wave induced advective transport below a rippled water sediment interface the exchange between the water column and the sediment bed and the transport inside the permeable sediment layer are important processes in the cycles of chemical elements in this paper we examine quantitatively the effects of modulations in the profile of the water sediment interface on this exchange and on the advective transport inside the sediment bed the flow field inside a sediment layer bounded between spatially periodic ripples on top and an impermeable bottom surface is modeled using darcy s law the forcing is due to progressive gravity waves in the water above the results of two different models for the pressure variation imposed on the upper boundary are compared the two pressure profiles are derived from potential flow theory and from a numerical solution to the navier stokes equations for the oscillatory flow over a rippled bed from an analytic solution to the two dimensional model the trajectories of pore water particles immediately below the ripple profile are found to be quite different from the simple elliptical pattern found below a flat bed the shapes of these trajectories can be quite complicated and vary considerably both along the length of the ripple and over the depth of the sediment layer close to its surface the total exchange across the water sediment interface averaged over one wave period is significantly higher across a rippled interface than across a flat bed this difference increases with increasing ripple slope and the strength of the wave motion and it decreases with increasing thickness of the sediment layer relative to the length of the gravity wave since rippled bed forms are commonly found in coastal waters the increase in the total exchange across a rippled water sediment boundary can enhance the exchange of solutes due to wave pumping immediately below the water sediment interface circulation cells with net advective transport over a wave period are found such net advection patterns can lead to spatial in the horizontal direction inhomogeneities of the vertical concentration or temperature profiles if the overlying water column and or the sediment bed act s as source or sink this gives a plausible physical mechanism to explain the spatial variations in vertical concentration profiles found in field measurements

holocene lake stages and thermokarst dynamics in a discontinuous permafrost affected region north eastern tibetan plateau abstract sediments of a thermokarst system on the north eastern tibetan plateau were studied to infer changes in the lacustrine depositional environment related to climatic changes since the early holocene the thermokarst pond with a length of 360 m is situated in a 14 5 6 km tectonically unaffected intermontane basin which is underlain by discontinuous permafrost a lake sediment core and bankside lacustrine onshore deposits were analysed additionally fossil lake sediments were investigated which document a former lake level high stand the sediments are mainly composed of marls with variable amounts of silt carbonate micrite and organic matter on the basis of sedimentological grain size data geochemical xrf mineralogical xrd and micropaleontological data ostracods and chironomide assemblages a reconstruction of a paleolake environment was achieved lacustrine sediments with endogenic carbonate precipitation suggest a lacustrine environment since at least 19 0 cal ka bp however because of relocation and reworking processes in the lake the sediments did not provide distinct information about the ultimate formation of the lake the high amount of endogenic carbonate suggests prolonged still water conditions at about 9 3 cal ka bp ostracod shells and chironomid head capsules in fossil lake sediments indicate at least one former lake level high stand which were developed between the early and middle holocene from the late holocene the area was possibly characterized by a lake level decline documented by a hiatus between lacustrine sediments and a reworked loess or loess like horizon after the lake level decline and the following warming period the area was affected by thermally induced subsidence and a re flooding of the basin because of thawing permafrost

dynamic response of surface water groundwater exchange to currents tides and waves in a shallow estuary 1 in shallow fetch limited estuaries variations in current and wave energy promote heterogeneous surface water groundwater mixing benthic exchange which influences biogeochemical activity here we characterize heterogeneity in benthic exchange within the subtidal zone of the delaware inland bays by linking hydrodynamic circulation models with mathematical solutions for benthic exchange forced by current bedform interactions tides and waves benthic fluxes oscillate over tidal cycles as fluctuating water depths alter fluid interactions with the bed maximum current driven fluxes 1 10 cm d occur in channels with strong tidal currents maximum wave driven fluxes 1 10 cm d occur in downwind shoals during high energy storms simulated wave pumping rates increase by orders of magnitude demonstrating the importance of storms in solute transfer through the benthic layer under moderate wind conditions 5 m s integrated benthic exchange rates due to wave current and tidal pumping are each 1 10 m3 s on the order of fluid contributions from runoff and fresh groundwater discharge to the estuary benthic exchange is thus a significant and dynamic component of an estuary s fluid budget that may influence estuarine geochemistry and ecology

