Bridging time scales: molecular simulations for the next decade
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2002
|
| Schriftenreihe: | Lecture notes in physics
605 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXVI, 500 S. Ill., graph. Darst. |
| ISBN: | 3540443177 |
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| 245 | 1 | 0 | |a Bridging time scales |b molecular simulations for the next decade |c P. Nielaba ... (eds.) |
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2002 | |
| 300 | |a XXVI, 500 S. |b Ill., graph. Darst. | ||
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| 490 | 1 | |a Lecture notes in physics |v 605 | |
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| 650 | 4 | |a Chemistry, Physical and theoretical |x Computer simulation | |
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Datensatz im Suchindex
| _version_ | 1804129584694689792 |
|---|---|
| adam_text | TABLE OF CONTENTS PART I PROTEIN FOLDING 1 SIDECHAIN DYNAMICS AND
PROTEIN FOLDING EDO KUSSELL, JUN SHIMADA, EUGENE I. SHAKHNOVICH
.................. 3 1.1 INTRODUCTION . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.2
RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 5 1.3 DISCUSSION . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . 18 1.4 METHODS. . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . 21 REFERENCES . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 23 PART II APPLICATIONS OF STATISTICAL
MECHANICS TO BIOLOGICAL SYSTEMS 2 A COARSE GRAIN MODEL FOR LIPID
MONOLAYER AND BILAYER STUDIES STEVE O. NIELSEN, MICHAEL L. KLEIN
................................ 27 2.1 INTRODUCTION . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. 27 2.2 CHALLENGES . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 28 2.3 MODELS . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 30 2.3.1 PREVIOUS WORK . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . 30 2.3.2 TOWARDS THE
CURRENT CG MODEL . . . . . . . . . . . . . . . . . . . . . . . . 32
2.3.3 A FIRST ATTEMPT . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 34 2.4 APPLICATIONS . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.4.1 FLUCTUATION MODES . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 41 2.4.2 BULK ALKANE AND WATER SURFACE TENSION .
. . . . . . . . . . . . . . . . 43 2.4.3 SELF-ASSEMBLY . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 2.4.4
TRANSMEMBRANE PEPTIDE INDUCED DOMAIN FORMATION . . . . . . 46 2.4.5
TRANSMEMBRANE PEPTIDE INDUCED L * TO H II PHASE TRANSITION . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 52 2.4.6 BUCKLING
INSTABILITIES IN LANGMUIR MONOLAYERS . . . . . . . . . . . . 54 2.5
FUTURE PERSPECTIVES . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 58 REFERENCES . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . 60 XIV TABLE OF CONTENTS PART III POLYMER STRUCTURE AND DYNAMICS
3VARIABLE-CONNECTIVITY MONTE CARLO ALGORITHMS FOR THE ATOMISTIC
SIMULATION OF LONG-CHAIN POLYMER SYSTEMS DOROS N. THEODOROU
............................................. 67 3.1 INTRODUCTION . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 67 3.2 THE BRIDGING CONSTRUCTION . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 71 3.3 MONTE CARLO ALGORITHMS
BASED ON THE BRIDGING CONSTRUCTION . . . . 77 3.3.1 CONCERTED ROTATION .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
3.3.2 DIRECTED INTERNAL BRIDGING . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 80 3.3.3 END-BRIDGING IN THE NNµ * PT ENSEMBLE . . . .
. . . . . . . . . . . . 81 3.3.4 DIRECTED END-BRIDGING . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 89 3.3.5 SAMPLING OF
ORIENTED CHAINS: NNBT µ * * MC SIMULATIONS . . 90 3.3.6 SCISSION AND
FUSION ALGORITHMS FOR PHASE EQUILIBRIA . . . . . . 92 3.3.7 DOUBLE
BRIDGING AND INTRAMOLECULAR DOUBLE REBRIDGING . . . 96 3.3.8
CONNECTIVITY-ALTERING MONTE CARLO AND PARALLEL TEMPERING 100 3.4
APPLICATIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . 103 3.4.1 STRUCTURE AND VOLUMETRIC
PROPERTIES OF LONG-CHAIN POLYETHYLENE MELTS . . . . . . . . . . . . . .
