Adrian, R. J.
2013
Structure of turbulent boundary layers. In Coherent Flow Structures at Earth’s Surface, 2nd edn (ed. Venditti, J. G., Best, J. L., Church, M. & Hardy, R. J.), pp. 17–24. John Wiley and Sons.

Adrian, R. J. & Liu, Z. C.
2002
Observation of vortex packets in direct numerical simulation of fully turbulent channel flow. J. Vis.
5, 9–19.

Adrian, R. J., Meinhart, C. D. & Tomkins, C. D.
2000
Vortex organization in the outer region of the turbulent boundary layer. J. Fluid Mech.
422, 1–54.

Ashurst, W. T. & Meiburg, E.
1988
Three-dimensional shear layers via vortex dynamics. J. Fluid Mech.
189, 87–116.

Bailey, B. N. & Stoll, R.
2013
Turbulence in sparse organized vegetative canopies: a large-eddy simulation study. Boundary-Layer Meteorol.
147, 369–400.

Bailey, B. N., Stoll, R., Pardyjak, E. R. & Mahaffee, W. F.
2014
Effect of canopy architecture on vertical transport of massless particles. Atmos. Environ.
95, 480–489.

Baldocchi, D. D. & Hutchinson, B. A.
1987
Turbulence in an almond orchard: vertical variation in turbulence statistics. Boundary-Layer Meteorol.
40, 127–146.

Barros, J. M. & Christensen, K. T.
2014
Observations of turbulent secondary flows in a rough-wall boundary layer. J. Fluid Mech.
748, R1–13.

Barthlott, C., Drobinski, P., Fesquet, C., Dubos, T. & Pietras, C.
2007
Long-term study of coherent structures in the atmospheric surface layer. Boundary-Layer Meteorol.
125, 1–24.

Bell, J. H. & Mehta, R. D.
1990
Development of a two-stream mixing layer from tripped and untriped boundary layers. AIAA J.
28, 2034–2042.

Bernal, L. P., Breidenthal, R. E., Brown, G. L., Konrad, J. H. & Roshko, A.
1979
On the development of three dimensional small scales in turbulent mixing layers. In Proceedings of the 2nd International Symposium on Turbulent Shear Flows, Imperial College, pp. 8.1–8.6.

Breidenthal, R. E.1978 A chemically reacting turbulent shear layer. PhD thesis, California Insitute of Technology.

Browand, F. K. & Troutt, T. R.
1980
A note on spanwise structure in the two-dimensional mixing layer. J. Fluid Mech.
97, 771–781.

Browand, F. K. & Troutt, T. R.
1985
The turbulent mixing layer: geometry of large vortices. J. Fluid Mech.
158, 489–509.

Brunet, Y., Finnigan, J. J. & Raupach, M. R.
1994
A wind tunnel study of air flow in waving wheat: single-point velocity statistics. Boundary-Layer Meteorol.
70, 95–132.

Brunet, Y. & Irvine, M. R.
2000
The control of coherent eddies in vegetation canopies: streamwise structure spacing, canopy shear scale and atmospheric stability. Boundary-Layer Meteorol.
94, 139–163.

Canuto, C., Hussaini, M. Y., Quarteroni, A. & Zang, T. A.
1988
Spectral Methods in Fluid Dynamics, p. 568. Springer.

Chen, C. H. P. & Blackwelder, R. F.
1978
Large-scale motion in a turbulent boundary layer: a study using temperature contamination. J. Fluid Mech.
89, 1–31.

Christen, A. & Vogt, R.
2004
Direct measurement of dispersive fluxes within a cork oak plantation. In Proceedings of the 26th Conference on Agricultural and Forest Meteorology, American Meteorological Society.

Clark, J. A. & Markland, E.
1971
Flow visualization in turbulent boundary layers. J. Hydraul. Div. ASCE
97, 1653–1664.

Coceal, O., Dobre, A., Thomas, T. G. & Belcher, S. E.
2007
Structure of turbulent flow over regular arrays of cubical roughness. J. Fluid Mech.
589, 375–409.

