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1. Plasma physics via computer simulation
by Birdsall, Charles K and Langdon, A. Bruce
1991, The Adam Hilger series on plasma physics., ISBN 0750301171, xxvi, 479
Computer simulation | Plasma (Ionized gases) | Simulation methods
Book
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2. Interactive dynamic-system simulation
by Korn, G.A
2011, 2nd ed., Numerical insights, ISBN 9781439836415, Volume 7., xvi, 204 p.4.
microcomputers | computer simulation | dynamics | interactive computer systems
Book
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3. Basic pharmacokinetics and pharmacodynamics
: an integrated textbook and computer simulations
by Rosenbaum, Sara (Sara E.)
2011, ISBN 9780470569061, xviii, 430
Drugs | Pharmacological Phenomena | Pharmacokinetics | Physiological effect | Computer Simulation
Book
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4. System dynamics
: modeling, analysis, simulation, design
by Doebelin, Ernest O
1998, ISBN 9780824701260, xiv, 755
Systems engineering | Dynamics
Book
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5. Full Text Atomically Detailed Simulations of Concentrated Protein Solutions:  The Effects of Salt, pH, Point Mutations, and Protein Concentration in Simulations of 1000-Molecule Systems
by McGuffee, Sean R and Elcock, Adrian H
Journal of the American Chemical Society, ISSN 0002-7863, 09/2006, Volume 128, Issue 37, pp. 12098 - 12110
An ability to accurately simulate the dynamic behavior of concentrated macromolecular solutions would be of considerable utility in studies of a wide range of... 
HYDROPHOBIC INTERACTIONS | CRYSTALLIZATION | MOLECULAR-DYNAMICS | 2ND VIRIAL-COEFFICIENT | DIFFUSIONAL ASSOCIATION | CHYMOTRYPSINOGEN | LYSOZYME | MONTE-CARLO SIMULATIONS | CHEMISTRY, MULTIDISCIPLINARY | BROWNIAN DYNAMICS | SCATTERING | Chymotrypsinogen - genetics | Models, Chemical | Muramidase - chemistry | Muramidase - genetics | Models, Molecular | Salts - chemistry | Point Mutation | Thermodynamics | Solutions | Computer Simulation | Bacteriophage T4 - enzymology | Chymotrypsinogen - chemistry | Protein Conformation | Kinetics | Hydrogen-Ion Concentration | Brownian motion | Protein research | Research | Analysis | Lysozyme
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6. Full Text Kinetic Monte Carlo simulations of the water gas shift reaction on Cu(111) from density functional theory based calculations
by Prats, Hèctor and Álvarez, Leny and Illas, Francesc and Sayós, Ramón
Journal of Catalysis, ISSN 0021-9517, 01/2016, Volume 333, pp. 217 - 226
A systematic first-principles kinetic Monte Carlo study of the water gas shift reaction taking place on the Cu(1 1 1) surface is presented including... 
Simulations | Mechanisms | Copper surface | Kinetic Monte Carlo | Associative | Microkinetic model | Carboxyl | Redox | Density functional theory | Water gas shift reaction | CHEMISTRY, PHYSICAL | TOTAL-ENERGY CALCULATIONS | COPPER | ENGINEERING, CHEMICAL | METALS | SUPPORTED CU | EXCHANGE | CATALYSTS | WAVE BASIS-SET | SURFACES | Density functionals | Monte Carlo method | Specific gravity
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7. Full Text Axisymmetric ab initio core-collapse supernova simulations of 12-25 M · stars
by Bruenn, Stephen W and Mezzacappa, Anthony and Hix, W. Raphael and Lentz, Eric J and Messer, O. E. Bronson and Lingerfelt, Eric J and Blondin, John M and Endeve, Eirik and Marronetti, Pedro and Yakunin, Konstantin N
Astrophysical Journal Letters, ISSN 2041-8205, 04/2013, Volume 767, Issue 1
We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our... 
neutrinos | supernovae: general | radiative transfer | RADIANT HEAT TRANSFER | AXIAL SYMMETRY | ASYMMETRY | EXPLOSIONS | INSTABILITY | ASTROPHYSICS, COSMOLOGY AND ASTRONOMY | CONVECTION | KINETIC ENERGY | MASS | NEUTRINOS | SIMULATION | SUPERNOVAE
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8. Full Text Simulations of thermophoretic nanoswimmers
by Yang, Mingcheng and Ripoll, Marisol
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, 12/2011, Volume 84, Issue 6, p. 061401
We consider a nanodimer in solution with asymmetric thermal properties that shows self-propelled motion. One monomer of the nanodimer can be heated to a fixed... 