. . . . . . . . 103 3.4.2 SIMULATIONS OF POLYPROPYLENE MELTS OF VARIOUS
TACTICITIES . . 107 3.4.3 SIMULATION OF POLYDIENES . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 110 3.4.4 PREDICTION OF MELT
ELASTICITY . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
3.4.5 SORPTION EQUILIBRIA OF ALKANES IN POLYETHYLENE . . . . . . . . . .
. 119 3.4.6 POLYMERS AT INTERFACES . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 121 3.5 CONCLUSIONS AND OUTLOOK . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 REFERENCES .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . 125 4 BRIDGING THE TIME SCALE GAP: HOW
DOES FOLDABLE POLYMER NAVIGATE ITS CONFORMATION SPACE? ALEXANDER
GROSBERG ............................................. 129 4.1
INTRODUCING THE CHARACTERS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 129 4.2 SETTING UP THE STAGE: CONFORMATION SPACE
AND REACTION COORDINATE . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 130 4.2.1 CONFORMATION SPACE: LATTICE POLYMER .
. . . . . . . . . . . . . . . . . . 130 4.2.2 CONFORMATION SPACE:
OFF-LATTICE POLYMER . . . . . . . . . . . . . . . . . 131 4.2.3 REACTION
COORDINATE PROBLEM . . . . . . . . . . . . . . . . . . . . . . . . . .
132 4.3 UNFOLDING THE DRAMA: COMMITOR, P FOLD , AND THE REACTION
COORDINATE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . 134 4.3.1 COMMITOR . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 134 4.3.2 DIRECT CURRENT ANALOGY .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 4.3.3
DIFFUSION EQUATION AND CONTINUOUS (OFF-LATTICE) MODELS . . . . 136 4.3.4
STATIONARY AND TRANSIENT REGIMES . . . . . . . . . . . . . . . . . . . .
. . . 137 TABLE OF CONTENTS XV 4.3.5 DIRECT CURRENT FORMULATION OF THE
FIRST RETURN PROBLEM: CASINO PROBLEM AND ITS EASY SOLUTION . . . . . . .
. . . . . . . . . . . . 138 4.3.6 DIRECT CURRENT FORMULATION OF THE
COMMITOR . . . . . . . . . . . . . 139 4.3.7 DIRECT CURRENT FORMULATION
OF THE LANDSCAPE . . . . . . . . . . . . . 139 4.4 CULMINATION: SO WHAT?
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. 141 REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . 141 5 MULTISCALE
COMPUTER SIMULATIONS FOR POLYMERIC MATERIALS IN BULK AND NEAR SURFACES
CAMERON ABRAMS, LUIGI DELLE SITE, KURT KREMER .................... 143
5.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 143 5.2 LENGTH AND TIME SCALES FOR
POLYMER SIMULATIONS . . . . . . . . . . . . . . . 144 5.3 DUAL-SCALE
MODELLING ANSATZ . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . 148 5.3.1 MESOSCOPIC MODELS IN BULK AND NEAR SURFACES . . . .
. . . . . . . . 148 5.3.2 SYSTEMATIC MOLECULAR COARSE-GRAINING . . . . .
. . . . . . . . . . . . . . 153 5.3.2.1 MAPPING SCHEMES . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 153 5.3.2.2 COARSE GRAINED
LIQUID STRUCTURE . . . . . . . . . . . . . . . . . 154 5.4 SPECIFIC
SURFACE EFFECTS: BPA-PC NEAR A NI SURFACE. . . . . . . . . . . . . 156
5.5 OTHER APPROACHES: AUTOMATIC COARSE-GRAINING . . . . . . . . . . . .
. . . . . 159 5.6 CONCLUSIONS, OUTLOOK . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 162 REFERENCES . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 163 PART IV COMPLEX AND MESOSCOPIC FLUIDS 6
EFFECTIVE INTERACTIONS FOR LARGE-SCALE SIMULATIONS OF COMPLEX FLUIDS
JEAN-PIERRE HANSEN, HARTMUT L¨ OWEN .............................. 167
6.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 167 6.2 EFFICIENT COARSE-GRAINING
THROUGH EFFECTIVE INTERACTIONS. . . . . . . . . 168 6.3 ELECTRIC
DOUBLE-LAYERS . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 172 6.4 SIMULATING THE POLARIZATION OF DIELECTRIC
MEDIA . . . . . . . . . . . . . . . . . 174 6.5 COARSE-GRAINING LINEAR
POLYMER SOLUTIONS . . . . . . . . . . . . . . . . . . . . . 176 6.6 STAR
POLYMERS AND DENDRIMERS . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 178 6.7 COLLOIDS AND POLYMERS: DEPLETION INTERACTIONS . .
