Quantum mechanical simulation methods for studying biological systems: Les Houches workshop, May 2 - 7, 1995
Saved in:
| Format: | Book |
|---|---|
| Language: | German |
| Published: |
Berlin [u.a.]
Springer [u.a.]
1996
|
| Series: | Centre de Physique des Houches
4 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Literaturangaben |
| Physical Description: | XIV, 311 S. graph. Darst. |
| ISBN: | 3540608699 2868832636 |
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MARC
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| 245 | 1 | 0 | |a Quantum mechanical simulation methods for studying biological systems |b Les Houches workshop, May 2 - 7, 1995 |c Ed. Dominique Bicout ... [Centre de Physiques des Houches] |
| 264 | 1 | |a Berlin [u.a.] |b Springer [u.a.] |c 1996 | |
| 300 | |a XIV, 311 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
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| 490 | 1 | |a Centre de Physique des Houches |v 4 | |
| 500 | |a Literaturangaben | ||
| 650 | 4 | |a Mathematisches Modell | |
| 650 | 4 | |a Biomolecules |x Structure |x Computer simulation |v Congresses | |
| 650 | 4 | |a Biomolecules |x Structure |x Mathematical models |v Congresses | |
| 650 | 4 | |a Proteins |x Structure |x Computer simulation |v Congresses | |
| 650 | 4 | |a Proteins |x Structure |x Mathematical models |v Congresses | |
| 650 | 4 | |a Structure-activity relationships (Biochemistry) |v Congresses | |
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Record in the Search Index
| _version_ | 1804125244641771520 |
|---|---|
| adam_text | CONTENTS
LECTURE
1
Density functional theory
by
N.
С
Handy
1.
Introduction
..................................................... 1
2.
E. Bright Wilson s observation and the Kohn-Hohenberg theorems
...... 2
3.
The Kohn-Sham equations
........................................ 5
4.
The uniform electron gas....the local density approximation
............. 6
5.
Beyond the LDA approximation
.................................... 8
5.1.
The Becke exchange correction
............................. 8
5.2.
The Lee-Yang-Parr correlation potential
..................... 10
6.
Numerical quadrature
............................................ 10
6.1.
Voronoi polyhedra
....................................... 11
6.2.
Radial quadrature
........................................ 12
6.3.
Two-dimensional angular quadrature schemes
................ 12
6.4.
The accuracy of the quadrature
............................. 13
7.
The implementation of the Kohn-Sham equations
..................... 13
8.
Derivative theory for the Kohn-Sham method
........................ 14
9.
The exact value for emax
.......................................... 15
10.
Quantum chemistry and density functional theory
.................... 16
11.
The Becke-Roussel exchange functional
............................ 17
12.
Becke-Roussel geometries and atomisation energies
.................. 19
13.
The neon exchange-hole function
.................................. 20
14.
The
7 = 0.80
Becke-Roussel model
................................ 23
15.
Molecular dissociation
........................................... 24
16.
Appendix: functional derivatives
.................................. 27
LECTURE!
Practical density functional approaches in chemistry and
biochemistry
by A. St-Amant
1.
Introduction
..................................................... 37
Z
The Hohenberg-Kohn theorem
..................................... 38
3.
The Kohn-Sham equations
........................................ 39
4.
Exchange-correlation functionals
................................... 41
5.
The LCAO approach
............................................. 44
6.
Handling the Coulomb potential
.................................... 46
7.
Handling exchange and correlation
................................. 51
8.
Evaluating the total energy
........................................ 54
9.
Grids
........................................................... 56
10.
Conclusion
..................................................... 58
LECTURES
A quantum chemical view of the initial photochemical event
in photosynthesis
by
M. C
Zerner
1.
Introduction
..................................................... 61
2.
Calculations on monomers
........................................ 67
3.
Calculations on the special pair
..................................... 70
4.
Calculations on the entire
ÄC...................................... 77
5.
Conclusions
..................................................... 81
LECTURE
4
Curve crossing in a protein: coupling of the elementary
quantum process to motions of the protein
by K.
Schulten
1.
Introduction
..................................................... 85
2.
The generic model: two-state quantum system coupled to an oscillator
... 87
3.
Two-state system coupled to a classical medium
[1].................... 90
4.
Two-state system coupled to a stochastic medium
[1]................... 93
5.