Collis, S. S., Lele, S. K., Moser, R. D. & Rogers, M. M.
1994
The evolution of a plane mixing layer with spanwise nonuniform forcing. Phys. Fluids
6, 381–396.

Comte, P., Lesieur, M. & Lamballais, E.
1992
Large- and small-scale stirring of vorticity and a passive scalar in a 3-D temporal mixing layer. Phys. Fluids A
4, 2761–2778.

Comte, P., Silvestrini, J. H. & Bégou, P.
1998
Steamwise vortices in large-eddy simulations of mixing layers. Eur. J. Mech. (B/Fluids)
4, 615–637.

Fang, J. & Porté-Agel, F.
2015
Large-eddy simulation of very-large-scale motinos in the neutrally stratified atmospheric boundary layer. Boundary-Layer Meteorol.
155, 397–416.

Finnigan, J. J.
2000
Turbulence in plant canopies. Annu. Rev. Fluid Mech.
32, 519–571.

Finnigan, J. J. & Shaw, R. H.
2000
A wind tunnel study of airflow in waving wheat: an EOF analysis of the structure of the large-eddy motion. Boundary-Layer Meteorol.
96, 211–255.

Finnigan, J. J. & Shaw, R. H.
2008
Double-averaging methodology and its application to turbulent flow in and above vegetation canopies. Environ. Sci. Technol.
56, 534–561.

Finnigan, J. J., Shaw, R. H. & Patton, E. G.
2009
Turbulence structure above a vegetation canopy. J. Fluid Mech.
637, 387–424.

Fitzmaurice, L., Shaw, R. H., Paw, U. K. T. & Patton, E. G.
2004
Three-dimensional scalar microfront systems in a large-eddy simulation of vegetation canopy flow. Boundary-Layer Meteorol.
112, 107–127.

Ganapathisubramani, B., Longmire, E. K. & Marusic, I.
2003
Characteristics of vortex packets in turbulent boundary layers. J. Fluid Mech.
478, 35–46.

Gao, W., Shaw, R. H. & Paw, U. K. T.
1989
Observation of organized structure in turbulent flow within and above a forest canopy. Boundary-Layer Meteorol.
47, 349–377.

Gerz, T., Howell, J. & Mahrt, L.
1994
Vortex structures and microfronts. Phys. Fluids
6, 1242–1251.

Ghisalberti, M.
2010
The three-dimensionality of obstructed shear flows. Environ. Fluid Mech.
10, 329–343.

Green, M. A., Rowley, C. W. & Haller, G.
2007
Detection of Lagrangian coherent structures in 3D turbulence. J. Fluid Mech.
572, 111–120.

Guala, M., Tomkins, C. D., Christensen, K. T. & Adrian, R. J.
2012
Vortex organization in a turbulent boundary layer overlying sparse roughness elements. J. Hydraul. Res.
50, 465–481.

Haller, G.
2005
An objective definition of a vortex. J. Fluid Mech.
525, 1–26.

Head, M. R. & Bandyopadhyay, P.
1981
New aspects of turbulent boundary layer structure. J. Fluid Mech.
107, 297–338.

Herbert, T.
1988
Secondary instability of boundary layers. Annu. Rev. Fluid Mech.
20, 487–526.

Holmes, P., Lumley, J. L., Berkooz, G. & Rowley, C. W.
2012
Turbulence, Coherent Structures, Dynamical Systems and Symmetry, 2nd edn. p. 386. Cambridge University Press.

Holt, J. T.
1998
Experiments on Kelvin–Helmholtz billows influenced by boundaries. Geophys. Astrophys. Fluid Dyn.
89, 205–233.

Hommema, S. E. & Adrian, R. J.
2003
Packet structure of surface eddies in the atmospheric boundary layer. Boundary-Layer Meteorol.
106, 147–170.

Huang, L.-S. & Ho, C.-M
1990
Small-scale transition in a plane mixing layer. J. Fluid Mech.
210, 475–500.

Huerre, P. & Monkewitz, P. A.
1985
Absolute and convective instabilities in free shear layers. J. Fluid Mech.
159, 151–168.