. . . . . . . . . . . . . . . . 183 6.8 BINARY COLLOIDAL *ALLOYS* . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
6.9 FROM COLLOIDAL TO NANOSCALES . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 187 6.10 CONCLUSIONS . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 192 XVI TABLE OF CONTENTS
PART V SLOW DYNAMICS AND REACTIVITY 7 SIMULATION OF MODELS FOR THE GLASS
TRANSITION: IS THERE PROGRESS? KURT BINDER, J¨ ORG BASCHNAGEL, WALTER
KOB, WOLFGANG PAUL .......... 199 7.1 INTRODUCTION . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
199 7.2 TOWARDS THE SIMULATION OF REAL GLASSY MATERIALS: THE CASE OF SIO
2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 204 7.3 PARALLEL TEMPERING . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . 209 7.4 AN ABSTRACT
MODEL FOR STATIC AND DYNAMIC GLASS TRANSITIONS: THE 10-STATE MEAN FIELD
POTTS GLASS . . . . . . . . . . . . . . . . . . . . . . . . . 212 7.5
THE BEAD-SPRING MODEL: A COARSE-GRAINED MODEL FOR THE STUDY OF THE GLASS
TRANSITION OF POLYMER MELTS . . . . . . . . . . 217 7.6 THE BOND
FLUCTUATION MODEL APPROACH TO GLASSFORMING POLYMER MELTS . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 219 7.7 CAN ONE MAP
COARSE-GRAINED MODELS ONTO ATOMISTICALLY REALISTIC ONES? . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 222 7.8 CONCLUDING REMARKS . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. 224 REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . 226 PART VI LATTICE
MODELS 8 MONTE CARLO METHODS FOR BRIDGING THE TIMESCALE GAP NIGEL
WILDING, DAVID P. LANDAU .................................. 231 8.1
GENERAL INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 231 8.2 PROBLEMS AND CHALLENGES . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232 8.2.1
INTRODUCTION TO METROPOLIS IMPORTANCE SAMPLING . . . . . . . . . . 232
8.2.2 ORIGIN OF TIME-SCALE PROBLEMS. . . . . . . . . . . . . . . . . . .
. . . . . . . 234 8.2.3 TRADITIONAL COMPUTATIONAL SOLUTIONS . . . . . .
. . . . . . . . . . . . . . 235 8.3 SOME *RECENT* DEVELOPMENTS . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . 236 8.3.1 SECOND
ORDER TRANSITIONS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . 236 8.3.1.1 CLUSTER FLIPPING . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 236 8.3.1.2 THE N-FOLD WAY AND EXTENSIONS . . .
. . . . . . . . . . . . . . 237 8.3.1.3 *WANG*LANDAU* SAMPLING . . . . .
. . . . . . . . . . . . . . . . . 239 8.3.2 FIRST ORDER TRANSITIONS . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240 8.3.2.1
FREE ENERGY COMPARISON: THE STATISTICAL MECHANICS PERSPECTIVE . . . . .
. . . . . . . 241 8.3.2.2 MULTICANONICAL MONTE CARLO . . . . . . . . . .
. . . . . . . . . . . 244 8.3.2.3 TRACKING PHASE BOUNDARIES: HISTOGRAM
EXTRAPOLATION . . . . . . . . . . . . . . . . . . . . . . . . 245
8.3.2.4 PHASE SWITCH MONTE CARLO . . . . . . . . . . . . . . . . . . . .
. . 247 TABLE OF CONTENTS XVII 8.3.2.5 FIRST ORDER TRANSITIONS AND
WANG*LANDAU SAMPLING . . . . . . . . . . . . . . . . . . . . 253 8.3.3
SYSTEMS WITH COMPLEX ORDER . . . . . . . . . . . . . . . . . . . . . . .