velocity measurements close to rippled beds in oscillatory flow the results are reported of velocity measurements in oscillatory flow over rippled beds velocities were measured with a laser doppler anemometer in both an oscillating tray rig and an oscillatory flow water channel both self formed and artificial ripples were examined in addition some measurements were made with an apparently plane bed with intense sediment motion the experimental results were compared with the predictions of kalkanis 1964 kajiura 1968 bakker 1973 1974 and sleath 1974 the closest agreement between theory and experiment was obtained with the method of sleath measurements of the eulerian drift velocities showed drift towards the adjacent ripple crest in the immediate vicinity of the bed and away from the crest further out

the mathematics of early diagenesis from worms to waves the changes that sediments undergo after deposition are collectively known as diagenesis diagenesis is not widely recognized as a source for mathematical ideas however the myriad processes responsible for these changes lead to a wide variety of mathematical models in fact most of the classical models and methods of applied mathematics emerge naturally from quantification of diagenesis for example small scale sediment mixing by bottom dwelling animals can be described by the diffusion equation the dissolution of biogenic opal in sediments leads to sets of coupled nonlinear ordinary differential equations and modeling organisms that eat at depth in the sediment and defecate at the surface suggests the one dimensional wave equation while the effect of waves on pore waters is governed by the two or three dimensional wave equation diagenetic modeling however is not restricted to classical methods diagenetic problems of concern to modern mathematics exist in abundance these include free boundary problems that predict the depth of biological mixing or the penetration of o2 into sediments algebraic differential equations that result from the fast reversible reactions that regulate ph in pore waters inverse calculations of input functions histories and the determination of the optimum choice in a hierarchy of possible diagenetic models this review highlights and explores these topics with the hope of encouraging further modeling and analysis of diagenetic phenomena

hydraulic control of pore water geochemistry within the oxic suboxic zone of a permeable sediment the geochemical behavior of the top 70 cm of permeable reef flat sediments on checker reef oahu hawai i was examined using spatial and temporal changes in pore water o2 no no nh and n2o concentrations 221 324 the shallow depth of the sediment water interface relative to the height of waves propagating across the reef creates an environment in which pore water mixing and transport are dominated by wave induced mechanisms dissolved oxygen penetrated 15 50 cm in the four sites studied the depth integrated concentration of dissolved oxygen was greater under larger wave conditions and in more permeable sediments which suggests that dissolved oxygen may be a good indicator of the relationship between sediment metabolism and the physical nature of the sediment environment the absence of any subsurface n2o maxima limited temporal variability in pore water n2o concentrations and vertically coherent profiles of o2 no no and n2o suggest that suboxic processes are typically 22 32 restricted to spatial scales that are smaller than for oxic processes in these sediments the geochemical response of the sediments to a natural perturbation was monitored by examining the composition of pore waters immediately following a large wave event and for several weeks thereafter significant changes in the depth integrated concentrations of o2 no no and nh were observed following the perturbation however only changes in no 22 1

influence of sea level rise on iron diagenesis in an east florida subterranean estuary abstract subterranean estuary occupies the transition zone between hypoxic fresh groundwater and oxic seawater and between terrestrial and marine sediment deposits consequently we hypothesize in a subterranean estuary biogeochemical reactions of fe respond to submarine groundwater discharge sgd and sea level rise porewater and sediment samples were collected across a 30 m wide freshwater discharge zone of the indian river lagoon florida usa subterranean estuary and at a site 250 m offshore porewater fe concentrations range from 0 5 m at the shoreline and 250 m offshore to about 286 m at the freshwater saltwater boundary sediment sulfur and porewater sulfide maxima occur in near surface oc rich black sediments of marine origin and dissolved fe maxima occur in underlying oc poor orange sediments of terrestrial origin freshwater sgd flow rates decrease offshore from around 1 to 0 1 cm day while bioirrigation exchange deepens with distance from about 10 cm at the shoreline to about 40 cm at the freshwater saltwater boundary doc concentrations increase from around 75 m at the shoreline to as much as 700 m at the freshwater saltwater boundary as a result of labile marine carbon inputs from marine sgd this labile doc reduces fe oxides which in conjunction with slow discharge of sgd at the boundary allows dissolved fe to accumulate upward advection of fresh sgd carries dissolved fe from the fe oxide reduction zone to the sulfate reduction zone where dissolved fe precipitates as fe sulfides saturation models of fe sulfides indicate some fractions of these fe sulfides get dissolved near the sediment water interface where bioirrigation exchanges oxic surface water the estimated dissolved fe flux is approximately 0 84 m fe day per meter of shoreline to lagoon surface waters accelerated sea level rise predictions are thus likely to increase the fe flux to surface waters and local primary productivity particularly along coastlines where groundwater discharges through sediments