Two-state system coupled to a single quantum mechanical oscillator
...... 97
6.
Two-state system coupled to a multi-modal bath of quantum mechanical
oscillators
...................................................... 102
7.
From the energy gap correlation function
A£ľ[R(ť)]
to the spectral density
ІМИ
........................................................ 105
8.
Evaluating the transfer rate
[2,3]................................... 109
8.1.
High temperature limit
....................................
Ill
8.2.
Low temperature limit
.................................... 112
8.3.
Results
................................................. 113
9.
Numerical evaluation of the line shape function
....................... 115
LECTURES
Quantum-classical molecular dynamics. Models and
applications
by P.
Bała,
P.
Grochowski,
В.
Lesyng
and
J.
A. McCammon
1.
Introduction
..................................................... 119
2. Abrief
overview of selected analytical models and theories
.,............ 121
2.1.
Evolution loops
.......................................... 121
2.2.
A quantum particle in a Penning trap and related models
....... 122
2.3.
Quantum harmonic oscillatorwith a time-dependent force constant
123
2.4.
Comments on theoretical tools used for studying formal quantum-
dynamical systems and perspectives for future studies
.......... 123
3.
Time-dependent Schroedinger equation. Overview of selected techniques
. 124
3.1.
The eigenfunction expansion method
........................ 125
3.2.
Second-order differencing scheme
.......................... 126
XI
3.3.
Split operator method
..................................... 126
3.4.
Cayley method
........................................... 126
3.5.
Chebychev polynomial method
............................. 127
4.
Quantum-classical molecular dynamics
.............................. 128
4.1.
Formulation of the model
................................. 128
4.2.
A classical particle colliding with a quantum harmonic oscillator.
The test-case for the QCMD method
........................ 131
5.
Application of the QCMD model to enzyme reactions
................. 137
5.1.
Phospholipase A2
-
a model enzymatic system
................ 137
5.2.
Potential energy surface for the enzymatic reaction
-
a fast valence
bond method
............................................ 139
5.3.
Simulations and results
.................................... 143
5.3.1.
Force fields
......................................... 143
5.3.2.
Energy minimization and thennalization
................ 144
5.3.3.
Dynamics of the enzyme
-
substrate complex
............. 145
5.3.4.
QCMD simulations of the proton transfer
............... 146
6.
Conclusions
..................................................... 153
LECTURE
б
Quantum dynamics simulation of a small quantum system
embedded in a classical environment
by H. J. C. Berendsen and J. Mavri
1.
Introduction
..................................................... 157
Z
Theory
......................................................... 159
2.1.
The Hamiltonian: mixing quantum-mechanical and classical
degrees of freedom
....................................... 159
ZZ The density matrix: principles
.............................. 160
2.3.
DME:
density matrix evolution and classical dynamics
.......... 163
Z4. Conservation properties
................................... 164
2.5.
The use of non-orthogonal basis sets
........................ 166
2.6.
The interaction representation
............................. 167
3.
Behaviour of a two-level system
.................................... 168
4.
Collision of particle with harmonic oscillator
......................... 170
5.
Proton transfer
.................................................. 173
6.
Perspectives
..................................................... 177
LECTURE?
A tubular view of electron transfer in azurin
by J. J. Regan and J.
N.
Onucbic
1.
Introduction
..................................................... 181
Z
The electron transfer model
....................................... 181
Zl.
Gđa
as a sum of pathways
.................................. 183
ZZ The pathway tube
........................................ 184
Z3. The sum of tubes
......................................... 185
хп
2.4.
The pathway approximation
................................ 185
2.4.1.
Renormalization
.................................... 185
2.4.2.
Decay per step
...................................... 188
2.5.
Pathways vs. tubes
........................................ 190
3.
An example in azurin
............................................. 190
3.1.
/3-strand calibration of tunneling energy
...................... 192
4.
The tubular breakdown
........................................... 198
LECTURE
8
Biological electron transfer: measurement, mechanism,
engineering requirements
by
С. С.
Moser
and P.
L. Dutton
1.
Introduction
..................................................... 201
1.1.
Electron transfer bioenergetics
............................. 201
2.
Lessons from the photosynthetic reaction center
...................... 202
2.1.
An electron transfer laboratory
............................. 202
2.2.
Marcus theory
........................................... 205
2.3.