. . . . 256 8.3.4 *DYNAMIC* BEHAVIOR: SPIN DYNAMICS WITH DECOMPOSITIONS
OF EXPONENTIAL OPERATORS . . . . . . . . . . . 258 8.4 SUMMARY AND
OUTLOOK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . 263 REFERENCES . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265 9
GO-WITH-THE-FLOW LATTICE BOLTZMANN METHODS FOR TRACER DYNAMICS
CHRISTOPHER P. LOWE, SAURO SUCCI ................................. 267
9.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 267 9.2 LBE SCHEMES WITH TRACER
DYNAMICS . . . . . . . . . . . . . . . . . . . . . . . . . . 269 9.2.1
EXTRA-DIMENSIONAL METHODS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . 269 9.2.2 HYBRID GRID*GRID . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 269 9.2.3 HYBRID GRID*PARTICLE . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
9.2.4 GO-WITH-THE-FLOW KINETIC METHODS . . . . . . . . . . . . . . . . .
. . . . . 270 9.3 HYDRODYNAMIC DISPERSION . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 270 9.3.1 THE MOMENT PROPAGATION
METHOD . . . . . . . . . . . . . . . . . . . . . . 272 9.3.2 GALILEAN
INVARIANCE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . 276 9.3.3 VARYING THE PECLET NUMBER. . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 276 9.3.4 THE VACF AT INFINITE TIME . . .
. . . . . . . . . . . . . . . . . . . . . . . . . 277 9.3.5
GENERALIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 278 9.4 APPLICATIONS OF THE MODEL . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . 279 9.4.1
DISPERSION IN A TUBE . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 279 9.4.2 DISPERSION IN CUBIC PERIODIC ARRAYS . . . . .
. . . . . . . . . . . . . . . . 282 9.5 CONCLUSIONS . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . 283 REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . 284 PART VII
MULTISCALE MODELLING IN MATERIALS SCIENCE 10 ATOMISTIC SIMULATIONS OF
SOLID FRICTION MARTIN H. M¨ USER
................................................ 289 10.1 INTRODUCTION .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 289 10.1.1 THE RELEVANCE OF DETAILS: A SIMPLE CASE
STUDY . . . . . . . . . . 291 10.2 SOLID FRICTION VERSUS STOKES FRICTION
. . . . . . . . . . . . . . . . . . . . . . . . . . 294 10.3 DRY
FRICTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 297 10.3.1 RIGID WALLS AND GEOMETRIC
INTERLOCKING . . . . . . . . . . . . . . . . . 297 10.3.2 ELASTIC
DEFORMATIONS: ROLE OF DISORDER AND DIMENSIONS . . . 298 10.3.3 EXTREME
CONDITIONS AND NON-ELASTIC DEFORMATIONS . . . . . . . . 299 10.4
LUBRICATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . 301 10.4.1 BOUNDARY LUBRICATION . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303 10.4.2
HYDRODYNAMIC LUBRICATION AND ITS BREAKDOWN. . . . . . . . . . . . 305
XVIII TABLE OF CONTENTS 10.5 SETTING UP A TRIBOLOGICAL SIMULATION . . .
. . . . . . . . . . . . . . . . . . . . . . 305 10.5.1 THE ESSENTIAL
INGREDIENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
305 10.5.2 PHYSO-CHEMICAL PROPERTIES . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 307 10.5.3 INITIAL GEOMETRY . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . 308 10.5.4 DRIVING
DEVICE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . 310 10.5.5 THERMOSTATING . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 311 10.5.6 METHODS TO TREAT
THE WALL*S ELASTICITY . . . . . . . . . . . . . . . . . . 311 10.5.7
CALCULATION OF THE FRICTION FORCE . . . . . . . . . . . . . . . . . . .
. . . . . 313 10.5.8 INTERPRETATION OF TIME SCALES AND VELOCITIES . . .
