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POPC:POPS (5:1) with 890 mM potassium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 890 mM potassium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4946 water molecules and 79 Na+ ions.

POPC:POPS (5:1) with 450 mM potassium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 450 mM potassium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4926 water molecules and 40 Na+ ions.

POPC:POPS (5:1) with 440 mM sodium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 440 mM sodium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4965 water molecules and 39 Na+ ions.

POPC:POPS (5:1) with 890 mM sodium simulation with CHARMM36 at 298K

POPC:POPS (5:1) with 890 mM sodium simulation with CHARMM36 at 298K. Trajectory 50-200ns. 110 POPC molecules, 22 POPS molecules, 4932 water molecules and 79 Na+ ions.

opencc-by-4.0Mar 2018View details →

Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 940 mM NaCl, 310K, GROMACS 5.1.4

Simulations of a POPC bilayer with 940 mM of NaC.  The sixth from the set of 6 simulations. The goal was to study the effect of scaling the CHARMM FF on the ion binding. Done for the NMRlipids project, see  http://nmrlipids.blogspot.fi for more information. A POPC bilayer consisting of 200 lipids (100 per leaflet)  is simulated in the presence of 945 mM NaCl. The scaled ECC-Charmm36  model  is employed for lipids, the Charmm compatible variant  of the tip3p model for water, and the ECC-ions  for NaCl. The new extra nonbonded parameters (NB-Fix) were removed.   The Charmm36 force field parameters were obtained from http://charmm-gui.org/ Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89. In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here. This is the same scaling as used for ECC-POPC –––––––––––––––––––––––––––––––––––––––––––––––––––––– The files are in GROMACS format. Trajectory (.xtc) is  610 ns long with data saved every 100 ps. the initial structure (.gro), topology (.top), index file (.ndx),  simulation paremeter file (.mdp), binary run input file  for GROMACS v. 5.1–> (.tpr) and the energy output file  (.edr) are provided.

opencc-by-4.0Mar 2018View details →

Simulation data for ECC-CHARMM36 POPC bilayer, 100 lipids/leaflet, 450 mM CaCl2, 310K, GROMACS 5.1.4

Simulations of a POPC bilayer with 450 mM of CaCl_2.  The fourth from the set of 6 simulations. The goal was to study the effect of scaling the CHARMM FF on the ion binding. Done for the NMRlipids project, see  http://nmrlipids.blogspot.fi for more information. A POPC bilayer consisting of 200 lipids (100 per leaflet)  is simulated in the presence of 450 mM CaCl_2. The scaled ECC-Charmm36  model  is employed for lipids, the Charmm compatible variant  of the tip3p model for water, and the ECC-ions  for CaCl_2. The new extra nonbonded parameters (NB-Fix) were removed.   The Charmm36 force field parameters were obtained from http://charmm-gui.org/ Charges of head group of POPC were scaled by 0.8, sigmas were scaled by 0.89. In the CHARMM FF, thera are extra sigma and epsilon parameters for 1,4 interactions (these are not present in the lipid14 FF). These parameters were not scaled here. This is the same scaling as used for ECC-POPC –––––––––––––––––––––––––––––––––––––––––––––––––––––– The files are in GROMACS format. Trajectory (.xtc) is  610 ns long with data saved every 100 ps. the initial structure (.gro), topology (.top), index file (.ndx),  simulation paremeter file (.mdp), binary run input file  for GROMACS v. 5.1–> (.tpr) and the energy output file  (.edr) are provided.

opennotspecifiedMay 2019View details →

lil, left ilium;; lti, left tibia; pd, pedal digits; and ub, unidentified bony element. The white box indicates the position from which the sample was taken for histological analysis. Scale bars, 10 mm (a, c, d), 20 mm (b). in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

lil, left ilium;; lti, left tibia; pd, pedal digits; and ub, unidentified bony element. The white box indicates the position from which the sample was taken for histological analysis. Scale bars, 10 mm (a, c, d), 20 mm (b).

opennotspecifiedMay 2019View details →

vertebra; po, postacetabular process of ilium; pp, pubic peduncle of ilium; pr, preacetabular process of ilium; ra, radius; ti, tibia; ul, ulna; I1, manual phalange I-1; II1, II2 and II3, manual phalanges II-1, II-2 and II-3; III1, III2, III3 and III4, manual phalanges III-1, III-2, III-3 and III-4. Scale bars, 10 mm. in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

vertebra; po, postacetabular process of ilium; pp, pubic peduncle of ilium; pr, preacetabular process of ilium; ra, radius; ti, tibia; ul, ulna; I1, manual phalange I-1; II1, II2 and II3, manual phalanges II-1, II-2 and II-3; III1, III2, III3 and III4, manual phalanges III-1, III-2, III-3 and III-4. Scale bars, 10 mm.