reactive transport modeling of iron diagenesis and associated organic carbon remineralization in a florida usa subterranean estuary article iron oxides are important terminal electron acceptors for organic carbon oc remineralization in subterranean estuaries particularly where oxygen and nitrate concentrations are low in indian river lagoon florida usa terrestrial fe oxides dissolve at the seaward edge of the seepage face and flow upward into overlying marine sediments where they precipitate as fe sulfides the dissolved fe concentrations vary by over three orders of magnitude but fe oxide dissolution rates are similar across the 25 m wide seepage face averaging around 0 21 mg cm 2 yr the constant dissolution rate but differing concentrations indicate fe dissolution is controlled by a combination of increasing lability of dissolved organic carbon doc and slower porewater flow velocities with distance offshore in contrast the average rate constants of fe sulfide precipitation decrease from 21 9 10 8 s 1 to 0 64 10 8 s 1 from the shoreline to the seaward edge of the seepage face as more oxygenated surface water circulates through the sediment the amount of oc

wave driven porewater and solute circulation through rippled elastic sediment under highly transient forcing waves induce porewater flow and solute transport through permeable marine sediment however past studies have ignored high frequency pressure pulses under the assumption that the porewater flow field is adequately represented by a time averaged one or that the saturated sediment is incompressible we modeled porewater flow and solute transport inside ripples forced by instantaneous pressure profiles along the sediment water interface swi with 0 1 s temporal resolution the transient pressure profiles were taken from a field data driven large eddy simulation model of wave driven oscillatory flow the simulations suggest that in elastic permeable and saturated sediment a time averaged representation of the flow field may be inadequate and that this also leads to shortcomings in how transport is modeled bursts in fluid flushing occur when high frequency pressure fluctuations were considered leading to larger long term average fluid fluxes compared to a steady flow field driven by a time averaged pressure profile the pressure perturbations along the swi propagate within a few milliseconds to meter depths within the sediment leading to strongly transient porewater velocity fields this leads to enhanced dispersion of solutes and larger time averaged solute fluxes however enhanced solute flux across the swi diminished through time with increasing permeability the high frequency transient pressures and sediment elastic properties we considered have been largely ignored and unrecognized future observational and modeling studies should consider these processes especially since they mediate timing sensitive biogeochemical reactions

aggregation of fine particles at the sediment water interface the presence of a bottom sediment layer agitated by mechanical stirring or by resident organisms tubificid oligochaetes significantly increases the rate at which fine 1 m cohesive particles are removed from suspension in laboratory columns measured rates of particle removal are equivalent to deposition velocities ranging from 0 23 m day 1 to 0 41 m day 1 these rates are an order of magnitude faster than deposition by gravitational settling or coagulation with larger particles in the water column as observed in experimental controls it is hypothesized that the increased removal rate is the result of aggregation in a sediment layer at the bed water interface characterized by loosely bound fluffy porous material hydrodynamically coupled to the water column according to this hypothesis particle removal occurs when motion of the overlying water or organism activity causes suspended fine particles to collide with and stick to the interfacial sediment this new hypothesis is supported by the mass and size distribution of tracer particles recovered in cores and sediment traps at a coastal site and by theoretical estimates of interfacial aggregation rates

impact of heterogeneity bed forms and stream curvature on subchannel hyporheic exchange 1 advection through hyporheic zones hz consisting of heterogeneous channel bend streambed deposits and their equivalent homogenous medium was investigated using finite difference groundwater flow and transport simulations and forward particle tracking the top prescribed head boundary was varied in order to mimic various stream channel head distributions resulting from the presence of bed forms and channel curvature flux calculations show that heterogeneity causes significant additional hz flux compared to an equivalent homogenous medium however the major cause of hz flux is a spatially periodic sinusoidal head distribution along the boundary representing the effect of bed forms the additional influence of heterogeneity on the total channel bed exchange and the overall hz geometry are increased when boundary head sinusoidal fluctuation is more subdued we present dimensionless numbers that summarize these relationships heterogeneity s influence is further magnified by considering the effect of channel curvature on boundary heads the simulations illustrate the dynamic influence of heterogeneity on the hyporheic zone since the various head boundaries employed in our modeling efforts are a proxy for different surface water conditions and bed form states that may occur during a single flood furthermore we show that residence times total tracking times of particles originating from the streambed follow a lognormal distribution in the presence of heterogeneity residence times can decrease or they can increase compared to residence times for homogeneous conditions depending on the relative positions of the heterogeneities and the bed forms hence streambed heterogeneity and stream curvature factors often neglected in previous modeling efforts combine with bed form configuration to dynamically determine hz geometry fluxes and residence time distributions