. . . . . . . . . . . 313 10.6 CONCLUSIONS . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 316 PART VIII METHODOLOGICAL
DEVELOPMENTS IN MD AND MC 11 BRIDGING THE TIME SCALE GAP WITH TRANSITION
PATH SAMPLING CHRISTOPH DELLAGO, DAVID CHANDLER
................................ 321 11.1 WHY TRANSITION PATH SAMPLING
IS NEEDED . . . . . . . . . . . . . . . . . . . . . 321 11.2 HOW
TRANSITION PATH SAMPLING WORKS . . . . . . . . . . . . . . . . . . . . .
. . . 323 11.2.1 PROBABILITIES OF TRAJECTORIES . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 323 11.2.2 DEFINING THE TRANSITION PATH
ENSEMBLE . . . . . . . . . . . . . . . . . . 324 11.2.3 SAMPLING THE
TRANSITION PATH ENSEMBLE . . . . . . . . . . . . . . . . . 325 11.3 WHAT
TRANSITION PATH SAMPLING CAN DO . . . . . . . . . . . . . . . . . . . .
. . 326 11.3.1 THE RARE EVENT PROBLEM . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 327 11.3.2 SOLVING THE RARE EVENT PROBLEM WITH
TRANSITION PATH SAMPLING . . . . . . . . . . . . . . . . . . . . . . . .
. 327 11.3.3 INTERPRETING THE ENSEMBLE OF HARVESTED PATHS . . . . . . .
. . . . . 329 11.3.4 RATE CONSTANTS . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 330 11.4 WHAT TRANSITION PATH
SAMPLING CANNOT DO (YET) . . . . . . . . . . . . . . 330 11.4.1 ONE AND
TWO POINT BOUNDARY PROBLEMS . . . . . . . . . . . . . . . . . 330 11.4.2
CHAINS OF STATES WITH LONG TIME STEPS . . . . . . . . . . . . . . . . .
. 331 11.4.3 PATTERN RECOGNITION . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 332 REFERENCES . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . 332 12 THE STOCHASTIC DIFFERENCE EQUATION AS A TOOL TO COMPUTE
LONG TIME DYNAMICS RON ELBER, AVIJIT GHOSH, ALFREDO C´ ARDENAS
......................... 335 12.1 INTRODUCTION . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
335 12.2 MOLECULAR DYNAMICS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . 335 12.2.1 INITIAL VALUE FORMULATION
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336 12.2.2 A
BOUNDARY VALUE FORMULATION IN TIME . . . . . . . . . . . . . . . . . 336
12.2.3 A BOUNDARY VALUE FORMULATION IN LENGTH . . . . . . . . . . . . .
. . . 340 12.3 THE STOCHASTIC DIFFERENCE EQUATION . . . . . . . . . . .
. . . . . . . . . . . . . . . . 341 TABLE OF CONTENTS XIX 12.3.1
STOCHASTIC DIFFERENCE IN TIME: DEFINITION . . . . . . . . . . . . . . .
. . 341 12.3.2 A STOCHASTIC MODEL FOR A TRAJECTORY . . . . . . . . . . .
. . . . . . . . . . 345 12.3.3 *STABILIZING* LONG TIME TRAJECTORIES, OR
FILTERING HIGH FREQUENCY MODES . . . . . . . . . . . . . . . . . . . . .
. 347 12.3.4 WEIGHTS OF TRAJECTORIES AND SAMPLING PROCEDURES . . . . . .
. . . 350 12.3.5 MEAN FIELD APPROACH, FAST EQUILIBRATION AND MOLECULAR
LABELING . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
353 12.3.6 STOCHASTIC DIFFERENCE IN LENGTH . . . . . . . . . . . . . . .