PHYSICS, FLUIDS & PLASMAS | MULTIPARTICLE COLLISION DYNAMICS | POLYMER-SOLUTIONS | PHYSICS, MATHEMATICAL | THERMAL-DIFFUSION | SOLVENT | MOLECULES | Models, Molecular | Motion | Temperature | Kinetics | Nanostructures | Dimerization
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9. Full Text Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
by Voelz, Vincent A and Bowman, Gregory R and Beauchamp, Kyle and Pande, Vijay S
Journal of the American Chemical Society, ISSN 0002-7863, 02/2010, Volume 132, Issue 5, pp. 1526 - 1528
To date, the slowest-folding proteins folded ab initio by all-atom molecular dynamics simulations have had folding times in the range of nanoseconds to... 
TRANSITION | HETEROGENEITY | DYNAMICS | DESIGN | CHEMISTRY, MULTIDISCIPLINARY | KINETICS | Markov Chains | Arabidopsis - chemistry | Transcription Factors - chemistry | Time Factors | Protein Conformation | Molecular Dynamics Simulation | Protein Folding | Molecular dynamics | Usage | Solvation | Chemical reaction, Rate of | Protein folding | Analysis
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10. Full Text Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(C pG) Steps
by Beveridge, David L and Barreiro, Gabriela and Suzie Byun, K and Case, David A and Cheatham, Thomas E and Dixit, Surjit B and Giudice, Emmanuel and Lankas, Filip and Lavery, Richard and Maddocks, John H and Osman, Roman and Seibert, Eleanore and Sklenar, Heinz and Stoll, Gautier and Thayer, Kelly M and Varnai, Péter and Young, Matthew A
Biophysical Journal, ISSN 0006-3495, 2004, Volume 87, Issue 6, pp. 3799 - 3813
We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA... 
Motion | DNA - chemistry | Models, Chemical | Base Sequence | Computer Simulation | Oligodeoxyribonucleotides - chemistry | Models, Molecular | Molecular Sequence Data | Structure-Activity Relationship | Kinetics | Nucleic Acid Conformation | DNA | Chemical properties | Research | Thermodynamics | Computer simulation | Deoxyribonucleic acid--DNA | Data bases | Life Sciences | Biochemistry, Molecular Biology | Biophysical Theory and Modeling
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11. Full Text Multiscale methods for macromolecular simulations
by Sherwood, Paul and Brooks, Bernard R and Sansom, Mark SP
Current Opinion in Structural Biology, ISSN 0959-440X, 10/2008, Volume 18, Issue 5, pp. 630 - 640
In this article we review the key modeling tools available for simulating biomolecular systems. We consider recent developments and representative applications... 
ELASTIC NETWORK MODEL | BIOCHEMISTRY & MOLECULAR BIOLOGY | AB-INITIO | FORCE-FIELD | REDOX PROPERTIES | CONFORMATIONAL DYNAMICS | MOLECULAR-DYNAMICS SIMULATIONS | MEMBRANE-PROTEINS | FREE-ENERGY | COARSE-GRAINED MODELS | LIPID-BILAYER | CELL BIOLOGY | Computational Biology - methods | Molecular Conformation | Computational Biology - trends | Elasticity | Electronics | Models, Molecular | Thermodynamics | Quantum Theory | Macromolecular Substances - chemistry | Computer Simulation | Kinetics | Lipid Bilayers - chemistry | Proteins - chemistry
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12. Full Text Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein
by Day, Ryan and Paschek, Dietmar and Garcia, Angel E
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 06/2010, Volume 78, Issue 8, pp. 1889 - 1899
We study the unbiased folding/unfolding thermodynamics of the Trp‐cage miniprotein using detailed molecular dynamics simulations of an all‐atom model of the... 
