See this document in CiteSeerX!

Novel Multiscale Algorithms for Molecular Dynamics (2003)  (Make Corrections)  (1 citation)
Qun Ma



  Home/Search   Context   Related

 
View or download:
nd.edu/~izaguirr/pape...qunMaThesis.pdf
Cached:  PS.gz  PS  PDF   Image  Update  Help

From:  nd.edu/~izaguirr/w...publications (more)
(Enter author homepages)

Rate this article: (best)
  Comment on this article  
(Enter summary)

Abstract: by Qun Ma In post-genomic computational biology and bioinformatics, long simulations of the dynamics of molecular systems, particularly biological molecules such as proteins and DNA, require advances in time stepping computational methods. The most severe problem of these algorithms is instability. The objective of this dissertation is to present original work in constructing multiscale multiple time stepping (MTS) algorithms for molecular dynamics (MD) that allow large time steps. First,... (Update)

Cited by:   More
Targeted Mollified Impulse - A Multiscale Stochastic.. - Ma, Izaguirre (2003)   (Correct)

Active bibliography (related documents):   More   All
5.9:   Verlet-I/r-RESPA/Impulse Is Limited by Nonlinear Instability - Ma, Izaguirre, Skeel   (Correct)
3.2:   Framework Design, Parallelization and Force Computation in.. - Matthey   (Correct)
2.1:   A Tutorial on the Prototyping of Multiple Time.. - Izaguirre.. (2001)   (Correct)

Similar documents based on text:   More   All
0.3:   Nonlinear Instability in Multiple Time Stepping Molecular.. - Ma, Izaguirre, Skeel (2002)   (Correct)
0.2:   Overcoming instabilities in Verlet-I/r-RESPA with.. - Izaguirre, Ma..   (Correct)
0.2:   Langevin Stabilization of Multiscale Mollified Molecular Dynamics - Izaguirre   (Correct)

Related documents from co-citation:   More   All
2:   Longer time steps for molecular dynamics (context) - Izaguirre, Reich et al. - 1999

BibTeX entry:   (Update)

Q. Ma. Novel Multiscale Algorithms for Molecular Dynamics. PhD thesis, University of Notre Dame, Notre Dame, Indiana, USA, 2003. http://citeseer.ist.psu.edu/ma03novel.html   More

