fluxes to a rocket engine combustor wall is the focus of the current effort. The FDNS and Loci-CHEM codes are used to simulate a shear coaxial single element G02/GH2 injector experiment. The experiment was conducted a t a chamber pressure of 750 psia using hot propellants from preburners. A measured wall temperature profile is used as a boundary condition to facilitate the calculations. Converged solutions, obtained from both codes by using wall functions with the K-E turbulence model and integrating to the wall using Mentor s baseline turbulence model, are compared to the experimental data. The initial solutions from both codes revealed significant issues with the wall function implementation associated with the recirculation zone between the shear coaxial jet and the chamber wall. The FDNS solution with a corrected implementation shows marked improvement in overall character and level of comparison to the data. With the FDNS code, integrating to the wall with Mentor s baseline turbulence model actually produce a degraded solution when compared to the wall function solution with the K--E model. The Loci-CHEM solution, produced by integrating to the wall with Mentor s baseline turbulence model, matches both the heat flux rise rate in the near injector region and the peak heat flux level very well. However, it moderately over predicts the heat fluxes downstream of the reattachment point. The Loci-CHEM solution achieved by integrating to the wall with Mentor s baseline turbulence model was clearly superior to the other solutions produced in this effort.

The Diffusion Simulator - Teaching Geomorphic and Geologic Problems Visually.

ERIC Educational Resources Information Center

Gilbert, R.

1979-01-01

Describes a simple hydraulic simulator based on more complex models long used by engineers to develop approximate solutions. It allows students to visualize non-steady transfer, to apply a model to solve a problem, and to compare experimentally simulated information with calculated values. (Author/MA)

Electrochemical studies on zirconium and its biocompatible alloys Ti-50Zr at.% and Zr-2.5Nb wt.% in simulated physiologic media.

PubMed

Oliveira, Nilson T C; Biaggio, Sonia R; Rocha-Filho, Romeu C; Bocchi, Nerilso

2005-09-01

Different electrochemical studies were carried out for Zr and its biocompatible alloys Ti-50Zr at.% and Zr-2.5Nb wt.% in solutions simulating physiologic media, Ringer and PBS (phosphate buffered saline) solutions. The results from rest-potential measurements showed that the three materials are spontaneously passivated in both solutions and that the Ti-50Zr alloy has the greatest tendency for spontaneous oxide formation. Some corrosion parameters (such as the pitting and repassivation potentials) were obtained via cyclic voltammetry in both solutions, revealing that the Ti-50Zr has the best corrosion protection while Zr has the worst. On the other hand, the pre-anodization (up to 8 V vs. SCE) of the alloys in a 0.15 mol/L Na2SO4 solution led to a significant improvement in their protection against pitting corrosion when exposed to the Ringer solution. Elemental analyses by EDX showed that during pitting corrosion, there is no preferential corrosion of any of the alloying elements (Zr, Ti, Nb). Copyright (c) 2005 Wiley Periodicals, Inc.

Structure and anomalous solubility for hard spheres in an associating lattice gas model.

PubMed

Szortyka, Marcia M; Girardi, Mauricio; Henriques, Vera B; Barbosa, Marcia C

2012-08-14

In this paper we investigate the solubility of a hard-sphere gas in a solvent modeled as an associating lattice gas. The solution phase diagram for solute at 5% is compared with the phase diagram of the original solute free model. Model properties are investigated both through Monte Carlo simulations and a cluster approximation. The model solubility is computed via simulations and is shown to exhibit a minimum as a function of temperature. The line of minimum solubility (TmS) coincides with the line of maximum density (TMD) for different solvent chemical potentials, in accordance with the literature on continuous realistic models and on the "cavity" picture.

PDE Nozzle Optimization Using a Genetic Algorithm

NASA Technical Reports Server (NTRS)

Billings, Dana; Turner, James E. (Technical Monitor)

2000-01-01

Genetic algorithms, which simulate evolution in natural systems, have been used to find solutions to optimization problems that seem intractable to standard approaches. In this study, the feasibility of using a GA to find an optimum, fixed profile nozzle for a pulse detonation engine (PDE) is demonstrated. The objective was to maximize impulse during the detonation wave passage and blow-down phases of operation. Impulse of each profile variant was obtained by using the CFD code Mozart/2.0 to simulate the transient flow. After 7 generations, the method has identified a nozzle profile that certainly is a candidate for optimum solution. The constraints on the generality of this possible solution remain to be clarified.

Chemical potentials of alkaline earth metal halide aqueous electrolytes and solubility of their hydrates by molecular simulation: Application to CaCl2, antarcticite, and sinjarite

NASA Astrophysics Data System (ADS)

Moučka, Filip; Kolafa, Jiří; Lísal, Martin; Smith, William R.

