From bioserv-owner@nic.funet.fi Mon Aug 26 03:07 EST 1991 Received: from iubio.bio.indiana.edu by cricket.bio.indiana.edu (5.64/A/UX-2.00) id AA12958; Mon, 26 Aug 91 03:07:12 EST From: "Rob \"bionaut\" Harper" To: bioserv@nic.funet.fi Subject: Environmental software. Message-Id: <91Aug26.110353eet_dst.57208@nic.funet.fi> Date: Mon, 26 Aug 1991 11:03:47 +0300 Status: R >Path: funic!fuug!mcsun!uunet!wupost!ukma!dftsrv!mimsy!ndcheg!nstar!crom2!jim >From: nstar!crom2!jim@ndcheg.cheg.nd.edu (James P. H. Fuller) >Newsgroups: bionet.biology.computational >Subject: Re: Contamination modeling in food chains >Message-ID: <9108260155.AA04959@crom2> >Date: 26 Aug 91 01:55:09 GMT >Sender: news@mimsy.umd.edu >Distribution: bionet >Lines: 486 >Approved: comp-bio-moderator@genbank.bio.net spatial!tim@uunet.uu.net (Tim Eckert) writes: > I am looking for any and all verifiable food chain models for tracing > metals and chemicals over various pathways. For ex., I want models > that can predict metal and chemical concentrations from soils and water > through plants, plankton, soil organisms, birds, terrestrial animals, > fish, bottom dwellers of ponds and lakes, up to people. Any models or > information on who might have these types of models for any part of any > pathway at is greatly appreciated. I'm posting the following (subject to the moderator's approval) rather than merely mailing it to the gentleman looking for models because it may be of interest to others to learn of the simulation and modeling software dis- tributed by the Environmental Protection Agency. The following has been HEAVILY edited before posting (the original is 85 kbytes long.) Please send me email to jim@crom2.rn.com if you wish more details about obtaining any of this software, either from the EPA on tape or disk, via modem from the CEAM BBS mentioned below (HST) or from the crom2 system (PEP/uucp or V.32/zmodem.) The CEAM BBS is not on the Internet and cannot be reached by telnet or ftp. P.S. For Dr. Eckert I particularly point out the "Food and Gill Exchange of Toxic Substances" model (FGETS) and the "WASP Food Chain" model (FCM2.) crom2 Athens GA Public Access Unix | i486 AT, 16mb RAM, 600mb online Molecular Biology | AT&T Unix System V release 3.2 Population Biology | Tbit PEP 19200bps V.32 V.42/V.42bis Ecological Modeling | admin: James P. H. Fuller Bionet/Usenet/cnews/nn | {jim,root}@crom2.rn.com ****************************************************************************** ENVIRONMENTAL SOFTWARE AT THE U. S. ENVIRONMENTAL PROTECTION AGENCY'S CENTER FOR EXPOSURE ASSESSMENT MODELING (Submitted to Environmental Software) (1 March 1989) Robert B. Ambrose, Jr., P.E., and Thomas O. Barnwell, Jr. Center for Exposure Assessment Modeling Environmental Research Laboratory U.S. Environmental Protection Agency Athens, GA 30613 ABSTRACT The Center for Exposure Assessment Modeling (CEAM) was established to meet the scientific and technical exposure assessment needs of the United States Environmental Protection Agency's (EPA) Program and Regional Offices and the various state environmental agencies. To support environmental risk-based decisions concerning protection of air, water, and soil, CEAM provides proven predictive exposure assessment techniques for aquatic, atmospheric, terrestrial, and multimedia pathways for organic chemicals and metals. A wide range of analysis techniques is provided, ranging from simple desk-top techniques suitable for screening analysis through computerized steady-state models to sophisticated, state-of-the-art continuous simulation models. This paper reviews the capabilities of 12 environmental simulation models for urban and rural nonpoint sources, conventional and toxic pollution of streams, lakes and estuaries, tidal hydrodynamics, geochemical equilibrium, and aquatic food chain bioaccumulation. [text deleted .....] SOFTWARE AVAILABILITY CEAM maintains a distribution center for continually updated models (codes and documentation) and databases for users. All computer code distributed by CEAM is considered to be in the public domain and is freely available to users. Persons interested in obtaining the software described in this article should send their requests to the Model Support Section at the authors' address. Requests for PC versions of the software should be accompanied by the proper number of diskettes (see Table I). [text deleted .....] In response to requests for software, the Center provides a copy of the model documentation and computer code on either a 9-track magnetic tape or, when appropriate, on user-supplied diskettes for IBM-PC compatible personal computers. The programs are written in standard FORTRAN 77 and are maintained for both the IBM PC-compatible and the DEC/VAX with VMS operating system. Executable code is available for the MS/DOS environment. Source code only is available for the VAX environment. These programs have been installed on a wide range of computers world-wide with, at most, minor modifications. [text deleted .....] CEAM operates an Electronic Bulletin Board System (BBS) to meet