Electronic coupling
....................................... 206
2.4.
Distance dependence of electron transfer rate
................ 207
3.
Design and construction of synthetic electron transfer proteins
.......... 209
3.1.
Assembly constraints
...................................... 209
3.2.
Designing with distance
................................... 211
LECTURE
9
The photodetachment of an electron from a chloride ion in
water studied by quantum molecular dynamics simulation
by A. Staib and D.
Borgis
1.
Introduction
..................................................... 215
2.
Quantum MD simulation method
................................... 217
11.
Model
.................................................. 217
2.2. Hydrated
electron
........................................ 219
2.3.
Aqueous chloride
........................................ 220
3.
Results
......................................................... 221
3.1.
Energetics
.............................................. 221
3.2.
Electron photodetachment
................................ 223
4.
Conclusions
..................................................... 232
хш
LECTURE
10
Quantum
chemistry
ofin
situ retinal: study of the spectral
properties and dark adaptation of Bacteriorhodopsin
by I. Logunov and K.
Schulten
1.
Introduction
..................................................... 236
2.
Quantum chemistry of in situ retinal
................................. 239
2.1.
Modelling spectral properties of Bacteriorhodopsin
............ 241
2.2.
Modelling the dark adaptation of Bacteriorhodopsin
........... 245
2.2.1.
Effective energy barrier of dark adaptation
.............. 248
3.
Further developments
............................................ 251
LECTURE
11
Towards an understanding of quantum factors in small
ligand geminate recombination to
heme
proteins
by W.
Nowak
and J.-L. Martin
1.
Introduction
..................................................... 257
2.
Model of the reaction center
....................................... 260
2.1.
Reaction coordinates
................................... 260
3.
Computational method
........................................... 261
3.1.
Basis sets
............................................... 262
4.
Results and discussion
............................................ 263
5.
Summary
....................................................... 267
LECTURED
A parallel direct SCF method for large molecular systems
by T. R. Furlani and H. F. King
1.
Introduction
..................................................... 271
2.
Computational methodology
....................................... 273
2.1.
Construction of the Fock matrix
............................ 273
2.2.
Dynamic load balance and memory requirements
.............. 277
3.
Results and discussion
............................................ 280
4.
Summary
....................................................... 283
XIV
LECTURE
13
Multigrid electrostatic
computations in density functional
theory
by M. P. Merrick, K. A. Iyer and
T. L.
Beck
1.
Introduction
..................................................... 285
2.
Method.
........................................................ 287
2.1.
Grid based minimization
.................................. 287
2.2.
Multigrid method
........................................ 287
2.3.
MG solution for KS equations
.............................. 289
3.
Applications
.................................................... 289
4.
Conclusions
..................................................... 291
LECTURED
Symmetry-oriented research of polymers PC program
POLSym and
DNA
by I. Milosevic,
A. Damjanović
and M.
Damnjanović
1.
Introduction
-
symmetry in polymer physics
.......................... 295
2.
Review of the line groups
.......................................... 297
2.1.
Structure of the line groups
................................ 298
2.2.
State transformations
-
Representations
..................... 299
2.3.
Line groups and computational physics
...................... 301
3.
Computing program POLSym
...................................... 302
3.1. 3 =
Invariant polynomials
.......................... 302
3.2. 4 =
Clebsch-Gordan coefficients
................... 303
3.3. 5 =
Normal vibrations
............................... 305
4.
The study of
DNA ............................................... 306
4.1.
Modeling of the system
.................................... 306
4.2.