2018-06-01

We present a molecular-level simulation study of CaCl2 in water and crystalline hydrates formed by CaCl2 at ambient (298.15 K, 1 bar) conditions and at a high-temperature high-pressure state (365 K, 275 bars) typical of hydraulic fracturing conditions in natural-gas extraction, at which experimental properties are poorly characterized. We focus on simulations of chemical potentials in both solution and crystalline phases and on the salt solubility, the first time to our knowledge that such properties have been investigated by molecular simulation for divalent aqueous electrolytes. We first extend our osmotic ensemble Monte Carlo simulation technique [F. Moučka et al., J. Phys. Chem. B 115, 7849-7861 (2011)] to such solutions. We then describe and apply new methodology for the simulation of the chemical potentials of the experimentally observed crystalline hydrates at ambient conditions (antarcticite, CaCl2.6H2O) and at high-temperature conditions (sinjarite, CaCl2.2H2O). We implement our methodologies using for both phases the CaCl2 transferable force field (FF) based on simple point charge-extended water developed by Mamatkulov et al. [J. Chem. Phys. 138, 024505 (2013)], based on training sets involving single-ion and ion-pair low-concentration solution properties at near-ambient conditions. We find that simulations of the solution chemical potentials at high concentrations are somewhat problematic, exhibiting densities diverging from experimental values and accompanied by dramatically decreasing particle mobility. For the solid phases, the sinjarite crystalline lattice differs from experiment only slightly, whereas the simulations of antarcticite completely fail, due to instability of the crystalline lattice. The FF thus only successfully yields the sinjarite solubility, but its value m = 8.0(7) mol kg-1H2O lies well below the experimentally observed solubility range at 1 bar pressure of (12m, 15m) in the temperature interval (320 K, 400 K). We conclude that the used FF does not provide a good description of the experimental properties considered and suggest that improvement must take into account the crystalline properties.

Chemical potentials of alkaline earth metal halide aqueous electrolytes and solubility of their hydrates by molecular simulation: Application to CaCl2, antarcticite, and sinjarite.

PubMed

Moučka, Filip; Kolafa, Jiří; Lísal, Martin; Smith, William R

2018-06-14

We present a molecular-level simulation study of CaCl 2 in water and crystalline hydrates formed by CaCl 2 at ambient (298.15 K, 1 bar) conditions and at a high-temperature high-pressure state (365 K, 275 bars) typical of hydraulic fracturing conditions in natural-gas extraction, at which experimental properties are poorly characterized. We focus on simulations of chemical potentials in both solution and crystalline phases and on the salt solubility, the first time to our knowledge that such properties have been investigated by molecular simulation for divalent aqueous electrolytes. We first extend our osmotic ensemble Monte Carlo simulation technique [F. Moučka et al., J. Phys. Chem. B 115, 7849-7861 (2011)] to such solutions. We then describe and apply new methodology for the simulation of the chemical potentials of the experimentally observed crystalline hydrates at ambient conditions (antarcticite, CaCl 2 ·6H 2 O) and at high-temperature conditions (sinjarite, CaCl 2 ·2H 2 O). We implement our methodologies using for both phases the CaCl 2 transferable force field (FF) based on simple point charge-extended water developed by Mamatkulov et al. [J. Chem. Phys. 138, 024505 (2013)], based on training sets involving single-ion and ion-pair low-concentration solution properties at near-ambient conditions. We find that simulations of the solution chemical potentials at high concentrations are somewhat problematic, exhibiting densities diverging from experimental values and accompanied by dramatically decreasing particle mobility. For the solid phases, the sinjarite crystalline lattice differs from experiment only slightly, whereas the simulations of antarcticite completely fail, due to instability of the crystalline lattice. The FF thus only successfully yields the sinjarite solubility, but its value m = 8.0(7) mol kg -1 H 2 O lies well below the experimentally observed solubility range at 1 bar pressure of (12m, 15m) in the temperature interval (320 K, 400 K). We conclude that the used FF does not provide a good description of the experimental properties considered and suggest that improvement must take into account the crystalline properties.

Determination of Earth rotation by the combination of data from different space geodetic systems

NASA Technical Reports Server (NTRS)

Archinal, Brent Allen

1987-01-01

Formerly, Earth Rotation Parameters (ERP), i.e., polar motion and UTI-UTC values, have been determined using data from only one observational system at a time, or by the combination of parameters previously obtained in such determinations. The question arises as to whether a simultaneous solution using data from several sources would provide an improved determination of such parameters. To pursue this reasoning, fifteen days of observations have been simulated using realistic networks of Lunar Laser Ranging (LLR), Satellite Laser Ranging (SLR) to Lageos, and Very Long Baseline Interferometry (VLBI) stations. A comparison has been done of the accuracy and precision of the ERP obtained from: (1) the individual system solutions, (2) the weighted means of those values, (3) all of the data by means of the combination of the normal equations obtained in 1, and (4) a grand solution with all the data. These simulations show that solutions done by the normal equation combination and grand solution methods provide the best or nearly the best ERP for all the periods considered, but that weighted mean solutions provide nearly the same accuracy and precision. VLBI solutions also provide similar accuracies.

A novel heterogeneous algorithm to simulate multiphase flow in porous media on multicore CPU-GPU systems

NASA Astrophysics Data System (ADS)

McClure, J. E.; Prins, J. F.; Miller, C. T.

2014-07-01

Multiphase flow implementations of the lattice Boltzmann method (LBM) are widely applied to the study of porous medium systems. In this work, we construct a new variant of the popular "color" LBM for two-phase flow in which a three-dimensional, 19-velocity (D3Q19) lattice is used to compute the momentum transport solution while a three-dimensional, seven velocity (D3Q7) lattice is used to compute the mass transport solution. Based on this formulation, we implement a novel heterogeneous GPU-accelerated algorithm in which the mass transport solution is computed by multiple shared memory CPU cores programmed using OpenMP while a concurrent solution of the momentum transport is performed using a GPU. The heterogeneous solution is demonstrated to provide speedup of 2.6 × as compared to multi-core CPU solution and 1.8 × compared to GPU solution due to concurrent utilization of both CPU and GPU bandwidths. Furthermore, we verify that the proposed formulation provides an accurate physical representation of multiphase flow processes and demonstrate that the approach can be applied to perform heterogeneous simulations of two-phase flow in porous media using a typical GPU-accelerated workstation.