EX-FIG. 45. Theropod tibiae in distal view, illustrating different states of character 208. a, Herrerasaurus ischigualastensis', left tibia (reversed); redrawn from Novas (1993). B, Dilophosaurus wetherilli: right tibia; based on UCMP V 6468. c, Piatnitzkysaurus foresi: left tibia (reversed); based on MACN CH 895. D, Rahonavis ostromi: right tibia; based on UA 8656. Abbreviations: ant, anterior; lat, lateral. Scale bars represent 10 mm (a-c) x and 5 mm (d). in The interrelationships and evolution of basal theropod dinosaurs

EX-FIG. 45. Theropod tibiae in distal view, illustrating different states of character 208. a, Herrerasaurus ischigualastensis', left tibia (reversed); redrawn from Novas (1993). B, Dilophosaurus wetherilli: right tibia; based on UCMP V 6468. c, Piatnitzkysaurus foresi: left tibia (reversed); based on MACN CH 895. D, Rahonavis ostromi: right tibia; based on UA 8656. Abbreviations: ant, anterior; lat, lateral. Scale bars represent 10 mm (a-c) x and 5 mm (d).

text-fig. 46. Segisaurus halli, UCMP V 338; stereophotographs of the left femur, tibia and fibula, illustrating state 1 of character 209. Abbreviations: fe, femur; fib, fibula; tib, tibia. Scale bar represents 10 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 46. Segisaurus halli, UCMP V 338; stereophotographs of the left femur, tibia and fibula, illustrating state 1 of character 209. Abbreviations: fe, femur; fib, fibula; tib, tibia. Scale bar represents 10 mm.

text-fig. 43. Right theropod tibiae in proximal yiew, illustrating states for characters 204 and 205. a, Dilophosaurus wetherilli; based on UCMP V 4214. B, Allosaurus fragilis; based on AMNH 680. Abbreviations: ant, anterior; cc, cnemial crest; fc, fibular condyle; lat, lateral. Scale bars represent 10 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 43. Right theropod tibiae in proximal yiew, illustrating states for characters 204 and 205. a, Dilophosaurus wetherilli; based on UCMP V 4214. B, Allosaurus fragilis; based on AMNH 680. Abbreviations: ant, anterior; cc, cnemial crest; fc, fibular condyle; lat, lateral. Scale bars represent 10 mm.

text-fig. 40. Left theropod ilia in ventral view, illustrating the differences in the development of the brevis fossa (character 176). a, Sinraptor dongi; redrawn from Currie and Zhao (1993b). B, Syntarsus rhodesiensis; based on QG 1. Abbreviations: bf, brevis fossa; ip, ischial peduncle; pp, pubic peduncle; sac, supraacetabular crest. Scale bars represent 100 mm (a) and 10 mm (b). in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 40. Left theropod ilia in ventral view, illustrating the differences in the development of the brevis fossa (character 176). a, Sinraptor dongi; redrawn from Currie and Zhao (1993b). B, Syntarsus rhodesiensis; based on QG 1. Abbreviations: bf, brevis fossa; ip, ischial peduncle; pp, pubic peduncle; sac, supraacetabular crest. Scale bars represent 100 mm (a) and 10 mm (b).

text-fig. 39. Theropod pelves in left lateral view, illustrating several pelvic characters, a, Herrerasaurus ischigualastensis; redrawn (reversed) from Novas (1993). B, Syntarsus rhodesiensis; based on QG 1, QG 691, and Raath (1990). c, Allosaurus fragilis; modified from Molnar et al. (1990). D, generalized tyrannosaurid; based on Osborn (1916) and ROM 807. E, Segnosaurus galbinensis', redrawn from Barsbold and Maryanska (1990). F, Rahonavis ostromi', based on UA 8656. Abbreviations: ac, acetabulum; bs, brevis shelf; il, ilium; ir, iliac ridge; is, ischium; of, obturator foramen; op, obturator process; pf, pubic fenestra; pip, posterior ischial process; pu, pubis. Scale bars represent 50 mm (a-b), 100 mm (c-e), and 10 mm (f). in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 39. Theropod pelves in left lateral view, illustrating several pelvic characters, a, Herrerasaurus ischigualastensis; redrawn (reversed) from Novas (1993). B, Syntarsus rhodesiensis; based on QG 1, QG 691, and Raath (1990). c, Allosaurus fragilis; modified from Molnar et al. (1990). D, generalized tyrannosaurid; based on Osborn (1916) and ROM 807. E, Segnosaurus galbinensis', redrawn from Barsbold and Maryanska (1990). F, Rahonavis ostromi', based on UA 8656. Abbreviations: ac, acetabulum; bs, brevis shelf; il, ilium; ir, iliac ridge; is, ischium; of, obturator foramen; op, obturator process; pf, pubic fenestra; pip, posterior ischial process; pu, pubis. Scale bars represent 50 mm (a-b), 100 mm (c-e), and 10 mm (f).