. . . . . . . . . . 355 12.3.7 *FRACTAL* REFINEMENT OF TRAJECTORIES
PARAMETERIZED BY LENGTH . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 358 12.4 NUMERICAL EXPERIMENTS .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
360 12.5 CONCLUDING REMARKS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . 363 13NUMERICAL SIMULATIONS OF
MOLECULAR SYSTEMS WITH LONG RANGE INTERACTIONS DOMINIQUE LEVESQUE
............................................ 367 13.1 INTRODUCTION . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 367 13.2 3-D SYSTEMS . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367 13.3
CONFINED SYSTEMS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 373 13.4 CONCLUSION. . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. 377 REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . 377 PART IX
PERPECTIVES IN AB INITIO MD 14 NEW DEVELOPMENTS IN PLANE-WAVE BASED AB
INITIO CALCULATIONS GLENN J. MARTYNA, MARK E. TUCKERMAN
............................ 381 14.1 INTRODUCTION . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
381 14.2 METHODS. . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 382 14.2.1 CLUSTERS,
SURFACES AND SOLIDS/LIQUIDS . . . . . . . . . . . . . . . . . . . . 382
14.2.1.1 SOLIDS/LIQUIDS . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 383 14.2.1.2 CLUSTERS . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 384 14.2.1.3 SURFACES . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
386 14.2.1.4 WIRES . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 388 14.2.1.5 SUMMARY . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . 389 14.2.1.6 APPLICATION
TO EWALD SUMMATION . . . . . . . . . . . . . . . . 390 14.2.1.7
APPLICATION TO PLANE-WAVE BASED DENSITY FUNCTIONAL THEORY . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 391 14.2.2 DUAL LENGTH SCALE
APPROACH . . . . . . . . . . . . . . . . . . . . . . . . . . . 392 14.3
RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 399 14.3.1 CLUSTERS . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . 400 14.3.1.1 HARTREE AND LOCAL PSEUDOPOTENTIAL ENERGIES FOR A
MODEL DENSITY . . . . . . . . . . . . . . . . . . . . . . . . . . . .
400 XX TABLE OF CONTENTS 14.3.1.2 WATER MOLECULE AND HYDRONIUM ION . . .
. . . . . . . . . . . 400 14.3.2 SURFACE EWALD SUMMATION . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 401 14.3.2.1 MODEL BCC SURFACE
. . . . . . . . . . . . . . . . . . . . . . . . . . . . 401 14.3.2.2 ICE
SURFACE WITH A DEFECT . . . . . . . . . . . . . . . . . . . . . . . 403
14.3.3 MIXED AB INITIO /EMPIRICAL FORCE FIELDS . . . . . . . . . . . . .
. . . . . 405 14.3.3.1 NEAT WATER . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . 405 14.3.3.2 HCA II IN WATER. . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . 407 14.4 CONCLUSION. .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 409 REFERENCES . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
410 15 TIME AND LENGTH SCALES IN AB INITIO MOLECULAR DYNAMICS URSULA R¨
OTHLISBERGER, MICHIEL SPRIK, J¨ URG HUTTER .................... 413 15.1
INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . 413 15.2 OVERCOMING THE TIME SCALE
BARRIER: ENHANCED SAMPLING TECHNIQUES FOR AB INITIO MOLECULAR DYNAMICS
SIMULATIONS . . . . . . . . 414 15.2.1 TIME SCALE LIMITATIONS IN AB
INITIO MOLECULAR DYNAMICS SIMULATIONS . . . . . . . . . . . . . 414
15.2.2 THE USE OF CLASSICAL FORCE FIELDS AS BIAS POTENTIALS FOR AN
ENHANCED SAMPLING OF CONFORMATIONAL TRANSITIONS . . 415 15.2.3 FINITE
ELECTRONIC TEMPERATURES AS ELECTRONIC BIAS POTENTIALS . . . . . . . . .
. . . . . . . . . . . . . . . . . . 417 15.3 COMPUTATION OF ACID
DISSOCIATION CONSTANTS . . . . . . . . . . . . . . . . . . 419 15.3.1
TIME AND LENGTH SCALES IN AQUEOUS CHEMISTRY . . . . . . . . . . 419
15.3.2 DETERMINATION OF FREE ENERGY PROFILES . . . . . . . . . . . . . .
. . . . . 420 15.3.3 STATISTICAL THERMODYNAMICS OF GAS-PHASE EQUILIBRIA
. . . . . . 421 15.3.4 REVERSIBLE WORK AND EQUILIBRIUM CONSTANTS . . . .
. . . . . . . . . 422 15.3.5 CONTROLLED DISSOCIATION IN A SMALL BOX . .