@misc{ ma03novel,
  author = "Q. Ma",
  title = "Novel Multiscale Algorithms for Molecular Dynamics",
  text = "Q. Ma. Novel Multiscale Algorithms for Molecular Dynamics. PhD thesis,
    University of Notre Dame, Notre Dame, Indiana, USA, 2003.",
  year = "2003",
  url = "citeseer.ist.psu.edu/ma03novel.html" }
Citations (may not include all citations):
306   Computer Simulation of Liquids (context) - Allen, Tildesley - 1987  ACM
306   Computer Simulation of Liquids (context) - Allen, Tildesley - 1987  ACM
109   Numerical Solution of Stochastic Differential Equations (context) - Kloeden, Platen - 1992
83   package automatic differentiation algorithm written CC++ - Juedes, package et al. - 1996
71   Solving Ordinary Differential Equations I: Non-stiff Systems (context) - Hairer, Nrsett et al. - 1987
52   Numerical Hamiltonian Problems (context) - Sanz-Serna, Calvo - 1994
49   A new kind of science (context) - Wolfram - 2002  ACM
25   NAMD2: Greater scalability for parallel molecular dynamics - Kale, Skeel et al. - 1999
25   NAMD2: Greater scalability for parallel molecular dynamics - Kale, Skeel et al. - 1999
24   Pathways to a protein folding intermediate observed in a 1 m.. (context) - Duan, Kollman - 1998
23   Proteins: A Theoretical Perspective of Dynamics (context) - Karplus, Pettitt - 1988
22   Vmd - visual molecular dynamics (context) - Humphrey, Dalke et al. - 1996
20   Generalized Verlet algorithm for efficient molecular dynamic.. (context) - Grubmuller, Heller et al. - 1991
20   Dangers of multiple-time-step methods (context) - Biesiadecki, Skeel - 1993
19   Symplectic integration with variable stepsize - Skeel, Biesiadecki - 1994
18   Molecular Modelling: Principles and Applications (context) - Leach - 1996
18   velocity' version of the shake algorithm for molecular dynam.. (context) - Andersen - 1983
17   A family of symplectic integrators: stability (context) - Skeel, Zhang et al. - 1997
17   object-oriented molecular dynamics program (context) - Nelson, Humphrey et al. - 1996
17   Longer Time Steps for Molecular Dynamics (context) - Izaguirre - 1999  ACM
17   Longer time steps for molecular dynamics (context) - Izaguirre, Reich et al. - 1999  ACM
16   Reversible multiple time scale molecular dynamics (context) - Tuckerman, Berne et al. - 1990
15   Comparison of simple potential functions for simulating liqu.. (context) - Jorgensen, Chandrasekhar et al. - 1983
14   Nonlinear resonance artifacts in molecular dynamics simulati.. (context) - Schlick, Mandziuk et al. - 1998  ACM
13   Protein folding by restrained energy minimization and molecu.. - Levitt - 1983
13   Molecular dynamics of native protein (context) - Levitt - 1983
13   Novel methods of sampling phase space in the simulation of b.. (context) - Berne, Straub - 1997
12   Computer simulation of protein folding (context) - Levitt, Warshel - 1975
10   Die Berechnung optischer und elektrostatischer Gitterpotenti.. (context) - Ewald - 1921
9   Multiple grid methods for classical molecular dynamics (context) - Skeel, Tezcan et al. - 2002  DBLP
9   Parallelization and Force Computation in Molecular Dynamics (context) - Matthey - 2002
9   PROTOMOL: an object-oriented framework for prototyping novel.. - Matthey, Cickovski et al. - 2003
9   method for Ewald sums in large systems (context) - Darden, York et al. - 1993
9   Langevin stabilization of molecular dynamics (context) - Izaguirre, Catarello et al. - 2090
9   Difficulties with multiple timestepping and the fast multipo.. (context) - Bishop, Skeel et al. - 1997
9   Integration schemes for molecular dynamics and related appli.. (context) - Skeel - 1999
9   Hybrid Monte Carlo method for condensed-matter systems (context) - Mehlig, Heermann et al. - 1992
8   Long-time energy conservation of numerical methods for oscil.. - Hairer, Lubich - 2000  ACM
8   An algorithm for the simulation of condensed matter which gr.. (context) - Perram, Petersen et al. - 1988
8   ProtoMol: A molecular dynamics framework with incremental pa.. - Matthey, Izaguirre - 2001
8   A new molecular dynamics method combining the reference syst.. - Zhou, Berne - 1995
8   Practical algorithms for dynamic simulations (context) - Berendsen, van Gunsteren - 1986
8   Extrapolation versus impulse in multiple-timestepping scheme.. (context) - Barth, Schlick - 1998
7   Geometric Numerical Integration: StructurePreserving Algorit.. (context) - Hairer, Lubich et al. - 2002
7   Error analysis of symplectic multiple time stepping (context) - Littell, Skeel et al. - 1997  ACM
7   Asymptotic expansions and backward analysis for numerical in.. - Hairer, Lubich - 2000
7   Mathematical analysis of coupled parallel simulations (context) - Shirts, Pande - 2001
7   Practical construction of modified Hamiltonians - Skeel, Hardy - 2001  ACM
7   Overcoming stability limitations in biomolecular dynamics (context) - Barth, Schlick - 1998
7   Statistical mechanics of dissipative particle dynamics - Espanol, Warren - 1995
6   Asynchronous variational integrators (context) - Lew, Marsden et al.
6   Long-time-step methods for oscillatory differential equation.. (context) - Garca-Archilla, Sanz-Serna et al. - 1998  ACM
6   On multiple time-step algorithms and the Ewald sum (context) - Forester, Smith - 1994
6   Stochastic boundary conditions for molecular dynamics simula.. (context) - Brunger, Brooks et al. - 1982
6   A multiple-time-step molecular dynamics algorithm for macrom.. (context) - Humphreys, Friesner et al. - 1994
6   Dissipative particle dynamics: Bridging the gap between atom.. (context) - Groot, Warren - 1997