text-fig. 38. Manual ungual II of two theropod dinosaurs in lateral view, illustrating states for characters 162 and 163. a, Allosaurus fragilis; MOR 693. B, Saurornitholestes längstem; MOR 660. Scale bars represent 10 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 38. Manual ungual II of two theropod dinosaurs in lateral view, illustrating states for characters 162 and 163. a, Allosaurus fragilis; MOR 693. B, Saurornitholestes längstem; MOR 660. Scale bars represent 10 mm.

text-fig. 48. Saurornitholestes langstoni; TMP 88.121.39; fibula, lateral view, showing state 1 for characters 211 and 212. Scale bar represents 10 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 48. Saurornitholestes langstoni; TMP 88.121.39; fibula, lateral view, showing state 1 for characters 211 and 212. Scale bar represents 10 mm.

text-fig. 36. Theropod mani in dorsal view, illustrating several manual characters, a, Dilophosaurus wetherillv, left manus; UCMP V 4214. B, Allosaurus fragilis', right manus; MOR 693. Scale bars represent 10 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 36. Theropod mani in dorsal view, illustrating several manual characters, a, Dilophosaurus wetherillv, left manus; UCMP V 4214. B, Allosaurus fragilis', right manus; MOR 693. Scale bars represent 10 mm.

text-fig. 34. Left theropod humeri in anterior (a-b, d) and lateral (c) views, illustrating several forelimb characters, a, Allosaurusfragilis; redrawn from Madsen (1976). B-c, Camotaurus sastrei; based on MACN CH 894. D, Deinonychus antirrhopus; redrawn (reversed) from Ostrom (1969/?). Abbreviations: af, articular facet on head of humans; dpc, deltopectoral crest; it, internal tuberosity. Scale bars represent 50 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 34. Left theropod humeri in anterior (a-b, d) and lateral (c) views, illustrating several forelimb characters, a, Allosaurusfragilis; redrawn from Madsen (1976). B-c, Camotaurus sastrei; based on MACN CH 894. D, Deinonychus antirrhopus; redrawn (reversed) from Ostrom (1969/?). Abbreviations: af, articular facet on head of humans; dpc, deltopectoral crest; it, internal tuberosity. Scale bars represent 50 mm.

text-fig. 50. Theropod metatarsals, illustrating several tarsal characters, a, Allosaurus sp.; DNM 116; left metatarsals II-IV, anterior view. B, Troödon formosus; MOR 748; right metatarsals II-IV, anterior view, c, Albertosaurus sarcophagus; ROM 807; left metatarsal V; lateral view, proximal is to the right. Scale bars represent 50 mm (a) and 10 mm (b-c). in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 50. Theropod metatarsals, illustrating several tarsal characters, a, Allosaurus sp.; DNM 116; left metatarsals II-IV, anterior view. B, Troödon formosus; MOR 748; right metatarsals II-IV, anterior view, c, Albertosaurus sarcophagus; ROM 807; left metatarsal V; lateral view, proximal is to the right. Scale bars represent 50 mm (a) and 10 mm (b-c).

text-fig. 31. Mid-caudal chevrons, illustrating states for characters 128 and 130. a, Majungatholus atopus-, based on FMNH/UA 96313. B, Allosaurus fragilis; redrawn from Madsen (1976). Scale bars represent 50 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 31. Mid-caudal chevrons, illustrating states for characters 128 and 130. a, Majungatholus atopus-, based on FMNH/UA 96313. B, Allosaurus fragilis; redrawn from Madsen (1976). Scale bars represent 50 mm.

text-fig. 30. Undetermined ornithomimosaur; mid-caudal vertebral column; Judith River Formation, southern Alberta; TMP unnumbered. Scale bar represents 50 mm. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 30. Undetermined ornithomimosaur; mid-caudal vertebral column; Judith River Formation, southern Alberta; TMP unnumbered. Scale bar represents 50 mm.