Dynamic Beam Solutions for Real-Time Simulation and Control Development of Flexible Rockets

NASA Technical Reports Server (NTRS)

Su, Weihua; King, Cecilia K.; Clark, Scott R.; Griffin, Edwin D.; Suhey, Jeffrey D.; Wolf, Michael G.

2016-01-01

In this study, flexible rockets are structurally represented by linear beams. Both direct and indirect solutions of beam dynamic equations are sought to facilitate real-time simulation and control development for flexible rockets. The direct solution is completed by numerically integrate the beam structural dynamic equation using an explicit Newmark-based scheme, which allows for stable and fast transient solutions to the dynamics of flexile rockets. Furthermore, in the real-time operation, the bending strain of the beam is measured by fiber optical sensors (FOS) at intermittent locations along the span, while both angular velocity and translational acceleration are measured at a single point by the inertial measurement unit (IMU). Another study in this paper is to find the analytical and numerical solutions of the beam dynamics based on the limited measurement data to facilitate the real-time control development. Numerical studies demonstrate the accuracy of these real-time solutions to the beam dynamics. Such analytical and numerical solutions, when integrated with data processing and control algorithms and mechanisms, have the potential to increase launch availability by processing flight data into the flexible launch vehicle's control system.

Molecular Dynamics and Neutron Scattering Studies of Mixed Solutions of Caffeine and Pyridine in Water.

PubMed

Tavagnacco, Letizia; Mason, Philip E; Neilson, George W; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W

2018-05-31

Insight into the molecular interactions of homotactic and heterotactic association of caffeine and pyridine in aqueous solution is given on the basis of both experimental and simulation studies. Caffeine is about 5 times more soluble in a 3 m aqueous pyridine solution than it is in pure water (an increase from ∼0.1 m to 0.5 m). At this elevated concentration the system becomes suitable for neutron scattering study. Caffeine-pyridine interactions were studied by neutron scattering and molecular dynamics simulations, allowing a detailed characterization of the spatial and orientational structure of the solution. It was found that while pyridine-caffeine interactions are not as strong as caffeine-caffeine interactions, the pyridine-caffeine interactions still significantly disrupted caffeine-caffeine stacking. The alteration of the caffeine-caffeine stacking, occasioned by the presence of pyridine molecules in solution and the consequent formation of heterotactic interactions, leads to the experimentally detected increase in caffeine solubility.

Numerical modeling of subsurface radioactive solute transport from waste seepage ponds at the Idaho National Engineering Laboratory

USGS Publications Warehouse

Robertson, John B.

1976-01-01

Aqueous chemical and low-level radioactive effluents have been disposed to seepage ponds since 1952 at the Idaho National Engineering Laboratory. The solutions percolate toward the Snake River Plain aquifer (135 m below) through interlayered basalts and unconsolidated sediments and an extensive zone of ground water perched on a sedimentary layer about 40 m beneath the ponds. A three-segment numerical model was developed to simulate the system, including effects of convection, hydrodynamic dispersion, radioactive decay, and adsorption. Simulated hydraulics and solute migration patterns for all segments agree adequately with the available field data. The model can be used to project subsurface distributions of waste solutes under a variety of assumed conditions for the future. Although chloride and tritium reached the aquifer several years ago, the model analysis suggests that the more easily sorbed solutes, such as cesium-137 and strontium-90, would not reach the aquifer in detectable concentrations within 150 years for the conditions assumed. (Woodard-USGS)

Selection of suitable fertilizer draw solute for a novel fertilizer-drawn forward osmosis-anaerobic membrane bioreactor hybrid system.

PubMed

Kim, Youngjin; Chekli, Laura; Shim, Wang-Geun; Phuntsho, Sherub; Li, Sheng; Ghaffour, Noreddine; Leiknes, TorOve; Shon, Ho Kyong

2016-06-01

In this study, a protocol for selecting suitable fertilizer draw solute for anaerobic fertilizer-drawn forward osmosis membrane bioreactor (AnFDFOMBR) was proposed. Among eleven commercial fertilizer candidates, six fertilizers were screened further for their FO performance tests and evaluated in terms of water flux and reverse salt flux. Using selected fertilizers, bio-methane potential experiments were conducted to examine the effect of fertilizers on anaerobic activity due to reverse diffusion. Mono-ammonium phosphate (MAP) showed the highest biogas production while other fertilizers exhibited an inhibition effect on anaerobic activity with solute accumulation. Salt accumulation in the bioreactor was also simulated using mass balance simulation models. Results showed that ammonium sulfate and MAP were the most appropriate for AnFDFOMBR since they demonstrated less salt accumulation, relatively higher water flux, and higher dilution capacity of draw solution. Given toxicity of sulfate to anaerobic microorganisms, MAP appears to be the most suitable draw solution for AnFDFOMBR. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transient Dupuit Interface Flow with partially penetrating features

NASA Astrophysics Data System (ADS)

Bakker, Mark

1998-11-01

A comprehensive potential is presented for Dupuit interface flow in coastal aquifers where both the fresh water and salt water are moving. The resulting potential flow problem may be solved, for incompressible confined aquifers, using analytic functions. The vertical velocity of the interface may then be computed analytically and the change of the position of the interface may be simulated by numerical integration through time, starting with a known (or estimated) initial position. The upconing of the interface below a partially penetrating ditch or well may be studied if Dupuit solutions for such features are available. A new Dupuit solution is derived for a ditch that penetrates the aquifer partially from above; a Dupuit solution for a partially penetrating well may be obtained following a similar derivation. The new Dupuit solution is combined with the interface solution to simulate the upconing of an initially horizontal interface below a series of partially penetrating ditches; the interface converges to the known steady state position.