force field | pressure denaturation | cold denaturation | molecular simulations | folding | Force field | Pressure denaturation | Folding | Cold denaturation | Molecular simulations | FOLDING SIMULATIONS | PRESSURE-DEPENDENCE | BIOCHEMISTRY & MOLECULAR BIOLOGY | FORCE-FIELDS | EXPLICIT SOLVENT | MINI-PROTEIN | BIOPHYSICS | UNFOLDED STATE | TEMPERATURE | REPLICA-EXCHANGE | MOLECULAR-DYNAMICS SIMULATIONS | STRUCTURE PREDICTION | Amino Acid Sequence | Thermodynamics | Peptides - metabolism | Peptides - chemistry | Time Factors | Computer Simulation | Models, Molecular | Molecular Sequence Data | Kinetics | Protein Stability | Protein Folding
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13. Full Text Simulations of the Small-Scale Turbulent Dynamo
by Schekochihin, Alexander A and Cowley, Steven C and Taylor, Samuel F and Maron, Jason L and McWilliams, James C
The Astrophysical Journal, ISSN 0004-637X, 09/2004, Volume 612, Issue 1 I, pp. 276 - 307
We report the results of an extensive numerical study of the small-scale turbulent dynamo. The primary focus is on the case of large magnetic Prandtl numbers... 
magnetic fields | plasmas | MAGNETIC-FIELDS | NONLINEAR DYNAMO | MHD | MODEL | turbulence | PRANDTL NUMBER | MAGNETOHYDRODYNAMIC TURBULENCE | INVERSE CASCADE | MHD TURBULENCE | ASTRONOMY & ASTROPHYSICS | methods : numerical | DIFFUSION | SPECTRUM | KINETIC HELICITY | Physics - Cosmology and Nongalactic Astrophysics | Physics - Earth and Planetary Astrophysics | Physics - Instrumentation and Methods for Astrophysics | Physics - High Energy Astrophysical Phenomena | Physics - Solar and Stellar Astrophysics | Physics - Astrophysics of Galaxies
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14. Full Text Accelerated molecular dynamics simulations of protein folding
by Miao, Yinglong and Feixas, Ferran and Eun, Changsun and McCammon, J. Andrew
Journal of Computational Chemistry, ISSN 0192-8651, 07/2015, Volume 36, Issue 20, pp. 1536 - 1549
Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD).... 
protein folding | free energy | accelerated molecular dynamics | enhanced sampling | reweighting | Enhanced sampling | Accelerated molecular dynamics | Protein folding | Reweighting | Free energy | FREE-ENERGY LANDSCAPE | MINIPROTEIN | TRP-CAGE | PARTICLE MESH EWALD | CHEMISTRY, MULTIDISCIPLINARY | WW DOMAIN | EXPLICIT-SOLVENT | KINETICS | FORCE-FIELD | BIOMOLECULAR SIMULATION | VILLIN HEADPIECE SUBDOMAIN | Molecular Dynamics Simulation | Protein Folding | Proteins - chemistry | Proteins | Chemical properties | Analysis
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15. Full Text Native contacts determine protein folding mechanisms in atomistic simulations
by Robert B. Best and Gerhard Hummer and William A. Eaton
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2013, Volume 110, Issue 44, pp. 17874 - 17879
The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key... 
Simulations | Protein folding | Ubiquitins | Molecular dynamics | Coordinate systems | Amino acids | Trajectories | Kinetics | Modeling | Free energy | reaction coordinate | MOLECULAR-DYNAMICS | funnel | internal friction | MULTIDISCIPLINARY SCIENCES | frustration | NONNATIVE INTERACTIONS | MODEL | RATES | Go models | THERMODYNAMICS | KINETICS | 3-HELIX BUNDLE PROTEIN | TRANSITION-STATE ENSEMBLE | ENERGY LANDSCAPE | Models, Chemical | Molecular Dynamics Simulation | Protein Folding | Bayes Theorem | Amino acid sequence | Research | Gō models | Biological Sciences | Physical Sciences
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