. . . . . . . . . . . . . . . . 424 15.3.6 COMPUTATION OF THE WATER
DISSOCIATION CONSTANT . . . . . . . . . 425 15.3.7 APPLICATION TO WEAK
ACIDS AND EVALUATION OF METHOD . . . . . 427 15.4 LINEAR SCALING
ELECTRONIC STRUCTURE METHODS FOR AB INITIO MOLECULAR DYNAMICS . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 428 15.4.1 KOHN*SHAM
MATRIX CALCULATION . . . . . . . . . . . . . . . . . . . . . . . . 429
15.4.2 WAVEFUNCTION OPTIMIZATION; SOLVING THE KOHN*SHAM EQUATIONS . . .
. . . . . . . . . . . . . . . . . . . 434 REFERENCES . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 440 PART X QUANTUM SIMULATIONS 16 A STATISTICAL MECHANICAL
THEORY OF QUANTUM DYNAMICS IN CLASSICAL ENVIRONMENTS RAYMOND KAPRAL,
GIOVANNI CICCOTTI ............................... 445 16.1 INTRODUCTION
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 445 16.2 QUANTUM DYNAMICS AND STATISTICAL MECHANICS
. . . . . . . . . . . . . . . . . 446 TABLE OF CONTENTS XXI 16.2.1 MIXED
REPRESENTATION OF QUANTUM STATISTICAL MECHANICS . . . 448 16.3
QUANTUM-CLASSICAL WORLD . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 451 16.4 NATURE OF QUANTUM-CLASSICAL DYNAMICS . .
. . . . . . . . . . . . . . . . . . . . . 453 16.5 TIME EVOLUTION OF
DYNAMICAL VARIABLES . . . . . . . . . . . . . . . . . . . . . . . 458
16.5.1 EQUATIONS FOR CANONICAL VARIABLES . . . . . . . . . . . . . . . .
. . . . . . . 461 16.6 QUANTUM-CLASSICAL EQUILIBRIUM DENSITY . . . . . .
. . . . . . . . . . . . . . . . . 462 16.7 QUANTUM-CLASSICAL TIME
CORRELATION FUNCTIONS . . . . . . . . . . . . . . . . 463 16.8
SIMULATION SCHEMES . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 467 16.8.1 SPIN*BOSON MODEL . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . 468 16.9
CONCLUSION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . 470 REFERENCES . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . 471 17 THE COUPLED ELECTRONIC*IONIC MONTE CARLO SIMULATION
METHOD DAVID CEPERLEY, MARK DEWING, CARLO PIERLEONI
...................... 473 17.1 INTRODUCTION . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473
17.2 THE COUPLED ELECTRONIC-IONIC MONTE CARLO METHOD . . . . . . . . . .
. . . 476 17.3 THE PENALTY METHOD . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 477 17.4 ENERGY DIFFERENCES .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . 478 17.4.1 DIRECT DIFFERENCE . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 479 17.4.2 REWEIGHTING . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . 479 17.4.3 IMPORTANCE SAMPLING . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 480 17.5 CHOICE OF TRIAL WAVE FUNCTION . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480 17.6 TWIST
AVERAGE BOUNDARY CONDITIONS . . . . . . . . . . . . . . . . . . . . . .
. . . . 482 17.7 FLUID MOLECULAR HYDROGEN . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 483 17.8 THE ATOMIC*METALLIC
PHASE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. 486 17.8.1 TRIAL WAVE FUNCTION AND OPTIMIZATION . . . . . . . . . . .
. . . . . . . 486 17.8.2 COMPARISON WITH PIMC . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . 491 17.8.3 HYDROGEN EQUATION OF
STATE AND SOLID*LIQUID PHASE TRANSITION OF THE PROTONS . . . . . . . . .