Use of the Marshall Space Flight Center solar simulator in collector performance evaluation

NASA Technical Reports Server (NTRS)

Humphries, W. R.

1978-01-01

Actual measured values from simulator checkout tests are detailed. Problems encountered during initial startup are discussed and solutions described. Techniques utilized to evaluate collector performance from simulator test data are given. Performance data generated in the simulator are compared to equivalent data generated during natural outdoor testing. Finally, a summary of collector performance parameters generated to date as a result of simulator testing are given.

Look-ahead Dynamic Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-10-20

Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.

A Solution Framework for Environmental Characterization Problems

EPA Science Inventory

This paper describes experiences developing a grid-enabled framework for solving environmental inverse problems. The solution approach taken here couples environmental simulation models with global search methods and requires readily available computational resources of the grid ...

How Does a Hydrophobic Macromolecule Respond to Mixed Osmolyte Environment?

PubMed

Tah, Indrajit; Mondal, Jagannath

2016-10-04

The role of the protecting osmolyte Trimethyl N-oxide (TMAO) in counteracting the denaturing effect of urea on a protein is quite well established. However, the mechanistic role of osmolytes on the hydrophobic interaction underlying protein folding is a topic of contention and is emerging as a key area of biophysical interest. Although recent experiment and computer simulation have established that individual aqueous solution of TMAO and urea respectively stabilizes and destabilizes the collapsed conformation of a hydrophobic polymer, it remains to be explored how a mixed aqueous solution of protecting and denaturing osmolytes influences the conformations of the polymer. In order to bridge the gap, we have simulated the conformational behavior of both a model hydrophobic polymer and a synthetic polymer polystyrene in an aqueous mixture of TMAO and urea. Intriguingly, our free energy based simulations on both the systems show that even though a pure aqueous solution of TMAO stabilizes the collapsed or globular conformation of the hydrophobic polymer, addition of TMAO to an aqueous solution of urea further destabilizes the collapsed conformation of the hydrophobic polymer. We also observe that the extent of destabilization in a mixed osmolyte solution is relatively higher than that in pure aqueous urea solution. The reinforcement of the denaturation effect of the hydrophobic macromolecule in a mixed osmolyte solution is in stark contrast to the well-known counteracting role of TMAO in proteins under denaturing condition of urea. In both model and realistic systems, our results show that in a mixed aqueous solution, greater number of cosolutes preferentially bind to the extended conformation of the polymer relative to that in the collapsed conformation, thereby complying with Tanford-Wyman preferential solvation theory disfavoring the collapsed conformation. The results are robust across a range of osmolyte concentrations and multiple cosolute forcefields. Our findings unequivocally imply that the action of mixed osmolyte solution on hydrophobic polymer is significantly distinct from that of proteins.

Ionic Effects on Supercritical CO2-Brine Interfacial Tensions: Molecular Dynamics Simulations and a Universal Correlation with Ionic Strength, Temperature, and Pressure.

PubMed

Zhao, Lingling; Ji, Jiayuan; Tao, Lu; Lin, Shangchao

2016-09-13

For geological CO2 storage in deep saline aquifers, the interfacial tension (IFT) between supercritical CO2 and brine is critical for the storage security and design of the storage capacitance. However, currently, no predictive model exists to determine the IFT of supercritical CO2 against complex electrolyte solutions involving various mixed salt species at different concentrations and compositions. In this paper, we use molecular dynamics (MD) simulations to investigate the effect of salt ions on the incremental IFT at the supercritical CO2-brine interface with respect to that at the reference supercritical CO2-water interface. Supercritical CO2-NaCl solution, CO2-CaCl2 solution and CO2-(NaCl+CaCl2) mixed solution systems are simulated at 343 K and 20 MPa under different salinities and salt compositions. We find that the valence of the cations is the primary contributor to the variation in IFT, while the Lennard-Jones potentials for the cations pose a smaller impact on the IFT. Interestingly, the incremental IFT exhibits a general linear correlation with the ionic strength in the above three electrolyte systems, and the slopes are almost identical and independent of the solution types. Based on this finding, a universal predictive formula for IFTs of CO2-complex electrolyte solution systems is established, as a function of ionic strength, temperature, and pressure. The predicted IFTs using the established formula agree perfectly (with a high statistical confidence level of ∼96%) with a wide range of experimental data for CO2 interfacing with different electrolyte solutions, such as those involving MgCl2 and Na2SO4. This work provides an efficient and accurate route to directly predict IFTs in supercritical CO2-complex electrolyte solution systems for practical engineering applications, such as geological CO2 sequestration in deep saline aquifers and other interfacial systems involving complex electrolyte solutions.

PERFORMANCE IMPROVEMENT OF CROSS-FLOW FILTRATION FOR HIGH LEVEL WASTE TREATMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duignan, M.; Nash, C.; Poirier, M.

