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opencc-zeroApr 2015View details →

MD simulation trajectories of Glycerol for different POPC/Cholesterol concentrations (0,10,15,20,25,35,50%). CHARMM36, Gromacs 4.6.3. 2014.

MD simulation trajectories files, for fully hydrated POPC + CHOLESTEROL bilayer. The CHARMM36 force field was used with Gromacs 4.6.3. Conditions: T=298K and different cholesterol concentrations described in the name of each file. 170 ns each trajectory, last 100 ns analyzed.

opencc-zeroApr 2015View details →

Hydrated DPPC, MD simulation trajectory and related files for UA charmm36 model by Lee et al 2014

MD simulation files 72 hydrated DPPC  + 2189 water TIP3P  NPgT P=1atm, gamma=0, T=323K (liquid crystalline phase) 20 ns equilibration (not here) 50 ns trajectory (dcd file) Model : Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB. CHARMM36 United Atom Chain Model for Lipids and Surfactants. J Phys Chem B. 2014;118(2):547-556. doi:10.1021/jp410344g. ---- * bilayer-72DPPC-c36-AU.psf : NAMD2.10 structure file Obtained with psfgen utility, using 1) topology from Lee et al.  2014 2) positions from J. Klauda. http://terpconnect.umd.edu/~jbklauda/research/download.html ---- * dppc_c36_AU.equil.2.dcd : trajectory file of 2635 frames every 20 ps. --- * measure_SCD_heads.tcl : file used to measure order parameters for the head hydrogens using vmd-1.9 --- *namd_input.tar files usefull to launch the simulations using NAMD(2.10).

opencc-zeroApr 2015View details →

Hydrated DPPC, MD simulation trajectory and related files for UA charmm36 model by Lee et al 2014

opencc-zeroFeb 2014View details →

Molecular dynamics derived side chain order parameters for Asp, Glu, Asn, and Gln residues in ribonucleases H, and molecular dynamics trajectories for E. coli ribonuclease H

This dataset contains tab-delimited text files reporting the complete calculated S2 side chain order parameters for carboxyl- and carbonyl-containing residues (Asp, Glu, Asn, Gln) in all RNase H homologs studied, as well as complete simulation trajectory data for the E. coli apo, site A, and site B simulations described in the text. We hope that easy access to the complete trajectory data for the experimentally best-characterized homolog will facilitate future comparison between simulation and experiments. order_parameters_magnesium.dat contains the calculated S2 side chain order parameters for carboxyl- and carbonyl-containing residues in each of the three E. coli trajectories supplied in this dataset. These data are sufficient to reproduce Figure 6. 2RN2.apo.pdb, 2RN2.MG.siteA.pdb, and 2RN2.MG.siteB.pdb define the equilibrated structure from which the E. coli apo, site A, and site B trajectories were initiated. All protein atoms, including hydrogens, are included, as well as Mg ions. Explicit waters and chloride counterions have been removed. 2RN2.apo.dcd, 2RN2.MG.siteA.dcd, and 2RN2.MG.siteB.dcd contain 100ns trajectories initiated from the starting structures in the corresponding pdb files. Frames were written every 4.5ps. Trajectories have been aligned to the initial structure of the apo trajectory to facilitate visualization. The remaining *.S2.CO.dat files contain the calculated S2 side chain order parameters for all apo RNases H simulated in this study. Each file is named for the PDB ID of its corresponding structure (see Table 1). These data are sufficient to reproduce Figure 8 (which reports on only the conserved active-site residues).

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 70 wt% C12E5, T=298K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 70 wt% C12E5, T=320K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 70 wt% C12E5, T=333K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 60 wt% C12E5, T=333K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 60 wt% C12E5, T=320K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 60 wt% C12E5, T=298K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

DOPC lipid bilayer simulation trajectory and files from Franova et al. BBA 1838 (2014) 1406–1411

Simulation files for pure DOPC (no pyrene present) simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411

DOPC lipid bilayer with PYR6 simulation trajectory and files from Franova et al. BBA 1838 (2014) 1406–1411

Simulation files for DOPC with PYR6 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411

DOPC lipid bilayer with PYR8 simulation trajectory and files from Franova et al. BBA 1838 (2014) 1406–1411

Simulation files for DOPC with PYR8 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411

DOPC lipid bilayer with PYR4 simulation trajectory and files from Franova et al. BBA 1838 (2014) 1406–1411

Simulation files for DOPC with PYR4 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411

DOPC lipid bilayer with PYR10 simulation trajectory and files from Franova et al. BBA 1838 (2014) 1406–1411

Simulation files for DOPC with PYR10 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411

opencc-zeroJan 2016View details →

3D Matching of resource vision tracking trajectories

Three dimensional (3D) paths of resources, have been proposed in construction management, as an efficient way for measuring labor productivity. These paths, are extracted either by using sensors such as Global Positioning System (GPS), Radio Frequency Identification (RFID), and Ultra-wideband (UWB), or based on cameras placed at jobsites for surveillance purposes. However, the tag based methods are seriously limited by privacy conflicts since they are not welcome from the personnel. On the other hand, the computer vision based methods have not achieved full automation in measuring labour productivity because they require prior knowledge of the type of tasks performed in specific working zones. This is associated with the lack of depth information. For this purpose, this paper proposes a computationally efficient computer vision method for matching construction workers across different frames. Entity matching, is a process that corresponds to a compulsory step prior to the calculation of the 3D position. The proposed matching method, is based on epipolar geometry, template and motion similarity features. The main result of this process, is to provide a method for the acquisition of the 3D paths that compose the detailed profile of a construction activity in terms of both time and space.

opencc-zeroApr 2016View details →

Myotis myotis baseline trajectory

Myotis myotis baseline trajectory Myotis myotis baseline trajectory  x(t), y(t), z(t)

opencc-by-4.0May 2016View details →

Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC

System: Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 6 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 94 mol-%) lipids in water. Number of DMPC: 120. Number of DMTAP: 8. Number of Cl--ions: 8. Number of waters: 5099. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)] with DMTAP modification by Gurtovenko et al. [Biophys. J. 86 3461 (2004)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 109 ns. Previously equilibrated for: 32 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.

opencc-by-4.0Dec 2012View details →

Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid bilayer

System: DMPC (dimyristoylphosphatidylcholine) bilayer in water. Number of lipids: 128. Number of waters: 5097. Lipid model: 'Berger' united-atom [Biophys. J. 72 2002 (1997)]. Water model: SPC [In Intermolecular Forces, ed. Pullman. 331 (1981)]. Simulation engine: Gromacs 3.x [www.gromacs.org] Trajectory length: 110 ns. Previously equilibrated for: 20 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with lipids and water coupled separately at T = 323 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984)] with xy and z coupled separately at p = 1.0 bar. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Phys. 103 8577 (1995)], real-space cutoff at 1.0 nm. Van der Waals: Truncated at 1.0 nm. Constraints: Covalent bond lengths in lipids using LINCS [J. Comput. Chem. 18 1463 (1997)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: [1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". J. Phys. Chem. B 113 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.