494 17.9 CONCLUSIONS AND OUTLOOK . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . 497 REFERENCES . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . 499
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| genre | (DE-588)1071861417 Konferenzschrift 2002 Konstanz gnd-content |
| genre_facet | Konferenzschrift 2002 Konstanz |
| id | DE-604.BV014811653 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T19:07:28Z |
| institution | BVB |
| isbn | 3540443177 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-010022256 |
| oclc_num | 50810614 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-384 DE-703 DE-11 |
| owner_facet | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-384 DE-703 DE-11 |
| physical | XXVI, 500 S. Ill., graph. Darst. |
| publishDate | 2002 |
| publishDateSearch | 2002 |
| publishDateSort | 2002 |
| publisher | Springer |
| record_format | marc |
| series | Lecture notes in physics |
| series2 | Lecture notes in physics |
| spelling | Bridging time scales molecular simulations for the next decade P. Nielaba ... (eds.) Berlin [u.a.] Springer 2002 XXVI, 500 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Lecture notes in physics 605 Física larpcal Chemistry, Physical and theoretical -- Computer simulation Chemistry, Physical and theoretical Computer simulation Molecular dynamics -- Computer simulation Molecular dynamics Computer simulation Molecules -- Computer simulation Molecules Computer simulation Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Statistische Physik (DE-588)4057000-9 gnd rswk-swf Kondensierte Materie (DE-588)4132810-3 gnd rswk-swf Molekulardynamik (DE-588)4170370-4 gnd rswk-swf Monte-Carlo-Simulation (DE-588)4240945-7 gnd rswk-swf (DE-588)1071861417 Konferenzschrift 2002 Konstanz gnd-content Proteinfaltung (DE-588)4324567-5 s Molekulardynamik (DE-588)4170370-4 s Monte-Carlo-Simulation (DE-588)4240945-7 s DE-604 Statistische Physik (DE-588)4057000-9 s Kondensierte Materie (DE-588)4132810-3 s Nielaba, Peter Sonstige oth Lecture notes in physics 605 (DE-604)BV000003166 605 SWB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010022256&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bridging time scales molecular simulations for the next decade Lecture notes in physics Física larpcal Chemistry, Physical and theoretical -- Computer simulation Chemistry, Physical and theoretical Computer simulation Molecular dynamics -- Computer simulation Molecular dynamics Computer simulation Molecules -- Computer simulation Molecules Computer simulation Proteinfaltung (DE-588)4324567-5 gnd Statistische Physik (DE-588)4057000-9 gnd Kondensierte Materie (DE-588)4132810-3 gnd Molekulardynamik (DE-588)4170370-4 gnd Monte-Carlo-Simulation (DE-588)4240945-7 gnd |
| subject_GND | (DE-588)4324567-5 (DE-588)4057000-9 (DE-588)4132810-3 (DE-588)4170370-4 (DE-588)4240945-7 (DE-588)1071861417 |
| title | Bridging time scales molecular simulations for the next decade |
| title_auth | Bridging time scales molecular simulations for the next decade |
| title_exact_search | Bridging time scales molecular simulations for the next decade |
| title_full | Bridging time scales molecular simulations for the next decade P. Nielaba ... (eds.) |
| title_fullStr | Bridging time scales molecular simulations for the next decade P. Nielaba ... (eds.) |
| title_full_unstemmed | Bridging time scales molecular simulations for the next decade P. Nielaba ... (eds.) |
| title_short | Bridging time scales |
| title_sort | bridging time scales molecular simulations for the next decade |
| title_sub | molecular simulations for the next decade |
| topic | Física larpcal Chemistry, Physical and theoretical -- Computer simulation Chemistry, Physical and theoretical Computer simulation Molecular dynamics -- Computer simulation Molecular dynamics Computer simulation Molecules -- Computer simulation Molecules Computer simulation Proteinfaltung (DE-588)4324567-5 gnd Statistische Physik (DE-588)4057000-9 gnd Kondensierte Materie (DE-588)4132810-3 gnd Molekulardynamik (DE-588)4170370-4 gnd Monte-Carlo-Simulation (DE-588)4240945-7 gnd |
| topic_facet | Física Chemistry, Physical and theoretical -- Computer simulation Chemistry, Physical and theoretical Computer simulation Molecular dynamics -- Computer simulation Molecular dynamics Computer simulation Molecules -- Computer simulation Molecules Computer simulation Proteinfaltung Statistische Physik Kondensierte Materie Molekulardynamik Monte-Carlo-Simulation Konferenzschrift 2002 Konstanz |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010022256&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000003166 |
| work_keys_str_mv | AT nielabapeter bridgingtimescalesmolecularsimulationsforthenextdecade |