Hunt, J. C., Wray, A. A. & Moin, P.1988 Eddies, stream, and convergence zones in turbulent flows. *Tech. Rep.* CTR-S88. Center for Turbulence Research, p. 193.

Hutchins, N. & Marusic, I.
2007
Evidence of very long meandering features in the logarithmic region of turbulent boundary layers. J. Fluid Mech.
579, 1–28.

Jeong, J. & Hussein, F.
1995
On the identification of a vortex. J. Fluid Mech.
285, 69–94.

Jiménez, J., Álamo, J. C. Del & Flores, O.
2004
The large-scale dynamics of near-wall turbulence. J. Fluid Mech.
505, 179–199.

Kim, J. & Moin, P.
1986
The structure of the vorticity field in turbulent channel flow. Part 2. Study of ensemble-averaged fields. J. Fluid Mech.
162, 339–363.

Kim, K. C. & Adrian, R. J.
1999
Very large-scale motion in the outer layer. Phys. Fluids
11, 417–422.

Klebanoff, P. S., Tidstrom, K. D. & Sargent, L. M.
1962
The three-dimensional nature of boundary-layer instability. J. Fluid Mech.
12, 1–34.

Lasheras, J. C. & Choi, H.
1988
Three-dimensional instability of a plane free shear layer: an experimental study of the formation and evolutionj of streamwise vortices. J. Fluid Mech.
189, 53–86.

Lin, S. J. & Corcos, G. M.
1984
The mixing layer: deterministic models of a turbulent flow. Part 3. The effect of plane strain on the dynamics of streamwise vortices. J. Fluid Mech.
141, 139–178.

Lindzen, R. S. & Rosenthal, A. J.
1976
On the instability of Helmholtz velocity profiles in stably stratified fluid when a lower boundary is present. J. Geophys. Res.
81, 1561–1571.

Lu, S. S. & Willmarth, W. W.
1973
Measurements of the structure of Reynolds stress in a turbulent boundary layer. J. Fluid Mech.
60, 481–571.

Mahrt, L.
1991
Eddy asymmetry in the sheared heated boundary layer. J. Atmos. Sci.
483, 472–492.

Mathis, R., Hutchins, N. & Marusic, I.
2009
Large-scale amplitude modulation of the small-scale structures in turbulent boundary layers. J. Fluid Mech.
628, 311–377.

Metcalfe, R. W., Hussain, F., Menon, S. & Hayakawa, M.
1985
Coherent structures in a turbulent mixing layer: a comparison between numerical simulations and experiments. In Turbulent Shear Flows 5 (ed. Durst, F., Launder, B. E., Lumley, J. L., Schmidt, F. W. & Whitelaw, J. H.), pp. 110–123. Springer.

Michalke, A.
1965
On the inviscid instability of the hyperbolic-tangent velocity profile. J. Fluid Mech.
19, 543–556.

Moser, R. D. & Rogers, M. M.
1991
Mixing transition and the cascade to small scales in a plane mixing layer. Phys. Fluids A
3, 1128.

Nyggard, K. J. & Glezer, A.
1991
Evolution of streamwise vortices and generation of small-scale motion in a plane mixing layer. J. Fluid Mech.
231, 257–301.

Offen, G. R. & Kline, S. J.
1975
A proposed model of the bursting process in turbulent boundary layers. J. Fluid Mech.
70, 209–228.

Pan, Y., Chamecki, M. & Isard, S. A.
2014
Large-eddy simulation of turbulence and particle dispersion inside the canopy roughness sublayer. J. Fluid Mech.
753, 499–534.

Paw, U. K. T., Brunet, Y., Collineau, S., Shaw, R. H., Maitani, T., Qiu, J. & Hipps, L.
1992
On coherent structures in turbulence above and within agricultural plant canopies. Agric. Forest Meteorol.
61, 55–68.

Perret, L. & Ruiz, T.
2013
SPIV analysis of coherent structures in a vegetation canopy model flow. In Coherent Flow Structures at Earth’s Surface (ed. Venditti, J. G., Best, J. L., Church, M. & Hardy, R. J.), pp. 161–174. John Wiley and Sons.