2011-01-12

In the interest of accelerating waste treatment processing, the DOE has funded studies to better understand filtration with the goal of improving filter fluxes in existing cross-flow equipment. The Savannah River National Laboratory (SRNL) was included in those studies, with a focus on start-up techniques, filter cake development, the application of filter aids (cake forming solid precoats), and body feeds (flux enhancing polymers). This paper discusses the progress of those filter studies. Cross-flow filtration is a key process step in many operating and planned waste treatment facilities to separate undissolved solids from supernate slurries. This separation technology generally has themore » advantage of self-cleaning through the action of wall shear stress created by the flow of waste slurry through the filter tubes. However, the ability of filter wall self-cleaning depends on the slurry being filtered. Many of the alkaline radioactive wastes are extremely challenging to filtration, e.g., those containing compounds of aluminum and iron, which have particles whose size and morphology reduce permeability. Unfortunately, low filter flux can be a bottleneck in waste processing facilities such as the Savannah River Modular Caustic Side Solvent Extraction Unit and the Hanford Waste Treatment Plant. Any improvement to the filtration rate would lead directly to increased throughput of the entire process. To date increased rates are generally realized by either increasing the cross-flow filter axial flowrate, limited by pump capacity, or by increasing filter surface area, limited by space and increasing the required pump load. SRNL set up both dead-end and cross-flow filter tests to better understand filter performance based on filter media structure, flow conditions, filter cleaning, and several different types of filter aids and body feeds. Using non-radioactive simulated wastes, both chemically and physically similar to the actual radioactive wastes, the authors performed several tests to demonstrate increases in filter performance. With the proper use of filter flow conditions and filter enhancers, filter flow rates can be increased over rates currently realized today.« less

Numerical Aerodynamic Simulation (NAS)

NASA Technical Reports Server (NTRS)

Peterson, V. L.; Ballhaus, W. F., Jr.; Bailey, F. R.

1983-01-01

The history of the Numerical Aerodynamic Simulation Program, which is designed to provide a leading-edge capability to computational aerodynamicists, is traced back to its origin in 1975. Factors motivating its development and examples of solutions to successively refined forms of the governing equations are presented. The NAS Processing System Network and each of its eight subsystems are described in terms of function and initial performance goals. A proposed usage allocation policy is discussed and some initial problems being readied for solution on the NAS system are identified.

Implementation and simulations of the sphere solution in FAST

NASA Astrophysics Data System (ADS)

Murgolo, F. P.; Schirone, M. G.; Lattanzi, M.; Bernacca, P. L.

1989-06-01

The details of the implementation of the sphere solution software in the Fundamental Astronomy by Space Techniques (FAST) consortium, are described. The simulation results for realistic data sets, both with and without grid-step errors are given. Expected errors on the astrometric parameters of the primary stars and the precision of the reference great circle zero points, are provided as a function of mission duration. The design matrix, the diagrams of the context processor and the processors experimental results are given.

Solution of non-continuum flows using BGK-type model with enforced relaxation of moments

NASA Astrophysics Data System (ADS)

Alekseenko, Alexander; Gimelshein, Sergey; Nguyen, Truong; Vedula, Prakash

2016-11-01

A BGK-type model with velocity dependent collision frequency and enforced relaxation rates for selected moments is applied to simulation of one- and two-dimensional super sonic flows. Relaxation rates of the moments are estimated by evaluating the full Boltzmann collision integral several times during the simulation. The solutions show improvements in velocity and temperature profiles as compared to the classical ES-BGK model. However, enforcement of relaxation rates for high order moments increases stiffness of the model.

Computer simulation of concentrated solid solution strengthening

NASA Technical Reports Server (NTRS)

Kuo, C. T. K.; Arsenault, R. J.

1976-01-01

The interaction forces between a straight edge dislocation moving through a three-dimensional block containing a random array of solute atoms were determined. The yield stress at 0 K was obtained by determining the average maximum solute-dislocation interaction force that is encountered by edge dislocation, and an expression relating the yield stress to the length of the dislocation and the solute concentration is provided. The magnitude of the solid solution strengthening due to solute atoms can be determined directly from the numerical results, provided the dislocation line length that moves as a unit is specified.

An open, object-based modeling approach for simulating subsurface heterogeneity

NASA Astrophysics Data System (ADS)

Bennett, J.; Ross, M.; Haslauer, C. P.; Cirpka, O. A.

2017-12-01

Characterization of subsurface heterogeneity with respect to hydraulic and geochemical properties is critical in hydrogeology as their spatial distribution controls groundwater flow and solute transport. Many approaches of characterizing subsurface heterogeneity do not account for well-established geological concepts about the deposition of the aquifer materials; those that do (i.e. process-based methods) often require forcing parameters that are difficult to derive from site observations. We have developed a new method for simulating subsurface heterogeneity that honors concepts of sequence stratigraphy, resolves fine-scale heterogeneity and anisotropy of distributed parameters, and resembles observed sedimentary deposits. The method implements a multi-scale hierarchical facies modeling framework based on architectural element analysis, with larger features composed of smaller sub-units. The Hydrogeological Virtual Reality simulator (HYVR) simulates distributed parameter models using an object-based approach. Input parameters are derived from observations of stratigraphic morphology in sequence type-sections. Simulation outputs can be used for generic simulations of groundwater flow and solute transport, and for the generation of three-dimensional training images needed in applications of multiple-point geostatistics. The HYVR algorithm is flexible and easy to customize. The algorithm was written in the open-source programming language Python, and is intended to form a code base for hydrogeological researchers, as well as a platform that can be further developed to suit investigators' individual needs. This presentation will encompass the conceptual background and computational methods of the HYVR algorithm, the derivation of input parameters from site characterization, and the results of groundwater flow and solute transport simulations in different depositional settings.