seawater circulation in sediments driven by interactions between seabed topography and fluid density 1 measurements of submarine groundwater discharge sgd in coastal areas often show that the saltwater discharge component is substantially greater than the freshwater discharge several mechanisms have been proposed to explain these high saltwater discharge values including saltwater circulation driven by wave and tidal pumping wave and tidal setup in intertidal areas currents over bedforms and density gradients resulting from mixing along the freshwater saltwater interface in this study a new mechanism for saltwater circulation and discharge is proposed and evaluated the process results from interaction between bedform topography and buoyancy forces even without flow or current over the bedform in this mechanism an inverted salinity and density profile in the presence of both a bedform on the seafloor and an upward flow of fresher groundwater from depth induces a downward flow of saline pore water under the troughs and upward flow under the adjacent crest of the bedform the magnitude and occurrence of the mechanism were tested using numerical methods the results indicate that this mechanism could drive seawater circulation under a limited range of conditions and contribute 20 30 of local sgd when and where the process is operative bedform shape hydraulic conductivity hydraulic head and salinity at depth in the porous media aquifer thickness effective porosity and hydrodynamic dispersion are among the factors that control the occurrence and magnitude of the circulation of seawater by this mechanism

the negligible effect of bed form migration on denitrification in hyporheic zones of permeable sediments bed form celerity the migration rate of ripples along a sediment bed has previously been shown to have dramatic effects on oxygen distribution and transport within the hyporheic zone of permeable sediments this has the potential to influence denitrification rates in particular by increasing the coupling of nitrification and denitrification to further understand this we numerically modeled nitrogen cycling under migrating ripples while the simulated oxygen profiles match with expected behavior almost no effect on denitrification or coupled nitrification denitrification was observed with increasing celerity instead denitrification rates were dominantly controlled by the flow velocity of water overlying the sediment

a wave induced transport process in marine sediments we show how surface wave action can increase the rate of transport of solutes into a sandy seabed by orders of magnitude via a mechanism known as mechanical dispersion it is most effective for large sediment permeability and thickness high surface wave amplitude and shallow water a method for setting up the appropriate transport equation valid when dispersion is well developed is given its dispersion term contains two mechanical dispersion parameters that can be estimated roughly from existing data when the sediments are well sorted the dispersion can be inhomogeneous and anisotropic in homogeneous isotropic sediments the effect of surface wave action on transport into sediments on the eastern u s shelf is shown to be significant under certain conditions the effect on thawing of subsea permafrost beneath prudhoe bay alaska seems negligible

on the elastic anatomy of heterogeneous fractures in rock abstract this study examines the feasibility of the full field ultrasonic characterization of fractures in rock to this end a slab like specimen of granite is subjected to in plane o 10 4 hz excitation while monitoring the induced 2d wavefield by a scanning laser doppler vibrometer sldv with sub centimeter spatial resolution upon suitable filtering and interpolation the observed wavefield is verified to conform with the plane stress approximation and used to i compute the maps of elastic modulus in the specimen before and after fracturing via a rudimentary application of the principle of elastography ii reconstruct the fracture geometry iii expose the fracture s primal traction displacement jump contact behavior and iv identify its profiles of shear and normal specific stiffness through the use of full field ultrasonic data the approach provides an unobscured high resolution insight into the fracture s contact behavior foreshadowing in depth laboratory exploration of interdependencies between the fracture geometry aperture interphase properties and its seismic characteristics

cycling of water through the sediment water interface by passive ventilation of relict biological structures abstract the biogeochemical environment of benthic sediments is affected by seawater transport across the sediment water interface and within the sediment pore spaces water circulation through the near surface sediments is produced by passive pumping of relict biostructures such as worm tubes and burrows this passive ventilation results from hydrodynamic interactions between structures that protrude from the sediment surface and flowing water in the overlying boundary layer flow over the end of a cylindrical worm tube projecting above the sediment surface into the benthic boundary layer results in lowered pressure in the tube and in sediments around the bottom end of the tube this induces flow of surface water through the adjacent sediment and back to the surface through tube a physical mechanism for this passive circulation is presented a mathematical model of interstitial water circulation produced by passive hydrodynamic effects has been solved analytically for steady flow in homogeneous isotropic sediments modflow a finite difference groundwater flow model is used to numerically determine the hydraulic gradients induced and the resulting flow through sediments near a structure under various conditions the magnitude of passive irrigation fluxes depends on the size and position of relict structures velocity of overlying surface water hydraulic conductivity of the sediments and the spatial distribution of tubes for a typical sandy sediment the hydraulic head in sediments near the bottom of a tube can be reduced by up to several centimeters and the zone of reduced head can extend over several hundred square centimeters around the tube surface water is drawn into the sediment throughout this area with a mean influx velocity of 10 3 cm s or greater yielding discharge rates on the order of tens to hundreds of milliliters per hour these passive fluxes are of the same magnitude as active pumping rates significantly greater than molecular diffusive fluxes and may represent a major driving mechanism for cycling water through surface sediments