the increasing demand for exposure assessment models supported by the Center. It allows efficient communication between users with modem-equipped computers and CEAM support staff as well as immediate acquisition of models by those under extreme time pressure. The services presently offered are: 1. downloading of CEAM supported models; 2. uploading of user input data sets for staff review and problem solving; 3. a bulletin area listing current CEAM activities and events, such as training courses, helpful hints about the models, and model documentation; and 4. a message area for discussion of computer modeling problems and enhancements. To access the CEAM BBS, a user must call 404/5463402 or FTS 250-3402 and follow the interactive prompts. The communications parameters are 9600/2400/1200 baud, no parity, 8 data bits, and 1 stop bit. CURRENTLY DISTRIBUTED MODELS The Center currently distributes 12 simulation models. These can be applied to urban runoff (SWMM4, HSPF9), leaching and runoff from soils (PRZM, HSPF9), conventional pollution of streams (QUAL2E, HSPF9, WASP4), toxic pollution of streams (HSPF9, WASP4, EXAMS2, DYNTOX, SARAH2), toxic pollution of lakes and estuaries (WASP4, EXAMS2), conventional pollution of lakes and estuaries (WASP4), tidal hydrodynamics (DYNHYD4), geochemical equilibrium (MINTEQA2), and aquatic food chain bioaccumulation (FGETS, WASP Food Chain Model). The remainder of this paper will summarize these simulation models. [text deleted .....] In addition, GCSOLAR and LC50 are distributed to aid in data analysis for environmental problems. Three new models are being tested and will be distributed in the next year. RUSTIC will simulate unsaturated and saturated transport of pollutants in ground water. MULTIMED will address multimedia exposure from hazardous waste sites. TEEAM will simulate ter- restrial exposure and food chain accumulation. STORM WATER MANAGEMENT MODEL The Storm Water Management Model (SWMM) was originally developed between 1969 and 1971 and was the first comprehensive model of its type for urban runoff analysis, although it has certainly not remained the only one. Maintenance and improvements to SWMM led to Version 2 in 1975, Version 3 in 1981 and now Version 4 (Huber et al., 1988). Version 4 of SWMM is the latest edition of this comprehensive computer model for analysis of quanti- ty and quality problems associated with urban runoff. Both single-event and continuous simulation may be performed on catch- ments having storm sewers, combined sewers and natural drainage, for prediction of flows, stages and pollutant concentration. The EXTRAN Block solves the complete dynamic flow routing equations (St. Venant equations) for accurate simulation of backwater, looped connections, surcharging, and pressure flow. Using SWMM, the modeler can simulate all aspects of the urban hydrologic and quality cycles, including rainfall, snowmelt, surface and subsurface runoff, flow routing through the drainage network, storage and treatment. Statistical analyses may be performed on long-term precipi- tation data and on output from continuous simulation. [text deleted .....] HYDROLOGIC SIMULATION PROGRAM - FORTRAN Hydrological Simulation Program - FORTRAN (HSPF; Johanson et al., 1984; Donigian et al., 1984) is a comprehensive package for simulation of watershed hydrology and water quality for both conventional and toxic organic pollutants. HSPF incorporates the watershed-scale ARM and NPS models into a basin-scale analysis framework that includes fate and transport in one-dimensional stream channels. It is the only comprehensive model of watershed hydrology and water quality that allows the integrated simulation of land and soil contaminant runoff processes with in-stream hydraulic and sediment-chemical interactions. The result of this simulation is a time history of the runoff flow rate, sediment load, and nutrient and pesticide concentrations, along with a time history of water quantity and quality at any point in a watershed. HSPF simulates three sediment types (sand, silt, and clay) in addition to a single organic chemical and transformation products of that chemical. The transfer and reaction processes included are hydrolysis, oxidation, photolysis, biodegradation, volatilization, and sorption. Sorption is modeled as a first-order kinetic process in which the user must specify a desorption rate and an equilibrium partition coefficient for each of the three solids types. Resuspension and settling of silts and clays (cohesive solids) are defined in terms of shear stress at the sedimentwater interface. The capacity of the system to transport sand at a particular flow is calculated and resuspension or settling is defined by the difference between the sand in suspension and the transport capacity. Calibration of the model requires data for each of the three solids types. Benthic exchange is modeled as sorption/desorption and deposition/scour with surficial benthic sediments. Underlying sediment and pore water are not modeled. [text deleted .....] PESTICIDE ROOT ZONE MODEL Pesticide