From single Debye-Hückel chains to polyelectrolyte solutions: Simulation results

NASA Astrophysics Data System (ADS)

Kremer, Kurt

1996-03-01

This lecture will present results from simulations of single weakly charged flexible chains, where the electrostatic part of the interaction is modeled by a Debye-Hückel potential,( with U. Micka, IFF, Forschungszentrum Jülich, 52425 Jülich, Germany) as well as simulations of polyelectrolyte solutions, where the counterions are explicitly taken into account( with M. J. Stevens, Sandia Nat. Lab., Albuquerque, NM 87185-1111) ( M. J. Stevens, K. Kremer, JCP 103), 1669 (1995). The first set of the simulations is meant to clear a recent contoversy on the dependency of the persistence length LP on the screening length Γ. While the analytic theories give Lp ~ Γ^x with either x=1 or x=2, the simulations find for all experimentally accessible chain lengths a varying exponent, which is significantly smaller than 1. This causes serious doubts on the applicability of this model for weakly charged polyelectrolytes in general. The second part deals with strongly charged flexible polyelectrolytes in salt free solution. These simulations are performed for multichain systems. The full Coulomb interactions of the monomers and counterions are treated explicitly. Experimental measurements of the osmotic pressure and the structure factor are reproduced and extended. The simulations reveal a new picture of the chain structure based on calculations of the structure factor, persistence length, end-to-end distance, etc. Even at very low density, the chains show significant bending. Furthermore, the chains contract significantly before they start to overlap. We also show that counterion condensation dramatically alters the chain structure, even for a good solvent backbone.

Sparse approximation problem: how rapid simulated annealing succeeds and fails

NASA Astrophysics Data System (ADS)

Obuchi, Tomoyuki; Kabashima, Yoshiyuki

2016-03-01

Information processing techniques based on sparseness have been actively studied in several disciplines. Among them, a mathematical framework to approximately express a given dataset by a combination of a small number of basis vectors of an overcomplete basis is termed the sparse approximation. In this paper, we apply simulated annealing, a metaheuristic algorithm for general optimization problems, to sparse approximation in the situation where the given data have a planted sparse representation and noise is present. The result in the noiseless case shows that our simulated annealing works well in a reasonable parameter region: the planted solution is found fairly rapidly. This is true even in the case where a common relaxation of the sparse approximation problem, the G-relaxation, is ineffective. On the other hand, when the dimensionality of the data is close to the number of non-zero components, another metastable state emerges, and our algorithm fails to find the planted solution. This phenomenon is associated with a first-order phase transition. In the case of very strong noise, it is no longer meaningful to search for the planted solution. In this situation, our algorithm determines a solution with close-to-minimum distortion fairly quickly.

Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution

NASA Astrophysics Data System (ADS)

Marchand, Gabriel; Soetens, Jean-Christophe; Jacquemin, Denis; Bopp, Philippe A.

2015-12-01

We demonstrate that different sets of Lennard-Jones parameters proposed for the Na+ ion, in conjunction with the empirical combining rules routinely used in simulation packages, can lead to essentially different equilibrium structures for a deprotonated poly-L-glutamic acid molecule (poly-L-glutamate) dissolved in a 0.3M aqueous NaCl solution. It is, however, difficult to discriminate a priori between these model potentials; when investigating the structure of the Na+-solvation shell in bulk NaCl solution, all parameter sets lead to radial distribution functions and solvation numbers in broad agreement with the available experimental data. We do not find any such dependency of the equilibrium structure on the parameters associated with the Cl- ion. This work does not aim at recommending a particular set of parameters for any particular purpose. Instead, it stresses the model dependence of simulation results for complex systems such as biomolecules in solution and thus the difficulties if simulations are to be used for unbiased predictions, or to discriminate between contradictory experiments. However, this opens the possibility of validating a model specifically in view of analyzing experimental data believed to be reliable.

Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution

PubMed Central

Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.

2011-01-01

Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions. PMID:21812485

Interactions of Organics within Hydrated Selective Layer of Reverse Osmosis Desalination Membrane: A Combined Experimental and Computational Study.

PubMed

Ghoufi, Aziz; Dražević, Emil; Szymczyk, Anthony

2017-03-07

In this work we have examined a computational approach in predicting the interactions between uncharged organic solutes and polyamide membranes. We used three model organic molecules with identical molecular weights (100.1 g/mol), 4-aminopiperidine, 3,3-dimethyl-2-butanone (pinacolone) and methylisobutyl ketone for which we obtained experimental data on partitioning, diffusion and separation on a typical seawater reverse osmosis (RO) membrane. The interaction energy between the solutes and the membrane phase (fully aromatic polyamide) was computed from molecular dynamics (MD) simulations and the resulting sequence was found to correlate well with the experimental rejections and sorption data. Sorption of the different organic solutes within the membrane skin layer determined from attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) nicely agreed with interaction energies computed from molecular simulations. Qualitative information about solute diffusivity inside the membrane was also extracted from MD simulations while ATR-FTIR experiments indicated strongly hindered diffusion with diffusion coefficients in the membrane about 10 -15 m 2 /s. The computational approach presented here could be a first step toward predicting rejections trends of, for example, hormones and pharmaceuticals by RO dense membranes.

Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation.

PubMed

Matubayasi, Nobuyuki; Takahashi, Hideaki

2012-01-28

The relationship is investigated for QM/MM (quantum-mechanical/molecular-mechanical) systems between the fluctuations of the electronic state of the QM subsystem and of the solvation effect due to the QM-MM interaction. The free-energy change due to the electron-density fluctuation around its average is highlighted, and is evaluated through an approximate functional formulated in terms of distribution functions of the many-body coupling (pairwise non-additive) part of the QM-MM interaction energy. A set of QM/MM simulations are conducted in MM water solvent for QM water solute in ambient and supercritical conditions and for QM glycine solute in the neutral and zwitterionic forms. The variation of the electronic distortion energy of the QM solute in the course of QM/MM simulation is then shown to be compensated by the corresponding variation of the free energy of solvation. The solvation free energy conditioned by the electronic distortion energy is further analyzed with its components. It is found that the many-body contribution is essentially equal between the free energy and the average sum of solute-solvent interaction energy. © 2012 American Institute of Physics

Plasma-Sheath-Surface Dynamics

DTIC Science & Technology

1990-09-01

Particle Simulations of Cross-Field Plasma Sheaths," Phys. Fluids B, pp 1069- 1082 , May 1990. IJ. Morey and C.K. Birdsall, "Traveling Wave-Tube Simulation...Theilhaber, "Analytic Solutions and Particle Simulations of Cross-Field Plasma Sheaths," Phys. Fluids B, pp 1069- 1082 , May 1990. S.E. Parker, and C.K

Use of a Computer Simulation To Develop Mental Simulations for Understanding Relative Motion Concepts.

ERIC Educational Resources Information Center

Monaghan, James M.; Clement, John

1999-01-01

Presents evidence for students' qualitative and quantitative difficulties with apparently simple one-dimensional relative-motion problems, students' spontaneous visualization of relative-motion problems, the visualizations facilitating solution of these problems, and students' memories of the online computer simulation used as a framework for…

Incorporation of Carrier Phase Global Positioning System Measurements into the Navigation Reference System for Improved Performance

DTIC Science & Technology

1993-12-01

5-6 5.6.1 Large Cycle Slip Simulation ............................. 5-7 5.6.2 Small Cycle Slip Simulation ........................... 5-9...Appendix J. Small Cycle Slip Simulation Results ............................. J-1 Bibliography ........................................................ BIB-I...when subjected to large and small cycle slips. Results of the simulations indicate that the PNRS can provide an improved navigation solution over

Solitary solutions including spatially localized chaos and their interactions in two-dimensional Kolmogorov flow.

PubMed

Hiruta, Yoshiki; Toh, Sadayoshi

2015-12-01

Two-dimensional Kolmogorov flow in wide periodic boxes is numerically investigated. It is shown that the total flow rate in the direction perpendicular to the force controls the characteristics of the flow, especially the existence of spatially localized solitary solutions such as traveling waves, periodic solutions, and chaotic solutions, which can behave as elementary components of the flow. We propose a procedure to construct approximate solutions consisting of solitary solutions. It is confirmed by direct numerical simulations that these solutions are stable and represent interactions between elementary components such as collisions, coexistence, and collapse of chaos.

A comparison of numerical methods for the prediction of two-dimensional heat transfer in an electrothermal deicer pad. M.S. Thesis. Final Contractor Report

NASA Technical Reports Server (NTRS)

Wright, William B.

1988-01-01

Transient, numerical simulations of the deicing of composite aircraft components by electrothermal heating have been performed in a 2-D rectangular geometry. Seven numerical schemes and four solution methods were used to find the most efficient numerical procedure for this problem. The phase change in the ice was simulated using the Enthalpy method along with the Method for Assumed States. Numerical solutions illustrating deicer performance for various conditions are presented. Comparisons are made with previous numerical models and with experimental data. The simulation can also be used to solve a variety of other heat conduction problems involving composite bodies.

78 FR 66099 - Petition for Exemption; Summary of Petition Received

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-04

..., Office of Rulemaking. Petition for Exemption Docket No.: FAA-2013-0818. Petitioner: ELITE Simulation Solutions. Section of 14 CFR Affected: Sec. 61.65(i) Description of Relief Sought: ELITE Simulation...

Analytical Applications of Monte Carlo Techniques.

ERIC Educational Resources Information Center

Guell, Oscar A.; Holcombe, James A.

1990-01-01

Described are analytical applications of the theory of random processes, in particular solutions obtained by using statistical procedures known as Monte Carlo techniques. Supercomputer simulations, sampling, integration, ensemble, annealing, and explicit simulation are discussed. (CW)

Nuclear quantum effects in water exchange around lithium and fluoride ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, David M.; Manolopoulos, David E.; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.« less

Panel summary report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gutjahr, A.L.; Kincaid, C.T.; Mercer, J.W.