The vibrational spectra
.................................... 309
|
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| callnumber-subject | QP - Physiology |
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| ctrlnum | (OCoLC)34667247 (DE-599)BVBBV010765056 |
| dewey-full | 530.12 572.6330113 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 530 - Physics 572 - Biochemistry |
| dewey-raw | 530.12 572.6330113 |
| dewey-search | 530.12 572.6330113 |
| dewey-sort | 3530.12 |
| dewey-tens | 530 - Physics 570 - Biology |
| discipline | Physik Biologie |
| format | Book |
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| genre | (DE-588)1071861417 Konferenzschrift 1995 Les Houches gnd-content |
| genre_facet | Konferenzschrift 1995 Les Houches |
| id | DE-604.BV010765056 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T17:58:29Z |
| institution | BVB |
| isbn | 3540608699 2868832636 |
| language | German |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-007188690 |
| oclc_num | 34667247 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-703 DE-83 DE-11 |
| owner_facet | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-703 DE-83 DE-11 |
| physical | XIV, 311 S. graph. Darst. |
| publishDate | 1996 |
| publishDateSearch | 1996 |
| publishDateSort | 1996 |
| publisher | Springer [u.a.] |
| record_format | marc |
| series | Centre de Physique des Houches |
| series2 | Centre de Physique des Houches |
| spelling | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 Ed. Dominique Bicout ... [Centre de Physiques des Houches] Berlin [u.a.] Springer [u.a.] 1996 XIV, 311 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Centre de Physique des Houches 4 Literaturangaben Mathematisches Modell Biomolecules Structure Computer simulation Congresses Biomolecules Structure Mathematical models Congresses Proteins Structure Computer simulation Congresses Proteins Structure Mathematical models Congresses Structure-activity relationships (Biochemistry) Congresses Biomolekül (DE-588)4135124-1 gnd rswk-swf Molekulardynamik (DE-588)4170370-4 gnd rswk-swf Quantenmechanisches System (DE-588)4300046-0 gnd rswk-swf Dichtefunktionalformalismus (DE-588)4258514-4 gnd rswk-swf (DE-588)1071861417 Konferenzschrift 1995 Les Houches gnd-content Biomolekül (DE-588)4135124-1 s Quantenmechanisches System (DE-588)4300046-0 s Dichtefunktionalformalismus (DE-588)4258514-4 s DE-604 Molekulardynamik (DE-588)4170370-4 s Bicout, Dominique Sonstige oth Centre de Physique des Houches 4 (DE-604)BV011876452 4 Digitalisierung TU Muenchen application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007188690&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 Centre de Physique des Houches Mathematisches Modell Biomolecules Structure Computer simulation Congresses Biomolecules Structure Mathematical models Congresses Proteins Structure Computer simulation Congresses Proteins Structure Mathematical models Congresses Structure-activity relationships (Biochemistry) Congresses Biomolekül (DE-588)4135124-1 gnd Molekulardynamik (DE-588)4170370-4 gnd Quantenmechanisches System (DE-588)4300046-0 gnd Dichtefunktionalformalismus (DE-588)4258514-4 gnd |
| subject_GND | (DE-588)4135124-1 (DE-588)4170370-4 (DE-588)4300046-0 (DE-588)4258514-4 (DE-588)1071861417 |
| title | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 |
| title_auth | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 |
| title_exact_search | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 |
| title_full | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 Ed. Dominique Bicout ... [Centre de Physiques des Houches] |
| title_fullStr | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 Ed. Dominique Bicout ... [Centre de Physiques des Houches] |
| title_full_unstemmed | Quantum mechanical simulation methods for studying biological systems Les Houches workshop, May 2 - 7, 1995 Ed. Dominique Bicout ... [Centre de Physiques des Houches] |
| title_short | Quantum mechanical simulation methods for studying biological systems |
| title_sort | quantum mechanical simulation methods for studying biological systems les houches workshop may 2 7 1995 |
| title_sub | Les Houches workshop, May 2 - 7, 1995 |
| topic | Mathematisches Modell Biomolecules Structure Computer simulation Congresses Biomolecules Structure Mathematical models Congresses Proteins Structure Computer simulation Congresses Proteins Structure Mathematical models Congresses Structure-activity relationships (Biochemistry) Congresses Biomolekül (DE-588)4135124-1 gnd Molekulardynamik (DE-588)4170370-4 gnd Quantenmechanisches System (DE-588)4300046-0 gnd Dichtefunktionalformalismus (DE-588)4258514-4 gnd |
| topic_facet | Mathematisches Modell Biomolecules Structure Computer simulation Congresses Biomolecules Structure Mathematical models Congresses Proteins Structure Computer simulation Congresses Proteins Structure Mathematical models Congresses Structure-activity relationships (Biochemistry) Congresses Biomolekül Molekulardynamik Quantenmechanisches System Dichtefunktionalformalismus Konferenzschrift 1995 Les Houches |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007188690&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV011876452 |
| work_keys_str_mv | AT bicoutdominique quantummechanicalsimulationmethodsforstudyingbiologicalsystemsleshouchesworkshopmay271995 |