Root Zone Model (PRZM) (Carsel et al., 1984; Carsel et al., 1985) is a dynamic compartment model that simulates the vertical movement of pesticides and other organic chemicals in unsaturated soil, both within and below the plant root zone. PRZM allows the user to perform dynamic simulations of potentially toxic chemicals that are applied to the soil or to plant foliage. Dynamic simulations allow the consideration of pulse loads, the prediction of peak events, and the estimation of time-varying mass emission or concentration profiles. Simulations may extend to the water table using generally available input data that are reasonable in spatial and temporal requirements. The model consists of hydrology and chemical transport components that simulate runoff, erosion, plant uptake, leaching, decay, foliar wash off, and volatilization (implicitly) of a pesticide. Predictions can be made daily, monthly, or annually. PRZM has a separate interactive processing module to develop and update parameter files for calibration, verification, and production runs. [text deleted .....] STREAM WATER QUALITY MODEL QUAL2E The Enhanced Stream Water Quality Model QUAL2E and QUAL2E-UNCAS (Brown and Barnwell, 1987) permits simulation of several water quality consti- tuents in a branching stream system using a finite difference solution to the one-dimensional advective- dispersive mass transport and reaction equation. The conceptual representation of a stream used in the QUAL2E formulation is a stream reach that has been divided into a number of sub- reaches or computational elements equivalent to finite differences. For each computational element, a hydrologic balance in terms of flow (Q), a heat balance in terms of temperature (T), and a materials balance in terms of concentration (C) is written. Both advective and dispersive transport are considered in the materials balance. Mass can be gained or lost from the element by transport processes, external sources and sinks (e.g., waste discharges or withdrawals) or by internal sources and sinks (e.g., benthic sources or biological transformations). The equation is solved for the steady-flow, steady state condition in a classical implicit backward difference method. The specific equations and solution technique are described in detail in the QUAL2E computer program documentation. [text deleted .....] WATER QUALITY ANALYSIS SIMULATION PROGRAM Water Quality Analysis Simulation Program, WASP4 (Ambrose et al., 1987) is a generalized framework for modeling contaminant fate and trans- port in surface waters. WASP4 is the latest of a series of WASP programs (Di Toro et al., 1983; Ambrose, et al., 1983; Connolly and Winfield, 1984; Ambrose et al., 1986). Based on the flexible compartment modeling approach, WASP can be applied in one, two, or three dimensions. WASP is designed to permit easy substitution of user-written routines into the program structure. Problems that have been studied using the WASP framework include biochemical oxygen demand and dissolved oxygen dynamics, nutrients and eutrophication, bacterial contamination, and organic chemical and heavy metal contamination. Two WASP models are provided with WASP4. The toxics WASP model, TOXI4, combines a kinetic structure adapted from EXAMS2 (Burns and Cline, 1985) with the WASP4 transport structure and simple sediment balance algorithms to predict dissolved and sorbed chemical concentrations in the bed and overlying waters. The dissolved oxygen/eutrophication WASP model EUTRO4 combines a kinetic structure adapted from the Potomac Eutrophication Model (Thomann and Fitzpatrick, 1982) with the WASP4 transport structure to predict DO and phytoplankton dynamics affected by nutrients and organic material. WASP4 input and output linkages also have been provided to other stand-alone models. Flows and volumes predicted by the link-node hydrodynamic model DYNHYD4 can be read and used by WASP4. Loading files from PRZM and HSPF can be reformatted and read by WASP4. Toxicant concentrations predicted by TOXI4 can be read and used by both the WASP Food Chain Model and the fish bioaccumulation model FGETS. [text deleted .....] TOXI4 TOXI4 simulates the transport and transformation of one to three chemicals and one to three types of particulate material. The three chemicals may be independent, such as isomers of PCB, or they may be linked with reaction yields, such as a parent compound-daughter product sequence. Each chemical exists as a neutral compound and up to four ionic species. The neutral and ionic species can exist in five phases: dissolved, sorbed to dissolved organic carbon (DOC), and sorbed to each of the up to three types of solids. Local equilibrium is assumed so that the distribution of the chemical between each of the species and phases is defined by distribution or partition coefficients. The model, then, is composed of up to six systems, three chemical and three solids, for which the general WASP4 mass balance equation is solved. In an aquatic environment a toxic chemical may be transferred between phases and may be degraded