1987-04-01

The objective of this report is to summarize the various modeling approaches that were used to simulate solute transport in a variably saturated emission. In particular, the technical strengths and weaknesses of each approach are discussed, and conclusions and recommendations for future studies are made. Five models are considered: (1) one-dimensional analytical and semianalytical solutions of the classical deterministic convection-dispersion equation (van Genuchten, Parker, and Kool, this report ); (2) one-dimensional simulation using a continuous-time Markov process (Knighton and Wagenet, this report); (3) one-dimensional simulation using the time domain method and the frequency domain method (Duffy and Al-Hassan, this report);more » (4) one-dimensional numerical approach that combines a solution of the classical deterministic convection-dispersion equation with a chemical equilibrium speciation model (Cederberg, this report); and (5) three-dimensional numerical solution of the classical deterministic convection-dispersion equation (Huyakorn, Jones, Parker, Wadsworth, and White, this report). As part of the discussion, the input data and modeling results are summarized. The models were used in a data analysis mode, as opposed to a predictive mode. Thus, the following discussion will concentrate on the data analysis aspects of model use. Also, all the approaches were similar in that they were based on a convection-dispersion model of solute transport. Each discussion addresses the modeling approaches in the order listed above.« less

Analytical solution and numerical simulation of the liquid nitrogen freezing-temperature field of a single pipe

NASA Astrophysics Data System (ADS)

Cai, Haibing; Xu, Liuxun; Yang, Yugui; Li, Longqi

2018-05-01

Artificial liquid nitrogen freezing technology is widely used in urban underground engineering due to its technical advantages, such as simple freezing system, high freezing speed, low freezing temperature, high strength of frozen soil, and absence of pollution. However, technical difficulties such as undefined range of liquid nitrogen freezing and thickness of frozen wall gradually emerge during the application process. Thus, the analytical solution of the freezing-temperature field of a single pipe is established considering the freezing temperature of soil and the constant temperature of freezing pipe wall. This solution is then applied in a liquid nitrogen freezing project. Calculation results show that the radius of freezing front of liquid nitrogen is proportional to the square root of freezing time. The radius of the freezing front also decreases with decreased the freezing temperature, and the temperature gradient of soil decreases with increased distance from the freezing pipe. The radius of cooling zone in the unfrozen area is approximately four times the radius of the freezing front. Meanwhile, the numerical simulation of the liquid nitrogen freezing-temperature field of a single pipe is conducted using the Abaqus finite-element program. Results show that the numerical simulation of soil temperature distribution law well agrees with the analytical solution, further verifies the reliability of the established analytical solution of the liquid nitrogen freezing-temperature field of a single pipe.

Numerical Simulation of the Freeze-Thaw Behavior of Mortar Containing Deicing Salt Solution

PubMed Central

Esmaeeli, Hadi S.; Farnam, Yaghoob; Bentz, Dale P.; Zavattieri, Pablo D.; Weiss, Jason

2016-01-01

This paper presents a one-dimensional finite difference model that is developed to describe the freeze-thaw behavior of an air-entrained mortar containing deicing salt solution. A phenomenological model is used to predict the temperature and the heat flow for mortar specimens during cooling and heating. Phase transformations associated with the freezing/melting of water/ice or transition of the eutectic solution from liquid to solid are included in this phenomenological model. The lever rule is used to calculate the quantity of solution that undergoes the phase transformation, thereby simulating the energy released/absorbed during phase transformation. Undercooling and pore size effects are considered in the numerical model. To investigate the effect of pore size distribution, this distribution is considered using the Gibbs-Thomson equation in a saturated mortar specimen. For an air-entrained mortar, the impact of considering pore size (and curvature) on freezing was relatively insignificant; however the impact of pore size is much more significant during melting. The fluid inside pores smaller than 5 nm (i.e., gel pores) has a relatively small contribution in the macroscopic freeze-thaw behavior of mortar specimens within the temperature range used in this study (i.e., +24 °C to −35 °C), and can therefore be neglected for the macroscopic freeze-thaw simulations. A heat sink term is utilized to simulate the heat dissipation during phase transformations. Data from experiments performed using a low-temperature longitudinal guarded comparative calorimeter (LGCC) on mortar specimens fully saturated with various concentration NaCl solutions or partially saturated with water is compared to the numerical results and a promising agreement is generally obtained. PMID:28082830

Numerical Simulation of the Freeze-Thaw Behavior of Mortar Containing Deicing Salt Solution.

PubMed

Esmaeeli, Hadi S; Farnam, Yaghoob; Bentz, Dale P; Zavattieri, Pablo D; Weiss, Jason

2017-02-01

This paper presents a one-dimensional finite difference model that is developed to describe the freeze-thaw behavior of an air-entrained mortar containing deicing salt solution. A phenomenological model is used to predict the temperature and the heat flow for mortar specimens during cooling and heating. Phase transformations associated with the freezing/melting of water/ice or transition of the eutectic solution from liquid to solid are included in this phenomenological model. The lever rule is used to calculate the quantity of solution that undergoes the phase transformation, thereby simulating the energy released/absorbed during phase transformation. Undercooling and pore size effects are considered in the numerical model. To investigate the effect of pore size distribution, this distribution is considered using the Gibbs-Thomson equation in a saturated mortar specimen. For an air-entrained mortar, the impact of considering pore size (and curvature) on freezing was relatively insignificant; however the impact of pore size is much more significant during melting. The fluid inside pores smaller than 5 nm (i.e., gel pores) has a relatively small contribution in the macroscopic freeze-thaw behavior of mortar specimens within the temperature range used in this study (i.e., +24 °C to -35 °C), and can therefore be neglected for the macroscopic freeze-thaw simulations. A heat sink term is utilized to simulate the heat dissipation during phase transformations. Data from experiments performed using a low-temperature longitudinal guarded comparative calorimeter (LGCC) on mortar specimens fully saturated with various concentration NaCl solutions or partially saturated with water is compared to the numerical results and a promising agreement is generally obtained.