6   Optimized particle mesh Ewaldmultipletime step integration m.. (context) - Case, particle et al. - 2001
6   Masking resonance artifacts in force-splitting methods for b.. - Sandu, Schlick - 1999
6   Cheap implicit symplectic integrators - Zhang, Skeel - 1997
5   Multigrid methods for classical molecular dynamics simulatio.. (context) - Sagui, Darden - 2001
5   Optimisation of the Ewald sum for large systems (context) - Fincham - 1994
5   Chaos and Integrability in Nonlinear Dynamics: An Introducti.. (context) - Tabor - 1989
5   MDSimAid: An automatic recommender for optimization of fast .. - Ko - 2002
5   Resonance in the dynamics of chemical systems simulated by t.. (context) - Mandziuk, Schlick - 1995
5   Acceptances and autocorrelations in hybrid monte carlo (context) - Kennedy, Pendleton - 1991
4   Ewald summation versus direct summation of shifted-force pot.. (context) - Dufner, Kast et al. - 1997
4   New splitting formulations for lattice summations (context) - Batcho, Schlick - 2001
4   An impulse integrator for Langevin dynamics - Skeel, Izaguirre - 2002
4   Time-reversible difference procedures (context) - Buneman - 1967
4   Electrostatic calculations and multiple time scales in molec.. (context) - Procacci, Marchi et al. - 1998
4   The mollified impulse method for oscillatory differential eq.. (context) - Garca-Archilla, Sanz-Serna et al. - 1997
4   Linearly scalable hybrid monte carlo method for conformation.. - Hampton, Izaguirre - 2003
4   Long time step molecular dynamics using targeted langevin st.. - Ma, Izaguirre - 2003
4   SETTLE: An analytical version of the SHAKE and RATTLE algori.. (context) - Miyamoto, Kollman - 1992
4   Taming the Ewald sum in molecular dynamics simulations of so.. (context) - Procacci, Marchi - 1996
4   The five femtosecond time step barrier - Skeel, Izaguirre - 1998
4   Dynamiksimulation sehr groer Makromolekule auf einem Paralle.. (context) - Grubmuller - 1989
4   Ewald summation of electrostatic interactions in molecular d.. (context) - Grzybowski, Gwozdz et al. - 2000
4   A reversible averaging integrator for multiple timescale dyn.. - Leimkuhler, Reich - 2001
4   Generalized mollified multiple time stepping methods for mol.. (context) - Izaguirre - 2001
3   Dissipative particle dynamics for interacting systems (context) - Pagonabarraga, Frenkel - 2001
3   Structure available httphttpwww (context) - Wesson, the et al. - 1990
3   Self-consistent dissipative particle dynamics algorithm (context) - Pagonabarraga, Hagen et al. - 1998
3   the effects of an uncertainty on the evolution law in dynami.. (context) - Crisanti, Falcioni et al. - 1989
3   Molecular dynamics of macromolecules in water (context) - Levitt - 1989
3   Algorithms for macromolecular dynamics and constraint dynami.. (context) - van Gunsteren, Berendsen - 1977
2   Structure of the ligandbinding domain of oestrogen receptor .. (context) - Pike, Brzozowski et al. - 1999
2   Nonlinear stability analysis of area-preserving integrators (context) - Skeel, Srinivas - 2000
2   Molecular dynamics simulations of a polyalanine octapeptide .. (context) - Weber, Hunenberger et al. - 2000
2   an object-oriented framework for algorithmic development (context) - Matthey, Ko et al. - 2003
2   Multiscale algorithms in molecular dynamics (context) - Bai, Brandt - 2001
2   Elastic rod model of a DNA loop in the lac operon (context) - Balaeff, Mahadevan et al. - 1999
2   Towards better integrators for dissipative particle dynamics.. (context) - Besold, Vattulainen et al. - 2000
2   Why does molecular dynamics work (context) - Skeel - 2002
2   A smoothparticle mesh ewald method for DL POLY molecular dyn.. (context) - Kholmurodov, Smith et al. - 2000
2   Explicit symplectic integrators using Hessian--vector produc.. (context) - Lopez-Marcos, Sanz-Serna et al. - 1997  ACM
2   Special stability advantages of position-verlet over velocit.. (context) - Batcho, Schlick - 2001
2   Targeted mollified impulse -- a multiscale integrator for mo.. (context) - Ma, Izaguirre - 2003
2   RESPAImpulse is limited by nonlinear instability (context) - Izaguirre, RESPA et al. - 1951
2   Symplectic energy-momentum integrators (context) - Kane, Marsden et al. - 1999
2   Efficient multiple time step method for use with Ewald and P.. (context) - Zhou, Harder et al. - 2001
1   Efficient multiple-time-step integrators with distancebased .. (context) - Qian, Schlick - 2002
1   Numerical integration of ordinary differential equations (context) - Milne - 1926
1   Intel announces super-fast transistors (context) - McDonald - 2000
1   A cluster model of liquid water and its ir spectroscopic res.. (context) - Bour - 2002
1   Nonlinear instability in multiple time stepping molecular dy.. - Ma, Izaguirre et al. - 2003
1   Targeted langevin stabilization of molecular dynamics (context) - Ma, Izaguirre - 2003
1   Long-range force molecular dynamics study on electrostatic a.. (context) - Zhou, Schulten - 1994
1   Stability of a numerical solution of differential equations (context) - Milne, Reynolds - 1959

Documents on the same site (http://www.nd.edu/~izaguirr/webpage_files/publications.htm):   More
MDSimAid: A Recommender System for Automatic Parameter.. - Crocker, Hampton.. (2004)   (Correct)
GIPSE: A Toolset for Streamlining the Management.. - Striegel, Shorts, ..   (Correct)
The Five Femtosecond Time Step Barrier - Skeel, Izaguirre (1998)   (Correct)

Online articles have much greater impact   More about CiteSeer.IST   Add search form to your site   Submit documents   Feedback  

CiteSeer.IST - Copyright Penn State and NEC