by any of a number of chemical and biological processes. Transfer processes defined in the model include sorption, ionization, and volatilization. Transformation processes defined include biodegradation, hydrolysis, photolysis and chemical oxidation. Sorption and ionization are treated as equilibrium reactions. All other processes are described by rate equations. Rate equations may be quantified either by first-order constants or by second-order chemical specific constants and environment-specific parameters that may vary in space and time. [text deleted .....] EUTRO4 EUTRO4 simulates the transport and transformation of up to eight state variables in the water column and sediment bed, including dissolved oxygen, carbonaceous biochemical oxygen demand, phytoplankton carbon and chlorophyll a, ammonia, nitrate, organic nitrogen, organic phosphorus, and orthophosphate. EUTRO4 can be used to simulate any or all of these variables and the interactions between them. Each variable may exist in both dissolved and particulate phases, as specified by the user for each segment. Solids transport fields describing settling and resuspension of organic solids, phytoplankton solids, and inorganic solids may be specified. The particulate concentration of each variable will be transported by the appropriate solids field. By bypassing variables and computations, EUTRO4 can be operated at various levels of complexity. The simplest level, equivalent to an en- hanced "Streeter-Phelps" equation, includes ultimate BOD, DO, and sediment oxygen demand (SOD). The reaeration rate constant is specified. The next level divides BOD into carbonaceous (CBOD) and nitrogenous (NBOD) fractions. Level 3 is a linear DO balance influenced by photosynthesis and respiration of user-specified phytoplankton and nitrification of ammonia to nitrate, as well as CBOD and SOD. The reaeration rate is computed from velocity, depth, and wind speed. Level 4 adds the phosphorus cycle and simulates phytoplankton dynamics subject to Michaelis-Menten nutrient limitation and light limitation. Level 5 adds benthic interactions explicitly. [text deleted .....] TIDAL HYDRODYNAMIC MODEL DYNHYD4 (Ambrose et al., 1987) is a simple link-node hydrodynamic model capable of handling variable tidal cycles, wind, and unsteady inflows. This program is an enhancement of the Potomac Estuary hydrodynamic model DYNHYD2 (Roesch et al., 1979), which was a component of the Dynamic Estuary Model (Feigner and Harris, 1970). DYNHYD4 solves the one-dimensional equations of continuity and momentum for a branching or channel-junction (link-node) computational network. Driven by variable upstream flows and downstream heads, simulations typically proceed at 1- to 5-minute intervals. The resulting unsteady flows and volumes are averaged over larger time intervals and stored for later use by the WASP4 water quality program. [text deleted .....] EXPOSURE ANALYSIS MODELING SYSTEM EXAMS is an interactive modeling system that allows a user to specify and store the properties of chemicals and ecosystems, modify either via simple commands, and conduct rapid evaluations and error analyses of the probable aquatic fate of synthetic organic chemicals (Burns and Cline, 1985). EXAMS combines the loadings, transport, and transformations of a chemical into a set of differential equations using the law of conservation of mass as an accounting principle. It accounts for all the chemical mass entering and leaving a system as the algebraic sum of external loadings, transport processes that export the compound from the system, and transformation processes within the system that convert the chemical to daughter products. The program produces output tables and simple graphics describing chemical exposure, fate, and persistence. [text deleted .....] DYNAMIC TOXICITY MODEL DYNTOX (Limno-Tech, 1985) is a waste load allocation computer program that uses probabilistic dilution techniques (Di Toro, 1984) to estimate concentrations of toxic substances or fractions of whole effluent toxicity. DYNTOX performs three types of simulations -- continuous, monte carlo, and log normal -- that, based on probabilities, can aid in analyzing the fre- quency and duration of toxic concentrations from a waste discharge. DYNTOX considers dilution and net first-order loss, but not sorption and benthic exchange. The net loss rate must be determined empirically on a case-by-case basis, and should not be extrapolated to different conditions of flow, temperature, solids, pH, or light. [text deleted .....] HAZARDOUS WASTE SCREENING MODEL SARAH2 is a nearfield surface water model that calculates maximum allowable concentrations of hazardous wastes discharged to land disposal or waste water treatment facilities based upon predicted exposure to humans or aquatic life (Vandergrift and Ambrose, 1988). The program has been used in regulatory applications for the U. S. EPA. Its core equations were developed in support of the Land Disposal Banning Rule published in proposal form in the January 14, 1986, Federal Register. The surface water