spatial periodicity in bed form scale solute and thermal transport models of the hyporheic zone spatially periodic solute boundaries force symmetry across a model domain by ensuring that concentrations and concentration gradients are identical at the same location on opposite boundaries they have been used in multiple publications on a hyporheic zone model of a single ripple or dune style bed form including variable density flow and reactive transport variants we evaluate simulations of multibed form models without imposing spatially periodic transport to demonstrate that nonphysical solute distributions arise from the periodic solute transport assumption that is the flow field within the single bed form model leads to a transport scenario that violates the forced symmetry of periodic solute boundary conditions culminating in a physically unrealistic solute distribution our results show that lack of symmetry between boundaries is a function of the vertical concentration gradient and two dimensionless parameters characterizing the hyporheic and underflow flow regimes and the solute exchange between them we assess the error associated with the spatially periodic assumption based on an analysis of solute fluxes across the lateral bed form model boundaries while the focus is on steady state concentration distributions the implications for transient solute transport models are also discussed we conclude that periodic solute transport boundary conditions should be applied only to bed form models that have minimal vertical dispersive and diffusive solute transfer this includes gaining systems and tracers such as temperature for which a temporally periodic flux reversal occurs across the top boundary

generalized analytical model for benthic water flux forced by surface gravity waves 1 a generalized analytical model for benthic water flux forced by linear surface gravity waves over a series of layered hydrogeologic units is developed by adapting a previous solution for a hydrogeologic unit with an infinite thickness case i to a unit with a finite thickness case ii and to a dual unit system case iii the model compares favorably with laboratory observations the amplitude of wave forced benthic water flux is shown to be directly proportional to the amplitude of the wave the permeability of the hydrogeologic unit and the wave number and inversely proportional to the kinematic viscosity of water a dimensionless amplitude parameter is introduced and shown to reach a maximum where the product of water depth and the wave number is 1 2 submarine groundwater discharge sgd is a benthic water discharge flux to a marine water body the case i model estimates an 11 5 cm d sgd forced by a wave with a 1 s period and 5 cm amplitude in water that is 0 5 m deep as this wave propagates into a region with a 0 3 m thick hydrogeologic unit with a no flow bottom boundary the case ii model estimates a 9 7 cm d wave forced sgd as this wave propagates into a region with a 0 2 m thick hydrogeologic unit over an infinitely thick more permeable unit the case iii quasi confined model estimates a 15 7 cm d wave forced sgd the quasi confined model has benthic constituent flux implications in coral reef karst and clastic regions waves may undermine tracer and seepage meter estimates of sgd at some locations

the driving forces of porewater and groundwater flow in permeable coastal sediments a review abstract advective flows rapidly transport water solutes and particles into and out of permeable sand beds and significantly affects the biogeochemistry of coastal environments in this paper we reviewed the drivers of porewater and groundwater advection in permeable shelf sediments in an attempt to bridge gaps among different disciplines studying similar problems we identified the following driving forces 1 terrestrial hydraulic gradients 2 seasonal changes in the aquifer level on land moving the location of the subterranean estuary 3 wave setup and tidal pumping 4 water level differences across permeable barriers 5 flow and topography induced pressure gradients 6 wave pumping 7 ripple and other bed form migration 8 fluid shear 9 density driven convection 10 bioirrigation and bioturbation 11 gas bubble upwelling and 12 sediment compaction while these drivers occur over spatial scales ranging from mm to km and temporal scales ranging from seconds to years their ultimate biogeochemical implications are very similar i e they are often a source of new or recycled nutrients to seawater and transform organic carbon into inorganic carbon drivers 2 12 result in no net water input into the ocean taking all these mechanisms into account we conservatively estimate that a volume equivalent to that of the entire ocean is filtered by permeable sediments at time scales of about 3000 years quantifying the relative contribution of these drivers is essential to understand the contribution of sediments to the global cycles of matter