Pierrehumbert, R. T. & Widnall, S. E.
1982
The two- and three-dimensional instabilities of a spatially periodic shear layer. J. Fluid Mech.
114, 59–82.

Raupach, M. R.
1981
Conditional statistics of Reynolds stress in rough-wall and smooth-wall turbulent boundary layers. J. Fluid Mech.
108, 363–382.

Raupach, M. R., Finnigan, J. J. & Brunet, Y.
1996
Coherent eddies and turbulence in vegetation canopies: the mixing-layer analogy. Boundary-Layer Meteorol.
78, 351–382.

Raupach, M. R. & Thom, A. S.
1981
Turbulence in and above plant canopies. Annu. Rev. Fluid Mech.
13, 97–129.

Reynolds, R. T., Hayden, P., Castro, I. P. & Robins, A. G.
2007
Spanwise variations in nominally two-dimensional rough-wall boundary layers. Exp. Fluids
42, 311–320.

Robinson, S. K.
1991
Coherent motions in the turbulent boundary layer. Annu. Rev. Fluid Mech.
23, 601–639.

Rogers, M. M. & Moin, P.
1987
The structure of the vorticity field in homogeneous turbulent flows. J. Fluid Mech.
176, 33–66.

Rogers, M. M. & Moser, R. D.
1992
The three-dimensional evolution of a plane mixing layer: the Kelvin–Helmholtz rollup. J. Fluid Mech.
243, 183–226.

Rogers, M. M. & Moser, R. D.
1994
Direct simulation of a self-similar turbulent mixing layer. Phys. Fluids
6, 903–923.

Saric, W. S. & Thomas, A. S. W.
1984
Experiments on the subharmonic route to turbulence in boundary layers. In Turbulence and Chaotic Phenomena in Fluids (ed. Tatsumi, T.), pp. 117–122. Elsevier.

Shaw, R. H., Brunet, Y., Finnigan, J. J. & Raupach, M. R.
1995
A wind tunnel study of air flow in waving wheat: two-point velocity statistics. Boundary-Layer Meteorol.
76, 349–376.

Shaw, R. H., Paw, U. K. T. & Gao, W.
1989
Detection of temperature ramps and flow structures at a deciduous forest site. Agric. Forest Meteorol.
47, 123–138.

Shaw, R. H. & Schumann, U.
1992
Large-eddy simulation of turbulent flow above and within a forest. Boundary-Layer Meteorol.
61, 47–64.

Stoll, R. & Porté-Agel, F.
2006a
Dynamic subgrid-scale models for momentum and scalar fluxes in large-eddy simulations of neutrally stratified atmospheric boundary layers over heterogeneous terrain. Water Resour. Res.
42, W01409.

Stoll, R. & Porté-Agel, F.
2006b
Effect of roughness on surface boundary conditions for large-eddy simulation. Boundary-Layer Meteorol.
118, 169–187.

Tanahashi, M., Iwase, S. & Miyauchi, T.
2001
Appearance and alignment with strain rate of coherent fine scale eddies in turbulent mixing layer. J. Turbul.
2, 006.

Tay, G. F. K., Kuhn, D. C. S. & Tachie, M. F.
2013
Surface roughness effects on the turbulence statistics in a low Reynolds number channel flow. J. Turbul.
14, 121–146.

Wang, Y., Tanahashi, M. & Miyauchi, T.
2007
Coherent fine scale eddies in turbulence transition of spatially-developing mixng layer. Intl J. Heat Fluid Flow
28, 1280–1290.

Watanabe, T.
2004
Large-eddy simulation of coherent turbulence structures associated with scalar ramps over plant canopies. Boundary-Layer Meteorol.
112, 307–341.

Wu, Y. & Christensen, K. T.
2010
Spatial structure of a turbulent boundary layer with irregular surface roughness. J. Fluid Mech.
655, 380–418.

Zhou, J., Adrian, R. J., Balachandar, S. & Kendall, T. M.
1999
Mechanisms for generating coherent packets of hairpin vortices in channel flow. J. Fluid Mech.
387, 353–396.