contamination pathways analyzed in SARAH2 include ground water leachate from a land disposal facility or lagoon, storm runoff from a land disposal facility or lagoon, and discharge through a waste water treatment facility or lagoon. The human exposure pathways considered include ingestion of treated drinking water and consumption of contaminated fish. Acceptable leachate or treated industrial waste discharge con- stituent concentrations are estimated by a "back calculation" procedure starting from chemical safety criteria in surface water, drinking water, or fish. "Forward calculations" predict the instream concentrations from leachate or discharge concentrations. [text deleted .....] METALS SPECIATION MODEL MINTEQA2 is an equilibrium chemical speciation model for dilute aqueous systems (Brown and Allison, 1987). The model is an update of MINTEQ (Felmy, et al., 1984), which itself was created from the models MINEQL (Westall, et al., 1976) and WATEQ3 (Ball et al., 1981). MINTEQA2 is appropriate for calculating the equilibrium composition of dilute solutions in the laboratory or in natural aquatic systems. It can be used to calculate the mass distribution at equilibrium among dissolved, adsorbed, and solid phases under a variety of conditions. The species distribution within each phase also is calculated. The aqueous equilibrium composition is obtained by calculating the concentrations of all dissolved species from an initial guess of the activity of each component and from the known stoichiometry of each component in each reaction with known formation constants. The total dissolved mass for each component implied by the calculated concentration of each species is compared with the known total dissolved mass supplied by the user. For each component, if the calculated total mass does not match the known total mass to within a pre-set tolerance level, the activity guess of each component is adjusted in such a way as to compensate for the mass imbalance and the entire procedure is repeated beginning with re- calculating the concentrations of all dissolved species using the new component activity guesses. This iterative procedure is continued until the mass imbalance for every component is less than the tolerance level. When that condition is met, the system is at equilibrium with respect to dissolved species. [text deleted .....] FOOD AND GILL EXCHANGE OF TOXIC SUBSTANCES FGETS (Barber et al., 1988a,b) is a toxicokinetic model that simulates the bioaccumulation of nonpolar organic chemicals by fish from both water and tainted food. Both of these routes of exchange are modeled as diffusion processes that depend upon physico-chemical properties of the pollutant and morphological/physiological characteristics of the fish. FGETS contains a moderately sized database of allometric relationships for gill morphology with which it can simulate the direct gill/water exchange of organic chemicals for essentially any fish species, assuming certain default values. FGETS also contains a limited database of physiological/- morphological relationships that are used to parameterize food exchange. In addition to simulating bioaccumulation of organic toxicants, FGETS also can calculate time to death from chemicals whose mode of action is narcosis. This calculation is based on the existence of a single, lethal, internal chemical activity for such chemicals. The concentrations of toxic chemical to which the food chain is exposed may be specified by the user or may be taken directly from the values calculated by the exposure concentration model WASP4. Thus FGETS may be executed as a separate model or as a post-processor to WASP4. [text deleted .....] WASP FOOD CHAIN MODEL The WASP Food Chain Model (FCM2) is a generalized model of the uptake and elimination of toxic chemicals by aquatic organisms (Connolly and Thomann, 1985). It is a mass balance calculation in which the rates of uptake and elimination are related to the bioenergetic parameters of the species. A linear food chain or a food web may be specified. Con- centrations are calculated as a function of time and age for each species included. Exposure to the toxic chemical in food is based on a consumption rate and predator-prey relationships that are specified as a function of age. Exposure to the toxic chemical in water is functionally related to the respiration rate. Steady state concentrations also may be calculated. The concentrations of toxic chemical to which the food chain is exposed may be specified by the user or may be taken directly from the values calculated by the exposure concentration model WASP4. Thus FCM2 may be executed as a separate model or as a post-processor to WASP4. Migratory species, as well as non-migratory species, may be considered. Separate non-migratory food chains may be specified and the migratory species is exposed sequentially to each based on its seasonal movements. [text deleted .....] -- Domain: curtiss@umiacs.umd.edu Phillip Curtiss UUCP: uunet!mimsy!curtiss UMIACS - Univ. of Maryland Phone: +1-301-405-6710 College Park, Md 20742 .