The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces.
暂无分享,去创建一个
Marcello Sega | Miguel Jorge | Pál Jedlovszky | M. Jorge | P. Jedlovszky | S. Kantorovich | M. Sega | Sofia S Kantorovich
[1] K. D. Gibson,et al. Surface area of the intersection of three spheres with unequal radii A simplified analytical formula , 1988 .
[2] R. Hancock,et al. Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles. , 2000, Biochemistry.
[3] Cyrus Levinthal,et al. A vectorized algorithm for calculating the accessible surface area of macromolecules , 1991 .
[4] Atsuyuki Okabe,et al. Spatial Tessellations: Concepts and Applications of Voronoi Diagrams , 1992, Wiley Series in Probability and Mathematical Statistics.
[5] J. J. Müller. Calculation of scattering curves for macromolecules in solution and comparison with results of methods using effective atomic scattering factors , 1983 .
[6] Mihaly Mezei,et al. A new method for mapping macromolecular topography. , 2003, Journal of molecular graphics & modelling.
[7] J. Janin,et al. Analytical approximation to the accessible surface area of proteins. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[8] B. Bush,et al. Macromolecular shape and surface maps by solvent exclusion. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[9] Johannes Quaas,et al. Global warming: The soot factor , 2011, Nature.
[10] Estanislao Silla,et al. GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set , 1990 .
[11] M. Cordeiro,et al. Intrinsic structure and dynamics of the water/nitrobenzene interface , 2007 .
[12] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[13] K. D. Gibson,et al. Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii , 1987 .
[14] S. Nosé. A molecular dynamics method for simulations in the canonical ensemble , 1984 .
[15] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[16] C. R. Watts,et al. The use of dodecylphosphocholine micelles in solution NMR. , 1995, Journal of magnetic resonance. Series B.
[17] W. C. Still,et al. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) , 1999 .
[18] Árpád Vincze,et al. A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid–vapor interface of water , 2008, J. Comput. Chem..
[19] A. Shrake,et al. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.
[20] Hai Wang,et al. On evolution of particle size distribution functions of incipient soot in premixed ethylene-oxygen-argon flames , 2008 .
[21] J. Gesell,et al. Two-dimensional 1H NMR experiments show that the 23-residue magainin antibiotic peptide is an α-helix in dodecylphosphocholine micelles, sodium dodecylsulfate micelles, and trifluoroethanol/water solution , 1997, Journal of biomolecular NMR.
[22] I. R. Mcdonald,et al. Molecular dynamics calculations for the liquid and cubic plastic crystal phases of carbon tetrachloride , 1982 .
[23] Jon Louis Bentley,et al. Multidimensional binary search trees used for associative searching , 1975, CACM.
[24] S. V. Renssen. The greenhouse-gas gang , 2012 .
[25] P. Jedlovszky,et al. New insight into the orientational order of water molecules at the water/1,2-dichloroethane interface: A Monte Carlo simulation study , 2002 .
[26] S. Kim,et al. Solvent-accessible surfaces of nucleic acids. , 1979, Journal of molecular biology.
[27] David G. Kirkpatrick,et al. On the shape of a set of points in the plane , 1983, IEEE Trans. Inf. Theory.
[28] P. Jedlovszky,et al. Morphology of bile salt micelles as studied by computer simulation methods. , 2007, Langmuir : the ACS journal of surfaces and colloids.
[29] P. Jedlovszky,et al. Molecular aggregates in aqueous solutions of bile acid salts. Molecular dynamics simulation study. , 2007, The journal of physical chemistry. B.
[30] A. C. Barone,et al. Detection of combustion formed nanoparticles. , 2003, Chemosphere.
[31] B. Lee,et al. The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.
[32] B. Ladanyi,et al. Water-hydrocarbon interfaces: effect of hydrocarbon branching on interfacial structure. , 2006, The journal of physical chemistry. B.
[33] Akbar Nayeem,et al. MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives , 1992 .
[34] Y. Liu,et al. Size distribution and morphology of nascent soot in premixed ethylene flames with and without benzene doping , 2009 .
[35] Herbert Edelsbrunner,et al. Measuring proteins and voids in proteins , 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.
[36] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[37] Frederic M. Richards,et al. Packing of α-helices: Geometrical constraints and contact areas☆ , 1978 .
[38] F M Richards,et al. Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.
[39] P. Tarazona,et al. Intrinsic profiles beyond the capillary wave theory: a Monte Carlo study. , 2003, Physical review letters.
[40] Kenneth M. Merz,et al. Rapid approximation to molecular surface area via the use of Boolean logic and look‐up tables , 1993, J. Comput. Chem..
[41] B. Fedorov,et al. Improved technique for calculating X‐ray scattering intensity of biopolymers in solution: Evaluation of the form, volume, and surface of a particle , 1983 .
[42] M. L. Connolly. Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.
[43] M. L. Connolly. Analytical molecular surface calculation , 1983 .
[44] David Chandler,et al. Instantaneous liquid interfaces. , 2009, The journal of physical chemistry. B.
[45] M. Cordeiro,et al. A critical assessment of methods for the intrinsic analysis of liquid interfaces. 1. surface site distributions , 2010 .
[46] George Horvai,et al. Full description of the orientational statistics of molecules near to interfaces. Water at the interface with CCl4Presented at the 81st International Bunsen Discussion Meeting on ?Interfacial Water in Chemistry and Biology?, Velen, Germany, September 19?23, 2003. , 2004 .
[47] A. Braun,et al. Electron microscopy investigation of carbonaceous particulate matter generated by combustion of fossil fuels , 2005 .
[48] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[49] Jon Louis Bentley,et al. Data Structures for Range Searching , 1979, CSUR.
[50] F. B. Usabiaga,et al. Applications of computational geometry to the molecular simulation of interfaces. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.
[51] Michael L. Connolly,et al. Computation of molecular volume , 1985 .
[52] D. Hibberd,et al. Quantitative imaging of aggregated emulsions. , 2006, Langmuir.
[53] Jay W. Ponder,et al. Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization , 1991 .
[54] S Subramaniam,et al. Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape , 1998, Proteins.
[55] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[56] Herbert Edelsbrunner,et al. Three-dimensional alpha shapes , 1994, ACM Trans. Graph..
[57] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[58] David P. Dobkin,et al. The quickhull algorithm for convex hulls , 1996, TOMS.
[59] G. B. Rulev,et al. Experimental characterization of aircraft combustor soot : Microstructure, surface area, porosity and water adsorption , 2000 .
[60] Kevin Q. Brown,et al. Voronoi Diagrams from Convex Hulls , 1979, Inf. Process. Lett..
[61] F. Richards. The interpretation of protein structures: total volume, group volume distributions and packing density. , 1974, Journal of molecular biology.
[62] T. Richmond,et al. Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.
[63] N. N. Medvedev,et al. Water adsorption isotherms on porous onionlike carbonaceous particles. Simulations with the grand canonical Monte Carlo method. , 2010, The Journal of chemical physics.
[64] Joseph O'Rourke,et al. Handbook of Discrete and Computational Geometry, Second Edition , 1997 .
[65] D. van der Spoel,et al. Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: Micellar structure and chain relaxation , 2000 .
[66] H. Vogel,et al. The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micelles. , 2001, Biochemistry.
[67] A critical assessment of methods for the intrinsic analysis of liquid interfaces: 2. Density profiles , 2010 .
[68] J. Tomasi,et al. Quantum mechanical continuum solvation models. , 2005, Chemical reviews.